diff --git a/.circleci/config.yml b/.circleci/config.yml index 725c78f5e7e8a..81ecb0653c316 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -239,6 +239,52 @@ jobs: # a basic unit of work in a run --skiplist-leafs conda clean -y --all + nightly_build: + parameters: + os: + type: executor + executor: << parameters.os >> + steps: + - add_ssh_keys: + fingerprints: + - 1e:85:74:42:35:5f:c5:a2:35:c2:ec:b7:80:c0:7c:40 + + - checkout + + - run: + name: Fetch bioconda install script + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh + + - run: + name: Install bioconda-utils + command: | + sudo mkdir -p /opt/ + sudo chmod o+rwx /opt + bash install-and-set-up-conda.sh + + - run: + name: Setup PATH + command: + echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" + + - run: + name: Configure conda + command: bash configure-conda.sh + + # For now, do not upload ARM images to biocontainers: --mulled-upload-target biocontainers + - run: + name: Build and push leftover packages + command: | + set -e + eval "$(conda shell.bash hook)" + conda activate bioconda + source common.sh + + # build and push all leftover packages + bioconda-utils build recipes config.yml \ + --docker --mulled-test --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \ + --anaconda-upload \ + --prelint --exclude bioconda-repodata-patches workflows: build and test (ARM): @@ -267,7 +313,6 @@ workflows: - osx-arm64 - linux-aarch64 - Bulk branch (ARM): jobs: - bulk_build: @@ -280,3 +325,21 @@ workflows: # - osx-arm64 Bulk is on GitHub Actions - linux-aarch64 runner: [0, 1, 2, 3, 4, 5] + + Nightly (ARM): + triggers: + - schedule: + cron: "0 0 * * *" + filters: + branches: + only: master + jobs: + - nightly_build: + filters: + branches: + only: master + matrix: + parameters: + os: + # - osx-arm64 Nightly is on GitHub Actions + - linux-aarch64 diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 38e3f8248cf8b..f04fc084c8a1e 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -128,9 +128,9 @@ jobs: runs-on: macOS-14 # M1 strategy: fail-fast: false - max-parallel: 4 + max-parallel: 1 # GHA free plan allows 5 concurrent Mac runners total, we still need most on osx-64. matrix: - runner: [0, 1, 2, 3] + runner: [0] steps: - uses: actions/checkout@v4 with: @@ -179,7 +179,7 @@ jobs: python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' echo '============' bioconda-utils build recipes config.yml \ - --worker-offset ${{ matrix.runner }} --n-workers 4 \ + --worker-offset ${{ matrix.runner }} --n-workers 1 \ --lint --anaconda-upload --record-build-failures --skiplist-leafs \ --exclude bioconda-repodata-patches conda clean -y --all diff --git a/.github/workflows/CommentResponder.yml b/.github/workflows/CommentResponder.yml index 2052f237029d0..2cc37b9226a99 100644 --- a/.github/workflows/CommentResponder.yml +++ b/.github/workflows/CommentResponder.yml @@ -1,28 +1,14 @@ name: CommentResponder on: - status: - # check_suite: - # types: - # - completed issue_comment: types: - created - # Runs too many times - # ( - # github.event_name == 'check_suite' && - # github.event.check_suite.conclusion == 'success' - # ) || - jobs: comment: runs-on: ubuntu-latest name: bioconda-bot comment if: >- - ( - github.event_name == 'status' && - github.event.state == 'success' - ) || ( github.event_name == 'issue_comment' && github.event.issue.pull_request && diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml index 11d48c1154598..850a5d83fc5ad 100644 --- a/.github/workflows/nightly.yml +++ b/.github/workflows/nightly.yml @@ -1,76 +1,17 @@ name: Nightly Uploader on: schedule: - - cron: '12 2 * * *' + - cron: "0 0 * * *" jobs: - build-linux: - name: Linux Upload + nightly-osx-arm: + name: Nightly OSX-ARM64 Builds if: github.repository == 'bioconda/bioconda-recipes' - runs-on: ubuntu-latest - strategy: - fail-fast: false - max-parallel: 13 - steps: - - uses: actions/checkout@v3 - with: - fetch-depth: 0 - - - name: set path - run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH - - - name: Fetch conda install script - run: | - wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh - - - name: Restore cache - id: cache - uses: actions/cache@v3 - with: - path: /opt/mambaforge - key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }} - - - name: Set up bioconda-utils - if: steps.cache.outputs.cache-hit != 'true' - run: bash install-and-set-up-conda.sh - - # This script can be used to reconfigure conda to use the right channel setup. - # This has to be done after the cache is restored, because - # the channel setup is not cached as it resides in the home directory. - # We could use a system-wide (and therefore cached) channel setup, - # but mamba does not support that at the time of implementation - # (it ignores settings made with --system). - - name: Configure conda - run: bash configure-conda.sh - - - name: Build and upload - env: - QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} - QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} - ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} - INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - # Mimic circleci - OSTYPE: "linux-gnu" - CI: "true" - run: | - set -ex - eval "$(conda shell.bash hook)" - conda activate bioconda - docker pull quay.io/dpryan79/mulled_container:latest - bioconda-utils build recipes config.yml \ - --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ - --prelint - docker rmi quay.io/dpryan79/mulled_container:latest - - build-osx: - name: OSX Tests - if: github.repository == 'bioconda/bioconda-recipes' - runs-on: macos-13 + runs-on: macOS-14 # M1 strategy: fail-fast: false max-parallel: 4 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 0 @@ -81,27 +22,13 @@ jobs: run: | wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh - - name: Restore cache - id: cache - uses: actions/cache@v3 - with: - path: /opt/mambaforge - key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }} - - name: Set up bioconda-utils - if: steps.cache.outputs.cache-hit != 'true' run: bash install-and-set-up-conda.sh - # This script can be used to reconfigure conda to use the right channel setup. - # This has to be done after the cache is restored, because - # the channel setup is not cached as it resides in the home directory. - # We could use a system-wide (and therefore cached) channel setup, - # but mamba does not support that at the time of implementation - # (it ignores settings made with --system). - name: Configure conda run: bash configure-conda.sh - - name: Build and Test + - name: Build and push leftover packages env: QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} @@ -116,9 +43,11 @@ jobs: eval "$(conda shell.bash hook)" conda activate bioconda - # The SDK isn't actually cached, so reinstall it + source common.sh + # Sets up OSX SDK run_conda_forge_build_setup + # build and push all leftover packages bioconda-utils build recipes config.yml \ --anaconda-upload \ - --prelint + --prelint --exclude bioconda-repodata-patches diff --git a/README.md b/README.md index 3d33a595046a4..ec75a3f5d9c15 100644 --- a/README.md +++ b/README.md @@ -20,3 +20,12 @@ Please visit https://bioconda.github.io for details. Please visit the new docs at https://bioconda.github.io/contributor/index.html for details. +## Nightly build status +The nightly uploader jobs build any recipes that exist on master but were not successfully uploaded to the [bioconda channel](https://anaconda.org/bioconda). Any failure in the nightly build should be resolved with a PR for the affected recipe. + +| arch | build status | +|------|--------------| +| linux-64 | [![Nightly linux-64](https://dev.azure.com/bioconda/bioconda-recipes/_apis/build/status/Nightly%20uploader?branchName=master&jobName=build_and_push_linux&label=Nightly%20linux-64)](https://dev.azure.com/bioconda/bioconda-recipes/_build/latest?definitionId=4) | +| osx-64 | [![Nightly osx-64](https://dev.azure.com/bioconda/bioconda-recipes/_apis/build/status/Nightly%20uploader?branchName=master&jobName=build_and_push_osx&label=Nightly%20osx-64)](https://dev.azure.com/bioconda/bioconda-recipes/_build/latest?definitionId=4) | +| osx-arm64 | [![Nightly osx-arm64](https://github.com/bioconda/bioconda-recipes/actions/workflows/nightly.yml/badge.svg)](https://github.com/bioconda/bioconda-recipes/actions/workflows/nightly.yml) | +| linux-aarch64 |[![CircleCI](https://dl.circleci.com/insights-snapshot/gh/bioconda/bioconda-recipes/master/Nightly%20(ARM)/badge.svg?window=24h)](https://app.circleci.com/insights/github/bioconda/bioconda-recipes/workflows/Nightly%20(ARM)/overview?branch=master&reporting-window=last-24-hours) | diff --git a/build-fail-blacklist b/build-fail-blacklist index f9e833ba2f1ce..3ec878a35f7ef 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -359,7 +359,6 @@ recipes/megagta # Unknown issues recipes/cmv recipes/fwdpp -recipes/parafly recipes/smashbenchmarking recipes/saffrontree @@ -633,10 +632,6 @@ recipes/tedna recipes/transtermhp recipes/carna -# stringify can't find libmysqlclient.18 -recipes/ucsc-overlapselect -recipes/ucsc-pslmap - # Source seems to have moved recipes/discovar @@ -658,9 +653,6 @@ recipes/ale # Pinned to biopython=1.65 which is only availble through pkgs/free. If it doesn't break the package, the requirement should be set to biopython=1.70 or higher. recipes/breakseq2 -# R package build segfaults: [2020-07-28 05:38:00] Plotting genome...\n\n*** caught segfault ***\naddress (nil), cause 'memory not mapped'\n\nTraceback:\n 1: cairoVersion()\n 2: grSoftVersion()\n 3: symbolType1support()\n 4: optionSymbolFont(d$symbolfamily)\n 5: png(paste0(xargs$out, ".cnv.png"), units = "px", width = 1600, height = 1600, res = 300) -recipes/cnv_facets - # Depends on r-base and mentalist. The latter has has pinned down dependencies preventing the installation alongside other packages like r-base. Need to fix mentalist! recipes/pathogist @@ -761,209 +753,6 @@ recipes/maker # Takes hours to solve the environment recipes/rop -# Need to redo the skeletons for these -recipes/ucsc-axttomaf -recipes/ucsc-bamtopsl -recipes/ucsc-bedcoverage -recipes/ucsc-bedextendranges -recipes/ucsc-bedintersect -recipes/ucsc-beditemoverlapcount -recipes/ucsc-bedjointaboffset -recipes/ucsc-bedpileups -recipes/ucsc-bedrestricttopositions -recipes/ucsc-bedtopsl -recipes/ucsc-bedweedoverlapping -recipes/ucsc-bigwigmerge -recipes/ucsc-blasttopsl -recipes/ucsc-catdir -recipes/ucsc-catuncomment -recipes/ucsc-chainbridge -recipes/ucsc-chainfilter -recipes/ucsc-chainnet -recipes/ucsc-chainprenet -recipes/ucsc-chainsplit -recipes/ucsc-chainstitchid -recipes/ucsc-chainswap -recipes/ucsc-chaintoaxt -recipes/ucsc-chaintopsl -recipes/ucsc-chaintopslbasic -recipes/ucsc-checkagpandfa -recipes/ucsc-checkcoveragegaps -recipes/ucsc-checkhgfindspec -recipes/ucsc-checktablecoords -recipes/ucsc-chopfalines -recipes/ucsc-chromgraphfrombin -recipes/ucsc-chromgraphtobin -recipes/ucsc-clustergenes -recipes/ucsc-coltransform -recipes/ucsc-countchars -recipes/ucsc-crtreeindexbed -recipes/ucsc-crtreesearchbed -recipes/ucsc-dbsnoop -recipes/ucsc-dbtrash -recipes/ucsc-endsinlf -recipes/ucsc-estorient -recipes/ucsc-expmatrixtobarchartbed -recipes/ucsc-faalign -recipes/ucsc-facmp -recipes/ucsc-facount -recipes/ucsc-fafilter -recipes/ucsc-fafiltern -recipes/ucsc-fafrag -recipes/ucsc-fanoise -recipes/ucsc-faonerecord -recipes/ucsc-fapolyasizes -recipes/ucsc-farandomize -recipes/ucsc-farc -recipes/ucsc-fasize -recipes/ucsc-fasplit -recipes/ucsc-fastqstatsandsubsample -recipes/ucsc-fastqtofa -recipes/ucsc-fatofastq -recipes/ucsc-fatotab -recipes/ucsc-fatrans -recipes/ucsc-featurebits -recipes/ucsc-findmotif -recipes/ucsc-gaptolift -recipes/ucsc-genepredfilter -recipes/ucsc-genepredhisto -recipes/ucsc-genepredsinglecover -recipes/ucsc-genepredtofakepsl -recipes/ucsc-genepredtomafframes -recipes/ucsc-genepredtoprot -recipes/ucsc-gensub2 -recipes/ucsc-getrna -recipes/ucsc-getrnapred -recipes/ucsc-gff3topsl -recipes/ucsc-gmtime -recipes/ucsc-headrest -recipes/ucsc-hgbbidblink -recipes/ucsc-hgfakeagp -recipes/ucsc-hgfindspec -recipes/ucsc-hggoldgapgl -recipes/ucsc-hgloadbed -recipes/ucsc-hgloadchain -recipes/ucsc-hgloadmaf -recipes/ucsc-hgloadnet -recipes/ucsc-hgloadout -recipes/ucsc-hgloadoutjoined -recipes/ucsc-hgloadsqltab -recipes/ucsc-hgloadwiggle -recipes/ucsc-hgspeciesrna -recipes/ucsc-hgsqldump -recipes/ucsc-hgtrackdb -recipes/ucsc-hgvstovcf -recipes/ucsc-htmlcheck -recipes/ucsc-hubcheck -recipes/ucsc-hubpubliccheck -recipes/ucsc-lavtoaxt -recipes/ucsc-lavtopsl -recipes/ucsc-ldhggene -recipes/ucsc-liftup -recipes/ucsc-linestora -recipes/ucsc-localtime -recipes/ucsc-mafaddirows -recipes/ucsc-mafaddqrows -recipes/ucsc-mafcoverage -recipes/ucsc-maffetch -recipes/ucsc-maffilter -recipes/ucsc-maffrag -recipes/ucsc-maffrags -recipes/ucsc-mafgene -recipes/ucsc-mafmefirst -recipes/ucsc-maforder -recipes/ucsc-mafranges -recipes/ucsc-mafsinregion -recipes/ucsc-mafspecieslist -recipes/ucsc-mafspeciessubset -recipes/ucsc-mafsplit -recipes/ucsc-mafsplitpos -recipes/ucsc-maftoaxt -recipes/ucsc-maftobigmaf -recipes/ucsc-maftopsl -recipes/ucsc-maftosnpbed -recipes/ucsc-maketablelist -recipes/ucsc-maskoutfa -recipes/ucsc-mktime -recipes/ucsc-mrnatogene -recipes/ucsc-netchainsubset -recipes/ucsc-netclass -recipes/ucsc-netfilter -recipes/ucsc-netsplit -recipes/ucsc-netsyntenic -recipes/ucsc-nettoaxt -recipes/ucsc-nettobed -recipes/ucsc-newprog -recipes/ucsc-newpythonprog -recipes/ucsc-nibsize -recipes/ucsc-overlapselect -recipes/ucsc-para -recipes/ucsc-parafetch -recipes/ucsc-parahub -recipes/ucsc-parahubstop -recipes/ucsc-paranode -recipes/ucsc-paranodestart -recipes/ucsc-paranodestatus -recipes/ucsc-paranodestop -recipes/ucsc-parasol -recipes/ucsc-parasync -recipes/ucsc-paratestjob -recipes/ucsc-positionaltblcheck -recipes/ucsc-pslcat -recipes/ucsc-pslcheck -recipes/ucsc-psldropoverlap -recipes/ucsc-pslfilter -recipes/ucsc-pslhisto -recipes/ucsc-pslliftsubrangeblat -recipes/ucsc-pslmap -recipes/ucsc-pslmappostchain -recipes/ucsc-pslmrnacover -recipes/ucsc-pslpairs -recipes/ucsc-pslpartition -recipes/ucsc-pslpretty -recipes/ucsc-pslrc -recipes/ucsc-pslrecalcmatch -recipes/ucsc-pslreps -recipes/ucsc-pslscore -recipes/ucsc-pslselect -recipes/ucsc-pslsomerecords -recipes/ucsc-pslstats -recipes/ucsc-pslswap -recipes/ucsc-psltobigpsl -recipes/ucsc-psltopslx -recipes/ucsc-pslxtofa -recipes/ucsc-qacagplift -recipes/ucsc-qactoqa -recipes/ucsc-qactowig -recipes/ucsc-qatoqac -recipes/ucsc-randomlines -recipes/ucsc-rasqlquery -recipes/ucsc-ratolines -recipes/ucsc-ratotab -recipes/ucsc-rmfadups -recipes/ucsc-rowstocols -recipes/ucsc-spacedtotab -recipes/ucsc-splitfile -recipes/ucsc-splitfilebycolumn -recipes/ucsc-sqltoxml -recipes/ucsc-subchar -recipes/ucsc-subcolumn -recipes/ucsc-taillines -recipes/ucsc-tdbquery -recipes/ucsc-texthistogram -recipes/ucsc-ticktodate -recipes/ucsc-toupper -recipes/ucsc-transmappsltogenepred -recipes/ucsc-trfbig -recipes/ucsc-twobitdup -recipes/ucsc-twobitmask -recipes/ucsc-validatefiles -recipes/ucsc-validatemanifest -recipes/ucsc-websync -recipes/ucsc-wigcorrelate -recipes/ucsc-wordline -recipes/ucsc-xmltosql - # Above v1.0.5 there are licensing restrictions and it cannot be distributed # via bioconda. See https://github.com/bioconda/bioconda-recipes/pull/23476. recipes/fishtaco diff --git a/recipes/abnumber/meta.yaml b/recipes/abnumber/meta.yaml index bf1cba8ad94cf..8a82abd0beb63 100644 --- a/recipes/abnumber/meta.yaml +++ b/recipes/abnumber/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.6" %} # Remember to update sha256 below +{% set version = "0.4.1" %} # Remember to update sha256 below package: name: abnumber @@ -6,7 +6,7 @@ package: source: url: https://github.com/prihoda/abnumber/archive/v{{ version }}.tar.gz - sha256: 'a3120224ca340c224085a8311ee9d5515fccdbadb156d769918bf86e06890d7d' + sha256: '240c7ccc1f85607ffdd0109f19761ab0488a059ae15e3ccd6066ef36c192a047' build: noarch: python diff --git a/recipes/abpoa/meta.yaml b/recipes/abpoa/meta.yaml index ad3e2d163205c..069ecd8444e2e 100644 --- a/recipes/abpoa/meta.yaml +++ b/recipes/abpoa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.2" %} +{% set version = "1.5.3" %} {% set name = "abPOA" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/yangao07/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 706f0ca0110f4974ae7b93157db560bb9beda4273d8c883fa6a03ccb19958149 + sha256: bb97de2dbdec014f2fb24beb0c85fa0b2073f717f3b68639e1edd89239729e6c build: number: 0 diff --git a/recipes/abritamr/meta.yaml b/recipes/abritamr/meta.yaml index 62bda213a61cf..edcc501e5cbc0 100644 --- a/recipes/abritamr/meta.yaml +++ b/recipes/abritamr/meta.yaml @@ -1,6 +1,6 @@ {% set name = "abritamr" %} -{% set version = "1.0.18" %} -{% set sha256 = "d7ea14271302177a4402f0b73ecb36212595960cbc3b2ce46cd50ac2af5b46f3" %} +{% set version = "1.0.19" %} +{% set sha256 = "a0571b3428186295ec27343fa4b648105be81a7fd871462a501c4c2bec43c335" %} package: name: "{{ name|lower }}" diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml index 0d927ebfebd75..813b1133e843f 100644 --- a/recipes/abyss/meta.yaml +++ b/recipes/abyss/meta.yaml @@ -1,18 +1,18 @@ {% set name = "abyss" %} -{% set version = "2.3.8" %} +{% set version = "2.3.9" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x") }} source: url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz - sha256: 3c262269043f619c79ec3dcd91f5595cb141229f9a13d1a76a952b9a0bfb0d84 + sha256: 55f0b27b67b4486dc6cbe132c0f4c228ee4f9e86c56292a7b50633df87e3212e patches: - config.patch diff --git a/recipes/acms/build.sh b/recipes/acms/build.sh new file mode 100644 index 0000000000000..00b12a00c829b --- /dev/null +++ b/recipes/acms/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +make -j ${CPU_COUNT} PREFIX=$PREFIX CC=$CC -C Misc/Applications/aCMs all +make PREFIX=$PREFIX CC=$CC -C Misc/Applications/aCMs install-program +make PREFIX=$PREFIX CC=$CC -C Misc/Applications/lib install +chmod 755 $PREFIX/bin/acmbuild* diff --git a/recipes/acms/meta.yaml b/recipes/acms/meta.yaml new file mode 100644 index 0000000000000..3c3dfbe30c7fd --- /dev/null +++ b/recipes/acms/meta.yaml @@ -0,0 +1,52 @@ +{% set fold_grammars_version = "2.3.2" %} +{% set acms_version = "1.3.0" %} +{% set packagename = "acms" %} +{% set sha256 = "d3e6cc8d2ecd31d4764b41fea589b98c637ff227d7ab3dcfe66f2ad3f24dece5" %} + +package: + name: {{ packagename }} + version: 1.3.0 + +source: + sha256: {{ sha256 }} + # the repository "fold-grammars" contains sources for several programs, i.e. pKiss, RNAshapes, ... + # thus, the version number does not correspond to the {{ packagename }} version number + #url: https://github.com/jlab/fold-grammars/archive/{{ version }}.tar.gz + url: https://github.com/jlab/fold-grammars/archive/refs/tags/{{ fold_grammars_version }}.tar.gz + +build: + number: 1 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('acms', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - ghc + host: + - perl + - bellmans-gapc >=2024.01.12 + - ghc + run: + - perl + - bellmans-gapc >=2024.01.12 + - ghc + +test: + commands: + - acmbuild -h + +about: + home: https://bibiserv.cebitec.uni-bielefeld.de/{{ packagename }} + license: 'GPL-3.0-or-later' + license_file: LICENSE + summary: 'Ambivalent Covariance Models (aCMs) are our prototypic suggestion to extend CMs with more than one consensus structure.' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - doi:10.1186/s12859-015-0569-1 + - doi:10.1093/bioinformatics/btu649 diff --git a/recipes/adapterremoval/meta.yaml b/recipes/adapterremoval/meta.yaml index e916bf3a3bd45..7f369ac53924a 100644 --- a/recipes/adapterremoval/meta.yaml +++ b/recipes/adapterremoval/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.3.3" %} -{% set sha256 = "a1bdc054319ede085fc8a4e9867c23ffed7df5e97b99d52221b7c587d19418fc" %} +{% set version = "2.3.4" %} +{% set sha256 = "a4433a45b73ead907aede22ed0c7ea6fbc080f6de6ed7bc00f52173dfb309aa1" %} package: name: adapterremoval @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 0 run_exports: - {{ pin_subpackage("adapterremoval", max_pin="x") }} diff --git a/recipes/afpdb/meta.yaml b/recipes/afpdb/meta.yaml new file mode 100644 index 0000000000000..0bfcfd3e0e7e6 --- /dev/null +++ b/recipes/afpdb/meta.yaml @@ -0,0 +1,61 @@ +{% set name = "afpdb" %} +{% set version = "0.2.2" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: fbdc60785aba0177a3766f952df8bc848aa03adcc0693506cc9f1f3601449e98 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + host: + - biopython + - dm-tree + - numpy + - pandas + - pip + - py3dmol + - python + - requests + - scipy + - tabulate + run: + - biopython + - dm-tree + - numpy + - pandas + - py3dmol + - python + - requests + - scipy + - tabulate + +test: + imports: + - afpdb + - afpdb.myalphafold + - afpdb.myalphafold.common + - afpdb.mycolabdesign + - afpdb.mycolabfold + +about: + home: "https://github.com/data2code/afpdb" + license: MIT + license_family: MIT + license_file: + summary: "A Numpy-based PDB structure manipulation package" + doc_url: "https://github.com/data2code/afpdb/blob/main/tutorial" + dev_url: + +extra: + recipe-maintainers: + - data2code diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml index a91fde31f4758..758b5d692e261 100755 --- a/recipes/agat/meta.yaml +++ b/recipes/agat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "AGAT" %} -{% set version = "1.4.0" %} -{% set sha256 = "d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77" %} +{% set version = "1.4.1" %} +{% set sha256 = "28dcdbcaac90164fbb75afdc41d34e3c997fbf0f46b0633e0ac653b3c6d2e409" %} package: name: "{{ name|lower }}" diff --git a/recipes/agfusion/meta.yaml b/recipes/agfusion/meta.yaml index 8aa1ba254810a..e75269053c624 100644 --- a/recipes/agfusion/meta.yaml +++ b/recipes/agfusion/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.4.1" %} -{% set sha256 = "fd04591d764deeff69978f9d495c3baf854ccfba27366aa0ae4859ad85ca2c60" %} +{% set version = "1.4.3" %} +{% set sha256 = "0fdace7fad64713173cac049af3783bdb3db406d5a6dafd4cc0c1948d0724c8f" %} package: name: agfusion diff --git a/recipes/alen/build.sh b/recipes/alen/build.sh new file mode 100644 index 0000000000000..c805061187cf0 --- /dev/null +++ b/recipes/alen/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash -euo + +set -xe + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . \ No newline at end of file diff --git a/recipes/alen/meta.yaml b/recipes/alen/meta.yaml new file mode 100644 index 0000000000000..a1fe8cc4ff58f --- /dev/null +++ b/recipes/alen/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.3.1" %} + +package: + name: alen + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("alen", max_pin="x.x") }} + +source: + url: https://github.com/jakobnissen/alen/archive/v{{ version }}.tar.gz + sha256: 30c55c0be3396647286ebfca8c46f88e5d7087482e19fb2e64404f87bad8a523 + +requirements: + build: + - {{ compiler('rust') }} + host: + run: + +test: + commands: + - alen --help + +about: + home: https://github.com/jakobnissen/alen + license: MIT + license_file: LICENSE + summary: Simple terminal sequence alignment viewer + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index 5d3625929f77e..d7ea18f44fdf3 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.1" %} -{% set sha256 = "6a84eef8cb737e856915c88b340304a22e5cc5013f89d3756026f93720f3c8cb" %} +{% set version = "0.3.2" %} +{% set sha256 = "506967a9588ee51911fb4ddd6d2d3274bff0140004b2473de32728de76567d05" %} package: name: alfred @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('alfred', max_pin="x.x") }} diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml index 70647c20c246d..cc6001b85a7db 100644 --- a/recipes/alignoth/meta.yaml +++ b/recipes/alignoth/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.12.1" %} +{% set version = "0.13.0" %} package: name: alignoth @@ -14,7 +14,7 @@ build: source: url: https://github.com/alignoth/alignoth/archive/v{{ version }}.tar.gz - sha256: 9bbff76754c3f183b63047f44995e72a356b0628aee3638addbf6eb15e9a4813 + sha256: a955e762d3593ac572424dbe775f1c554bb5ab10f391fb643c7d613cca416cc4 requirements: build: diff --git a/recipes/allo/meta.yaml b/recipes/allo/meta.yaml index f87b34e141165..5b5ad70173d76 100644 --- a/recipes/allo/meta.yaml +++ b/recipes/allo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "allo" %} -{% set version = "1.1.2" %} +{% set version = "1.2.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/b/bio-{{ name }}/bio_allo-{{ version }}.tar.gz - sha256: 116390a306d76ae8986762292b51e85de710a36e56d532ae7e3cc4df5796befc + sha256: d5ec3b33975743022447ac4cefb9f2b75d188b6f8ece0e8073b636ce6c969f3d build: run_exports: @@ -24,7 +24,7 @@ requirements: - python >=3.10 - numpy - joblib - - tensorflow >=2.11 + - tensorflow >=2.17 - pysam test: diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 5916971d38193..b037d25c280b4 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,22 +1,22 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.3.3" %} +{% set AS_version="1.3.4" %} {% set AA_version="1.4.r2" %} -{% set AC_version="1.2.0" %} +{% set AC_version="1.2.1" %} package: name: {{ name }} version: {{ AS_version }} source: - # the sha256 sum is generated by doing + # the sha256 sum is generated by running the following on the release .tar.gz from Github. # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: c29f159cb641068b5c38529eeb49a975d63b3369407603cf30f3d8cf49a380d5 + sha256: 58f2b74eac0116e0830bceea66a854071e2a205b6f5b8e57ce61a0e358434a61 - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz sha256: 987390d7a32a6c118e6c7fea5c7a5aba2db1b3e64fc3ece5f68f50c7cabf01fa folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz - sha256: 85052324376756ca3558325dce45635276af3f41dd292601f673abaf9990790a + sha256: 5cd6b9f4e2239631b8f11adda99d8858c29de64cf6f1c7a38121946db06803c9 build: noarch: python diff --git a/recipes/anchorwave/meta.yaml b/recipes/anchorwave/meta.yaml index d4e34368db76c..7e9ee0a0d0817 100644 --- a/recipes/anchorwave/meta.yaml +++ b/recipes/anchorwave/meta.yaml @@ -1,7 +1,7 @@ {% set name = "anchorwave" %} -{% set version = "1.2.3" %} -{% set tag = "v1.2.3" %} -{% set sha256 = "1f689c06f9bbc8e1ed64c0addf4aaf5d172a2fea1e55660b8d3f6dfdffe3f157" %} +{% set version = "1.2.5" %} +{% set tag = "v1.2.5" %} +{% set sha256 = "440e233739582f1e3d7a3847a421919b4c426d4f4332f4d812ea4d23b9958cfa" %} package: name: {{ name }} diff --git a/recipes/anglerfish/meta.yaml b/recipes/anglerfish/meta.yaml index d15537aa287a2..d8fccb5046b12 100644 --- a/recipes/anglerfish/meta.yaml +++ b/recipes/anglerfish/meta.yaml @@ -1,36 +1,37 @@ {% set name = "anglerfish" %} -{% set version = "0.6.1" %} +{% set version = "0.7.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://pypi.io/packages/source/b/bio-{{ name }}/bio-{{ name }}-{{ version }}.tar.gz" - sha256: 91a62cbbc388009bd503df0d3f64441c0e86ab377da46f721f5fcf82b9cce331 + url: "https://pypi.io/packages/source/b/bio-{{ name }}/bio_{{ name }}-{{ version }}.tar.gz" + sha256: f756fbc32a55cc98b2fd5e315f503bdebe52d85cc36eb3d12771d0deb2fce846 build: number: 0 noarch: python script: "cp ${RECIPE_DIR}/requirements.txt ${SRC_DIR} && {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" entry_points: - - anglerfish=anglerfish.anglerfish:anglerfish + - anglerfish=anglerfish.cli:app run_exports: - {{ pin_subpackage('anglerfish', max_pin="x.x") }} requirements: host: - pip - - python >=3.7 + - python >=3.12 run: - biopython - - click - minimap2 - numpy - pandas - - python >=3.7 + - python >=3.12 - python-levenshtein - pyyaml + - typer + - typing_extensions test: imports: @@ -42,7 +43,7 @@ test: - anglerfish --help about: - home: "https://github.com/remiolsen/anglerfish" + home: "https://github.com/NationalGenomicsInfrastructure/anglerfish" license: MIT license_family: MIT summary: "Anglerfish, a tool to demultiplex Illumina libraries from ONT data" diff --git a/recipes/anglerfish/requirements.txt b/recipes/anglerfish/requirements.txt index db39464867253..0dfb12778f82a 100644 --- a/recipes/anglerfish/requirements.txt +++ b/recipes/anglerfish/requirements.txt @@ -1,6 +1,7 @@ biopython==1.83 -click==8.1.7 levenshtein==0.23.0 numpy==1.26.3 pandas==2.1.4 -pyyaml==6.0.1 \ No newline at end of file +pyyaml==6.0.1 +typer==0.9.0 +typing_extensions==4.12.2 \ No newline at end of file diff --git a/recipes/anndata2ri/meta.yaml b/recipes/anndata2ri/meta.yaml index b9c15422687c7..a4e795ebc53cd 100644 --- a/recipes/anndata2ri/meta.yaml +++ b/recipes/anndata2ri/meta.yaml @@ -1,12 +1,12 @@ {% set name = "anndata2ri" %} -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps -vvv" run_exports: @@ -14,7 +14,7 @@ build: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42 + sha256: 34a767b16abfac1aacb6edcd394eaf565f53fff6de3e6f47961a3901d3890d93 requirements: host: diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index f0329a528357d..c6fd696b3a026 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.40.0" %} +{% set version = "0.41.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1860e69f89935aa5d5456e55070d4c172cd4b29bdf07ad16b6b4dcf95b4ef7b2 + sha256: 11cf6d760c9a4f5896c5a6883fda2bd39b734862a6acf6af004704edb0752569 requirements: build: diff --git a/recipes/annotsv/meta.yaml b/recipes/annotsv/meta.yaml index 81da5cb827871..16048ac117689 100644 --- a/recipes/annotsv/meta.yaml +++ b/recipes/annotsv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "annotsv" %} -{% set version = "3.4.2" %} -{% set sha256 = "a8a06fc60bd4c8fb380598097f644f02ed22051b5b30f4eb42b2474b170fe91d" %} +{% set version = "3.4.4" %} +{% set sha256 = "ab7afcdddc1aa1215d3d77cdab74d6db4f24f2c56de9b820a6bbf668f48b1d88" %} package: name: {{ name }} diff --git a/recipes/apscale/meta.yaml b/recipes/apscale/meta.yaml index 35804d0fc32bf..e91738cdd3c3a 100644 --- a/recipes/apscale/meta.yaml +++ b/recipes/apscale/meta.yaml @@ -1,5 +1,5 @@ {% set name = "apscale" %} -{% set version = "1.7.1" %} +{% set version = "2.0.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/apscale-{{ version }}.tar.gz - sha256: 99ea723823313e33ee69373fbb9b12d7a62765fe6d74c9f69d61a2d4dc2ea69f + sha256: 52cf592e1446c958b781e5a134a2945989b33008805f46a071c97d073d330f00 build: entry_points: diff --git a/recipes/apu-label-propagation/build.sh b/recipes/apu-label-propagation/build.sh new file mode 100644 index 0000000000000..11f2d38047bb7 --- /dev/null +++ b/recipes/apu-label-propagation/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +set -xe + +mkdir -p ${PREFIX}/bin + +cd src + +$CC -o $PREFIX/bin/apu-label-propagation apu_label_propagation.c -lm + +chmod u+x ${PREFIX}/bin/apu-label-propagation diff --git a/recipes/apu-label-propagation/meta.yaml b/recipes/apu-label-propagation/meta.yaml new file mode 100644 index 0000000000000..d8e15873d5b8d --- /dev/null +++ b/recipes/apu-label-propagation/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.2" %} + +package: + name: apu-label-propagation + version: {{ version }} + +source: + url: https://github.com/anuprulez/NIAPU/archive/refs/tags/{{ version }}.tar.gz + sha256: 50424bf7df99b51dc71a4121beae89ef69b2bb4eaba559c99643baecb8544806 + +build: + number: 2 + run_exports: + - {{ pin_subpackage('apu-label-propagation', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + +test: + commands: + - apu-label-propagation + +about: + home: https://github.com/AndMastro/NIAPU + license: MIT + summary: Adaptive Positive-Unlabelled label propagation + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/architeuthis/meta.yaml b/recipes/architeuthis/meta.yaml index 44e0523a764f2..4b437bd62bb10 100644 --- a/recipes/architeuthis/meta.yaml +++ b/recipes/architeuthis/meta.yaml @@ -1,5 +1,5 @@ {% set name = "architeuthis" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/cdiener/{{ name }}/archive/{{ version }}.tar.gz - sha256: 63aba50c66188202debc822d0ded57d2398f5e4e9d8535f83a2c5e982bb4999f + sha256: 11b0e09785f23e479f3de55e12dfbe788c938a497a64c7293d8c4ce41d57ef2b build: - number: 1 + number: 0 script: - go build -v -ldflags "-w -s -X 'main.version={{ version }}'" -o $PREFIX/bin/architeuthis run_exports: diff --git a/recipes/argnorm/meta.yaml b/recipes/argnorm/meta.yaml index 3eaff5920960f..2349661f642da 100644 --- a/recipes/argnorm/meta.yaml +++ b/recipes/argnorm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "argnorm" %} -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 60589492f01c000a5b8b4c2608cd607d8bc922786b2b3fc0cfbc5a4575cb9baf + sha256: 85b54bff237943af418a4f6fedd83c1c67c14522f9ef81e1b750bbd5aec2051b build: noarch: python diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml index ef376602011c1..321d4a53e99df 100644 --- a/recipes/argo/meta.yaml +++ b/recipes/argo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "argo" %} -{% set version = "0.0.1" %} +{% set version = "0.1.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz - sha256: 88d4993c1509442a933db4a5d406ac5af1d0816637e3d05e53735c188291a1b4 + sha256: 9ddc3bea602e3bdcd3518bb3ecd7795b680addaa513eff0fff83e1010ba4e253 build: noarch: python diff --git a/recipes/art/build.sh b/recipes/art/build.sh index 0ed4c0e67646f..ee2131550a5ab 100644 --- a/recipes/art/build.sh +++ b/recipes/art/build.sh @@ -8,7 +8,11 @@ export CPATH=${PREFIX}/include mkdir -p $PREFIX/bin -./configure --prefix=$PREFIX +if [[ "$HOST" == "arm64-apple-"* ]]; then + ./configure --prefix=$PREFIX --host=arm +else + ./configure --prefix=$PREFIX +fi make -j ${CPU_COUNT} make install diff --git a/recipes/art/meta.yaml b/recipes/art/meta.yaml index cefbaaa1b2e1e..84123e4e38846 100644 --- a/recipes/art/meta.yaml +++ b/recipes/art/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 11 + number: 12 run_exports: - {{ pin_subpackage(name, max_pin=None) }} @@ -40,3 +40,4 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index 481c55de1362a..af993fa78011c 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.7.5" %} +{% set version = "0.7.7" %} package: name: "{{ name|lower }}" @@ -7,14 +7,14 @@ package: source: url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5b5d6ec619775e419c6875215c71a3a1e8c4e745c4a7ddb6847a2c03313a1470 + sha256: 0c6542253464b8ba406aeddc630f5625db74a5e1e07911534be3add0500a1f02 build: number: 0 noarch: python entry_points: - assembly_finder=assembly_finder.__main__:main - script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: - {{ pin_subpackage('assembly_finder', max_pin="x.x") }} @@ -24,9 +24,9 @@ requirements: - pip run: - python >=3.10 - - snakemake-minimal >=7.32.4 - - pulp <2.8 - - snaketool-utils >=0.0.4 + - mamba >=1.5.8 + - snakemake-minimal >=8.0.0 + - snaketool-utils >=0.0.5 - attrmap >=0.0.7 - pyyaml >=6.0 - pandas >=2.2.1 @@ -52,3 +52,5 @@ extra: recipe-maintainers: - farchaab - tpillone + identifiers: + - biotools:assembly_finder diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index 582384a73f4d2..ba381bb2d3dea 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "25.2.0" %} +{% set version = "26.0.0" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz - sha256: 2869033bf551476859792e6fa442204dcd03c37e5a8a6239a19fe2da9e307248 + sha256: 0040d881eca4d695b75ba87c07a6c7abbdd13cc3e200606d77b38b875348cb07 build: number: 0 diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml index 3d686e8bf8ffe..ee058b1597a18 100644 --- a/recipes/auspice/meta.yaml +++ b/recipes/auspice/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.56.0" %} +{% set version = "2.58.0" %} {% set name = "auspice" %} package: @@ -7,10 +7,10 @@ package: source: url: https://registry.npmjs.org/{{ name }}/-/{{ name }}-{{ version }}.tgz - sha256: 89c620bc790c5e3f28969a253f41e36bf35a13346cb8c6ab55868d9c6ee08714 + sha256: cb746010b28de5d0232258113820c551f6f4287e5b0ff67a1e5854adc381ac96 build: - number: 3 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -46,7 +46,7 @@ about: extra: identifiers: # Generic Nextstrain paper, for lack of specific Auspice one - - doi:10.1093/bioinformatics/bty407 + - doi:10.1093/bioinformatics/bty407 additional-platforms: - linux-aarch64 - osx-arm64 diff --git a/recipes/aviary/meta.yaml b/recipes/aviary/meta.yaml index 0b0c688982b3c..bc5287938478b 100644 --- a/recipes/aviary/meta.yaml +++ b/recipes/aviary/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.9.1" %} +{% set version = "0.9.2" %} {% set name = "aviary" %} -{% set sha256 = "51b7096f7e031e0d4cf465249ca6959eda28f66bd8ca24fd5e0989b131a6f9ce" %} +{% set sha256 = "83e18bbd2abf347ae7e0d83d81d671031a6a98324b01053e79c0d86b989c95ba" %} package: name: aviary diff --git a/recipes/bactopia-qc/meta.yaml b/recipes/bactopia-qc/meta.yaml index c353c88a8c8f5..8d3df3e550414 100644 --- a/recipes/bactopia-qc/meta.yaml +++ b/recipes/bactopia-qc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: bactopia-qc @@ -7,10 +7,12 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('bactopia-qc', max_pin='x.x') }} source: url: https://github.com/bactopia/bactopia-qc/archive/v{{version}}.tar.gz - sha256: e30768ecd3f46d84d36d2db8c931db83b350e988822eeb3594db4031e015c7e1 + sha256: f1c07ee9aadd35cc9689070f236617afdc39f28210313675794e21a74f098244 requirements: run: @@ -27,7 +29,7 @@ requirements: - pigz - porechop >=0.2.4 - python >=3.7,<3.11 - - rasusa >=0.7.1 + - rasusa >=1 - rename - sed diff --git a/recipes/bactopia-teton/meta.yaml b/recipes/bactopia-teton/meta.yaml index d1b1ab3117925..1232947ff15cf 100644 --- a/recipes/bactopia-teton/meta.yaml +++ b/recipes/bactopia-teton/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.4" %} +{% set version = "1.1.1" %} package: name: bactopia-teton @@ -12,7 +12,7 @@ build: source: url: https://github.com/bactopia/bactopia-teton/archive/v{{version}}.tar.gz - sha256: 648b476bcf15bc177df1a814d782d318ee6b78a38e2ccb8268c569cbd1576504 + sha256: c62d0f74d5d4f48573af055424368de4ec4f88b744c7e3d451f818838f3b2da1 requirements: run: @@ -28,12 +28,14 @@ requirements: - pigz - python >=3.6,<3.11 - sed + - sizemeup >=1.2.3 - sra-human-scrubber >=2.2 test: commands: - "bactopia-teton" - "kraken-bracken-summary.py --help" + - "teton-prepare.py --help" about: home: https://bactopia.github.io/ diff --git a/recipes/bactopia/meta.yaml b/recipes/bactopia/meta.yaml index 55a6a219c4b5d..f4e2686493bf6 100644 --- a/recipes/bactopia/meta.yaml +++ b/recipes/bactopia/meta.yaml @@ -1,23 +1,23 @@ {% set name = "bactopia" %} -{% set version = "3.0.1" %} +{% set version = "3.1.0" %} package: name: {{ name }} version: {{ version }} build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} source: url: https://github.com/bactopia/bactopia/archive/v{{version}}.tar.gz - sha256: f3f152294555c05ec37c20041385034b02a79a709d7801b07d2115f50115fa4a + sha256: a8134a5de2aa2e3d8131188420dadc034c5dcf4559c5c752148a103ddc47f463 requirements: run: - - bactopia-py 1.0.9 + - bactopia-py 1.1.1 - conda >=22.11.0 - coreutils - mamba >=1.1.0 diff --git a/recipes/baltic/meta.yaml b/recipes/baltic/meta.yaml index 1838b30e463fb..724178253314a 100644 --- a/recipes/baltic/meta.yaml +++ b/recipes/baltic/meta.yaml @@ -1,5 +1,5 @@ {% set name = "baltic" %} -{% set version = "0.2.2" %} +{% set version = "0.3.0" %} package: name: "{{ name|lower }}" @@ -7,21 +7,23 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 095045aeb0f86f7668df5d7f163ab9fec30e59a564fc77c06b5cb756027a1e79 + sha256: d7fd92d0a40840f15826416e5aaaa3b9e40db07df99f9d4add2eeaf683ae385d build: number: 0 - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv noarch: python + run_exports: + - {{ pin_subpackage('baltic', max_pin="x.x") }} requirements: host: - pip - - python + - python >=3.5 run: - matplotlib-base >=2.0.0 - numpy >=1.16 - - python + - python >=3.5 test: imports: @@ -29,7 +31,8 @@ test: about: home: "https://github.com/evogytis/baltic" - license: GPL-3.0 + license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE - summary: "Lightweight package for analyzing, manipulating and visualizing annotated phylogenetic trees" + summary: "Lightweight package for analyzing, manipulating and visualizing annotated phylogenetic trees." + dev_url: "https://github.com/evogytis/baltic" diff --git a/recipes/bambamc/build.sh b/recipes/bambamc/build.sh index e0ae564e50a1c..19c2086ceb10f 100644 --- a/recipes/bambamc/build.sh +++ b/recipes/bambamc/build.sh @@ -1,7 +1,12 @@ #!/usr/bin/env bash +set -xe + +# use newer config.guess and config.sub that support osx arm64 +cp ${RECIPE_DIR}/config.* . + export C_INCLUDE_PATH=${PREFIX}/include export LIBRARY_PATH=${PREFIX}/lib ./configure --prefix=${PREFIX} -make +make -j ${CPU_COUNT} make install diff --git a/recipes/bambamc/config.guess b/recipes/bambamc/config.guess new file mode 100644 index 0000000000000..1972fda8eb05d --- /dev/null +++ b/recipes/bambamc/config.guess @@ -0,0 +1,1700 @@ +#! /bin/sh +# Attempt to guess a canonical system name. +# Copyright 1992-2021 Free Software Foundation, Inc. + +timestamp='2021-01-25' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see . +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). +# +# Originally written by Per Bothner; maintained since 2000 by Ben Elliston. +# +# You can get the latest version of this script from: +# https://git.savannah.gnu.org/cgit/config.git/plain/config.guess +# +# Please send patches to . + + +me=$(echo "$0" | sed -e 's,.*/,,') + +usage="\ +Usage: $0 [OPTION] + +Output the configuration name of the system \`$me' is run on. + +Options: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.guess ($timestamp) + +Originally written by Per Bothner. +Copyright 1992-2021 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + * ) + break ;; + esac +done + +if test $# != 0; then + echo "$me: too many arguments$help" >&2 + exit 1 +fi + +# CC_FOR_BUILD -- compiler used by this script. Note that the use of a +# compiler to aid in system detection is discouraged as it requires +# temporary files to be created and, as you can see below, it is a +# headache to deal with in a portable fashion. + +# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still +# use `HOST_CC' if defined, but it is deprecated. + +# Portable tmp directory creation inspired by the Autoconf team. + +tmp= +# shellcheck disable=SC2172 +trap 'test -z "$tmp" || rm -fr "$tmp"' 0 1 2 13 15 + +set_cc_for_build() { + # prevent multiple calls if $tmp is already set + test "$tmp" && return 0 + : "${TMPDIR=/tmp}" + # shellcheck disable=SC2039 + { tmp=$( (umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null) && test -n "$tmp" && test -d "$tmp" ; } || + { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir "$tmp" 2>/dev/null) ; } || + { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir "$tmp" 2>/dev/null) && echo "Warning: creating insecure temp directory" >&2 ; } || + { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } + dummy=$tmp/dummy + case ${CC_FOR_BUILD-},${HOST_CC-},${CC-} in + ,,) echo "int x;" > "$dummy.c" + for driver in cc gcc c89 c99 ; do + if ($driver -c -o "$dummy.o" "$dummy.c") >/dev/null 2>&1 ; then + CC_FOR_BUILD="$driver" + break + fi + done + if test x"$CC_FOR_BUILD" = x ; then + CC_FOR_BUILD=no_compiler_found + fi + ;; + ,,*) CC_FOR_BUILD=$CC ;; + ,*,*) CC_FOR_BUILD=$HOST_CC ;; + esac +} + +# This is needed to find uname on a Pyramid OSx when run in the BSD universe. +# (ghazi@noc.rutgers.edu 1994-08-24) +if test -f /.attbin/uname ; then + PATH=$PATH:/.attbin ; export PATH +fi + +UNAME_MACHINE=$( (uname -m) 2>/dev/null) || UNAME_MACHINE=unknown +UNAME_RELEASE=$( (uname -r) 2>/dev/null) || UNAME_RELEASE=unknown +UNAME_SYSTEM=$( (uname -s) 2>/dev/null) || UNAME_SYSTEM=unknown +UNAME_VERSION=$( (uname -v) 2>/dev/null) || UNAME_VERSION=unknown + +case "$UNAME_SYSTEM" in +Linux|GNU|GNU/*) + LIBC=unknown + + set_cc_for_build + cat <<-EOF > "$dummy.c" + #include + #if defined(__UCLIBC__) + LIBC=uclibc + #elif defined(__dietlibc__) + LIBC=dietlibc + #elif defined(__GLIBC__) + LIBC=gnu + #else + #include + /* First heuristic to detect musl libc. */ + #ifdef __DEFINED_va_list + LIBC=musl + #endif + #endif + EOF + eval "$($CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g')" + + # Second heuristic to detect musl libc. + if [ "$LIBC" = unknown ] && + command -v ldd >/dev/null && + ldd --version 2>&1 | grep -q ^musl; then + LIBC=musl + fi + + # If the system lacks a compiler, then just pick glibc. + # We could probably try harder. + if [ "$LIBC" = unknown ]; then + LIBC=gnu + fi + ;; +esac + +# Note: order is significant - the case branches are not exclusive. + +case "$UNAME_MACHINE:$UNAME_SYSTEM:$UNAME_RELEASE:$UNAME_VERSION" in + *:NetBSD:*:*) + # NetBSD (nbsd) targets should (where applicable) match one or + # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*, + # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently + # switched to ELF, *-*-netbsd* would select the old + # object file format. This provides both forward + # compatibility and a consistent mechanism for selecting the + # object file format. + # + # Note: NetBSD doesn't particularly care about the vendor + # portion of the name. We always set it to "unknown". + UNAME_MACHINE_ARCH=$( (uname -p 2>/dev/null || \ + /sbin/sysctl -n hw.machine_arch 2>/dev/null || \ + /usr/sbin/sysctl -n hw.machine_arch 2>/dev/null || \ + echo unknown)) + case "$UNAME_MACHINE_ARCH" in + aarch64eb) machine=aarch64_be-unknown ;; + armeb) machine=armeb-unknown ;; + arm*) machine=arm-unknown ;; + sh3el) machine=shl-unknown ;; + sh3eb) machine=sh-unknown ;; + sh5el) machine=sh5le-unknown ;; + earmv*) + arch=$(echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,') + endian=$(echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p') + machine="${arch}${endian}"-unknown + ;; + *) machine="$UNAME_MACHINE_ARCH"-unknown ;; + esac + # The Operating System including object format, if it has switched + # to ELF recently (or will in the future) and ABI. + case "$UNAME_MACHINE_ARCH" in + earm*) + os=netbsdelf + ;; + arm*|i386|m68k|ns32k|sh3*|sparc|vax) + set_cc_for_build + if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ELF__ + then + # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). + # Return netbsd for either. FIX? + os=netbsd + else + os=netbsdelf + fi + ;; + *) + os=netbsd + ;; + esac + # Determine ABI tags. + case "$UNAME_MACHINE_ARCH" in + earm*) + expr='s/^earmv[0-9]/-eabi/;s/eb$//' + abi=$(echo "$UNAME_MACHINE_ARCH" | sed -e "$expr") + ;; + esac + # The OS release + # Debian GNU/NetBSD machines have a different userland, and + # thus, need a distinct triplet. However, they do not need + # kernel version information, so it can be replaced with a + # suitable tag, in the style of linux-gnu. + case "$UNAME_VERSION" in + Debian*) + release='-gnu' + ;; + *) + release=$(echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2) + ;; + esac + # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: + # contains redundant information, the shorter form: + # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. + echo "$machine-${os}${release}${abi-}" + exit ;; + *:Bitrig:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/Bitrig.//') + echo "$UNAME_MACHINE_ARCH"-unknown-bitrig"$UNAME_RELEASE" + exit ;; + *:OpenBSD:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/OpenBSD.//') + echo "$UNAME_MACHINE_ARCH"-unknown-openbsd"$UNAME_RELEASE" + exit ;; + *:LibertyBSD:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/^.*BSD\.//') + echo "$UNAME_MACHINE_ARCH"-unknown-libertybsd"$UNAME_RELEASE" + exit ;; + *:MidnightBSD:*:*) + echo "$UNAME_MACHINE"-unknown-midnightbsd"$UNAME_RELEASE" + exit ;; + *:ekkoBSD:*:*) + echo "$UNAME_MACHINE"-unknown-ekkobsd"$UNAME_RELEASE" + exit ;; + *:SolidBSD:*:*) + echo "$UNAME_MACHINE"-unknown-solidbsd"$UNAME_RELEASE" + exit ;; + *:OS108:*:*) + echo "$UNAME_MACHINE"-unknown-os108_"$UNAME_RELEASE" + exit ;; + macppc:MirBSD:*:*) + echo powerpc-unknown-mirbsd"$UNAME_RELEASE" + exit ;; + *:MirBSD:*:*) + echo "$UNAME_MACHINE"-unknown-mirbsd"$UNAME_RELEASE" + exit ;; + *:Sortix:*:*) + echo "$UNAME_MACHINE"-unknown-sortix + exit ;; + *:Twizzler:*:*) + echo "$UNAME_MACHINE"-unknown-twizzler + exit ;; + *:Redox:*:*) + echo "$UNAME_MACHINE"-unknown-redox + exit ;; + mips:OSF1:*.*) + echo mips-dec-osf1 + exit ;; + alpha:OSF1:*:*) + case $UNAME_RELEASE in + *4.0) + UNAME_RELEASE=$(/usr/sbin/sizer -v | awk '{print $3}') + ;; + *5.*) + UNAME_RELEASE=$(/usr/sbin/sizer -v | awk '{print $4}') + ;; + esac + # According to Compaq, /usr/sbin/psrinfo has been available on + # OSF/1 and Tru64 systems produced since 1995. I hope that + # covers most systems running today. This code pipes the CPU + # types through head -n 1, so we only detect the type of CPU 0. + ALPHA_CPU_TYPE=$(/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1) + case "$ALPHA_CPU_TYPE" in + "EV4 (21064)") + UNAME_MACHINE=alpha ;; + "EV4.5 (21064)") + UNAME_MACHINE=alpha ;; + "LCA4 (21066/21068)") + UNAME_MACHINE=alpha ;; + "EV5 (21164)") + UNAME_MACHINE=alphaev5 ;; + "EV5.6 (21164A)") + UNAME_MACHINE=alphaev56 ;; + "EV5.6 (21164PC)") + UNAME_MACHINE=alphapca56 ;; + "EV5.7 (21164PC)") + UNAME_MACHINE=alphapca57 ;; + "EV6 (21264)") + UNAME_MACHINE=alphaev6 ;; + "EV6.7 (21264A)") + UNAME_MACHINE=alphaev67 ;; + "EV6.8CB (21264C)") + UNAME_MACHINE=alphaev68 ;; + "EV6.8AL (21264B)") + UNAME_MACHINE=alphaev68 ;; + "EV6.8CX (21264D)") + UNAME_MACHINE=alphaev68 ;; + "EV6.9A (21264/EV69A)") + UNAME_MACHINE=alphaev69 ;; + "EV7 (21364)") + UNAME_MACHINE=alphaev7 ;; + "EV7.9 (21364A)") + UNAME_MACHINE=alphaev79 ;; + esac + # A Pn.n version is a patched version. + # A Vn.n version is a released version. + # A Tn.n version is a released field test version. + # A Xn.n version is an unreleased experimental baselevel. + # 1.2 uses "1.2" for uname -r. + echo "$UNAME_MACHINE"-dec-osf"$(echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz)" + # Reset EXIT trap before exiting to avoid spurious non-zero exit code. + exitcode=$? + trap '' 0 + exit $exitcode ;; + Amiga*:UNIX_System_V:4.0:*) + echo m68k-unknown-sysv4 + exit ;; + *:[Aa]miga[Oo][Ss]:*:*) + echo "$UNAME_MACHINE"-unknown-amigaos + exit ;; + *:[Mm]orph[Oo][Ss]:*:*) + echo "$UNAME_MACHINE"-unknown-morphos + exit ;; + *:OS/390:*:*) + echo i370-ibm-openedition + exit ;; + *:z/VM:*:*) + echo s390-ibm-zvmoe + exit ;; + *:OS400:*:*) + echo powerpc-ibm-os400 + exit ;; + arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) + echo arm-acorn-riscix"$UNAME_RELEASE" + exit ;; + arm*:riscos:*:*|arm*:RISCOS:*:*) + echo arm-unknown-riscos + exit ;; + SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) + echo hppa1.1-hitachi-hiuxmpp + exit ;; + Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) + # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. + if test "$( (/bin/universe) 2>/dev/null)" = att ; then + echo pyramid-pyramid-sysv3 + else + echo pyramid-pyramid-bsd + fi + exit ;; + NILE*:*:*:dcosx) + echo pyramid-pyramid-svr4 + exit ;; + DRS?6000:unix:4.0:6*) + echo sparc-icl-nx6 + exit ;; + DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) + case $(/usr/bin/uname -p) in + sparc) echo sparc-icl-nx7; exit ;; + esac ;; + s390x:SunOS:*:*) + echo "$UNAME_MACHINE"-ibm-solaris2"$(echo "$UNAME_RELEASE" | sed -e 's/[^.]*//')" + exit ;; + sun4H:SunOS:5.*:*) + echo sparc-hal-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) + echo sparc-sun-solaris2"$(echo "$UNAME_RELEASE" | sed -e 's/[^.]*//')" + exit ;; + i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) + echo i386-pc-auroraux"$UNAME_RELEASE" + exit ;; + i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) + set_cc_for_build + SUN_ARCH=i386 + # If there is a compiler, see if it is configured for 64-bit objects. + # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. + # This test works for both compilers. + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + SUN_ARCH=x86_64 + fi + fi + echo "$SUN_ARCH"-pc-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:6*:*) + # According to config.sub, this is the proper way to canonicalize + # SunOS6. Hard to guess exactly what SunOS6 will be like, but + # it's likely to be more like Solaris than SunOS4. + echo sparc-sun-solaris3"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:*:*) + case "$(/usr/bin/arch -k)" in + Series*|S4*) + UNAME_RELEASE=$(uname -v) + ;; + esac + # Japanese Language versions have a version number like `4.1.3-JL'. + echo sparc-sun-sunos"$(echo "$UNAME_RELEASE"|sed -e 's/-/_/')" + exit ;; + sun3*:SunOS:*:*) + echo m68k-sun-sunos"$UNAME_RELEASE" + exit ;; + sun*:*:4.2BSD:*) + UNAME_RELEASE=$( (sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null) + test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3 + case "$(/bin/arch)" in + sun3) + echo m68k-sun-sunos"$UNAME_RELEASE" + ;; + sun4) + echo sparc-sun-sunos"$UNAME_RELEASE" + ;; + esac + exit ;; + aushp:SunOS:*:*) + echo sparc-auspex-sunos"$UNAME_RELEASE" + exit ;; + # The situation for MiNT is a little confusing. The machine name + # can be virtually everything (everything which is not + # "atarist" or "atariste" at least should have a processor + # > m68000). The system name ranges from "MiNT" over "FreeMiNT" + # to the lowercase version "mint" (or "freemint"). Finally + # the system name "TOS" denotes a system which is actually not + # MiNT. But MiNT is downward compatible to TOS, so this should + # be no problem. + atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) + echo m68k-milan-mint"$UNAME_RELEASE" + exit ;; + hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) + echo m68k-hades-mint"$UNAME_RELEASE" + exit ;; + *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) + echo m68k-unknown-mint"$UNAME_RELEASE" + exit ;; + m68k:machten:*:*) + echo m68k-apple-machten"$UNAME_RELEASE" + exit ;; + powerpc:machten:*:*) + echo powerpc-apple-machten"$UNAME_RELEASE" + exit ;; + RISC*:Mach:*:*) + echo mips-dec-mach_bsd4.3 + exit ;; + RISC*:ULTRIX:*:*) + echo mips-dec-ultrix"$UNAME_RELEASE" + exit ;; + VAX*:ULTRIX*:*:*) + echo vax-dec-ultrix"$UNAME_RELEASE" + exit ;; + 2020:CLIX:*:* | 2430:CLIX:*:*) + echo clipper-intergraph-clix"$UNAME_RELEASE" + exit ;; + mips:*:*:UMIPS | mips:*:*:RISCos) + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" +#ifdef __cplusplus +#include /* for printf() prototype */ + int main (int argc, char *argv[]) { +#else + int main (argc, argv) int argc; char *argv[]; { +#endif + #if defined (host_mips) && defined (MIPSEB) + #if defined (SYSTYPE_SYSV) + printf ("mips-mips-riscos%ssysv\\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_SVR4) + printf ("mips-mips-riscos%ssvr4\\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) + printf ("mips-mips-riscos%sbsd\\n", argv[1]); exit (0); + #endif + #endif + exit (-1); + } +EOF + $CC_FOR_BUILD -o "$dummy" "$dummy.c" && + dummyarg=$(echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p') && + SYSTEM_NAME=$("$dummy" "$dummyarg") && + { echo "$SYSTEM_NAME"; exit; } + echo mips-mips-riscos"$UNAME_RELEASE" + exit ;; + Motorola:PowerMAX_OS:*:*) + echo powerpc-motorola-powermax + exit ;; + Motorola:*:4.3:PL8-*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:Power_UNIX:*:*) + echo powerpc-harris-powerunix + exit ;; + m88k:CX/UX:7*:*) + echo m88k-harris-cxux7 + exit ;; + m88k:*:4*:R4*) + echo m88k-motorola-sysv4 + exit ;; + m88k:*:3*:R3*) + echo m88k-motorola-sysv3 + exit ;; + AViiON:dgux:*:*) + # DG/UX returns AViiON for all architectures + UNAME_PROCESSOR=$(/usr/bin/uname -p) + if test "$UNAME_PROCESSOR" = mc88100 || test "$UNAME_PROCESSOR" = mc88110 + then + if test "$TARGET_BINARY_INTERFACE"x = m88kdguxelfx || \ + test "$TARGET_BINARY_INTERFACE"x = x + then + echo m88k-dg-dgux"$UNAME_RELEASE" + else + echo m88k-dg-dguxbcs"$UNAME_RELEASE" + fi + else + echo i586-dg-dgux"$UNAME_RELEASE" + fi + exit ;; + M88*:DolphinOS:*:*) # DolphinOS (SVR3) + echo m88k-dolphin-sysv3 + exit ;; + M88*:*:R3*:*) + # Delta 88k system running SVR3 + echo m88k-motorola-sysv3 + exit ;; + XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) + echo m88k-tektronix-sysv3 + exit ;; + Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) + echo m68k-tektronix-bsd + exit ;; + *:IRIX*:*:*) + echo mips-sgi-irix"$(echo "$UNAME_RELEASE"|sed -e 's/-/_/g')" + exit ;; + ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. + echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id + exit ;; # Note that: echo "'$(uname -s)'" gives 'AIX ' + i*86:AIX:*:*) + echo i386-ibm-aix + exit ;; + ia64:AIX:*:*) + if test -x /usr/bin/oslevel ; then + IBM_REV=$(/usr/bin/oslevel) + else + IBM_REV="$UNAME_VERSION.$UNAME_RELEASE" + fi + echo "$UNAME_MACHINE"-ibm-aix"$IBM_REV" + exit ;; + *:AIX:2:3) + if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + #include + + main() + { + if (!__power_pc()) + exit(1); + puts("powerpc-ibm-aix3.2.5"); + exit(0); + } +EOF + if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=$("$dummy") + then + echo "$SYSTEM_NAME" + else + echo rs6000-ibm-aix3.2.5 + fi + elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then + echo rs6000-ibm-aix3.2.4 + else + echo rs6000-ibm-aix3.2 + fi + exit ;; + *:AIX:*:[4567]) + IBM_CPU_ID=$(/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }') + if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then + IBM_ARCH=rs6000 + else + IBM_ARCH=powerpc + fi + if test -x /usr/bin/lslpp ; then + IBM_REV=$(/usr/bin/lslpp -Lqc bos.rte.libc | + awk -F: '{ print $3 }' | sed s/[0-9]*$/0/) + else + IBM_REV="$UNAME_VERSION.$UNAME_RELEASE" + fi + echo "$IBM_ARCH"-ibm-aix"$IBM_REV" + exit ;; + *:AIX:*:*) + echo rs6000-ibm-aix + exit ;; + ibmrt:4.4BSD:*|romp-ibm:4.4BSD:*) + echo romp-ibm-bsd4.4 + exit ;; + ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and + echo romp-ibm-bsd"$UNAME_RELEASE" # 4.3 with uname added to + exit ;; # report: romp-ibm BSD 4.3 + *:BOSX:*:*) + echo rs6000-bull-bosx + exit ;; + DPX/2?00:B.O.S.:*:*) + echo m68k-bull-sysv3 + exit ;; + 9000/[34]??:4.3bsd:1.*:*) + echo m68k-hp-bsd + exit ;; + hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) + echo m68k-hp-bsd4.4 + exit ;; + 9000/[34678]??:HP-UX:*:*) + HPUX_REV=$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//') + case "$UNAME_MACHINE" in + 9000/31?) HP_ARCH=m68000 ;; + 9000/[34]??) HP_ARCH=m68k ;; + 9000/[678][0-9][0-9]) + if test -x /usr/bin/getconf; then + sc_cpu_version=$(/usr/bin/getconf SC_CPU_VERSION 2>/dev/null) + sc_kernel_bits=$(/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null) + case "$sc_cpu_version" in + 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0 + 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1 + 532) # CPU_PA_RISC2_0 + case "$sc_kernel_bits" in + 32) HP_ARCH=hppa2.0n ;; + 64) HP_ARCH=hppa2.0w ;; + '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20 + esac ;; + esac + fi + if test "$HP_ARCH" = ""; then + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + + #define _HPUX_SOURCE + #include + #include + + int main () + { + #if defined(_SC_KERNEL_BITS) + long bits = sysconf(_SC_KERNEL_BITS); + #endif + long cpu = sysconf (_SC_CPU_VERSION); + + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1"); break; + case CPU_PA_RISC2_0: + #if defined(_SC_KERNEL_BITS) + switch (bits) + { + case 64: puts ("hppa2.0w"); break; + case 32: puts ("hppa2.0n"); break; + default: puts ("hppa2.0"); break; + } break; + #else /* !defined(_SC_KERNEL_BITS) */ + puts ("hppa2.0"); break; + #endif + default: puts ("hppa1.0"); break; + } + exit (0); + } +EOF + (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=$("$dummy") + test -z "$HP_ARCH" && HP_ARCH=hppa + fi ;; + esac + if test "$HP_ARCH" = hppa2.0w + then + set_cc_for_build + + # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating + # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler + # generating 64-bit code. GNU and HP use different nomenclature: + # + # $ CC_FOR_BUILD=cc ./config.guess + # => hppa2.0w-hp-hpux11.23 + # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess + # => hppa64-hp-hpux11.23 + + if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | + grep -q __LP64__ + then + HP_ARCH=hppa2.0w + else + HP_ARCH=hppa64 + fi + fi + echo "$HP_ARCH"-hp-hpux"$HPUX_REV" + exit ;; + ia64:HP-UX:*:*) + HPUX_REV=$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//') + echo ia64-hp-hpux"$HPUX_REV" + exit ;; + 3050*:HI-UX:*:*) + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + #include + int + main () + { + long cpu = sysconf (_SC_CPU_VERSION); + /* The order matters, because CPU_IS_HP_MC68K erroneously returns + true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct + results, however. */ + if (CPU_IS_PA_RISC (cpu)) + { + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; + case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; + default: puts ("hppa-hitachi-hiuxwe2"); break; + } + } + else if (CPU_IS_HP_MC68K (cpu)) + puts ("m68k-hitachi-hiuxwe2"); + else puts ("unknown-hitachi-hiuxwe2"); + exit (0); + } +EOF + $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=$("$dummy") && + { echo "$SYSTEM_NAME"; exit; } + echo unknown-hitachi-hiuxwe2 + exit ;; + 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*) + echo hppa1.1-hp-bsd + exit ;; + 9000/8??:4.3bsd:*:*) + echo hppa1.0-hp-bsd + exit ;; + *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) + echo hppa1.0-hp-mpeix + exit ;; + hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*) + echo hppa1.1-hp-osf + exit ;; + hp8??:OSF1:*:*) + echo hppa1.0-hp-osf + exit ;; + i*86:OSF1:*:*) + if test -x /usr/sbin/sysversion ; then + echo "$UNAME_MACHINE"-unknown-osf1mk + else + echo "$UNAME_MACHINE"-unknown-osf1 + fi + exit ;; + parisc*:Lites*:*:*) + echo hppa1.1-hp-lites + exit ;; + C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) + echo c1-convex-bsd + exit ;; + C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit ;; + C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) + echo c34-convex-bsd + exit ;; + C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) + echo c38-convex-bsd + exit ;; + C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) + echo c4-convex-bsd + exit ;; + CRAY*Y-MP:*:*:*) + echo ymp-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*[A-Z]90:*:*:*) + echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \ + | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ + -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ + -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*TS:*:*:*) + echo t90-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*T3E:*:*:*) + echo alphaev5-cray-unicosmk"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*SV1:*:*:*) + echo sv1-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + *:UNICOS/mp:*:*) + echo craynv-cray-unicosmp"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) + FUJITSU_PROC=$(uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz) + FUJITSU_SYS=$(uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///') + FUJITSU_REL=$(echo "$UNAME_RELEASE" | sed -e 's/ /_/') + echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + 5000:UNIX_System_V:4.*:*) + FUJITSU_SYS=$(uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///') + FUJITSU_REL=$(echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/') + echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) + echo "$UNAME_MACHINE"-pc-bsdi"$UNAME_RELEASE" + exit ;; + sparc*:BSD/OS:*:*) + echo sparc-unknown-bsdi"$UNAME_RELEASE" + exit ;; + *:BSD/OS:*:*) + echo "$UNAME_MACHINE"-unknown-bsdi"$UNAME_RELEASE" + exit ;; + arm:FreeBSD:*:*) + UNAME_PROCESSOR=$(uname -p) + set_cc_for_build + if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_PCS_VFP + then + echo "${UNAME_PROCESSOR}"-unknown-freebsd"$(echo ${UNAME_RELEASE}|sed -e 's/[-(].*//')"-gnueabi + else + echo "${UNAME_PROCESSOR}"-unknown-freebsd"$(echo ${UNAME_RELEASE}|sed -e 's/[-(].*//')"-gnueabihf + fi + exit ;; + *:FreeBSD:*:*) + UNAME_PROCESSOR=$(/usr/bin/uname -p) + case "$UNAME_PROCESSOR" in + amd64) + UNAME_PROCESSOR=x86_64 ;; + i386) + UNAME_PROCESSOR=i586 ;; + esac + echo "$UNAME_PROCESSOR"-unknown-freebsd"$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')" + exit ;; + i*:CYGWIN*:*) + echo "$UNAME_MACHINE"-pc-cygwin + exit ;; + *:MINGW64*:*) + echo "$UNAME_MACHINE"-pc-mingw64 + exit ;; + *:MINGW*:*) + echo "$UNAME_MACHINE"-pc-mingw32 + exit ;; + *:MSYS*:*) + echo "$UNAME_MACHINE"-pc-msys + exit ;; + i*:PW*:*) + echo "$UNAME_MACHINE"-pc-pw32 + exit ;; + *:Interix*:*) + case "$UNAME_MACHINE" in + x86) + echo i586-pc-interix"$UNAME_RELEASE" + exit ;; + authenticamd | genuineintel | EM64T) + echo x86_64-unknown-interix"$UNAME_RELEASE" + exit ;; + IA64) + echo ia64-unknown-interix"$UNAME_RELEASE" + exit ;; + esac ;; + i*:UWIN*:*) + echo "$UNAME_MACHINE"-pc-uwin + exit ;; + amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) + echo x86_64-pc-cygwin + exit ;; + prep*:SunOS:5.*:*) + echo powerpcle-unknown-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + *:GNU:*:*) + # the GNU system + echo "$(echo "$UNAME_MACHINE"|sed -e 's,[-/].*$,,')-unknown-$LIBC$(echo "$UNAME_RELEASE"|sed -e 's,/.*$,,')" + exit ;; + *:GNU/*:*:*) + # other systems with GNU libc and userland + echo "$UNAME_MACHINE-unknown-$(echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]")$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')-$LIBC" + exit ;; + *:Minix:*:*) + echo "$UNAME_MACHINE"-unknown-minix + exit ;; + aarch64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + aarch64_be:Linux:*:*) + UNAME_MACHINE=aarch64_be + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + alpha:Linux:*:*) + case $(sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' /proc/cpuinfo 2>/dev/null) in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep -q ld.so.1 + if test "$?" = 0 ; then LIBC=gnulibc1 ; fi + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + arc:Linux:*:* | arceb:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + arm*:Linux:*:*) + set_cc_for_build + if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_EABI__ + then + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + else + if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_PCS_VFP + then + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabi + else + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabihf + fi + fi + exit ;; + avr32*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + cris:Linux:*:*) + echo "$UNAME_MACHINE"-axis-linux-"$LIBC" + exit ;; + crisv32:Linux:*:*) + echo "$UNAME_MACHINE"-axis-linux-"$LIBC" + exit ;; + e2k:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + frv:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + hexagon:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + i*86:Linux:*:*) + echo "$UNAME_MACHINE"-pc-linux-"$LIBC" + exit ;; + ia64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + k1om:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + loongarch32:Linux:*:* | loongarch64:Linux:*:* | loongarchx32:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + m32r*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + m68*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + mips:Linux:*:* | mips64:Linux:*:*) + set_cc_for_build + IS_GLIBC=0 + test x"${LIBC}" = xgnu && IS_GLIBC=1 + sed 's/^ //' << EOF > "$dummy.c" + #undef CPU + #undef mips + #undef mipsel + #undef mips64 + #undef mips64el + #if ${IS_GLIBC} && defined(_ABI64) + LIBCABI=gnuabi64 + #else + #if ${IS_GLIBC} && defined(_ABIN32) + LIBCABI=gnuabin32 + #else + LIBCABI=${LIBC} + #endif + #endif + + #if ${IS_GLIBC} && defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 + CPU=mipsisa64r6 + #else + #if ${IS_GLIBC} && !defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 + CPU=mipsisa32r6 + #else + #if defined(__mips64) + CPU=mips64 + #else + CPU=mips + #endif + #endif + #endif + + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + MIPS_ENDIAN=el + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + MIPS_ENDIAN= + #else + MIPS_ENDIAN= + #endif + #endif +EOF + eval "$($CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU\|^MIPS_ENDIAN\|^LIBCABI')" + test "x$CPU" != x && { echo "$CPU${MIPS_ENDIAN}-unknown-linux-$LIBCABI"; exit; } + ;; + mips64el:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + openrisc*:Linux:*:*) + echo or1k-unknown-linux-"$LIBC" + exit ;; + or32:Linux:*:* | or1k*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + padre:Linux:*:*) + echo sparc-unknown-linux-"$LIBC" + exit ;; + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-"$LIBC" + exit ;; + parisc:Linux:*:* | hppa:Linux:*:*) + # Look for CPU level + case $(grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2) in + PA7*) echo hppa1.1-unknown-linux-"$LIBC" ;; + PA8*) echo hppa2.0-unknown-linux-"$LIBC" ;; + *) echo hppa-unknown-linux-"$LIBC" ;; + esac + exit ;; + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-"$LIBC" + exit ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-"$LIBC" + exit ;; + ppc64le:Linux:*:*) + echo powerpc64le-unknown-linux-"$LIBC" + exit ;; + ppcle:Linux:*:*) + echo powerpcle-unknown-linux-"$LIBC" + exit ;; + riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo "$UNAME_MACHINE"-ibm-linux-"$LIBC" + exit ;; + sh64*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + sh*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + sparc:Linux:*:* | sparc64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + tile*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + vax:Linux:*:*) + echo "$UNAME_MACHINE"-dec-linux-"$LIBC" + exit ;; + x86_64:Linux:*:*) + set_cc_for_build + LIBCABI=$LIBC + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __ILP32__'; echo IS_X32; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_X32 >/dev/null + then + LIBCABI="$LIBC"x32 + fi + fi + echo "$UNAME_MACHINE"-pc-linux-"$LIBCABI" + exit ;; + xtensa*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + i*86:DYNIX/ptx:4*:*) + # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. + # earlier versions are messed up and put the nodename in both + # sysname and nodename. + echo i386-sequent-sysv4 + exit ;; + i*86:UNIX_SV:4.2MP:2.*) + # Unixware is an offshoot of SVR4, but it has its own version + # number series starting with 2... + # I am not positive that other SVR4 systems won't match this, + # I just have to hope. -- rms. + # Use sysv4.2uw... so that sysv4* matches it. + echo "$UNAME_MACHINE"-pc-sysv4.2uw"$UNAME_VERSION" + exit ;; + i*86:OS/2:*:*) + # If we were able to find `uname', then EMX Unix compatibility + # is probably installed. + echo "$UNAME_MACHINE"-pc-os2-emx + exit ;; + i*86:XTS-300:*:STOP) + echo "$UNAME_MACHINE"-unknown-stop + exit ;; + i*86:atheos:*:*) + echo "$UNAME_MACHINE"-unknown-atheos + exit ;; + i*86:syllable:*:*) + echo "$UNAME_MACHINE"-pc-syllable + exit ;; + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) + echo i386-unknown-lynxos"$UNAME_RELEASE" + exit ;; + i*86:*DOS:*:*) + echo "$UNAME_MACHINE"-pc-msdosdjgpp + exit ;; + i*86:*:4.*:*) + UNAME_REL=$(echo "$UNAME_RELEASE" | sed 's/\/MP$//') + if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then + echo "$UNAME_MACHINE"-univel-sysv"$UNAME_REL" + else + echo "$UNAME_MACHINE"-pc-sysv"$UNAME_REL" + fi + exit ;; + i*86:*:5:[678]*) + # UnixWare 7.x, OpenUNIX and OpenServer 6. + case $(/bin/uname -X | grep "^Machine") in + *486*) UNAME_MACHINE=i486 ;; + *Pentium) UNAME_MACHINE=i586 ;; + *Pent*|*Celeron) UNAME_MACHINE=i686 ;; + esac + echo "$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}" + exit ;; + i*86:*:3.2:*) + if test -f /usr/options/cb.name; then + UNAME_REL=$(sed -n 's/.*Version //p' /dev/null >/dev/null ; then + UNAME_REL=$( (/bin/uname -X|grep Release|sed -e 's/.*= //')) + (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 + (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ + && UNAME_MACHINE=i586 + (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ + && UNAME_MACHINE=i686 + (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ + && UNAME_MACHINE=i686 + echo "$UNAME_MACHINE"-pc-sco"$UNAME_REL" + else + echo "$UNAME_MACHINE"-pc-sysv32 + fi + exit ;; + pc:*:*:*) + # Left here for compatibility: + # uname -m prints for DJGPP always 'pc', but it prints nothing about + # the processor, so we play safe by assuming i586. + # Note: whatever this is, it MUST be the same as what config.sub + # prints for the "djgpp" host, or else GDB configure will decide that + # this is a cross-build. + echo i586-pc-msdosdjgpp + exit ;; + Intel:Mach:3*:*) + echo i386-pc-mach3 + exit ;; + paragon:*:*:*) + echo i860-intel-osf1 + exit ;; + i860:*:4.*:*) # i860-SVR4 + if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then + echo i860-stardent-sysv"$UNAME_RELEASE" # Stardent Vistra i860-SVR4 + else # Add other i860-SVR4 vendors below as they are discovered. + echo i860-unknown-sysv"$UNAME_RELEASE" # Unknown i860-SVR4 + fi + exit ;; + mini*:CTIX:SYS*5:*) + # "miniframe" + echo m68010-convergent-sysv + exit ;; + mc68k:UNIX:SYSTEM5:3.51m) + echo m68k-convergent-sysv + exit ;; + M680?0:D-NIX:5.3:*) + echo m68k-diab-dnix + exit ;; + M68*:*:R3V[5678]*:*) + test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; + 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) + OS_REL='' + test -r /etc/.relid \ + && OS_REL=.$(sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; + 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4; exit; } ;; + NCR*:*:4.2:* | MPRAS*:*:4.2:*) + OS_REL='.3' + test -r /etc/.relid \ + && OS_REL=.$(sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; + m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) + echo m68k-unknown-lynxos"$UNAME_RELEASE" + exit ;; + mc68030:UNIX_System_V:4.*:*) + echo m68k-atari-sysv4 + exit ;; + TSUNAMI:LynxOS:2.*:*) + echo sparc-unknown-lynxos"$UNAME_RELEASE" + exit ;; + rs6000:LynxOS:2.*:*) + echo rs6000-unknown-lynxos"$UNAME_RELEASE" + exit ;; + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) + echo powerpc-unknown-lynxos"$UNAME_RELEASE" + exit ;; + SM[BE]S:UNIX_SV:*:*) + echo mips-dde-sysv"$UNAME_RELEASE" + exit ;; + RM*:ReliantUNIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + RM*:SINIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + *:SINIX-*:*:*) + if uname -p 2>/dev/null >/dev/null ; then + UNAME_MACHINE=$( (uname -p) 2>/dev/null) + echo "$UNAME_MACHINE"-sni-sysv4 + else + echo ns32k-sni-sysv + fi + exit ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says + echo i586-unisys-sysv4 + exit ;; + *:UNIX_System_V:4*:FTX*) + # From Gerald Hewes . + # How about differentiating between stratus architectures? -djm + echo hppa1.1-stratus-sysv4 + exit ;; + *:*:*:FTX*) + # From seanf@swdc.stratus.com. + echo i860-stratus-sysv4 + exit ;; + i*86:VOS:*:*) + # From Paul.Green@stratus.com. + echo "$UNAME_MACHINE"-stratus-vos + exit ;; + *:VOS:*:*) + # From Paul.Green@stratus.com. + echo hppa1.1-stratus-vos + exit ;; + mc68*:A/UX:*:*) + echo m68k-apple-aux"$UNAME_RELEASE" + exit ;; + news*:NEWS-OS:6*:*) + echo mips-sony-newsos6 + exit ;; + R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) + if test -d /usr/nec; then + echo mips-nec-sysv"$UNAME_RELEASE" + else + echo mips-unknown-sysv"$UNAME_RELEASE" + fi + exit ;; + BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. + echo powerpc-be-beos + exit ;; + BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. + echo powerpc-apple-beos + exit ;; + BePC:BeOS:*:*) # BeOS running on Intel PC compatible. + echo i586-pc-beos + exit ;; + BePC:Haiku:*:*) # Haiku running on Intel PC compatible. + echo i586-pc-haiku + exit ;; + x86_64:Haiku:*:*) + echo x86_64-unknown-haiku + exit ;; + SX-4:SUPER-UX:*:*) + echo sx4-nec-superux"$UNAME_RELEASE" + exit ;; + SX-5:SUPER-UX:*:*) + echo sx5-nec-superux"$UNAME_RELEASE" + exit ;; + SX-6:SUPER-UX:*:*) + echo sx6-nec-superux"$UNAME_RELEASE" + exit ;; + SX-7:SUPER-UX:*:*) + echo sx7-nec-superux"$UNAME_RELEASE" + exit ;; + SX-8:SUPER-UX:*:*) + echo sx8-nec-superux"$UNAME_RELEASE" + exit ;; + SX-8R:SUPER-UX:*:*) + echo sx8r-nec-superux"$UNAME_RELEASE" + exit ;; + SX-ACE:SUPER-UX:*:*) + echo sxace-nec-superux"$UNAME_RELEASE" + exit ;; + Power*:Rhapsody:*:*) + echo powerpc-apple-rhapsody"$UNAME_RELEASE" + exit ;; + *:Rhapsody:*:*) + echo "$UNAME_MACHINE"-apple-rhapsody"$UNAME_RELEASE" + exit ;; + arm64:Darwin:*:*) + echo aarch64-apple-darwin"$UNAME_RELEASE" + exit ;; + *:Darwin:*:*) + UNAME_PROCESSOR=$(uname -p) + case $UNAME_PROCESSOR in + unknown) UNAME_PROCESSOR=powerpc ;; + esac + if command -v xcode-select > /dev/null 2> /dev/null && \ + ! xcode-select --print-path > /dev/null 2> /dev/null ; then + # Avoid executing cc if there is no toolchain installed as + # cc will be a stub that puts up a graphical alert + # prompting the user to install developer tools. + CC_FOR_BUILD=no_compiler_found + else + set_cc_for_build + fi + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + case $UNAME_PROCESSOR in + i386) UNAME_PROCESSOR=x86_64 ;; + powerpc) UNAME_PROCESSOR=powerpc64 ;; + esac + fi + # On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc + if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_PPC >/dev/null + then + UNAME_PROCESSOR=powerpc + fi + elif test "$UNAME_PROCESSOR" = i386 ; then + # uname -m returns i386 or x86_64 + UNAME_PROCESSOR=$UNAME_MACHINE + fi + echo "$UNAME_PROCESSOR"-apple-darwin"$UNAME_RELEASE" + exit ;; + *:procnto*:*:* | *:QNX:[0123456789]*:*) + UNAME_PROCESSOR=$(uname -p) + if test "$UNAME_PROCESSOR" = x86; then + UNAME_PROCESSOR=i386 + UNAME_MACHINE=pc + fi + echo "$UNAME_PROCESSOR"-"$UNAME_MACHINE"-nto-qnx"$UNAME_RELEASE" + exit ;; + *:QNX:*:4*) + echo i386-pc-qnx + exit ;; + NEO-*:NONSTOP_KERNEL:*:*) + echo neo-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSE-*:NONSTOP_KERNEL:*:*) + echo nse-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSR-*:NONSTOP_KERNEL:*:*) + echo nsr-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSV-*:NONSTOP_KERNEL:*:*) + echo nsv-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSX-*:NONSTOP_KERNEL:*:*) + echo nsx-tandem-nsk"$UNAME_RELEASE" + exit ;; + *:NonStop-UX:*:*) + echo mips-compaq-nonstopux + exit ;; + BS2000:POSIX*:*:*) + echo bs2000-siemens-sysv + exit ;; + DS/*:UNIX_System_V:*:*) + echo "$UNAME_MACHINE"-"$UNAME_SYSTEM"-"$UNAME_RELEASE" + exit ;; + *:Plan9:*:*) + # "uname -m" is not consistent, so use $cputype instead. 386 + # is converted to i386 for consistency with other x86 + # operating systems. + # shellcheck disable=SC2154 + if test "$cputype" = 386; then + UNAME_MACHINE=i386 + else + UNAME_MACHINE="$cputype" + fi + echo "$UNAME_MACHINE"-unknown-plan9 + exit ;; + *:TOPS-10:*:*) + echo pdp10-unknown-tops10 + exit ;; + *:TENEX:*:*) + echo pdp10-unknown-tenex + exit ;; + KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) + echo pdp10-dec-tops20 + exit ;; + XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) + echo pdp10-xkl-tops20 + exit ;; + *:TOPS-20:*:*) + echo pdp10-unknown-tops20 + exit ;; + *:ITS:*:*) + echo pdp10-unknown-its + exit ;; + SEI:*:*:SEIUX) + echo mips-sei-seiux"$UNAME_RELEASE" + exit ;; + *:DragonFly:*:*) + echo "$UNAME_MACHINE"-unknown-dragonfly"$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')" + exit ;; + *:*VMS:*:*) + UNAME_MACHINE=$( (uname -p) 2>/dev/null) + case "$UNAME_MACHINE" in + A*) echo alpha-dec-vms ; exit ;; + I*) echo ia64-dec-vms ; exit ;; + V*) echo vax-dec-vms ; exit ;; + esac ;; + *:XENIX:*:SysV) + echo i386-pc-xenix + exit ;; + i*86:skyos:*:*) + echo "$UNAME_MACHINE"-pc-skyos"$(echo "$UNAME_RELEASE" | sed -e 's/ .*$//')" + exit ;; + i*86:rdos:*:*) + echo "$UNAME_MACHINE"-pc-rdos + exit ;; + *:AROS:*:*) + echo "$UNAME_MACHINE"-unknown-aros + exit ;; + x86_64:VMkernel:*:*) + echo "$UNAME_MACHINE"-unknown-esx + exit ;; + amd64:Isilon\ OneFS:*:*) + echo x86_64-unknown-onefs + exit ;; + *:Unleashed:*:*) + echo "$UNAME_MACHINE"-unknown-unleashed"$UNAME_RELEASE" + exit ;; +esac + +# No uname command or uname output not recognized. +set_cc_for_build +cat > "$dummy.c" < +#include +#endif +#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) +#if defined (vax) || defined (__vax) || defined (__vax__) || defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) +#include +#if defined(_SIZE_T_) || defined(SIGLOST) +#include +#endif +#endif +#endif +main () +{ +#if defined (sony) +#if defined (MIPSEB) + /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, + I don't know.... */ + printf ("mips-sony-bsd\n"); exit (0); +#else +#include + printf ("m68k-sony-newsos%s\n", +#ifdef NEWSOS4 + "4" +#else + "" +#endif + ); exit (0); +#endif +#endif + +#if defined (NeXT) +#if !defined (__ARCHITECTURE__) +#define __ARCHITECTURE__ "m68k" +#endif + int version; + version=$( (hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null); + if (version < 4) + printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); + else + printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); + exit (0); +#endif + +#if defined (MULTIMAX) || defined (n16) +#if defined (UMAXV) + printf ("ns32k-encore-sysv\n"); exit (0); +#else +#if defined (CMU) + printf ("ns32k-encore-mach\n"); exit (0); +#else + printf ("ns32k-encore-bsd\n"); exit (0); +#endif +#endif +#endif + +#if defined (__386BSD__) + printf ("i386-pc-bsd\n"); exit (0); +#endif + +#if defined (sequent) +#if defined (i386) + printf ("i386-sequent-dynix\n"); exit (0); +#endif +#if defined (ns32000) + printf ("ns32k-sequent-dynix\n"); exit (0); +#endif +#endif + +#if defined (_SEQUENT_) + struct utsname un; + + uname(&un); + if (strncmp(un.version, "V2", 2) == 0) { + printf ("i386-sequent-ptx2\n"); exit (0); + } + if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ + printf ("i386-sequent-ptx1\n"); exit (0); + } + printf ("i386-sequent-ptx\n"); exit (0); +#endif + +#if defined (vax) +#if !defined (ultrix) +#include +#if defined (BSD) +#if BSD == 43 + printf ("vax-dec-bsd4.3\n"); exit (0); +#else +#if BSD == 199006 + printf ("vax-dec-bsd4.3reno\n"); exit (0); +#else + printf ("vax-dec-bsd\n"); exit (0); +#endif +#endif +#else + printf ("vax-dec-bsd\n"); exit (0); +#endif +#else +#if defined(_SIZE_T_) || defined(SIGLOST) + struct utsname un; + uname (&un); + printf ("vax-dec-ultrix%s\n", un.release); exit (0); +#else + printf ("vax-dec-ultrix\n"); exit (0); +#endif +#endif +#endif +#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) +#if defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) +#if defined(_SIZE_T_) || defined(SIGLOST) + struct utsname *un; + uname (&un); + printf ("mips-dec-ultrix%s\n", un.release); exit (0); +#else + printf ("mips-dec-ultrix\n"); exit (0); +#endif +#endif +#endif + +#if defined (alliant) && defined (i860) + printf ("i860-alliant-bsd\n"); exit (0); +#endif + + exit (1); +} +EOF + +$CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null && SYSTEM_NAME=$($dummy) && + { echo "$SYSTEM_NAME"; exit; } + +# Apollos put the system type in the environment. +test -d /usr/apollo && { echo "$ISP-apollo-$SYSTYPE"; exit; } + +echo "$0: unable to guess system type" >&2 + +case "$UNAME_MACHINE:$UNAME_SYSTEM" in + mips:Linux | mips64:Linux) + # If we got here on MIPS GNU/Linux, output extra information. + cat >&2 <&2 <&2 </dev/null || echo unknown) +uname -r = $( (uname -r) 2>/dev/null || echo unknown) +uname -s = $( (uname -s) 2>/dev/null || echo unknown) +uname -v = $( (uname -v) 2>/dev/null || echo unknown) + +/usr/bin/uname -p = $( (/usr/bin/uname -p) 2>/dev/null) +/bin/uname -X = $( (/bin/uname -X) 2>/dev/null) + +hostinfo = $( (hostinfo) 2>/dev/null) +/bin/universe = $( (/bin/universe) 2>/dev/null) +/usr/bin/arch -k = $( (/usr/bin/arch -k) 2>/dev/null) +/bin/arch = $( (/bin/arch) 2>/dev/null) +/usr/bin/oslevel = $( (/usr/bin/oslevel) 2>/dev/null) +/usr/convex/getsysinfo = $( (/usr/convex/getsysinfo) 2>/dev/null) + +UNAME_MACHINE = "$UNAME_MACHINE" +UNAME_RELEASE = "$UNAME_RELEASE" +UNAME_SYSTEM = "$UNAME_SYSTEM" +UNAME_VERSION = "$UNAME_VERSION" +EOF +fi + +exit 1 + +# Local variables: +# eval: (add-hook 'before-save-hook 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/recipes/bambamc/config.sub b/recipes/bambamc/config.sub new file mode 100644 index 0000000000000..38f3d037a785f --- /dev/null +++ b/recipes/bambamc/config.sub @@ -0,0 +1,1885 @@ +#! /bin/sh +# Configuration validation subroutine script. +# Copyright 1992-2021 Free Software Foundation, Inc. + +# shellcheck disable=SC2006,SC2268 # see below for rationale + +timestamp='2021-10-27' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see . +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). + + +# Please send patches to . +# +# Configuration subroutine to validate and canonicalize a configuration type. +# Supply the specified configuration type as an argument. +# If it is invalid, we print an error message on stderr and exit with code 1. +# Otherwise, we print the canonical config type on stdout and succeed. + +# You can get the latest version of this script from: +# https://git.savannah.gnu.org/cgit/config.git/plain/config.sub + +# This file is supposed to be the same for all GNU packages +# and recognize all the CPU types, system types and aliases +# that are meaningful with *any* GNU software. +# Each package is responsible for reporting which valid configurations +# it does not support. The user should be able to distinguish +# a failure to support a valid configuration from a meaningless +# configuration. + +# The goal of this file is to map all the various variations of a given +# machine specification into a single specification in the form: +# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM +# or in some cases, the newer four-part form: +# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM +# It is wrong to echo any other type of specification. + +# The "shellcheck disable" line above the timestamp inhibits complaints +# about features and limitations of the classic Bourne shell that were +# superseded or lifted in POSIX. However, this script identifies a wide +# variety of pre-POSIX systems that do not have POSIX shells at all, and +# even some reasonably current systems (Solaris 10 as case-in-point) still +# have a pre-POSIX /bin/sh. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS + +Canonicalize a configuration name. + +Options: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.sub ($timestamp) + +Copyright 1992-2021 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + + *local*) + # First pass through any local machine types. + echo "$1" + exit ;; + + * ) + break ;; + esac +done + +case $# in + 0) echo "$me: missing argument$help" >&2 + exit 1;; + 1) ;; + *) echo "$me: too many arguments$help" >&2 + exit 1;; +esac + +# Split fields of configuration type +# shellcheck disable=SC2162 +saved_IFS=$IFS +IFS="-" read field1 field2 field3 field4 <&2 + exit 1 + ;; + *-*-*-*) + basic_machine=$field1-$field2 + basic_os=$field3-$field4 + ;; + *-*-*) + # Ambiguous whether COMPANY is present, or skipped and KERNEL-OS is two + # parts + maybe_os=$field2-$field3 + case $maybe_os in + nto-qnx* | linux-* | uclinux-uclibc* \ + | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* \ + | netbsd*-eabi* | kopensolaris*-gnu* | cloudabi*-eabi* \ + | storm-chaos* | os2-emx* | rtmk-nova*) + basic_machine=$field1 + basic_os=$maybe_os + ;; + android-linux) + basic_machine=$field1-unknown + basic_os=linux-android + ;; + *) + basic_machine=$field1-$field2 + basic_os=$field3 + ;; + esac + ;; + *-*) + # A lone config we happen to match not fitting any pattern + case $field1-$field2 in + decstation-3100) + basic_machine=mips-dec + basic_os= + ;; + *-*) + # Second component is usually, but not always the OS + case $field2 in + # Prevent following clause from handling this valid os + sun*os*) + basic_machine=$field1 + basic_os=$field2 + ;; + zephyr*) + basic_machine=$field1-unknown + basic_os=$field2 + ;; + # Manufacturers + dec* | mips* | sequent* | encore* | pc533* | sgi* | sony* \ + | att* | 7300* | 3300* | delta* | motorola* | sun[234]* \ + | unicom* | ibm* | next | hp | isi* | apollo | altos* \ + | convergent* | ncr* | news | 32* | 3600* | 3100* \ + | hitachi* | c[123]* | convex* | sun | crds | omron* | dg \ + | ultra | tti* | harris | dolphin | highlevel | gould \ + | cbm | ns | masscomp | apple | axis | knuth | cray \ + | microblaze* | sim | cisco \ + | oki | wec | wrs | winbond) + basic_machine=$field1-$field2 + basic_os= + ;; + *) + basic_machine=$field1 + basic_os=$field2 + ;; + esac + ;; + esac + ;; + *) + # Convert single-component short-hands not valid as part of + # multi-component configurations. + case $field1 in + 386bsd) + basic_machine=i386-pc + basic_os=bsd + ;; + a29khif) + basic_machine=a29k-amd + basic_os=udi + ;; + adobe68k) + basic_machine=m68010-adobe + basic_os=scout + ;; + alliant) + basic_machine=fx80-alliant + basic_os= + ;; + altos | altos3068) + basic_machine=m68k-altos + basic_os= + ;; + am29k) + basic_machine=a29k-none + basic_os=bsd + ;; + amdahl) + basic_machine=580-amdahl + basic_os=sysv + ;; + amiga) + basic_machine=m68k-unknown + basic_os= + ;; + amigaos | amigados) + basic_machine=m68k-unknown + basic_os=amigaos + ;; + amigaunix | amix) + basic_machine=m68k-unknown + basic_os=sysv4 + ;; + apollo68) + basic_machine=m68k-apollo + basic_os=sysv + ;; + apollo68bsd) + basic_machine=m68k-apollo + basic_os=bsd + ;; + aros) + basic_machine=i386-pc + basic_os=aros + ;; + aux) + basic_machine=m68k-apple + basic_os=aux + ;; + balance) + basic_machine=ns32k-sequent + basic_os=dynix + ;; + blackfin) + basic_machine=bfin-unknown + basic_os=linux + ;; + cegcc) + basic_machine=arm-unknown + basic_os=cegcc + ;; + convex-c1) + basic_machine=c1-convex + basic_os=bsd + ;; + convex-c2) + basic_machine=c2-convex + basic_os=bsd + ;; + convex-c32) + basic_machine=c32-convex + basic_os=bsd + ;; + convex-c34) + basic_machine=c34-convex + basic_os=bsd + ;; + convex-c38) + basic_machine=c38-convex + basic_os=bsd + ;; + cray) + basic_machine=j90-cray + basic_os=unicos + ;; + crds | unos) + basic_machine=m68k-crds + basic_os= + ;; + da30) + basic_machine=m68k-da30 + basic_os= + ;; + decstation | pmax | pmin | dec3100 | decstatn) + basic_machine=mips-dec + basic_os= + ;; + delta88) + basic_machine=m88k-motorola + basic_os=sysv3 + ;; + dicos) + basic_machine=i686-pc + basic_os=dicos + ;; + djgpp) + basic_machine=i586-pc + basic_os=msdosdjgpp + ;; + ebmon29k) + basic_machine=a29k-amd + basic_os=ebmon + ;; + es1800 | OSE68k | ose68k | ose | OSE) + basic_machine=m68k-ericsson + basic_os=ose + ;; + gmicro) + basic_machine=tron-gmicro + basic_os=sysv + ;; + go32) + basic_machine=i386-pc + basic_os=go32 + ;; + h8300hms) + basic_machine=h8300-hitachi + basic_os=hms + ;; + h8300xray) + basic_machine=h8300-hitachi + basic_os=xray + ;; + h8500hms) + basic_machine=h8500-hitachi + basic_os=hms + ;; + harris) + basic_machine=m88k-harris + basic_os=sysv3 + ;; + hp300 | hp300hpux) + basic_machine=m68k-hp + basic_os=hpux + ;; + hp300bsd) + basic_machine=m68k-hp + basic_os=bsd + ;; + hppaosf) + basic_machine=hppa1.1-hp + basic_os=osf + ;; + hppro) + basic_machine=hppa1.1-hp + basic_os=proelf + ;; + i386mach) + basic_machine=i386-mach + basic_os=mach + ;; + isi68 | isi) + basic_machine=m68k-isi + basic_os=sysv + ;; + m68knommu) + basic_machine=m68k-unknown + basic_os=linux + ;; + magnum | m3230) + basic_machine=mips-mips + basic_os=sysv + ;; + merlin) + basic_machine=ns32k-utek + basic_os=sysv + ;; + mingw64) + basic_machine=x86_64-pc + basic_os=mingw64 + ;; + mingw32) + basic_machine=i686-pc + basic_os=mingw32 + ;; + mingw32ce) + basic_machine=arm-unknown + basic_os=mingw32ce + ;; + monitor) + basic_machine=m68k-rom68k + basic_os=coff + ;; + morphos) + basic_machine=powerpc-unknown + basic_os=morphos + ;; + moxiebox) + basic_machine=moxie-unknown + basic_os=moxiebox + ;; + msdos) + basic_machine=i386-pc + basic_os=msdos + ;; + msys) + basic_machine=i686-pc + basic_os=msys + ;; + mvs) + basic_machine=i370-ibm + basic_os=mvs + ;; + nacl) + basic_machine=le32-unknown + basic_os=nacl + ;; + ncr3000) + basic_machine=i486-ncr + basic_os=sysv4 + ;; + netbsd386) + basic_machine=i386-pc + basic_os=netbsd + ;; + netwinder) + basic_machine=armv4l-rebel + basic_os=linux + ;; + news | news700 | news800 | news900) + basic_machine=m68k-sony + basic_os=newsos + ;; + news1000) + basic_machine=m68030-sony + basic_os=newsos + ;; + necv70) + basic_machine=v70-nec + basic_os=sysv + ;; + nh3000) + basic_machine=m68k-harris + basic_os=cxux + ;; + nh[45]000) + basic_machine=m88k-harris + basic_os=cxux + ;; + nindy960) + basic_machine=i960-intel + basic_os=nindy + ;; + mon960) + basic_machine=i960-intel + basic_os=mon960 + ;; + nonstopux) + basic_machine=mips-compaq + basic_os=nonstopux + ;; + os400) + basic_machine=powerpc-ibm + basic_os=os400 + ;; + OSE68000 | ose68000) + basic_machine=m68000-ericsson + basic_os=ose + ;; + os68k) + basic_machine=m68k-none + basic_os=os68k + ;; + paragon) + basic_machine=i860-intel + basic_os=osf + ;; + parisc) + basic_machine=hppa-unknown + basic_os=linux + ;; + psp) + basic_machine=mipsallegrexel-sony + basic_os=psp + ;; + pw32) + basic_machine=i586-unknown + basic_os=pw32 + ;; + rdos | rdos64) + basic_machine=x86_64-pc + basic_os=rdos + ;; + rdos32) + basic_machine=i386-pc + basic_os=rdos + ;; + rom68k) + basic_machine=m68k-rom68k + basic_os=coff + ;; + sa29200) + basic_machine=a29k-amd + basic_os=udi + ;; + sei) + basic_machine=mips-sei + basic_os=seiux + ;; + sequent) + basic_machine=i386-sequent + basic_os= + ;; + sps7) + basic_machine=m68k-bull + basic_os=sysv2 + ;; + st2000) + basic_machine=m68k-tandem + basic_os= + ;; + stratus) + basic_machine=i860-stratus + basic_os=sysv4 + ;; + sun2) + basic_machine=m68000-sun + basic_os= + ;; + sun2os3) + basic_machine=m68000-sun + basic_os=sunos3 + ;; + sun2os4) + basic_machine=m68000-sun + basic_os=sunos4 + ;; + sun3) + basic_machine=m68k-sun + basic_os= + ;; + sun3os3) + basic_machine=m68k-sun + basic_os=sunos3 + ;; + sun3os4) + basic_machine=m68k-sun + basic_os=sunos4 + ;; + sun4) + basic_machine=sparc-sun + basic_os= + ;; + sun4os3) + basic_machine=sparc-sun + basic_os=sunos3 + ;; + sun4os4) + basic_machine=sparc-sun + basic_os=sunos4 + ;; + sun4sol2) + basic_machine=sparc-sun + basic_os=solaris2 + ;; + sun386 | sun386i | roadrunner) + basic_machine=i386-sun + basic_os= + ;; + sv1) + basic_machine=sv1-cray + basic_os=unicos + ;; + symmetry) + basic_machine=i386-sequent + basic_os=dynix + ;; + t3e) + basic_machine=alphaev5-cray + basic_os=unicos + ;; + t90) + basic_machine=t90-cray + basic_os=unicos + ;; + toad1) + basic_machine=pdp10-xkl + basic_os=tops20 + ;; + tpf) + basic_machine=s390x-ibm + basic_os=tpf + ;; + udi29k) + basic_machine=a29k-amd + basic_os=udi + ;; + ultra3) + basic_machine=a29k-nyu + basic_os=sym1 + ;; + v810 | necv810) + basic_machine=v810-nec + basic_os=none + ;; + vaxv) + basic_machine=vax-dec + basic_os=sysv + ;; + vms) + basic_machine=vax-dec + basic_os=vms + ;; + vsta) + basic_machine=i386-pc + basic_os=vsta + ;; + vxworks960) + basic_machine=i960-wrs + basic_os=vxworks + ;; + vxworks68) + basic_machine=m68k-wrs + basic_os=vxworks + ;; + vxworks29k) + basic_machine=a29k-wrs + basic_os=vxworks + ;; + xbox) + basic_machine=i686-pc + basic_os=mingw32 + ;; + ymp) + basic_machine=ymp-cray + basic_os=unicos + ;; + *) + basic_machine=$1 + basic_os= + ;; + esac + ;; +esac + +# Decode 1-component or ad-hoc basic machines +case $basic_machine in + # Here we handle the default manufacturer of certain CPU types. It is in + # some cases the only manufacturer, in others, it is the most popular. + w89k) + cpu=hppa1.1 + vendor=winbond + ;; + op50n) + cpu=hppa1.1 + vendor=oki + ;; + op60c) + cpu=hppa1.1 + vendor=oki + ;; + ibm*) + cpu=i370 + vendor=ibm + ;; + orion105) + cpu=clipper + vendor=highlevel + ;; + mac | mpw | mac-mpw) + cpu=m68k + vendor=apple + ;; + pmac | pmac-mpw) + cpu=powerpc + vendor=apple + ;; + + # Recognize the various machine names and aliases which stand + # for a CPU type and a company and sometimes even an OS. + 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) + cpu=m68000 + vendor=att + ;; + 3b*) + cpu=we32k + vendor=att + ;; + bluegene*) + cpu=powerpc + vendor=ibm + basic_os=cnk + ;; + decsystem10* | dec10*) + cpu=pdp10 + vendor=dec + basic_os=tops10 + ;; + decsystem20* | dec20*) + cpu=pdp10 + vendor=dec + basic_os=tops20 + ;; + delta | 3300 | motorola-3300 | motorola-delta \ + | 3300-motorola | delta-motorola) + cpu=m68k + vendor=motorola + ;; + dpx2*) + cpu=m68k + vendor=bull + basic_os=sysv3 + ;; + encore | umax | mmax) + cpu=ns32k + vendor=encore + ;; + elxsi) + cpu=elxsi + vendor=elxsi + basic_os=${basic_os:-bsd} + ;; + fx2800) + cpu=i860 + vendor=alliant + ;; + genix) + cpu=ns32k + vendor=ns + ;; + h3050r* | hiux*) + cpu=hppa1.1 + vendor=hitachi + basic_os=hiuxwe2 + ;; + hp3k9[0-9][0-9] | hp9[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + hp9k2[0-9][0-9] | hp9k31[0-9]) + cpu=m68000 + vendor=hp + ;; + hp9k3[2-9][0-9]) + cpu=m68k + vendor=hp + ;; + hp9k6[0-9][0-9] | hp6[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + hp9k7[0-79][0-9] | hp7[0-79][0-9]) + cpu=hppa1.1 + vendor=hp + ;; + hp9k78[0-9] | hp78[0-9]) + # FIXME: really hppa2.0-hp + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) + # FIXME: really hppa2.0-hp + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[0-9][13679] | hp8[0-9][13679]) + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[0-9][0-9] | hp8[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + i*86v32) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv32 + ;; + i*86v4*) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv4 + ;; + i*86v) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv + ;; + i*86sol2) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=solaris2 + ;; + j90 | j90-cray) + cpu=j90 + vendor=cray + basic_os=${basic_os:-unicos} + ;; + iris | iris4d) + cpu=mips + vendor=sgi + case $basic_os in + irix*) + ;; + *) + basic_os=irix4 + ;; + esac + ;; + miniframe) + cpu=m68000 + vendor=convergent + ;; + *mint | mint[0-9]* | *MiNT | *MiNT[0-9]*) + cpu=m68k + vendor=atari + basic_os=mint + ;; + news-3600 | risc-news) + cpu=mips + vendor=sony + basic_os=newsos + ;; + next | m*-next) + cpu=m68k + vendor=next + case $basic_os in + openstep*) + ;; + nextstep*) + ;; + ns2*) + basic_os=nextstep2 + ;; + *) + basic_os=nextstep3 + ;; + esac + ;; + np1) + cpu=np1 + vendor=gould + ;; + op50n-* | op60c-*) + cpu=hppa1.1 + vendor=oki + basic_os=proelf + ;; + pa-hitachi) + cpu=hppa1.1 + vendor=hitachi + basic_os=hiuxwe2 + ;; + pbd) + cpu=sparc + vendor=tti + ;; + pbb) + cpu=m68k + vendor=tti + ;; + pc532) + cpu=ns32k + vendor=pc532 + ;; + pn) + cpu=pn + vendor=gould + ;; + power) + cpu=power + vendor=ibm + ;; + ps2) + cpu=i386 + vendor=ibm + ;; + rm[46]00) + cpu=mips + vendor=siemens + ;; + rtpc | rtpc-*) + cpu=romp + vendor=ibm + ;; + sde) + cpu=mipsisa32 + vendor=sde + basic_os=${basic_os:-elf} + ;; + simso-wrs) + cpu=sparclite + vendor=wrs + basic_os=vxworks + ;; + tower | tower-32) + cpu=m68k + vendor=ncr + ;; + vpp*|vx|vx-*) + cpu=f301 + vendor=fujitsu + ;; + w65) + cpu=w65 + vendor=wdc + ;; + w89k-*) + cpu=hppa1.1 + vendor=winbond + basic_os=proelf + ;; + none) + cpu=none + vendor=none + ;; + leon|leon[3-9]) + cpu=sparc + vendor=$basic_machine + ;; + leon-*|leon[3-9]-*) + cpu=sparc + vendor=`echo "$basic_machine" | sed 's/-.*//'` + ;; + + *-*) + # shellcheck disable=SC2162 + saved_IFS=$IFS + IFS="-" read cpu vendor <&2 + exit 1 + ;; + esac + ;; +esac + +# Here we canonicalize certain aliases for manufacturers. +case $vendor in + digital*) + vendor=dec + ;; + commodore*) + vendor=cbm + ;; + *) + ;; +esac + +# Decode manufacturer-specific aliases for certain operating systems. + +if test x$basic_os != x +then + +# First recognize some ad-hoc cases, or perhaps split kernel-os, or else just +# set os. +case $basic_os in + gnu/linux*) + kernel=linux + os=`echo "$basic_os" | sed -e 's|gnu/linux|gnu|'` + ;; + os2-emx) + kernel=os2 + os=`echo "$basic_os" | sed -e 's|os2-emx|emx|'` + ;; + nto-qnx*) + kernel=nto + os=`echo "$basic_os" | sed -e 's|nto-qnx|qnx|'` + ;; + *-*) + # shellcheck disable=SC2162 + saved_IFS=$IFS + IFS="-" read kernel os <&2 + exit 1 + ;; +esac + +# As a final step for OS-related things, validate the OS-kernel combination +# (given a valid OS), if there is a kernel. +case $kernel-$os in + linux-gnu* | linux-dietlibc* | linux-android* | linux-newlib* \ + | linux-musl* | linux-relibc* | linux-uclibc* ) + ;; + uclinux-uclibc* ) + ;; + -dietlibc* | -newlib* | -musl* | -relibc* | -uclibc* ) + # These are just libc implementations, not actual OSes, and thus + # require a kernel. + echo "Invalid configuration \`$1': libc \`$os' needs explicit kernel." 1>&2 + exit 1 + ;; + kfreebsd*-gnu* | kopensolaris*-gnu*) + ;; + vxworks-simlinux | vxworks-simwindows | vxworks-spe) + ;; + nto-qnx*) + ;; + os2-emx) + ;; + *-eabi* | *-gnueabi*) + ;; + -*) + # Blank kernel with real OS is always fine. + ;; + *-*) + echo "Invalid configuration \`$1': Kernel \`$kernel' not known to work with OS \`$os'." 1>&2 + exit 1 + ;; +esac + +# Here we handle the case where we know the os, and the CPU type, but not the +# manufacturer. We pick the logical manufacturer. +case $vendor in + unknown) + case $cpu-$os in + *-riscix*) + vendor=acorn + ;; + *-sunos*) + vendor=sun + ;; + *-cnk* | *-aix*) + vendor=ibm + ;; + *-beos*) + vendor=be + ;; + *-hpux*) + vendor=hp + ;; + *-mpeix*) + vendor=hp + ;; + *-hiux*) + vendor=hitachi + ;; + *-unos*) + vendor=crds + ;; + *-dgux*) + vendor=dg + ;; + *-luna*) + vendor=omron + ;; + *-genix*) + vendor=ns + ;; + *-clix*) + vendor=intergraph + ;; + *-mvs* | *-opened*) + vendor=ibm + ;; + *-os400*) + vendor=ibm + ;; + s390-* | s390x-*) + vendor=ibm + ;; + *-ptx*) + vendor=sequent + ;; + *-tpf*) + vendor=ibm + ;; + *-vxsim* | *-vxworks* | *-windiss*) + vendor=wrs + ;; + *-aux*) + vendor=apple + ;; + *-hms*) + vendor=hitachi + ;; + *-mpw* | *-macos*) + vendor=apple + ;; + *-*mint | *-mint[0-9]* | *-*MiNT | *-MiNT[0-9]*) + vendor=atari + ;; + *-vos*) + vendor=stratus + ;; + esac + ;; +esac + +echo "$cpu-$vendor-${kernel:+$kernel-}$os" +exit + +# Local variables: +# eval: (add-hook 'before-save-hook 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/recipes/bambamc/meta.yaml b/recipes/bambamc/meta.yaml index 333d2989bd85e..113f9b83fe42e 100644 --- a/recipes/bambamc/meta.yaml +++ b/recipes/bambamc/meta.yaml @@ -7,7 +7,9 @@ source: md5: 4de1f030fab1de54387f68e4fbd2cd35 build: - number: 7 + number: 8 + run_exports: + - {{ pin_subpackage('bambamc', max_pin="x.x.x") }} requirements: build: @@ -31,3 +33,8 @@ about: license: GPLv3 license_file: COPYING summary: lightweight C implementation of name collating BAM file input and BAM file output + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/bamdash/meta.yaml b/recipes/bamdash/meta.yaml index c245a749ceb5c..e583fa3f821fc 100644 --- a/recipes/bamdash/meta.yaml +++ b/recipes/bamdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bamdash" %} -{% set version = "0.3" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/bamdash-{{ version }}.tar.gz - sha256: aca6cf247961b7d1e50afa7fe121056ed6039c918d68d8c816f60bc331a7d876 + sha256: db8ff295b8e16bb290e3cd53fa04aa86d9a2cfd18c053f62a6379bb6c8272b26 build: entry_points: diff --git a/recipes/bbmap/build.sh b/recipes/bbmap/build.sh index 3cad42d6b4a27..c7989d9fdf823 100755 --- a/recipes/bbmap/build.sh +++ b/recipes/bbmap/build.sh @@ -12,8 +12,8 @@ mkdir -p $DATA_HOME chmod a+x *.sh -cp -R * $BBMAP_HOME/ +cp -Rf * $BBMAP_HOME/ -find *.sh -type f -exec ln -s $BBMAP_HOME/{} $BINARY_HOME/{} \; +find *.sh -type f -exec ln -sf $BBMAP_HOME/{} $BINARY_HOME/{} \; -cp -R $BBMAP_HOME/resources $DATA_HOME +cp -Rf $BBMAP_HOME/resources $DATA_HOME diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml index 7cc8eb01e781e..96c8679f42e91 100644 --- a/recipes/bbmap/meta.yaml +++ b/recipes/bbmap/meta.yaml @@ -1,17 +1,17 @@ {% set name = "BBMap" %} -{% set version = "39.06" %} -{% set sha256 = "61d45bd59a543b90a143c5c7dbfec0ff6163dce54194b8c4b648fb6aac67d42e" %} +{% set version = "39.09" %} +{% set sha256 = "df7871a18eff981d405472ff4bba3db8f99cac106acf3bb84d7435f260b33e54" %} package: name: {{ name|lower }} version: {{ version }} source: - url: http://downloads.sourceforge.net/project/{{ name|lower }}/{{ name }}_{{ version }}.tar.gz + url: https://downloads.sourceforge.net/project/{{ name|lower }}/{{ name }}_{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} @@ -23,10 +23,9 @@ requirements: - pbzip2 - bzip2 - samtools + - patchelf # [osx] run: - openjdk >=7.0 - - pbzip2 - - bzip2 - samtools test: @@ -45,16 +44,19 @@ about: home: https://sourceforge.net/projects/bbmap doc_url: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ license: "UC-LBL license (see package)" - license_file: license.txt + license_file: "license.txt" summary: "BBMap is a short read aligner, as well as various other bioinformatic tools." + dev_url: https://sourceforge.net/projects/bbmap extra: additional-platforms: - linux-aarch64 + - osx-arm64 notes: | BBMap is a series of Java programs, but they come with a number of custom wrapper shell scripts. Each of these is symlinked to the conda bin directory during install. identifiers: - biotools:bbmap + - usegalaxy-eu:bbtools_bbmap - doi:10.1371/journal.pone.0185056 diff --git a/recipes/bbmix/meta.yaml b/recipes/bbmix/meta.yaml new file mode 100644 index 0000000000000..300260eec6617 --- /dev/null +++ b/recipes/bbmix/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "bbmix" %} +{% set version = "0.2.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/bbmix-{{ version }}.tar.gz + sha256: 33b8891b4e1f7f1c5059c755ad888af2412b79738ec0cfb2f194ba7329c9bce6 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('bbmix', max_pin="x.x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - numpy >=1.9.0 + - scipy >=1.4.0 + - matplotlib-base + +test: + imports: + - bbmix + +about: + home: "https://github.com/statbiomed/betabinmix" + summary: 'BBMix: inference of beta-binomial mixture model' + license: "Apache-2.0" + license_family: APACHE + license_file: LICENSE + dev_url: "https://github.com/statbiomed/betabinmix" diff --git a/recipes/bcbio-gff/0.6.2/meta.yaml b/recipes/bcbio-gff/0.6.2/meta.yaml index 9a88bf7a0c348..97d545454cf69 100644 --- a/recipes/bcbio-gff/0.6.2/meta.yaml +++ b/recipes/bcbio-gff/0.6.2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -22,7 +22,7 @@ requirements: run: - python - six - - biopython + - biopython <=1.78 - bx-python test: diff --git a/recipes/bcbio-gff/0.6.4/meta.yaml b/recipes/bcbio-gff/0.6.4/meta.yaml index 293650e9cf2de..11ad4bd1be87a 100644 --- a/recipes/bcbio-gff/0.6.4/meta.yaml +++ b/recipes/bcbio-gff/0.6.4/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -22,7 +22,7 @@ requirements: run: - python - six - - biopython + - biopython <=1.78 - bx-python test: diff --git a/recipes/bcbio-gff/meta.yaml b/recipes/bcbio-gff/meta.yaml index cceb7684f852b..24d4a1716f553 100644 --- a/recipes/bcbio-gff/meta.yaml +++ b/recipes/bcbio-gff/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d1dc3294147b95baced6033f6386a0fed45c43767ef02d1223df5ef497e9cca6 build: - number: 1 + number: 2 noarch: python run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} @@ -23,12 +23,13 @@ requirements: run: - python - six - - biopython + - biopython <=1.86 - bx-python test: imports: - BCBio.GFF + about: home: https://github.com/chapmanb/bcbb/tree/master/gff license: Biopython License Agreement diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index 61846b556ed34..c2d6bc3961469 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -1,17 +1,17 @@ -{% set version="1.20" %} +{% set version="1.21" %} package: name: bcftools version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("bcftools", max_pin="x") }} source: url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - sha256: 312b8329de5130dd3a37678c712951e61e5771557c7129a70a327a300fda8620 + sha256: 528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282 requirements: build: diff --git a/recipes/bcgtree/build.sh b/recipes/bcgtree/build.sh new file mode 100755 index 0000000000000..76615afda3810 --- /dev/null +++ b/recipes/bcgtree/build.sh @@ -0,0 +1,18 @@ +#!/bin/sh +set -e + +mkdir -pv "$PREFIX/bin" +mkdir -pv "$PREFIX/SeqFilter" +mkdir -pv "$PREFIX/data" +mkdir -pv "$PREFIX/lib" + +sed -i 's/\/usr\/bin\/perl/\/bin\/env perl/' bin/*.pl +sed -i 's/\/usr\/bin\/python/\/bin\/env python/' bin/*.py +sed -i 's/\/bin\/bash/\/bin\/env bash/' bin/*.sh + +cp bin/* "$PREFIX/bin/" +cp -R SeqFilter/* "$PREFIX/SeqFilter/" +cp -R data/* "$PREFIX/data/" +cp -R lib/* "$PREFIX/lib" + + diff --git a/recipes/bcgtree/meta.yaml b/recipes/bcgtree/meta.yaml new file mode 100755 index 0000000000000..b6650dcf4cf90 --- /dev/null +++ b/recipes/bcgtree/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "bcgtree" %} +{% set version = "1.2.1" %} +{% set sha256 = "7739da7bf8e36933a45ee62e72cdf5988626595223baab96ec24a657a814b4a2" %} + +package: + name: '{{ name }}' + version: '{{ version }}' + +source: + url: https://github.com/molbiodiv/{{ name }}/archive/v{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('bcgtree', max_pin="x") }} + +requirements: + host: + - perl + run: + - perl + - python + - bash + - prodigal + - hmmer + - muscle =3.8.1551 + - gblocks + - raxml + +test: + commands: + - bcgTree.pl --version + +about: + home: https://github.com/molbiodiv/{{ name }} + summary: Automatized phylogenetic tree building from bacterial core genomes + license: MIT + license_family: MIT + license_file: LICENSE + diff --git a/recipes/beacon2-import/meta.yaml b/recipes/beacon2-import/meta.yaml index 30562965cc5d4..e82608f48d1d5 100644 --- a/recipes/beacon2-import/meta.yaml +++ b/recipes/beacon2-import/meta.yaml @@ -1,13 +1,13 @@ {% set name = "beacon2-import" %} -{% set version = "2.2.1" %} +{% set version = "2.2.4" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/beacon2-import-{{ version }}.tar.gz - sha256: 1c8e26beaed158563dbf46f86aec89be385fa79c40f05e081edcb5a91c954290 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/beacon2_import-{{ version }}.tar.gz + sha256: 238fe76cc0a82ff1c3881ea4a376f664885761e0e211477064147209442f7201 build: entry_points: diff --git a/recipes/beav/meta.yaml b/recipes/beav/meta.yaml index a677a34fc3bd4..6c2f22c6c1890 100644 --- a/recipes/beav/meta.yaml +++ b/recipes/beav/meta.yaml @@ -1,6 +1,6 @@ {% set name = "beav" %} -{% set version = "1.3.0" %} -{% set sha256 = "d691635cc861560c7ae272b4ee2023534e35b43e8764a8fb7f5691ab6202fe3e" %} +{% set version = "1.4.0" %} +{% set sha256 = "fb76843ea670121f901af3c1fb1c7742f0523b47c18dd633c3477802fc2d4c81" %} {% set dbscan_git = "condabeav0.5" %} {% set dbscan_sha256 = "2fe08873026fe63a9992bfb997e59fecce7facb903778983dc6917c962573463" %} {% set gapmind_git = "Beav0.5.1conda" %} @@ -64,6 +64,9 @@ requirements: - perl-file-spec - perl-ipc-run3 +variables: + BEAV_DIR: {{ PREFIX }}/share/{{ name }}-{{ version }} + test: commands: - beav -h diff --git a/recipes/bifrost/build.sh b/recipes/bifrost/build.sh index 7e8ce5cc81850..eb160feeb9e96 100644 --- a/recipes/bifrost/build.sh +++ b/recipes/bifrost/build.sh @@ -1,16 +1,31 @@ -#!/bin/bash +#!/bin/bash -ex -mkdir build -pushd build +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -# Cmake is having trouble finding the sysroot with conda so we're giving it a little help... -if [[ ${HOST} =~ .*darwin.* ]]; then - cmake -DCMAKE_BUILD_TYPE=Release -DCOMPILATION_ARCH=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}" .. +export CXXFLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64 -I${PREFIX}/include" + +ARCH=$(uname -m) +case ${ARCH} in + x86_64) ARCH_FLAGS="-DCOMPILATION_ARCH=OFF" ;; + aarch64) ARCH_FLAGS="-DCOMPILATION_ARCH=OFF" ;; + *) ARCH_FLAGS="-DCOMPILATION_ARCH=ON" ;; +esac + +if [ `uname` == Darwin ]; then + export CONFIG_ARGS="-DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT} -DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" + export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" else - cmake -DCMAKE_BUILD_TYPE=Release -DCOMPILATION_ARCH=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake" .. + export CONFIG_ARGS="-DCMAKE_TOOLCHAIN_FILE=${RECIPE_DIR}/cross-linux.cmake" fi -make VERBOSE=1 -make install +cmake -S . -B build \ + -DCMAKE_INSTALL_PREFIX=${PREFIX} \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + "${CONFIG_ARGS}" \ + "${ARCH_FLAGS}" -popd +cmake --build build --target install -j "${CPU_COUNT}" -v diff --git a/recipes/bifrost/meta.yaml b/recipes/bifrost/meta.yaml index 8ee624077f1c1..1dc9bb202eea2 100644 --- a/recipes/bifrost/meta.yaml +++ b/recipes/bifrost/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e1b2491328b0cc1a32e433a8a9780f05547fa4b8d674b58abdda9ac8809f5341 build: - number: 0 + number: 1 # v1.3.0 breaks Bifrost Index File (.bfi) compatibility with previous Bifrost versions run_exports: - {{ pin_subpackage('bifrost', max_pin="x.x") }} @@ -24,22 +24,24 @@ requirements: host: - zlib - pthread-stubs - run: - - zlib - - pthread-stubs test: commands: - - Bifrost --version + - "Bifrost --version" about: - home: https://github.com/pmelsted/bifrost - license: BSD-2-Clause + home: "https://github.com/pmelsted/bifrost" + license: "BSD-2-Clause" license_family: BSD license_file: LICENSE - summary: Highly parallel construction and indexing of colored and compacted de Bruijn graphs + summary: "Highly parallel construction and indexing of colored and compacted de Bruijn graphs." + dev_url: "https://github.com/pmelsted/bifrost" + doc_url: "https://github.com/pmelsted/bifrost/blob/v{{ version }}/README.md" extra: identifiers: - doi:10.1101/695338 - biotools:bifrost + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/bigtools/meta.yaml b/recipes/bigtools/meta.yaml index 103e8822e7ec1..89cd9389aeb41 100644 --- a/recipes/bigtools/meta.yaml +++ b/recipes/bigtools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.1" %} +{% set version = "0.5.2" %} package: name: bigtools @@ -11,7 +11,7 @@ build: source: url: https://github.com/jackh726/bigtools/archive/refs/tags/v{{ version }}.tar.gz - sha256: "dc006ee7037420e9cd279b2aaaf3a2859c81c07eb08c3ce6b1598b1962f055a3" + sha256: "f5b50a4d717f93242541673bbdeb1fa67b8b9175b0f72d8ff5c52f1563b5cd4e" requirements: build: diff --git a/recipes/binchicken/meta.yaml b/recipes/binchicken/meta.yaml index c19d5f3a24cf6..b64097ecd7181 100644 --- a/recipes/binchicken/meta.yaml +++ b/recipes/binchicken/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.12.1" %} +{% set version = "0.12.5" %} {% set name = "binchicken" %} -{% set sha256 = "99466aafa8037f683f02c5c68ffc689ba9137709e130cf434cd0d4b8a829a67f" %} +{% set sha256 = "80e39d2aae136dc949e504923c270314d60023124499214e30a4669d88c26add" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: @@ -32,7 +32,7 @@ requirements: - bird_tool_utils_python - extern - ruamel.yaml >=0.15.99 - - polars =0.20.31 + - polars =1.2.* - pigz - pyarrow - parallel diff --git a/recipes/binette/meta.yaml b/recipes/binette/meta.yaml index 7c516ff19ef72..9e3f94dfe7e32 100644 --- a/recipes/binette/meta.yaml +++ b/recipes/binette/meta.yaml @@ -1,12 +1,12 @@ {% set name = "Binette" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://github.com/genotoul-bioinfo/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 968c6568b862f4586388fbc63d8fd6054fb2dd0b177d5594099235f48ddea7ab + sha256: 2ed4b5927d7d523db752bdd2ed9e6654e672963ead7a562e0dc2252cbf402191 build: noarch: python diff --git a/recipes/biobb_structure_checking/meta.yaml b/recipes/biobb_structure_checking/meta.yaml index 56a00c5124d72..5e13c55af3867 100644 --- a/recipes/biobb_structure_checking/meta.yaml +++ b/recipes/biobb_structure_checking/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_structure_checking" %} -{% set version = "3.13.4" %} +{% set version = "3.13.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d819819d13c7ad219411b70b043555dcd65d5535f696a1121db562646931f445 + sha256: 4ba074da556a7aecac215f2020a04274c05f155413ed467177b9c9f31a53d4d0 build: number: 0 diff --git a/recipes/biobox_add_taxid/meta.yaml b/recipes/biobox_add_taxid/meta.yaml new file mode 100644 index 0000000000000..2fb85616b6e75 --- /dev/null +++ b/recipes/biobox_add_taxid/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "biobox_add_taxid" %} +{% set version = "0.6" %} +{% set sha256 = "9ca7fca41aa53c3ae26d15328944954419b894e1ee7a4745222c808b5e4ff147" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/SantaMcCloud/{{ name }}/archive/refs/tags/release-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage("biobox_add_taxid", max_pin="x.x") }} + +requirements: + host: + - pip + - python + run: + - python + +test: + commands: + - biobox_add_taxid.py --help + - biobox_add_taxid.py --version + +about: + home: https://github.com/SantaMcCloud/biobox_add_taxid + license: MIT + license_family: MIT + license_file: LICENSE + summary: "CAMI amber utility script for adding the taxid output from GTDB and BAT" diff --git a/recipes/bioconda-repodata-patches/gen_patch_json.py b/recipes/bioconda-repodata-patches/gen_patch_json.py index a6413dcc044c4..34c0225e0f599 100755 --- a/recipes/bioconda-repodata-patches/gen_patch_json.py +++ b/recipes/bioconda-repodata-patches/gen_patch_json.py @@ -169,7 +169,7 @@ def _gen_new_index(repodata, subdir): if has_dep(record, 'htslib'): # skip deps prior to 1.10, which was the first with soversion 3 # TODO adjust replacement (exclusive) upper bound with each new compatible HTSlib - _pin_looser(fn, record, 'htslib', min_lower_bound='1.10', upper_bound='1.21') + _pin_looser(fn, record, 'htslib', min_lower_bound='1.10', upper_bound='1.22') # future libdeflate versions are compatible until they bump their soversion; relax dependencies accordingly if record_name in ['htslib', 'staden_io_lib', 'fastp', 'pysam'] and has_dep(record, 'libdeflate'): diff --git a/recipes/bioconda-repodata-patches/meta.yaml b/recipes/bioconda-repodata-patches/meta.yaml index dfacdaf368a45..0610ed44e66ce 100644 --- a/recipes/bioconda-repodata-patches/meta.yaml +++ b/recipes/bioconda-repodata-patches/meta.yaml @@ -1,6 +1,6 @@ package: name: bioconda-repodata-patches - version: 20240805 # ensure that this is the "current" date, and always higher than the latest version in master + version: 20240913 # ensure that this is the "current" date, and always higher than the latest version in master source: path: . diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 49d272da820fb..c8a92fc0b1c12 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "bioconda-utils" %} -{% set version = "3.3.1" %} -{% set sha256 = "db6b99456a334b958ba61fcfc6e717e5f22848342f99fecb1f6f2b0113165054" %} +{% set version = "3.3.2" %} +{% set sha256 = "6c6dcac689a2fb0f8142546aa9021bfd620fe484e724e4844a2d2e55c337747c" %} package: name: {{ name }} @@ -21,7 +21,7 @@ build: requirements: host: - - python + - python <3.12 - pip run: - conda-forge-pinning 2024.06.01.05.54.15 diff --git a/recipes/bioconvert/meta.yaml b/recipes/bioconvert/meta.yaml index c8ce7d429faf8..1894031152828 100644 --- a/recipes/bioconvert/meta.yaml +++ b/recipes/bioconvert/meta.yaml @@ -11,13 +11,15 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --use-pep517 -vv entry_points: - bioconvert=bioconvert.scripts.converter:main - bioconvert_init=bioconvert.scripts.init_convert:main - bioconvert_stats=bioconvert.scripts.stats:main + run_exports: + - {{ pin_subpackage("bioconvert", max_pin="x.x") }} requirements: host: @@ -31,6 +33,8 @@ requirements: - colorlog - deeptools - gffread + - goalign + - gotree - pandas - biopython >=1.70 - mappy diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index 58dd9b847dd6f..382819362ccd1 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.11" %} +{% set version = "1.0.12" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 14883379dbae1a7cd80b1e19e7593db0f9966413c2a1ffb97f58690fec5dc929 + sha256: 7625c3087677cee45b04bda27542d3436348ae194c938d2a1c2388941471f3b8 build: noarch: python diff --git a/recipes/biophi/meta.yaml b/recipes/biophi/meta.yaml index cf9b788553cb9..e86252f4f51f6 100644 --- a/recipes/biophi/meta.yaml +++ b/recipes/biophi/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.9" %} # Remember to update sha256 below +{% set version = "1.0.10" %} # Remember to update sha256 below package: name: biophi @@ -6,22 +6,21 @@ package: source: url: https://github.com/Merck/BioPhi/archive/v{{ version }}.tar.gz - sha256: 'dd0662ce1e8ff750487493c23db7ac2fa0e9b7cf0868f479996300aec2e2acd2' + sha256: '553c238753281be106b9ad5d470fce71b3d79517734e0ebb85ffd15b4eb7dfe7' build: noarch: python - number: 3 + number: 0 entry_points: - biophi = biophi.common.cli.main:main - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv run_exports: - - {{ pin_subpackage("biophi", max_pin="x.x") }} + - {{ pin_subpackage("biophi", max_pin="x") }} requirements: host: - python >=3.8 - - pip - - setuptools + - pip <24.1 # due to error in omegaconf (dependency of fairseq) - pytest run: - python >=3.8 @@ -50,8 +49,14 @@ test: - biophi oasis --help about: - home: https://github.com/Merck/BioPhi + home: "https://github.com/Merck/BioPhi" license: MIT license_family: MIT license_file: LICENSE - summary: BioPhi open-source antibody design platform + summary: "BioPhi open-source antibody design platform." + dev_url: "https://github.com/Merck/BioPhi" + doc_url: "https://biophi.dichlab.org" + +extra: + identifiers: + - biotools:biophi diff --git a/recipes/bioutils/meta.yaml b/recipes/bioutils/meta.yaml index 6ceda44c8f345..284dd3259c795 100644 --- a/recipes/bioutils/meta.yaml +++ b/recipes/bioutils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioutils" %} -{% set version = "0.5.7" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,23 +7,27 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2610f8d940a613bc9fb0f400fd21b27a4a4f2795a86de26a38b6857577aaabf2 + sha256: 6487a5565bb798b88202d1f5aa3a4ee6b229151e86dc8ff77cbf0e3b4f4dad4b build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv --no-deps --ignore-installed" + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir" + run_exports: + - {{ pin_subpackage('bioutils', max_pin="x.x") }} requirements: host: - pip - - python >=3.6 - - setuptools_scm #to avoid: ERROR: Could not find a version that satisfies the requirement setuptools_scm - - pytest-runner #to avoid: ERROR: Could not find a version that satisfies the requirement pytest-runner + - python >=3.10 + - setuptools-scm run: - - python >=3.6 + - python >=3.10 - attrs - requests + - urllib3 >=1.26,<2.dev0 test: imports: diff --git a/recipes/blast-legacy/2.2.26/fix-osx-build.patch b/recipes/blast-legacy/2.2.26/fix-osx-build.patch index a297ebd103209..0edf78005c26c 100644 --- a/recipes/blast-legacy/2.2.26/fix-osx-build.patch +++ b/recipes/blast-legacy/2.2.26/fix-osx-build.patch @@ -44,12 +44,12 @@ +++ ncbi/corelib/ncbimisc.c 2021-05-21 18:20:54.000000000 -0700 @@ -1266,7 +1266,7 @@ if (len < 1) return NULL; - + rsult = (Nlm_CharPtr) MemNew (len + 3); - if (rsult == NULL) return; + if (rsult == NULL) return NULL; tmp = rsult; - + for (i = 0; /* local [i] != NULL */ i < numitems; i++) { --- ncbi/make/makedis.csh.orig 2021-05-25 19:09:16.000000000 -0700 +++ ncbi/make/makedis.csh 2021-05-25 19:32:11.000000000 -0700 @@ -75,18 +75,92 @@ @@ -300,7 +299,7 @@ echo platform is $platform uname -a - + -set NCBI_DOT_MK = ncbi/platform/${platform}.ncbi.mk +set NCBI_DOT_MK = platform/${platform}.ncbi.mk - + if (! -r "$NCBI_DOT_MK") then goto BADPLATFORM @@ -323,7 +322,7 @@ echo "Enabling assert()." endif - + -cd ncbi/build +cd build ln -s ../make/*.unx . ln -s ../make/ln-if-absent . mv makeall.unx makefile +--- ncbi/corelib/ncbimain.c.orig 2002-07-09 09:20:17 ++++ ncbi/corelib/ncbimain.c 2024-09-18 14:28:01 +@@ -75,7 +75,7 @@ + * setups argc and argv + * + *****************************************************************************/ +-#ifdef OS_MSWIN ++#if defined OS_MSWIN || defined OS_UNIX_DARWIN + int + #endif + main(int argc, char *argv[]) +--- ncbi/tools/kappa.c.orig 2012-04-30 06:45:01 ++++ ncbi/tools/kappa.c 2024-09-18 14:58:32 +@@ -2197,7 +2197,7 @@ + /** + * Callbacks used by Blast_RedoOneMatch and + * Blast_RedoOneMatchSmithWaterman */ +-static const Blast_RedoAlignCallbacks ++static const Blast_RedoAlignCallbacks * + redo_align_callbacks = { + Kappa_CalcLambda, + Kappa_SequenceGetRange, +--- ncbi/tools/ncbisort.c.orig 2006-05-10 14:47:17 ++++ ncbi/tools/ncbisort.c 2024-09-18 14:40:01 +@@ -689,7 +689,7 @@ + of the fraction. Strings not of this form are considered to be zero. */ + static Int4 SORTFracCompare(register UcharPtr a, register UcharPtr b) + { +- register tmpa = UCHAR(*a), tmpb = UCHAR(*b); ++ register int tmpa = UCHAR(*a), tmpb = UCHAR(*b); + + if (tmpa == '.' && tmpb == '.') { + do +--- ncbi/tools/pattern1.c.orig 2006-08-04 15:11:17 ++++ ncbi/tools/pattern1.c 2024-09-18 14:42:18 +@@ -741,7 +741,7 @@ + + /*Do a word-by-word bit-wise or of a and b and put the result in + result; return 1 if there are any non-zero words*/ +-static and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch) ++static Int4 and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch) + { + Int4 i; /*index over words*/ + Int4 returnValue = 0; +--- ncbi/api/asn2ff4.c.orig 2001-10-02 10:13:15 ++++ ncbi/api/asn2ff4.c 2024-09-18 14:36:13 +@@ -1344,7 +1344,7 @@ + * Compare two ImpFeats by name and location + * returns 1 for matching features otherwise returns 0 + ******************************************************************************/ +-static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2) ++static int CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2) + { + if (f1 == NULL && f2) + return 0; +--- ncbi/api/asn2ff2.c.orig 2024-09-18 22:02:18 ++++ ncbi/api/asn2ff2.c 2024-09-18 22:36:29 +@@ -220,6 +220,7 @@ + #include + #include + #include ++#include + + + NLM_EXTERN Int2 GetGenDate PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, CharPtr buffer)); +@@ -1355,7 +1356,7 @@ + return newstring; + } + +-static ChoicePID(SeqIdPtr sid) ++static bool ChoicePID(SeqIdPtr sid) + { + + DbtagPtr db; diff --git a/recipes/blast-legacy/2.2.26/meta.yaml b/recipes/blast-legacy/2.2.26/meta.yaml index 1138152050e28..be2f140d0a9a9 100644 --- a/recipes/blast-legacy/2.2.26/meta.yaml +++ b/recipes/blast-legacy/2.2.26/meta.yaml @@ -10,7 +10,9 @@ source: patches: - fix-osx-build.patch # [osx] build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage('blast-legacy', max_pin='x.x') }} test: commands: diff --git a/recipes/blast/meta.yaml b/recipes/blast/meta.yaml index a637fdd91d09e..da0a582f155e8 100644 --- a/recipes/blast/meta.yaml +++ b/recipes/blast/meta.yaml @@ -16,7 +16,7 @@ source: - update_configsub.patch build: - number: 1 + number: 2 run_exports: # Now, the point releases seem to be only bugfixes at least (but this definitely was not the # case up to v2.2.31) diff --git a/recipes/blast2galaxy/meta.yaml b/recipes/blast2galaxy/meta.yaml new file mode 100644 index 0000000000000..ffc343984a7bb --- /dev/null +++ b/recipes/blast2galaxy/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "blast2galaxy" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/blast2galaxy-{{ version }}.tar.gz + sha256: 6831f00319c18dc338df18fccd279c6a6dc8d725b4afc414f5bb34d16e8317f3 + +build: + entry_points: + - blast2galaxy = blast2galaxy.cli:cli + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('blast2galaxy', max_pin="x.x") }} + +requirements: + host: + - python >=3.10,<4.0 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.10,<4.0 + - typer >=0.9.0,<0.10.0 + - bioblend >=1.2.0,<2.0.0 + - rich >=13.6.0,<14.0.0 + - tomli >=2.0.1,<3.0.0 + +test: + imports: + - blast2galaxy + commands: + - pip check + - blast2galaxy --help + requires: + - pip + +about: + summary: A Python package with a CLI and API to perform BLAST queries against Galaxy servers + license: MIT + license_file: LICENSE + home: "https://github.com/IPK-BIT/blast2galaxy" + doc_url: "https://blast2galaxy.readthedocs.io/" + dev_url: "https://github.com/IPK-BIT/blast2galaxy" + +extra: + recipe-maintainers: + - patrick-koenig diff --git a/recipes/blaze2/meta.yaml b/recipes/blaze2/meta.yaml index 90649b463cac0..098c5e8149ec3 100644 --- a/recipes/blaze2/meta.yaml +++ b/recipes/blaze2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "BLAZE2" %} -{% set version = "2.2.1" %} +{% set version = "2.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/shimlab/BLAZE/archive/refs/tags/v{{ version }}.tar.gz - sha256: 30a3f7ede0237d5fbb1e1fa7155c2505d0ce560ba92ea61654ae0ff18f7453e4 + sha256: f47175997742562add1deb9524e468b6709e40c92f74165a1a0fe1897b2919fc build: number: 0 diff --git a/recipes/bowtie2/build.sh b/recipes/bowtie2/build.sh index 78e79f68ac4c8..62175c7a09ec7 100644 --- a/recipes/bowtie2/build.sh +++ b/recipes/bowtie2/build.sh @@ -7,8 +7,8 @@ git clone https://github.com/ch4rr0/libsais third_party/libsais LDFLAGS="" make CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -O3" CPP="${CXX} -I${PREFIX}/include" CC="${CC} -L${PREFIX}/lib" \ - CFLAGS="${CFLAGS} -O3" LDLIBS="-L$PREFIX/lib -lz -lzstd -ltbb -ltbbmalloc -lpthread" \ - WITH_ZSTD=1 USE_SAIS_OPENMP=1 + CFLAGS="${CFLAGS} -O3" LDLIBS="-L$PREFIX/lib -lz -lzstd -lpthread" \ + WITH_ZSTD=1 USE_SRA=1 USE_SAIS_OPENMP=1 binaries="\ bowtie2 \ diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml index e4fde80b6a4f3..64a7124009d3a 100644 --- a/recipes/bowtie2/meta.yaml +++ b/recipes/bowtie2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 841a6a60111b690c11d1e123cb5c11560b4cd1502b5cee7e394fd50f83e74e13 build: - number: 2 + number: 4 run_exports: - {{ pin_subpackage('bowtie2', max_pin="x") }} @@ -25,8 +25,6 @@ requirements: - libgomp # [linux] - zlib - zstd - - tbb-devel - - tbb run: - python - perl diff --git a/recipes/bpipe/meta.yaml b/recipes/bpipe/meta.yaml index 9bc00b7316519..68230c4b19867 100644 --- a/recipes/bpipe/meta.yaml +++ b/recipes/bpipe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bpipe" %} -{% set version = "0.9.12" %} +{% set version = "0.9.13" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/ssadedin/bpipe/releases/download/{{ version }}/bpipe-{{ version }}.tar.gz - sha256: '2c8b004e8bcc6bc85c14b699ee011af8a9f9e19f252260a14561492dadc5878b' + sha256: '206939fe11d47d3d5d93667317d6acfdf23fb0bdc3ffb0e7a891c3010d390339' build: number: 0 diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index 528eb257d49c9..301a04bc398ed 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -30,7 +30,6 @@ requirements: - biopython >=1.79 - prodigal - sepp >=4.3.10 - - dendropy <4.6.0 # necessary temporarily until SEPP updates their codebase or recipe - metaeuk >=6.a5d39d9 # needed for gff bug fix - pandas - bbmap @@ -47,7 +46,6 @@ requirements: - r-ggplot2 >=2.2.1 - prodigal - sepp >=4.3.10 - - dendropy <4.6.0 # necessary temporarily until SEPP updates their codebase or recipe - metaeuk >=6.a5d39d9 # needed for gff bug fix - pandas - bbmap diff --git a/recipes/busco_phylogenomics/meta.yaml b/recipes/busco_phylogenomics/meta.yaml new file mode 100644 index 0000000000000..ed1764337ae39 --- /dev/null +++ b/recipes/busco_phylogenomics/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "busco_phylogenomics" %} +{% set version = "20240919" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/jamiemcg/{{ name }}/archive/refs/tags/{{ version }}.tar.gz + sha256: 989cfb137cc06e0014daa4475e9b6bd070bd3ea77baed8fd6f26562ee84b9f5b + +build: + number: 0 + noarch: python + script: bash conda_build_package.sh + entry_points: + - BUSCO_phylogenomics = BUSCO_phylogenomics.BUSCO_phylogenomics:main + - count_buscos = BUSCO_phylogenomics.count_buscos:main + run_exports: + - {{ pin_subpackage('busco_phylogenomics', max_pin=None) }} + +requirements: + build: + - python >=3.8 + run: + - python >=3.8 + - biopython + - muscle >=5.1 + - iqtree + - fasttree + - trimal +test: + commands: + - BUSCO_phylogenomics.py -h + - count_buscos.py -h + +about: + home: https://github.com/jamiemcg/BUSCO_phylogenomics + license: MIT + license_file: LICENSE + license_family: MIT + summary: 'Utility script to construct species phylogenies using BUSCO proteins.' + +extra: + maintainers: + - jamiemcg diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml index d2bfdf335da0a..fed8ae7701f0b 100644 --- a/recipes/bustools/meta.yaml +++ b/recipes/bustools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.43.2" %} +{% set version = "0.44.0" %} package: name: bustools @@ -6,10 +6,10 @@ package: source: url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz - sha256: ad5816152644ee615316daecf5883183994bd7cc96e6c008439123f4cd750b1f + sha256: e9a12be416d5d3940dd0ec3bfb0be3a481f2eea7d4411df1ab24c814332d99b8 build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('bustools', max_pin="x.x") }} @@ -33,3 +33,8 @@ about: license_file: LICENSE summary: | bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/bwa-aln-interactive/build.sh b/recipes/bwa-aln-interactive/build.sh new file mode 100644 index 0000000000000..f7f3b28babaf1 --- /dev/null +++ b/recipes/bwa-aln-interactive/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +make CC="$CC" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS" -j "${CPU_COUNT}" +mkdir -p $PREFIX/bin +cp bwa $PREFIX/bin/bwa-aln-interactive diff --git a/recipes/bwa-aln-interactive/meta.yaml b/recipes/bwa-aln-interactive/meta.yaml new file mode 100644 index 0000000000000..14d6175ede952 --- /dev/null +++ b/recipes/bwa-aln-interactive/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.7.18" %} +{% set sha256 = "9a1baef6d08da234a96466a1023dae53154fe0b2358f9ff7ad5307e63f4e89ba" %} + + +package: + name: bwa-aln-interactive + version: {{ version }} + +source: + url: https://github.com/fulcrumgenomics/bwa-aln-interactive/archive/refs/tags/v0.7.18-r1243-1.tar.gz + sha256: {{ sha256 }} + +build: + number: 1 + run_exports: + - {{ pin_subpackage("bwa-aln-interactive", max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + host: + - zlib + +test: + commands: + - bwa-aln-interactive 2>&1 | grep "This fork of bwa supports interactive \`bwa aln\`" + +about: + home: https://github.com/fulcrumgenomics/bwa-aln-interactive + license: GPL-3.0-only + license_file: COPYING + summary: Version of the BWA aln read mapper for interactive alignment. + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index fb05bc7948ff6..187536a7dee88 100644 --- a/recipes/bx-python/meta.yaml +++ b/recipes/bx-python/meta.yaml @@ -1,6 +1,6 @@ {% set name = "bx-python" %} -{% set version = "0.12.0" %} -{% set sha256 = "aac2405a7b6f0d74a0a38d0e589205ed4e5ecee12df23e2076d40d41cc8335c2" %} +{% set version = "0.13.0" %} +{% set sha256 = "ce04696543367efc6b7995d9463efeda691b9a58f6f55a7bd831e642159b0644" %} package: name: {{ name|lower }} @@ -32,6 +32,7 @@ requirements: run: - python - {{ pin_compatible('numpy') }} + - pyparsing test: imports: @@ -50,6 +51,7 @@ test: - bx.motif.io - bx.motif.logo - bx.phylo + - bx.phylo.newick - bx.pwm - bx.seq - bx.tabular diff --git a/recipes/cagee/build.sh b/recipes/cagee/build.sh index 5d921656c8975..79aff1ef6a196 100755 --- a/recipes/cagee/build.sh +++ b/recipes/cagee/build.sh @@ -1,28 +1,28 @@ #!/bin/bash -set -e -set -x +set -ex -if [ "$(uname)" = "Darwin" ]; then - # LDFLAGS fix: https://github.com/AnacondaRecipes/intel_repack-feedstock/issues/8 - export LDFLAGS="-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib" +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I{PREFIX}/include" + +if [[ "$(uname)" == "Darwin" ]]; then + # LDFLAGS fix: https://github.com/AnacondaRecipes/intel_repack-feedstock/issues/8 + export LDFLAGS="${LDFLAGS} -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib" + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" else - export LDFLAGS="-L$PREFIX/lib" - export MKL_THREADING_LAYER="GNU" + export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + export MKL_THREADING_LAYER="GNU" + export CONFIG_ARGS="" fi -# https://bioconda.github.io/contributor/troubleshooting.html#zlib-errors -export CFLAGS="-I$PREFIX/include" -export CPATH=${PREFIX}/include - -mkdir -p build -cd build - -cmake -DCMAKE_PREFIX_PATH:PATH=${PREFIX} \ - -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \ - -DCMAKE_BUILD_TYPE="Release" \ - .. +# https://bioconda.github.io/contributor/troubleshooting.html#zlib-errors +export CFLAGS="${CFLAGS} -O3 -I$PREFIX/include" +export INCLUDE_PATH="${PREFIX}/include" -make -make install +cmake -S . -B build \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DCMAKE_BUILD_TYPE="Release" \ + -DCMAKE_CXX_COMPILER="${CXX}" -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + "${CONFIG_ARGS}" +cmake --build build --target install -j "${CPU_COUNT}" -v diff --git a/recipes/cagee/meta.yaml b/recipes/cagee/meta.yaml index ff080b956e86b..cdc593579ee6c 100755 --- a/recipes/cagee/meta.yaml +++ b/recipes/cagee/meta.yaml @@ -1,6 +1,6 @@ {% set name = "CAGEE" %} -{% set version = "1.0" %} -{% set sha256 = "3aec98af3552ef86df03d42a068925e2becd69daac3720ea9fd136b084198f57" %} +{% set version = "1.2" %} +{% set sha256 = "fc1db60d8d9478ef53b38f310a687453c6f8f2f50d3c68ec6a0747e822c2a481" %} package: name: {{ name|lower }} @@ -11,27 +11,30 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('cagee', max_pin="x") }} requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} - binutils >=2.33.1 # [linux] + - binutils_impl_linux-aarch64 # [osx] - cmake >=3.13 - make - - llvm-openmp # [osx] host: - eigen >=3.4.0 - boost-cpp - mkl >=2020.4 - mkl-include + - libgomp # [linux] + - llvm-openmp # [osx] - zlib - zstd run: - boost-cpp - mkl >=2020.4 - - zlib test: commands: @@ -49,4 +52,3 @@ about: extra: recipe-maintainers: - benfulton - diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index 5fa8e90fbbc22..658e9faaff4dd 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.7.1" %} +{% set version = "1.8.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 45dee48898336883b91cae93f9a34db68b1992a0f16a436d7f904f71ab061999 + sha256: 4be2d211751482c7d8618be6974a69ec711c9d9f55e0739e277bd41c6194cb05 build: noarch: python diff --git a/recipes/cami-amber/meta.yaml b/recipes/cami-amber/meta.yaml index 0c4f04ed2f084..65e1b263966d8 100644 --- a/recipes/cami-amber/meta.yaml +++ b/recipes/cami-amber/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.4" %} +{% set version = "2.0.7" %} package: name: cami-amber @@ -6,18 +6,18 @@ package: source: url: https://pypi.io/packages/source/c/cami-amber/cami-amber-{{ version }}.tar.gz - sha256: a671517d1ea2d43b74f0bd1934621b59b9d6e160f64ef485c03f612c9de21e3a + sha256: 01f11fbab7cb0f24497932669b00981292b1dc0df2ce6cd4b707a7ddd675bf8d build: noarch: python - number: 1 + number: 0 run_exports: - - {{ pin_subpackage("cami-amber", max_pin="x.x") }} + - {{ pin_subpackage("cami-amber", max_pin="x") }} script: - - python -m pip install --no-deps --ignore-installed . - - cp ./src/utils/add_length_column.py $PREFIX/bin - - cp ./src/utils/convert_fasta_bins_to_biobox_format.py $PREFIX/bin - - cp ./src/utils/argparse_parents.py $PREFIX/bin + - {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + - cp -rf ./cami_amber/utils/add_length_column.py $PREFIX/bin + - cp -rf ./cami_amber/utils/convert_fasta_bins_to_biobox_format.py $PREFIX/bin + - cp -rf ./cami_amber/utils/argparse_parents.py $PREFIX/bin requirements: host: @@ -25,14 +25,14 @@ requirements: - pip run: - python >=3.6 - - numpy >=1.24.2 - - biopython >=1.81 - - matplotlib-base >=3.7.1 - - pandas >=1.5.3 - - bokeh >=3.1.0 - - seaborn >=0.12.2 - - jinja2 >=3.1.2 - - pyarrow >=11.0.0 + - numpy >=2.0.1 + - biopython >=1.84 + - matplotlib-base >=3.8.4 + - pandas >=2.2.2 + - bokeh >=3.5.1 + - seaborn-base >=0.13.2 + - jinja2 >=3.1.4 + - pyarrow >=17.0.0 test: commands: @@ -42,6 +42,8 @@ test: about: home: https://github.com/CAMI-challenge/AMBER - license: GPL v3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: 'AMBER: Assessment of Metagenome BinnERs' + dev_url: https://github.com/CAMI-challenge/AMBER diff --git a/recipes/cami-opal/meta.yaml b/recipes/cami-opal/meta.yaml index 8e9d6ea40ba94..099c010d085a0 100644 --- a/recipes/cami-opal/meta.yaml +++ b/recipes/cami-opal/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cami-opal" %} -{% set version = "1.0.12" %} -{% set sha256 = "f8ed286472106332d309ced2504b8fa729c03f6b9d72d8db4faabe726f033f87" %} +{% set version = "1.0.13" %} +{% set sha256 = "bbb869b739c555fbbfc26d2771fa1b501f671b620bcbf743c15327a51debd408" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: python script: {{ PYTHON }} -m pip install . --no-deps -vvv run_exports: diff --git a/recipes/camlhmp/meta.yaml b/recipes/camlhmp/meta.yaml index 4a40b11a65bb0..ff176d7dbb452 100644 --- a/recipes/camlhmp/meta.yaml +++ b/recipes/camlhmp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "camlhmp" %} -{% set version = "0.3.1" %} +{% set version = "1.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/camlhmp/camlhmp-{{ version }}.tar.gz - sha256: 5add4f82f4cc70bb5192a0bbe4fc3a6263aaa51353ddd0eb17833ec75ec1d008 + sha256: 0f20b94fc0bd469299bd9bec6fe384013bd7043cb4dd97e9df827895f2d06fb2 build: noarch: python diff --git a/recipes/catfasta2phyml/meta.yaml b/recipes/catfasta2phyml/meta.yaml index 0127661fa44c0..44d06ac51bcaf 100644 --- a/recipes/catfasta2phyml/meta.yaml +++ b/recipes/catfasta2phyml/meta.yaml @@ -1,14 +1,16 @@ package: name: catfasta2phyml - version: "1.2.0" + version: "1.2.1" source: - url: https://github.com/nylander/catfasta2phyml/archive/refs/tags/v.1.2.0.tar.gz - sha256: f4ea5aef5aa21d15d84436262f06b79a004b7017ab7a433019fe903aec995fdb + url: https://github.com/nylander/catfasta2phyml/archive/refs/tags/v1.2.1.tar.gz + sha256: 2647985192b05df49e10bfce64d6843fe7916b0395199dfd2ac4f80910c5a91f build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('catfasta2phyml', max_pin="x") }} requirements: run: diff --git a/recipes/cellbender/meta.yaml b/recipes/cellbender/meta.yaml index 68183da020015..b70653de9be49 100644 --- a/recipes/cellbender/meta.yaml +++ b/recipes/cellbender/meta.yaml @@ -1,27 +1,26 @@ -{% set name = "cellbender" %} -{% set version = "0.3.0" %} +{% set name = "CellBender" %} +{% set version = "0.3.2" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cellbender-{{ version }}.tar.gz - sha256: 94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42 + url: https://github.com/broadinstitute/CellBender/archive/v{{ version }}.tar.gz + sha256: 3bd4bf77c82a5817bb09ac3db236e9795e3e71c99cbe34c8baef04272a7d1717 build: number: 0 noarch: python entry_points: - cellbender = cellbender.base_cli:main - script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir run_exports: - {{ pin_subpackage('cellbender', max_pin="x.x") }} requirements: host: - python 3.7 - - setuptools >=61.2 - pip run: - python 3.7 @@ -45,16 +44,16 @@ test: imports: - cellbender commands: - - cellbender --help + - "cellbender --help" about: - home: https://github.com/broadinstitute/CellBender + home: "https://github.com/broadinstitute/CellBender" summary: "A software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data" - license: BSD-3-Clause + license: "BSD-3-Clause" license_family: BSD license_file: LICENSE - doc_url: https://cellbender.readthedocs.io/en/latest/ - dev_url: https://github.com/broadinstitute/CellBender + doc_url: "https://cellbender.readthedocs.io/en/latest" + dev_url: "https://github.com/broadinstitute/CellBender" extra: recipe-maintainers: diff --git a/recipes/cellprofiler-core/meta.yaml b/recipes/cellprofiler-core/meta.yaml index f439833bd2fb8..3d571207beeff 100644 --- a/recipes/cellprofiler-core/meta.yaml +++ b/recipes/cellprofiler-core/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cellprofiler-core" %} -{% set version = "4.2.7" %} +{% set version = "4.2.8" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cellprofiler_core-{{ version }}.tar.gz - sha256: b1a4c232a7d6237726ec3f5a5d5b9c06b177d3b37020c14b2179b690aef1f772 + sha256: 80e7465edf7b3c9d09b36156ba163d3a30769951f3724b924a504c9289ed7848 build: number: 0 diff --git a/recipes/cellsnp-lite/LICENSE b/recipes/cellsnp-lite/LICENSE deleted file mode 100644 index 261eeb9e9f8b2..0000000000000 --- a/recipes/cellsnp-lite/LICENSE +++ /dev/null @@ -1,201 +0,0 @@ - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/recipes/cellsnp-lite/build.sh b/recipes/cellsnp-lite/build.sh index dc3736b1c75a4..ce213a712a2cf 100755 --- a/recipes/cellsnp-lite/build.sh +++ b/recipes/cellsnp-lite/build.sh @@ -1,20 +1,18 @@ #!/bin/bash -export C_INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib -export LD_LIBRARY_PATH=${PREFIX}/lib - -./configure -make +mkdir -p ${PREFIX}/bin -#cflags="-g -Wall -O2 -Wno-unused-function -fgnu89-inline -I${PREFIX}/include" +export M4="$BUILD_PREFIX/bin/m4" +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -g -Wall -O3 -Wno-implicit-function-declaration" -#if [ "`uname`" == "Darwin" ]; then -# make CC=${CC} CFLAGS="-fgnu89-inline -fcommon ${CFLAGS}" LDFLAGS="${LDFLAGS}" -#else -# make CC=${CC} CFLAGS="${cflags}" htslib_lib_dir=${PREFIX}/lib -#fi +autoreconf -if +./configure --prefix="${PREFIX}" CC="${CC}" CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" -mkdir -p ${PREFIX}/bin -cp -f cellsnp-lite ${PREFIX}/bin +make -j"${CPU_COUNT}" +make install +chmod 0755 ${PREFIX}/bin/cellsnp-lite diff --git a/recipes/cellsnp-lite/build_failure.osx-64.yaml b/recipes/cellsnp-lite/build_failure.osx-64.yaml deleted file mode 100644 index a7e45f3dd22d7..0000000000000 --- a/recipes/cellsnp-lite/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: dd6a23ac00183a8e28b55aa29a5ede942ba044cd21b1bfb29d5e7425e0fd6d8c # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - checking for a BSD-compatible install... /usr/bin/install -c - checking whether build environment is sane... yes - checking for a thread-safe mkdir -p... ./install-sh -c -d - checking for gawk... no - checking for mawk... no - checking for nawk... no - checking for awk... awk - checking whether make sets $(MAKE)... yes - checking whether make supports nested variables... yes - checking for gawk... (cached) awk - checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... - checking whether we are cross compiling... no - checking for suffix of object files... o - checking whether we are using the GNU C compiler... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed - checking for style of include used by make... GNU - checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 - checking for math.h... yes - checking for log in -lm... yes - checking for zlib.h... yes - checking for inflate in -lz... yes - checking for bzlib.h... yes - checking for BZ2_bzBuffToBuffCompress in -lbz2... yes - checking for lzma.h... yes - checking for lzma_easy_buffer_encode in -llzma... yes - checking for curl_easy_pause in -lcurl... yes - checking for HMAC in -lcrypto... yes - checking location of HTSlib installation... none found - checking for htslib/sam.h... yes - checking for sam_hdr_init in -lhts... yes - checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E - checking for grep that handles long lines and -e... /usr/bin/grep - checking for egrep... /usr/bin/grep -E - checking for ANSI C header files... yes - checking for sys/types.h... yes - checking for sys/stat.h... yes - checking for stdlib.h... yes - checking for string.h... yes - checking for memory.h... yes - checking for strings.h... yes - checking for inttypes.h... yes - checking for stdint.h... yes - checking for unistd.h... yes - checking for stdlib.h... (cached) yes - checking for string.h... (cached) yes - checking for unistd.h... (cached) yes - checking for inline... inline - checking for int32_t... yes - checking for int8_t... yes - checking for size_t... yes - checking for ssize_t... yes - checking for uint32_t... yes - checking for uint8_t... yes - checking for stdlib.h... (cached) yes - checking for GNU libc compatible malloc... (cached) yes - checking for stdlib.h... (cached) yes - checking for GNU libc compatible realloc... (cached) yes - checking for memset... yes - checking for mkdir... yes - checking for pow... yes - checking for strdup... yes - checking that generated files are newer than configure... done - configure: creating ./config.status - config.status: creating Makefile - config.status: creating conf.h - config.status: executing depfiles commands - make all-am - make[1]: Entering directory '$SRC_DIR' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-cellsnp.o -MD -MP -MF src/.deps/cellsnp_lite-cellsnp.Tpo -c -o src/cellsnp_lite-cellsnp.o test -f 'src/cellsnp.c' || echo './'src/cellsnp.c - mv -f src/.deps/cellsnp_lite-cellsnp.Tpo src/.deps/cellsnp_lite-cellsnp.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-csp.o -MD -MP -MF src/.deps/cellsnp_lite-csp.Tpo -c -o src/cellsnp_lite-csp.o test -f 'src/csp.c' || echo './'src/csp.c - mv -f src/.deps/cellsnp_lite-csp.Tpo src/.deps/cellsnp_lite-csp.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-csp_fetch.o -MD -MP -MF src/.deps/cellsnp_lite-csp_fetch.Tpo -c -o src/cellsnp_lite-csp_fetch.o test -f 'src/csp_fetch.c' || echo './'src/csp_fetch.c - mv -f src/.deps/cellsnp_lite-csp_fetch.Tpo src/.deps/cellsnp_lite-csp_fetch.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-csp_pileup.o -MD -MP -MF src/.deps/cellsnp_lite-csp_pileup.Tpo -c -o src/cellsnp_lite-csp_pileup.o test -f 'src/csp_pileup.c' || echo './'src/csp_pileup.c - mv -f src/.deps/cellsnp_lite-csp_pileup.Tpo src/.deps/cellsnp_lite-csp_pileup.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-jfile.o -MD -MP -MF src/.deps/cellsnp_lite-jfile.Tpo -c -o src/cellsnp_lite-jfile.o test -f 'src/jfile.c' || echo './'src/jfile.c - mv -f src/.deps/cellsnp_lite-jfile.Tpo src/.deps/cellsnp_lite-jfile.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-jsam.o -MD -MP -MF src/.deps/cellsnp_lite-jsam.Tpo -c -o src/cellsnp_lite-jsam.o test -f 'src/jsam.c' || echo './'src/jsam.c - mv -f src/.deps/cellsnp_lite-jsam.Tpo src/.deps/cellsnp_lite-jsam.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-jstring.o -MD -MP -MF src/.deps/cellsnp_lite-jstring.Tpo -c -o src/cellsnp_lite-jstring.o test -f 'src/jstring.c' || echo './'src/jstring.c - mv -f src/.deps/cellsnp_lite-jstring.Tpo src/.deps/cellsnp_lite-jstring.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-mplp.o -MD -MP -MF src/.deps/cellsnp_lite-mplp.Tpo -c -o src/cellsnp_lite-mplp.o test -f 'src/mplp.c' || echo './'src/mplp.c - mv -f src/.deps/cellsnp_lite-mplp.Tpo src/.deps/cellsnp_lite-mplp.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-snp.o -MD -MP -MF src/.deps/cellsnp_lite-snp.Tpo -c -o src/cellsnp_lite-snp.o test -f 'src/snp.c' || echo './'src/snp.c - mv -f src/.deps/cellsnp_lite-snp.Tpo src/.deps/cellsnp_lite-snp.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Isrc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -g -Wall -O2 -Wno-unused-function -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT src/cellsnp_lite-thpool.o -MD -MP -MF src/.deps/cellsnp_lite-thpool.Tpo -c -o src/cellsnp_lite-thpool.o test -f 'src/thpool.c' || echo './'src/thpool.c - make[1]: Leaving directory '$SRC_DIR' -# Last 100 lines of the build log. diff --git a/recipes/cellsnp-lite/meta.yaml b/recipes/cellsnp-lite/meta.yaml index 5a2d55ecac7cd..f44ac346eecc8 100644 --- a/recipes/cellsnp-lite/meta.yaml +++ b/recipes/cellsnp-lite/meta.yaml @@ -1,8 +1,9 @@ +{% set name = "cellsnp-lite" %} {% set version = "1.2.3" %} {% set sha256 = "baf84ee8fc80e5a11d31e266ed6087e7dcba65be6b8583b025c628a9ff9d9dd7" %} package: - name: cellsnp-lite + name: {{ name }} version: {{ version }} source: @@ -10,27 +11,42 @@ source: sha256: {{ sha256 }} build: - number: 3 - #skip: True # [osx] + number: 4 + run_exports: + - {{ pin_subpackage('cellsnp-lite', max_pin="x") }} requirements: build: - make - {{ compiler('c') }} + - autoconf + - automake + - libtool host: - htslib + - libcurl + - bzip2 - zlib run: - htslib - - zlib test: commands: - cellsnp-lite 2>&1 | grep -i 'options' about: - home: https://github.com/single-cell-genetics/cellsnp-lite - license: Apache-2.0 + home: "https://github.com/single-cell-genetics/cellsnp-lite" + license: "Apache-2.0" + license_family: APACHE license_file: LICENSE - summary: Efficient genotyping bi-allelic SNPs on single cells + summary: "Efficient genotyping bi-allelic SNPs on single cells." + dev_url: "https://github.com/single-cell-genetics/cellsnp-lite" + doc_url: "https://cellsnp-lite.readthedocs.io/en/latest" +extra: + identifiers: + - doi:10.1093/bioinformatics/btab358 + - biotools:cellsnp-lite + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/cellxgene/meta.yaml b/recipes/cellxgene/meta.yaml index c0c0b3cf36172..6356ce82759b0 100644 --- a/recipes/cellxgene/meta.yaml +++ b/recipes/cellxgene/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cellxgene" %} -{% set version = "1.2.0" %} -{% set sha256 = "1a4c5e93106283ecd1d6bd38170942d298ce8087ace533c2a6e294b67fb13c53" %} +{% set version = "1.3.0" %} +{% set sha256 = "4c220c5b34f121c17b94a302119ac30fc31a308c3eb9101d05fa905cd133925e" %} package: name: "{{ name|lower }}" @@ -15,14 +15,14 @@ build: noarch: python entry_points: - cellxgene = server.cli.cli:cli - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('cellxgene', max_pin="x") }} requirements: host: - pip - - python >=3.6 + - python >=3.6,<3.12 run: - anndata >=0.7.6 - boto3 >=1.12.18 @@ -43,7 +43,7 @@ requirements: - numpy >=1.17.5 - packaging >=20.0 - pandas >=1.0,!=1.1 - - python >=3.6 + - python >=3.6,<3.12 - pyyaml >=5.4 - requests >=2.22.0 - s3fs ==0.4.2 diff --git a/recipes/cgpbigwig/meta.yaml b/recipes/cgpbigwig/meta.yaml index d2bfb03682261..6b1022168b253 100644 --- a/recipes/cgpbigwig/meta.yaml +++ b/recipes/cgpbigwig/meta.yaml @@ -1,18 +1,18 @@ -{% set version = "1.6.0" %} +{% set version = "1.7.0" %} package: name: cgpbigwig version: {{ version }} build: - number: 9 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage('cgpbigwig', max_pin="x") }} source: url: https://github.com/cancerit/cgpBigWig/archive/{{ version }}.tar.gz - sha256: d92a27f34a7a58cc16adc7244a97d53d98e0efd5fac1f676ef18181e47fc7b0d + sha256: d1dff8cdf35b8ffa231b999e79c44f8a4897e469224652da50d2a116c45b2b8b requirements: build: @@ -44,4 +44,4 @@ test: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/checkm-genome/meta.yaml b/recipes/checkm-genome/meta.yaml index fd74a342a3ec5..1a7aeba1e7066 100644 --- a/recipes/checkm-genome/meta.yaml +++ b/recipes/checkm-genome/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: @@ -22,7 +22,7 @@ requirements: - python >=3.6 - pip run: - - python >=3.6 + - python >=3.6, <3.12 - numpy >=1.21.3 - scipy >=1.7.3 - matplotlib-base >=3.5.1 diff --git a/recipes/checkqc/meta.yaml b/recipes/checkqc/meta.yaml index 5eb9c3ce6caa5..4b0cb5b4016dd 100644 --- a/recipes/checkqc/meta.yaml +++ b/recipes/checkqc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "checkQC" %} -{% set version = "4.0.4" %} -{% set sha256 = "26fdd9e649f25df757cacab2263b814df45cb2531e35850930df3c90183609cb" %} +{% set version = "4.0.5" %} +{% set sha256 = "f5ff8985baeb079d2e6731fbfebc0a26a2d14c752cdcddffd322b251053acd71" %} package: name: "{{ name|lower }}" diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index 0e07a8938b6ad..6b0161564da8c 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,5 +1,5 @@ {% set name = 'chewBBACA' %} -{% set version = '3.3.9' %} +{% set version = '3.3.10' %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: url: https://github.com/B-UMMI/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz # url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 7afef83a3e2bd7e451443073ce6f08bc2a9c2149ec9b23bc2be488553bc62169 + sha256: bb3f3bbc81d3469c36d2038302ee32964c630d261dd9e5954aa3fdcb46728c0c # sha256: b54c5f4fb2f3c943f9ec51e5b81f4fb9a312fcc87fdea6e0a9f3edbebdf62308 build: diff --git a/recipes/chopper/meta.yaml b/recipes/chopper/meta.yaml index d3d1d006ac7f4..00dbb1806606e 100644 --- a/recipes/chopper/meta.yaml +++ b/recipes/chopper/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.0" %} +{% set version = "0.9.0" %} package: name: chopper @@ -11,7 +11,7 @@ build: source: url: https://github.com/wdecoster/chopper/archive/v{{ version }}.tar.gz - sha256: d79c3a3af8daf9e81f4a209061629e823a3cb0275ff13f9f7e800b9f62c19bab + sha256: ae5b6f8f5ffde45582998b63cb45b4221b25ee37a9fde7a256e653c7f3f12075 requirements: build: diff --git a/recipes/chromap/build.sh b/recipes/chromap/build.sh index 85c7748feac5e..fd60e56ba057e 100644 --- a/recipes/chromap/build.sh +++ b/recipes/chromap/build.sh @@ -1,5 +1,15 @@ #!/bin/bash -# -msse4.1 needed for _mm_min_epi32 -make CXX=$CXX CXXFLAGS="-O3 -Wall -I$PREFIX/include -std=c++11 -msse4.1 -fopenmp" LDFLAGS="-L$PREFIX/lib -lm -lz" + +set -xe +case $(uname -m) in + x86_64) + # -msse4.1 needed for _mm_min_epi32 + ARCH_OPTS="-msse4.1" + ;; + *) + ;; +esac + +make -j ${CPU_COUNT} CXX=$CXX CXXFLAGS="-O3 -Wall -I$PREFIX/include -std=c++11 ${ARCH_OPTS} -fopenmp" LDFLAGS="-L$PREFIX/lib -lm -lz" mkdir -p $PREFIX/bin mv chromap $PREFIX/bin diff --git a/recipes/r-stitch/seqlib-aarch64.patch b/recipes/chromap/chromap-aarch64.patch similarity index 99% rename from recipes/r-stitch/seqlib-aarch64.patch rename to recipes/chromap/chromap-aarch64.patch index b52fd6c6937ed..f7683e7c8badc 100644 --- a/recipes/r-stitch/seqlib-aarch64.patch +++ b/recipes/chromap/chromap-aarch64.patch @@ -1,8 +1,40 @@ -diff --git c/SeqLib/sse2neon.h i/SeqLib/sse2neon.h +diff --git c/src/alignment.cc i/src/alignment.cc +index 8abb4a6..a71f434 100644 +--- c/src/alignment.cc ++++ i/src/alignment.cc +@@ -1,6 +1,10 @@ + #include "alignment.h" + ++#ifdef __ARM_NEON ++#include "sse2neon.h" ++#else + #include ++#endif + + namespace chromap { + +diff --git c/src/ksw.cc i/src/ksw.cc +index 26cdb04..a5b7432 100644 +--- c/src/ksw.cc ++++ i/src/ksw.cc +@@ -26,7 +26,12 @@ + #include + #include + #include ++#ifdef __ARM_NEON ++#include "sse2neon.h" ++#else + #include ++#endif ++ + #include "ksw.h" + #include "sequence_batch.h" + +diff --git c/src/sse2neon.h i/src/sse2neon.h new file mode 100644 index 0000000..2b12721 --- /dev/null -+++ i/SeqLib/sse2neon.h ++++ i/src/sse2neon.h @@ -0,0 +1,9301 @@ +#ifndef SSE2NEON_H +#define SSE2NEON_H @@ -9305,36 +9337,3 @@ index 0000000..2b12721 +#endif + +#endif -diff --git c/SeqLib/ssw.h i/SeqLib/ssw.h -index 583442a..5a962c2 100644 ---- c/SeqLib/ssw.h -+++ i/SeqLib/ssw.h -@@ -11,7 +11,11 @@ - #ifndef SSW_H - #define SSW_H - -+#ifdef __ARM_NEON -+#include "sse2neon.h" -+#else - #include -+#endif - #include - #include - #include -diff --git c/src/ssw.c i/src/ssw.c -index 5851613..2fb43b1 100644 ---- c/src/ssw.c -+++ i/src/ssw.c -@@ -36,7 +36,12 @@ - */ - - #include "SeqLib/ssw.h" -+#ifdef __ARM_NEON -+#include "SeqLib/sse2neon.h" -+#else - #include -+#endif -+#include - #include - #include - #include diff --git a/recipes/chromap/meta.yaml b/recipes/chromap/meta.yaml index 05010a6f787c2..db405e9472056 100644 --- a/recipes/chromap/meta.yaml +++ b/recipes/chromap/meta.yaml @@ -5,13 +5,15 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('chromap', max_pin="x.x") }} source: url: https://github.com/haowenz/chromap/archive/refs/tags/v{{ version }}.tar.gz sha256: bea2fc76bd7d8931f69db0b63aef19e50070b24c0ab1415569b59d490fff42e8 + patches: + - chromap-aarch64.patch # [aarch64 or arm64] requirements: build: @@ -35,3 +37,8 @@ about: license_file: LICENSE summary: Fast alignment and preprocessing of chromatin profiles doc_url: https://zhanghaowen.com/chromap/ + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/chromsize/build.sh b/recipes/chromsize/build.sh new file mode 100644 index 0000000000000..9543cf881c80c --- /dev/null +++ b/recipes/chromsize/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +set -xe + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --path ./chromsize/ --root ${PREFIX} diff --git a/recipes/chromsize/meta.yaml b/recipes/chromsize/meta.yaml new file mode 100644 index 0000000000000..e28195bb187a3 --- /dev/null +++ b/recipes/chromsize/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "chromsize" %} +{% set version = "0.0.2" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz + sha256: e0358a7a36a74b24b8cbb9034b8060de90d1af867baa66bc093192df9734bd40 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('chromsize', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - {{ compiler("rust") }} + - pkg-config + +test: + commands: + - chromsize --help + - chromsize --version + +about: + home: https://github.com/alejandrogzi/chromsize + license: MIT + license_family: MIT + license_file: LICENSE + summary: "just get your chrom sizes" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - alejandrogzi diff --git a/recipes/clinker-py/meta.yaml b/recipes/clinker-py/meta.yaml index 20abe45bf5912..88ceab35216f8 100644 --- a/recipes/clinker-py/meta.yaml +++ b/recipes/clinker-py/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clinker" %} -{% set version = "0.0.29" %} +{% set version = "0.0.30" %} package: name: {{ name }}-py @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: cca735b27da29fc676517d5578c771d05dd2be4f00ea25221747088185bd860d + sha256: 42901ab26945d436ff462528579f7354abe2bb1df7910d6bf16669a57fcfb1ff build: number: 0 diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index e073332a1cf96..7902d97a06e40 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.17.1" %} -{% set sha256 = "9fc21858d673a9f4daa459741a5425790402ad7ef12544d62c13e750d73888af" %} +{% set version = "0.18.2" %} +{% set sha256 = "b3064769e3cf62bd19d12523d391496bce96ce2c057df2b49e53f922ef1369fb" %} package: name: clinvar-this diff --git a/recipes/clipandmerge/LICENSE b/recipes/clipandmerge/LICENSE new file mode 100644 index 0000000000000..9cecc1d4669ee --- /dev/null +++ b/recipes/clipandmerge/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + {one line to give the program's name and a brief idea of what it does.} + Copyright (C) {year} {name of author} + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/clipandmerge/clipandmerge.py b/recipes/clipandmerge/clipandmerge.py index 4ee16451cc972..7c28c1f5f1081 100755 --- a/recipes/clipandmerge/clipandmerge.py +++ b/recipes/clipandmerge/clipandmerge.py @@ -11,7 +11,7 @@ import sys import subprocess from os import access, getenv, X_OK -jar_file = 'ClipAndMerge-1.7.8.jar' +jar_file = 'ClipAndMerge-1.7.9.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] diff --git a/recipes/clipandmerge/meta.yaml b/recipes/clipandmerge/meta.yaml index 85cd37f69f1ed..285ccf03cd358 100644 --- a/recipes/clipandmerge/meta.yaml +++ b/recipes/clipandmerge/meta.yaml @@ -1,16 +1,18 @@ -{% set version = "1.7.8" %} +{% set version = "1.7.9" %} package: name: clipandmerge version: {{ version }} source: - url: https://github.com/apeltzer/ClipAndMerge/releases/download/v{{ version }}/ClipAndMerge-{{ version }}.jar - md5: 548e403bf12d9709949fd74236205a01 + url: https://github.com/apeltzer/ClipAndMerge/releases/download/{{ version }}/ClipAndMerge-{{ version }}.jar + md5: 2951ba364b4a5add18caf21459291cfe build: noarch: generic - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('clipandmerge', max_pin="x") }} requirements: run: @@ -24,4 +26,5 @@ test: about: home: https://github.com/apeltzer/ClipAndMerge license: GPLv3 + license_file: LICENSE summary: Clip&Merge is a tool to clip off adapters from sequencing reads and merge overlapping paired end reads together. diff --git a/recipes/cloci/meta.yaml b/recipes/cloci/meta.yaml index 99e3b7b279aee..ca9f38a84593d 100644 --- a/recipes/cloci/meta.yaml +++ b/recipes/cloci/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cloci" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,9 +7,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cloci-{{ version }}.tar.gz - sha256: 46f5387ff625b79038a130f5d501e6dd18b3ccd8ec79d027e6ca78d97e8ad0c2 + sha256: 2bf3eff7a017174633337d72b1c221098aca161b6d55d362e34a4c5bcc62c17d build: + number: 1 + noarch: python entry_points: - cloci = cloci.main:cli - cloci2enrich = cloci.tools.cloci2enrich:cli @@ -17,18 +19,19 @@ build: - hg2hg_net = cloci.tools.hg2hg_net:cli - hlg2biofile = cloci.tools.hlg2biofile:cli - hlg2hlg_net = cloci.tools.hlg2hlg_net:cli - noarch: python - script: python -m pip install . -vv --no-deps --no-build-isolation - number: 0 + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} run_exports: - {{ pin_subpackage('cloci', max_pin="x.x") }} requirements: host: + - python >=3 - setuptools-scm - pip run: - - python >=3.0,<4.0 + - python >=3 - mycotools - cogent3 - tqdm @@ -39,17 +42,16 @@ test: imports: - cloci commands: - - pip check - cloci --help - update_mtdb --help - requires: - - pip about: home: https://github.com/xonq/cloci - summary: Co-occurrence Locus and Orthologous Cluster Identifier + summary: "Co-occurrence Locus and Orthologous Cluster Identifier." license: AGPL-3.0-only + license_family: AGPL license_file: LICENSE + dev_url: https://github.com/xonq/cloci extra: recipe-maintainers: diff --git a/recipes/cnmf/meta.yaml b/recipes/cnmf/meta.yaml new file mode 100644 index 0000000000000..42c0284e02d37 --- /dev/null +++ b/recipes/cnmf/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "cnmf" %} +{% set version = "1.6.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/cnmf-{{ version }}.tar.gz + sha256: a38dfe82261087ed1945aac069a77a04fc12f5e8621bfa1c9b3e662339432c2a + +build: + number: 0 + noarch: python + entry_points: + - cnmf = cnmf:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('cnmf', max_pin="x") }} + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - scikit-learn >=1.0 + - anndata >=0.9 + - scanpy + - pandas + - numpy + - fastcluster + - matplotlib-base + - palettable + - scipy + - pyyaml + +test: + imports: + - cnmf + commands: + - cnmf --help + +about: + home: https://github.com/dylkot/cNMF + summary: "Consensus NMF for scRNA-Seq data." + license: MIT + license_family: MIT + license_file: LICENSE + dev_url: https://github.com/dylkot/cNMF + +extra: + identifiers: + - doi:10.7554/eLife.43803 diff --git a/recipes/cnv_facets/build.sh b/recipes/cnv_facets/build.sh index 37d48cafb138b..cd500288f600e 100644 --- a/recipes/cnv_facets/build.sh +++ b/recipes/cnv_facets/build.sh @@ -1,16 +1,12 @@ #!/bin/bash -set -e +set -xe FACETS_GIT_REF=`grep -P ' *^FACETS_REF' install/install_pkgs.R \ | sed 's/ //g; s/<-//; s/=//;' \ | tr "'" '"' \ | sed 's/FACETS_REF"//; s/".*//'` -$R -e "devtools::install_github('mskcc/facets', ref= '$FACETS_GIT_REF', lib= NULL, repos= 'https://cran.r-project.org')" - -$R -e 'install.packages(c("argparse"), lib= NULL, repos= "https://cran.r-project.org")' - mkdir -p $PREFIX/bin chmod a+x bin/cnv_facets.R cp bin/cnv_facets.R $PREFIX/bin/ diff --git a/recipes/cnv_facets/meta.yaml b/recipes/cnv_facets/meta.yaml index f4a0bec2d5da0..33bfbf683e95c 100644 --- a/recipes/cnv_facets/meta.yaml +++ b/recipes/cnv_facets/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.16.0" %} -{% set sha256 = "3628bc0970942e79292d60a972df85f75c7a8699c633f79fb96ba071e83600a2" %} +{% set version = "0.16.1" %} +{% set sha256 = "64c29e2719306cc8e20318ff9a857fa2bb4fcd2af5eea30e733dad4867475972" %} package: name: cnv_facets @@ -10,7 +10,9 @@ source: sha256: '{{sha256}}' build: - number: 2 + number: 1 + run_exports: + - {{ pin_subpackage('cnv_facets', max_pin="x") }} skip: True # [not linux] requirements: @@ -19,6 +21,8 @@ requirements: - {{ compiler('cxx') }} - {{ compiler('fortran') }} host: + - r-argparse >=2.1.6 + - r-facets - r-base - r-devtools - r-data.table @@ -31,6 +35,8 @@ requirements: - bcftools >=1.9 - snp-pileup run: + - r-argparse >=2.1.6 + - r-facets - r-base - r-data.table - r-ggplot2 @@ -54,5 +60,7 @@ about: license_family: MIT extra: + additional-platforms: + - linux-aarch64 maintainers: - Dario Beraldi diff --git a/recipes/cogent3/meta.yaml b/recipes/cogent3/meta.yaml index d475b58bcaa0b..9e74412a866f8 100644 --- a/recipes/cogent3/meta.yaml +++ b/recipes/cogent3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cogent3" %} -{% set version = "2024.7.19a1" %} +{% set version = "2024.7.19a6" %} package: name: {{ name|lower }} @@ -7,24 +7,26 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: fdf62233b60eb28e16a7aa8a58abdc6b98b594a596b220316875cb3d31f34dda + sha256: dae78c99be59e4a2283cd1e60ea1e35029132296c1b2c4fc750a5f28f809a72b build: noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv number: 0 run_exports: - {{ pin_subpackage(name, max_pin=None) }} requirements: host: - - python >=3.9, <3.12 + - python >=3.9,<3.13 - pip - - flit-core >=3.2, <4 + - flit-core >=3.2,<4 run: - - python >=3.9, <3.12 + - python >=3.9,<3.13 + - charset-normalizer - scipy - chardet + - loky - numpy - numba >0.53.0 - scitrack @@ -38,10 +40,13 @@ test: - cogent3 about: - home: https://pypi.org/project/cogent3/ + home: "https://github.com/cogent3/cogent3" summary: 'COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems with 1000s of CPUs.' - license: BSD-3-Clause + license: "BSD-3-Clause" + license_family: BSD license_file: LICENSE + dev_url: "https://github.com/cogent3/cogent3" + doc_url: "https://github.com/cogent3/cogent3/blob/{{ version }}/README.md" extra: recipe-maintainers: diff --git a/recipes/comet-ms/meta.yaml b/recipes/comet-ms/meta.yaml index 66057b41ec387..addbd48fa6ffe 100644 --- a/recipes/comet-ms/meta.yaml +++ b/recipes/comet-ms/meta.yaml @@ -1,20 +1,20 @@ {% set name = "comet-ms" %} -{% set version = "2023012" %} -{% set md5 = "d60433652e5a5e682288ddbdfb014eb4" %} +{% set version = "2024011" %} +{% set md5 = "3f0dc29582792620b0cc916c2117965f" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/UWPR/Comet/archive/refs/tags/v2023.01.2.zip + url: https://github.com/UWPR/Comet/archive/refs/tags/v2024.01.1.zip md5: {{ md5 }} build: run_exports: - {{ pin_subpackage('comet-ms', max_pin=None) }} skip: True # [osx] - number: 1 + number: 0 requirements: build: diff --git a/recipes/commec/meta.yaml b/recipes/commec/meta.yaml new file mode 100644 index 0000000000000..676f15e6479c5 --- /dev/null +++ b/recipes/commec/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "commec" %} +{% set version = "0.1.2" %} +{% set sha256 = "33e99060dca151cb9d5481f47e02f1b5276b2cdf61804e7093f0cfc32bef1188" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: https://github.com/ibbis-screening/common-mechanism/archive/refs/tags/v{{version}}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + # consider using "x.x.x" rather than "x.x", or "x" considering alpha software and liklihood of change. + - {{ pin_subpackage('commec', max_pin="x.x") }} + +requirements: + host: + - python >=3.1 + - pip >=24 + run: + - python >=3.1 + # Runtime Python dependencies + - biopython >=1.8 + - numpy >=2.0.0 + - pandas >=2.2 + - pytaxonkit >=0.8 + # Runtime non-Python dependencies + - bedtools >=2.31 + - blast >=2.16 + - emboss >=6.6 + - diamond >=0.9 + - hmmer >=3.4 + - infernal >=1.1 + - parallel >=20240722 + - perl-list-moreutils >=0.430 + - taxonkit >=0.17 + +test: + commands: + - commec screen --help + - commec flag --help + - commec split --help + +about: + home: https://github.com/ibbis-screening/common-mechanism + license: MIT + license_family: MIT + doc_url: https://github.com/ibbis-screening/common-mechanism/wiki + summary: "commec: a free, open-source, globally available tool for DNA sequence screening" + dev_url: https://github.com/ibbis-screening/common-mechanism diff --git a/recipes/consensify/build.sh b/recipes/consensify/build.sh new file mode 100755 index 0000000000000..1bded391fb320 --- /dev/null +++ b/recipes/consensify/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +set -xe + +## compile +${CXX} -c consensify_c.cpp -I./ ${CXXFLAGS} + +## link +${CXX} consensify_c.o -o consensify_c -lz ${LDFLAGS} + +## install +mkdir -p $PREFIX/bin +cp consensify_c ${PREFIX}/bin/consensify_c diff --git a/recipes/consensify/meta.yaml b/recipes/consensify/meta.yaml new file mode 100644 index 0000000000000..be77f31b16102 --- /dev/null +++ b/recipes/consensify/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "2.4.0" %} + +package: + name: consensify + version: {{ version }} + +source: + url: https://github.com/jlapaijmans/Consensify/archive/refs/tags/{{ version }}.tar.gz + sha256: 2b88cda2c6ad44b6fd749d86485d3f16418b189b9c8ff4d20dd19640792dac1e + +build: + number: 1 + run_exports: + - {{ pin_subpackage('consensify', max_pin="x") }} + +requirements: + build: + - {{ compiler('cxx') }} + host: + - zlib + run: + - zlib + +test: + commands: + - consensify_c -h + +about: + home: https://github.com/jlapaijmans/Consensify + license: GPL-3.0-or-later + license_family: GPL + license_file: LICENCE.txt + dev_url: https://github.com/jlapaijmans/Consensify + doc_url: https://github.com/jlapaijmans/Consensify + summary: A method for generating a consensus pseudohaploid genome sequence + about: Consensify is a method for generating a consensus pseudohaploid genome sequence with greatly reduced error rates compared to standard pseudohaploidisation. The method is described in full and tested in the associated publication (Barlow et al. (2020), Genes 11:50, doi 10.3390/genes11010050). + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/cpstools/meta.yaml b/recipes/cpstools/meta.yaml index f8dbea9224cbb..e9c88674e0521 100644 --- a/recipes/cpstools/meta.yaml +++ b/recipes/cpstools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cpstools" %} -{% set version = "1.0.13" %} -{% set sha256 = "767f5739416f290726ed459bf82969b453ffd2c04aa9171e5dc7c842a8d6b81e" %} +{% set version = "2.0.0" %} +{% set sha256 = "1c2c729d4979402d9f7835dea70e47c77d2e2ef6b1e822cfd1e6e008f3b98ba1" %} package: name: {{ name|lower }} @@ -21,13 +21,14 @@ build: requirements: host: - - python >=3.10 + - python >=3.9 - poetry-core - pip run: - - python >=3.10.0 + - python >=3.9 - biopython >=1.84.0 - numpy >=1.26.4 + - tqdm >=4.66.5 test: imports: diff --git a/recipes/crisprme/meta.yaml b/recipes/crisprme/meta.yaml index 6997ee9a682b8..77d798dc99338 100644 --- a/recipes/crisprme/meta.yaml +++ b/recipes/crisprme/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1.4" %} +{% set version = "2.1.5" %} package: name: crisprme @@ -6,7 +6,7 @@ package: source: url: https://github.com/pinellolab/CRISPRme/archive/refs/tags/v{{ version }}.tar.gz - sha256: a2d8d374365ba90eeb81548b16b589f23bc9ee184cca447306efc12b3d1a97f8 + sha256: 788cca9caff4d9c3a3c7ace21a62891d052bd23513addd72c34dc577dde1e375 build: run_exports: diff --git a/recipes/cryptkeeper/meta.yaml b/recipes/cryptkeeper/meta.yaml new file mode 100644 index 0000000000000..bd612a21cc2c6 --- /dev/null +++ b/recipes/cryptkeeper/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "cryptkeeper" %} +{% set version = "1.0.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cryptkeeper-{{ version }}.tar.gz + sha256: 7e43d858043073a98903b890846636c3b7c9e5ce289fe97c00ff5734d47357e8 + +build: + entry_points: + - cryptkeeper = cryptkeeper.cryptkeeper:main + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + number: 0 + run_exports: + - {{ pin_subpackage("cryptkeeper", max_pin="x") }} + +requirements: + host: + - python >=3.9 + - pip + run: + - python >=3.9 + - ostir + - rhotermpredict + - promotercalculator + - bokeh + - biopython + +test: + imports: + - cryptkeeper + commands: + - cryptkeeper --help + +about: + home: https://github.com/barricklab/cryptkeeper + summary: "A negative design tool for predicting and visualizing undesired gene expression" + license: "GPL-3.0-only" + license_file: LICENSE + license_family: GPL3 + dev_url: https://github.com/barricklab/cryptkeeper + +extra: + recipe-maintainers: + - croots + - jeffreybarrick diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index 6c35dd340e3da..b68dacf543faa 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -9,7 +9,7 @@ source: sha256: da3b45775b07334d2e2580a7b154d19ea7e872f0da813bb1ac2a4da712bfc223 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" skip: True # [py < 38] run_exports: @@ -45,6 +45,7 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 recipe-maintainers: - marcelm identifiers: diff --git a/recipes/cyrcular/build.sh b/recipes/cyrcular/build.sh new file mode 100644 index 0000000000000..4bbfddb620755 --- /dev/null +++ b/recipes/cyrcular/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash -xeuo + +# Make sure bindgen passes on our compiler flags. +export BINDGEN_EXTRA_CLANG_ARGS="${CPPFLAGS} ${CFLAGS} ${LDFLAGS}" + +cargo install --no-track --locked --root "${PREFIX}" --path . diff --git a/recipes/cyrcular/meta.yaml b/recipes/cyrcular/meta.yaml new file mode 100644 index 0000000000000..26a83c54f2525 --- /dev/null +++ b/recipes/cyrcular/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "0.3.0" %} +{% set sha256 = "eba1dea2e13601b5bc18183fff7d5bf3c07e9ed98f62272453a5473e7bbd36cb" %} + +package: + name: cyrcular + version: {{ version }} + +source: + url: https://github.com/tedil/cyrcular/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage("cyrcular", max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('rust') }} + - cmake + - make + - pkg-config + host: + - clangdev + - openssl + - zlib + - xz + - bzip2 + - gsl + - libcblas + - blis + +test: + commands: + - cyrcular -h + +about: + home: https://github.com/tedil/cyrcular + license: MIT + license_family: MIT + summary: Tool for calling circles from nanopore reads + dev_url: https://github.com/tedil/cyrcular + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/cytotrace2-python/meta.yaml b/recipes/cytotrace2-python/meta.yaml new file mode 100644 index 0000000000000..a0e51187a6d66 --- /dev/null +++ b/recipes/cytotrace2-python/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "cytotrace2-python" %} +{% set version = "0.0.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/digitalcytometry/cytotrace2/archive/refs/tags/v1.0.0.tar.gz + sha256: a0e238320fc0f310f6c16b1d2ad3fd2cc556e5ee3a04d24c490c4e46c34053e1 + +build: + number: 0 + entry_points: + - cytotrace2=cytotrace2_py.cytotrace2_py:run_cytotrace2 + noarch: python + script: cd cytotrace2_python && {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('cytotrace2-python', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - pip + run: + - python >=3.9 + - anndata + - numpy + - pandas + - scanpy + - scipy + - scikit-learn + - pytorch + - r-rann + - r-seurat + - r-seuratobject + - r-matrix + - r-ggplot2 + - r-data.table + - r-dplyr + - r-argparse + +test: + imports: + - cytotrace2_py + commands: + - cytotrace2 --help + +about: + license: Custom + license_file: LICENSE + summary: "CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data." + home: "https://github.com/digitalcytometry/cytotrace2" + dev_url: "https://github.com/digitalcytometry/cytotrace2" + doc_url: "https://github.com/digitalcytometry/cytotrace2/blob/v{{ version }}/cytotrace2_python/README.md" diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index 139cbd9408afd..a79b51679e3a0 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -14,11 +14,12 @@ source: - patches/setup.py.patch build: - number: 0 + number: 1 skip: True # [py < 37] script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv script_env: - CFLAGS=-Wno-implicit-function-declaration -Wno-int-conversion # [osx and py == 38] + - M4=$BUILD_PREFIX/bin/m4 # [osx and arm64] entry_points: - cyvcf2 = cyvcf2.__main__:cli run_exports: @@ -67,3 +68,4 @@ extra: - biotools:cyvcf2 additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/d4tools/meta.yaml b/recipes/d4tools/meta.yaml index 54a4335bead4b..185f9b3671124 100644 --- a/recipes/d4tools/meta.yaml +++ b/recipes/d4tools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.10" %} +{% set version = "0.3.11" %} package: name: d4tools @@ -6,10 +6,10 @@ package: source: url: https://github.com/38/d4-format/archive/refs/tags/v{{ version }}.tar.gz - sha256: d3fbe8f063ed1f89148ae0333abc1d5b955f499fc429254f83af464012678d33 + sha256: 376e61c93cfe2efc15f5e74b75214e065e278146555e67b8769818bf49594726 build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('d4tools', max_pin="x.x") }} diff --git a/recipes/dbcanlight/meta.yaml b/recipes/dbcanlight/meta.yaml index feb9db4e3aac6..913d6bd54f1e3 100644 --- a/recipes/dbcanlight/meta.yaml +++ b/recipes/dbcanlight/meta.yaml @@ -1,5 +1,5 @@ -{% set name = "dbcanLight" %} -{% set version = "1.0.2" %} +{% set name = "dbcanlight" %} +{% set version = "1.1.0" %} package: name: {{ name|lower }} @@ -7,40 +7,58 @@ package: source: url: https://github.com/chtsai0105/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: da8a46553010e625e0a8c5db218876b1b339a153750341f110f7883dd961c340 + sha256: dee95b9e8295fc749013283af43706b777646beb55d0881360b68b7efc7a60b6 build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + entry_points: + - dbcanlight = dbcanlight.__main__:main + - dbcanlight-hmmparser = dbcanlight.hmmsearch_parser:main + - dbcanlight-subparser = dbcanlight.substrate_parser:main run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: host: - pip - - python - - setuptools + - python >=3.7 + - pytest >=6.0 run: - - biopython >=1.79 + - biopython >=1.81 + - importlib-metadata + - pyhmmer >=0.10.4 - python >=3.7 - - importlib_metadata - - pyhmmer >=0.10.2 test: commands: - - dbcanLight -h - - dbcanLight-hmmparser -h - - dbcanLight-subparser -h + - dbcanlight -h + - dbcanlight-hmmparser -h + - dbcanlight-subparser -h about: - home: https://github.com/chtsai0105/dbcanLight/tree/main + home: https://github.com/chtsai0105/dbcanlight license: MIT + license_family: MIT license_file: LICENSE - summary: A lightweight rewrite of run_dbcan + summary: A lightweight CAZyme annotation tool description: | - dbcanlight uses the hmmsearch module in pyhmmer to discover CAZymes and - potential substrates from a peptide sequences. + Dbcanlight is a lightweight rewrite of a widely used CAZyme annotation tool run_dbcan. It uses pyhmmer, a Cython bindings to + HMMER3, to instead the cli version of HMMER3 suite as the backend for the search processes, which improves the multithreading + performance. In addition, it also solves the inconvenience process in the run dbcan that the large sequence file required + manual splitting beforehand. + + The main program dbcanlight comprises 3 modules - build, search and conclude. The build module help to download the required + databases from dbcan website; the search module searches against protein HMM, substrate HMM or diamond databases and reports + the hits separately; and the conclude module gathers all the results made by each module and provides a brief overview. The + output of dbcanlight is resemble to run_dbcan with slight cleanup. Run_dbcan output the same substrate several times for a + gene that hits multiple profiles with the same substrate; in dbcanlight we only report it once. + + Dbcanlight only re-implemented the core features of run_dbcan, that is searching for CAZyme and substrate matches by + hmmer/diamond/dbcansub. Submodules like signalP, CGCFinder, etc. are not implemented. + dev_url: https://github.com/chtsai0105/dbcanlight + doc_url: https://github.com/chtsai0105/dbcanlight/blob/v{{ version }}/README.md extra: recipe-maintainers: diff --git a/recipes/dbghaplo/build.sh b/recipes/dbghaplo/build.sh new file mode 100644 index 0000000000000..17d5db214e9a0 --- /dev/null +++ b/recipes/dbghaplo/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +cargo-bundle-licenses --format yaml --output THIRDPARTY.yml +RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . +cp scripts/* $PREFIX/bin diff --git a/recipes/dbghaplo/meta.yaml b/recipes/dbghaplo/meta.yaml new file mode 100644 index 0000000000000..f14ef02373001 --- /dev/null +++ b/recipes/dbghaplo/meta.yaml @@ -0,0 +1,47 @@ +{% set version="0.0.2" %} + +package: + name: dbghaplo + version: {{ version }} + +source: + url: https://github.com/bluenote-1577/dbghaplo/archive/v{{ version }}.tar.gz + sha256: e7e2741afb0c7f12718ec969815d3c8f18ce7ba66517e21c6fcfb3fe4262780b + +build: + number: 0 + run_exports: + - {{ pin_subpackage('dbghaplo', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - {{ compiler('rust') }} + - cargo-bundle-licenses + - make + - cmake >=3.12 + run: + - python + - samtools + - minimap2 + - lofreq >=2.1.5 + - tabix + - pysam >=0.16 + +test: + commands: + - dbghaplo -h + - run_dbghaplo_pipeline -h + - haplotag_bam -h + +about: + home: https://github.com/bluenote-1577/dbghaplo + license: MIT + license_file: + - LICENSE + - THIRDPARTY.yml + summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn Graph. + +extra: + recipe-maintainers: + - bluenote-1577 diff --git a/recipes/dedup/LICENSE b/recipes/dedup/LICENSE new file mode 100644 index 0000000000000..9cecc1d4669ee --- /dev/null +++ b/recipes/dedup/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + {one line to give the program's name and a brief idea of what it does.} + Copyright (C) {year} {name of author} + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/dedup/dedup.py b/recipes/dedup/dedup.py index eb372e90b3c0f..3ae3773987d7b 100755 --- a/recipes/dedup/dedup.py +++ b/recipes/dedup/dedup.py @@ -11,7 +11,7 @@ import sys import subprocess from os import access, getenv, X_OK -jar_file = 'DeDup-0.12.8.jar' +jar_file = 'DeDup-0.12.9.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] diff --git a/recipes/dedup/meta.yaml b/recipes/dedup/meta.yaml index 25bf9cf7d20cd..8c9d2229145cc 100644 --- a/recipes/dedup/meta.yaml +++ b/recipes/dedup/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.12.8" %} +{% set version = "0.12.9" %} package: name: dedup @@ -6,11 +6,13 @@ package: source: url: https://github.com/apeltzer/dedup/releases/download/{{ version }}/DeDup-{{ version }}.jar - md5: 2a5fdca4754de6a3526740f4c55fb8dc + md5: 5c398758f28e77c3544cdeadade31d6d build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('dedup', max_pin="x") }} requirements: run: @@ -25,4 +27,5 @@ test: about: home: https://github.com/apeltzer/dedup license: GPLv3 + license_file: LICENSE summary: "DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments)." diff --git a/recipes/deeplc/meta.yaml b/recipes/deeplc/meta.yaml index eab5e428730fa..a06a3a30d25e1 100644 --- a/recipes/deeplc/meta.yaml +++ b/recipes/deeplc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLC" %} -{% set version = "2.2.38" %} -{% set sha256 = "9c66dd629246ce422ca57a8628c122765770c8eeebdc2f6a71a8f88d9a9193a5" %} +{% set version = "3.0.8" %} +{% set sha256 = "49f579fd96d937f7c62b99044b8bf12085ccc9b6d123b93ab2c4417189106ca0" %} package: name: {{ name|lower }} diff --git a/recipes/deeplcretrainer/meta.yaml b/recipes/deeplcretrainer/meta.yaml index 635792b35745b..27dd7f6bf8b00 100644 --- a/recipes/deeplcretrainer/meta.yaml +++ b/recipes/deeplcretrainer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLCRetrainer" %} -{% set version = "0.2.12" %} -{% set sha256 = "bd31124518f6b5d1f1ec2f0983c0885b44e235b93134cc61c5eab52e2519bdff" %} +{% set version = "1.0.0" %} +{% set sha256 = "a12d46baec788b46437692f941260ec8956aaa55618030c26ebf2d1681f69954" %} package: name: {{ name|lower }} diff --git a/recipes/delly/build.sh b/recipes/delly/build.sh index 2947d72ca81d5..89d206cac27f5 100644 --- a/recipes/delly/build.sh +++ b/recipes/delly/build.sh @@ -1,4 +1,3 @@ #!/bin/sh -make CXX="$CXX" all -make prefix="$PREFIX" install +CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS" make -j${CPU_COUNT} CXX="${CXX}" prefix="${PREFIX}" install diff --git a/recipes/delly/meta.yaml b/recipes/delly/meta.yaml index 084b2579dcc44..21458f52a32ed 100644 --- a/recipes/delly/meta.yaml +++ b/recipes/delly/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.6" %} -{% set sha256 = "1a71fcc5f2a55649c2104086f3f7163ed58c5868eaf040a25e45c777b0e1abb7" %} +{% set version = "1.2.9" %} +{% set sha256 = "084aec699f266e21b457db2cb86c75d73e29b071bdd837cb987561942aa01510" %} package: name: delly @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 3 + number: 0 run_exports: - {{ pin_subpackage("delly", max_pin="x.x") }} @@ -18,13 +18,18 @@ requirements: build: - make - {{ compiler('cxx') }} - - wget host: - zlib - - boost-cpp >=1.85.0 + - bzip2 + - libdeflate + - boost-cpp - htslib run: - - libboost >=1.85.0 + - zlib + - bzip2 + - libdeflate + - boost-cpp + - htslib test: commands: diff --git a/recipes/derna/build.sh b/recipes/derna/build.sh index a56e54179f0d9..7898ddc35f18f 100644 --- a/recipes/derna/build.sh +++ b/recipes/derna/build.sh @@ -1,4 +1,6 @@ -#! /bin/sh +#!/bin/bash + +set -xe export C_INCLUDE_PATH=${PREFIX}/include export LIBRARY_PATH=${PREFIX}/lib @@ -6,6 +8,6 @@ export LIBRARY_PATH=${PREFIX}/lib mkdir build cd build cmake .. -make +make -j ${CPU_COUNT} mkdir -p $PREFIX/bin cp derna $PREFIX/bin diff --git a/recipes/derna/meta.yaml b/recipes/derna/meta.yaml index 1ea6fe69b1979..ffafda5a12a70 100644 --- a/recipes/derna/meta.yaml +++ b/recipes/derna/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: derna @@ -6,10 +6,12 @@ package: source: url: https://github.com/elkebir-group/derna/archive/refs/tags/v{{ version }}.tar.gz - sha256: 29e6bd6588a3e6d4d48fc2d08ff69a5eddeccbe281c3f802d2052c4c1945230a + sha256: d7e2fdbe733d03f9e617ea325a43283c0e4e298780253cf2e7da7ad07d3aafc5 build: number: 1 + run_exports: + - {{ pin_subpackage('derna', max_pin="x") }} requirements: build: @@ -17,9 +19,6 @@ requirements: - {{ compiler('cxx') }} - make - cmake - host: - run: - test: commands: @@ -28,5 +27,12 @@ test: about: home: https://github.com/elkebir-group/derna license: BSD-3-Clause + license_family: BSD license_file: LICENSE - summary: "RNA sequence design for a target protein sequence" + summary: "RNA sequence design for a target protein sequence." + dev_url: https://github.com/elkebir-group/derna + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/dfast/meta.yaml b/recipes/dfast/meta.yaml index 36eb6d765c65d..63eb3ed37c582 100644 --- a/recipes/dfast/meta.yaml +++ b/recipes/dfast/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: dfast @@ -6,7 +6,7 @@ package: source: url: https://github.com/nigyta/dfast_core/archive/{{ version }}.tar.gz - sha256: afee0c4e13482b519203c2bedbf48375788aa17ef7f340f0c52165d10931efcb + sha256: d889e00c6870cdb7229cc91fe8f52b6dafc95535948669b91f0a0b276501adb7 build: number: 0 diff --git a/recipes/dfast_qc/build.sh b/recipes/dfast_qc/build.sh index ffe64f11c0e4a..73a9d9b560a5d 100755 --- a/recipes/dfast_qc/build.sh +++ b/recipes/dfast_qc/build.sh @@ -19,8 +19,9 @@ cp -Rv ./* ${APPROOT}/ # cd ${PREFIX}/bin ln -s ${APPROOT}/dfast_qc ${PREFIX}/bin/ ln -s ${APPROOT}/dqc_admin_tools.py ${PREFIX}/bin/ -ln -s ${APPROOT}/initial_setup.sh ${PREFIX}/bin/dqc_initial_setup.sh +ln -s ${APPROOT}/dqc_initial_setup.sh ${PREFIX}/bin/ ln -s ${APPROOT}/dqc_ref_manager.py ${PREFIX}/bin/ +ln -s ${APPROOT}/dqc_multi ${PREFIX}/bin/ # ${PREFIX}/bin/dfast_qc --version dfast_qc --version diff --git a/recipes/dfast_qc/meta.yaml b/recipes/dfast_qc/meta.yaml index 5481d28e3c43b..37f9b57bd3975 100644 --- a/recipes/dfast_qc/meta.yaml +++ b/recipes/dfast_qc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.0.5" %} package: name: dfast_qc @@ -12,7 +12,7 @@ build: source: url: https://github.com/nigyta/dfast_qc/archive/{{ version }}.tar.gz - sha256: 60cc0badf7b2aa8a464b92db717b2853e343b09a18f2c4bf6eeced3c79b0ba7b + sha256: 7a4bb1139268c5bcfcc0a94a653cb0b7e8cbb9c0e9fb89dbde8ab6fa2b84162f requirements: diff --git a/recipes/dice/meta.yaml b/recipes/dice/meta.yaml index 3bb08800d67bd..491b95d5b6b15 100644 --- a/recipes/dice/meta.yaml +++ b/recipes/dice/meta.yaml @@ -1,13 +1,13 @@ {% set name = "dice" %} -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} package: name: '{{ name }}' version: '{{ version }}' source: - url: https://github.com/samsonweiner/DICE/archive/refs/tags/v1.0.0.tar.gz - sha256: 67288b5b73c61a66b2d4fd04329974c529a3744b57f0a59606d610403010213f + url: https://github.com/samsonweiner/DICE/archive/refs/tags/v1.1.0.tar.gz + sha256: 4130efd20af8726544350cef76015b4f9d1f1755fef1a4f63576a73755a0d8c0 build: noarch: python @@ -38,4 +38,4 @@ about: license_file: LICENSE summary: Cell lineage reconstruction from single-cell CNA data description: | - DICE (short for Distance-based Inference of Copy-number Evolution) is a collection of fast and accurate methods for reconstructing cell lineage trees from single-cell copy number aberration data. \ No newline at end of file + DICE (short for Distance-based Inference of Copy-number Evolution) is a collection of fast and accurate methods for reconstructing cell lineage trees from single-cell copy number aberration data. diff --git a/recipes/dicey/build.sh b/recipes/dicey/build.sh index 54987ee3ba11a..38a203670614e 100644 --- a/recipes/dicey/build.sh +++ b/recipes/dicey/build.sh @@ -1,5 +1,3 @@ -#!/bin/sh +#!/bin/bash -make all CXX=$CXX CXXFLAGS="-D__STDC_FORMAT_MACROS -I${SRC_DIR}/src/sdslLite/include -L${SRC_DIR}/src/sdslLite/lib -I${PREFIX}/include -L${PREFIX}/lib -Isrc/jlib/ -std=c++14" -mkdir -p $PREFIX/bin -cp src/dicey $PREFIX/bin +CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS -I${SRC_DIR}/src/sdslLite/include -L${SRC_DIR}/src/sdslLite/lib -I${PREFIX}/include -L${PREFIX}/lib -Isrc/jlib/ -std=c++17" make -j${CPU_COUNT} CXX="${CXX}" prefix="${PREFIX}" install diff --git a/recipes/dicey/build_failure.linux-64.yaml b/recipes/dicey/build_failure.linux-64.yaml deleted file mode 100644 index 7a7c7fc2685d4..0000000000000 --- a/recipes/dicey/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c8389fa92d55fba29aa3e922321084ba770fc8c234a709c8b440b779fa5268d0 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Sample programs can be found in the examples-directory. - A program 'example.cpp' can be compiled with the command: - g -std=c14 -D__STDC_FORMAT_MACROS -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib -I$PREFIX/include -L$PREFIX/lib -Isrc/jlib/ -std=c14 -O3 -DNDEBUG -msse4.2 -Wall -Wextra -pedantic -ffast-math -funroll-loops -D__extern_always_inline="extern __always_inline" \ - -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib \ - example.cpp -ldivsufsort -ldivsufsort64 - - Tests in the test-directory - A cheat sheet in the extras/cheatsheet-directory. - Have fun! - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -D__STDC_FORMAT_MACROS -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib -I$PREFIX/include -L$PREFIX/lib -Isrc/jlib/ -std=c14 src/dicey.cpp -o src/dicey -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/src/htslib/ -L$SRC_DIR/src/htslib//lib -L$SRC_DIR/src/sdslLite//lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -ldl -lpthread -lhts -lz -llzma -lbz2 -Wl,-rpath,$SRC_DIR/src/htslib/ - In file included from src/bed.h:6, - from src/dicey.cpp:12: - /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/progress.hpp:23:3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) - 23 | # error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) - | ^~~~~ - In file included from /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/progress.hpp:29: - /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/timer.hpp:21:3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) - 21 | # error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) - | ^~~~~ - In file included from /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/smart_ptr/intrusive_ptr.hpp:16, - from /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/filesystem/exception.hpp:20, - from /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/filesystem.hpp:17, - from src/bed.h:4: - /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config/pragma_message.hpp:24:34: note: '#pragma message: This header is deprecated. Use the facilities in or instead.' - 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) - | ^~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro 'BOOST_PRAGMA_MESSAGE' - 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") - | ^~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/progress.hpp:27:1: note: in expansion of macro 'BOOST_HEADER_DEPRECATED' - 27 | BOOST_HEADER_DEPRECATED( "the facilities in or " ) - | ^~~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config/pragma_message.hpp:24:34: note: '#pragma message: This header is deprecated. Use the facilities in instead.' - 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) - | ^~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro 'BOOST_PRAGMA_MESSAGE' - 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") - | ^~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/timer.hpp:25:1: note: in expansion of macro 'BOOST_HEADER_DEPRECATED' - 25 | BOOST_HEADER_DEPRECATED( "the facilities in " ) - | ^~~~~~~~~~~~~~~~~~~~~~~ - In file included from src/dicey.cpp:17: - src/hunter.h:65:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | struct SortDnaHit : public std::binary_function { - | ^~~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/string:48, - from /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/bits/locale_classes.h:40, - from /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/bits/ios_base.h:41, - from /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/ios:42, - from /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/ostream:38, - from /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/iostream:39, - from src/dicey.cpp:3: - /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - In file included from src/dicey.cpp:18: - src/silica.h:80:37: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 80 | struct SortPrimer : public std::binary_function - | ^~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - src/silica.h:100:39: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 100 | struct SortProducts : public std::binary_function - | ^~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - In file included from src/padlock.h:34, - from src/dicey.cpp:21: - src/gtf.h:53:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 53 | struct SortIntervalLabel : public std::binary_function { - | ^~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - src/gtf.h:60:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 60 | struct SortIntervalStart : public std::binary_function { - | ^~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718311588591/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - make: *** [Makefile:60: src/dicey] Error 1 - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/dicey_1718311588591/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/dicey/build_failure.linux-aarch64.yaml b/recipes/dicey/build_failure.linux-aarch64.yaml deleted file mode 100644 index c0c5be81f9cf2..0000000000000 --- a/recipes/dicey/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c8389fa92d55fba29aa3e922321084ba770fc8c234a709c8b440b779fa5268d0 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Sample programs can be found in the examples-directory. - A program 'example.cpp' can be compiled with the command: - g -std=c14 -D__STDC_FORMAT_MACROS -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib -I$PREFIX/include -L$PREFIX/lib -Isrc/jlib/ -std=c14 -O3 -DNDEBUG -Wall -Wextra -pedantic -ffast-math -funroll-loops -D__extern_always_inline="extern __always_inline" \ - -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib \ - example.cpp -ldivsufsort -ldivsufsort64 - - Tests in the test-directory - A cheat sheet in the extras/cheatsheet-directory. - Have fun! - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -D__STDC_FORMAT_MACROS -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib -I$PREFIX/include -L$PREFIX/lib -Isrc/jlib/ -std=c14 src/dicey.cpp -o src/dicey -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/src/htslib/ -L$SRC_DIR/src/htslib//lib -L$SRC_DIR/src/sdslLite//lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -ldl -lpthread -lhts -lz -llzma -lbz2 -Wl,-rpath,$SRC_DIR/src/htslib/ - In file included from src/bed.h:6, - from src/dicey.cpp:12: - /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/progress.hpp:23:3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) - 23 | # error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) - | ^~~~~ - In file included from /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/progress.hpp:29: - /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/timer.hpp:21:3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) - 21 | # error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) - | ^~~~~ - In file included from /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/smart_ptr/intrusive_ptr.hpp:16, - from /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/filesystem/exception.hpp:20, - from /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/filesystem.hpp:17, - from src/bed.h:4: - /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config/pragma_message.hpp:24:34: note: '#pragma message: This header is deprecated. Use the facilities in or instead.' - 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) - | ^~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro 'BOOST_PRAGMA_MESSAGE' - 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") - | ^~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/progress.hpp:27:1: note: in expansion of macro 'BOOST_HEADER_DEPRECATED' - 27 | BOOST_HEADER_DEPRECATED( "the facilities in or " ) - | ^~~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config/pragma_message.hpp:24:34: note: '#pragma message: This header is deprecated. Use the facilities in instead.' - 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) - | ^~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro 'BOOST_PRAGMA_MESSAGE' - 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") - | ^~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/boost/timer.hpp:25:1: note: in expansion of macro 'BOOST_HEADER_DEPRECATED' - 25 | BOOST_HEADER_DEPRECATED( "the facilities in " ) - | ^~~~~~~~~~~~~~~~~~~~~~~ - In file included from src/dicey.cpp:17: - src/hunter.h:65:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | struct SortDnaHit : public std::binary_function { - | ^~~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/string:48, - from /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/bits/locale_classes.h:40, - from /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/bits/ios_base.h:41, - from /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/ios:42, - from /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/ostream:38, - from /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/iostream:39, - from src/dicey.cpp:3: - /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - In file included from src/dicey.cpp:18: - src/silica.h:80:37: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 80 | struct SortPrimer : public std::binary_function - | ^~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - src/silica.h:100:39: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 100 | struct SortProducts : public std::binary_function - | ^~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - In file included from src/padlock.h:34, - from src/dicey.cpp:21: - src/gtf.h:53:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 53 | struct SortIntervalLabel : public std::binary_function { - | ^~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - src/gtf.h:60:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 60 | struct SortIntervalStart : public std::binary_function { - | ^~~~~~~~~~~~~~~ - /opt/conda/conda-bld/dicey_1718314872467/_build_env/lib/gcc/aarch64-conda-linux-gnu/12.3.0/include/c/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - make: *** [Makefile:60: src/dicey] Error 1 - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/dicey_1718314872467/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/dicey/build_failure.osx-64.yaml b/recipes/dicey/build_failure.osx-64.yaml deleted file mode 100644 index bd4b827824d0d..0000000000000 --- a/recipes/dicey/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c8389fa92d55fba29aa3e922321084ba770fc8c234a709c8b440b779fa5268d0 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [ 91%] Building CXX object tutorial/CMakeFiles/expl-20.dir/expl-20.cpp.o - [ 91%] Linking CXX executable expl-20 - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [ 91%] Built target expl-20 - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [ 91%] Building CXX object tutorial/CMakeFiles/expl-21.dir/expl-21.cpp.o - [ 91%] Linking CXX executable expl-21 - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [ 91%] Built target expl-21 - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [ 91%] Building CXX object tutorial/CMakeFiles/expl-22.dir/expl-22.cpp.o - [ 91%] Linking CXX executable expl-22 - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [ 91%] Built target expl-22 - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [ 91%] Building CXX object tutorial/CMakeFiles/expl-23.dir/expl-23.cpp.o - [ 91%] Linking CXX executable expl-23 - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [ 91%] Built target expl-23 - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [ 91%] Building CXX object tutorial/CMakeFiles/expl-24.dir/expl-24.cpp.o - [ 95%] Linking CXX executable expl-24 - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [ 95%] Built target expl-24 - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [ 95%] Building CXX object tutorial/CMakeFiles/expl-25.dir/expl-25.cpp.o - [ 95%] Linking CXX executable expl-25 - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [ 95%] Built target expl-25 - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [ 95%] Building CXX object tutorial/CMakeFiles/expl-26.dir/expl-26.cpp.o - [ 95%] Linking CXX executable expl-26 - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [ 95%] Built target expl-26 - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [100%] Building CXX object tutorial/CMakeFiles/int-vector-tutorial.dir/int-vector-tutorial.cpp.o - [100%] Linking CXX executable int-vector-tutorial - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [100%] Built target int-vector-tutorial - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [100%] Building CXX object tutorial/CMakeFiles/rmq-example.dir/rmq-example.cpp.o - [100%] Linking CXX executable rmq-example - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [100%] Built target rmq-example - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - make[3]: Entering directory '$SRC_DIR/src/xxsds/build' - [100%] Building CXX object tutorial/CMakeFiles/use-a-wavelet-tree.dir/use-a-wavelet-tree.cpp.o - [100%] Linking CXX executable use-a-wavelet-tree - make[3]: Leaving directory '$SRC_DIR/src/xxsds/build' - [100%] Built target use-a-wavelet-tree - make[2]: Leaving directory '$SRC_DIR/src/xxsds/build' - Install the project... - -- Install configuration: "Release" - make[1]: Leaving directory '$SRC_DIR/src/xxsds/build' - Copy pre-commit into .git/hooks - SUCCESS: sdsl was installed successfully! - The sdsl include files are located in '$SRC_DIR/src/sdslLite/include'. - The library files are located in '$SRC_DIR/src/sdslLite/lib'. - - Sample programs can be found in the examples-directory. - A program 'example.cpp' can be compiled with the command: - g -std=c14 -D__STDC_FORMAT_MACROS -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib -I$PREFIX/include -L$PREFIX/lib -Isrc/jlib/ -std=c14 -O3 -DNDEBUG -msse4.2 -Wall -Wextra -pedantic -ffast-math -funroll-loops -D__extern_always_inline="extern __always_inline" -stdlib=libc \ - -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib \ - example.cpp -ldivsufsort -ldivsufsort64 - - Tests in the test-directory - A cheat sheet in the extras/cheatsheet-directory. - Have fun! - x86_64-apple-darwin13.4.0-clang -D__STDC_FORMAT_MACROS -I$SRC_DIR/src/sdslLite/include -L$SRC_DIR/src/sdslLite/lib -I$PREFIX/include -L$PREFIX/lib -Isrc/jlib/ -std=c14 src/dicey.cpp -o src/dicey -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/src/htslib/ -L$SRC_DIR/src/htslib//lib -L$SRC_DIR/src/sdslLite//lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -ldl -lpthread -lhts -lz -llzma -lbz2 -Wl,-rpath,$SRC_DIR/src/htslib/ - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/dicey_1718321691422/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/dicey/meta.yaml b/recipes/dicey/meta.yaml index d4c5c3060bf24..aff17789c7676 100644 --- a/recipes/dicey/meta.yaml +++ b/recipes/dicey/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.1" %} -{% set sha256 = "11ac3b8b6dd1a7dc83bd4fd32ecb4781b6a63c4eedb7870a40bc989f8734914b" %} +{% set version = "0.3.3" %} +{% set sha256 = "69e84d07c2e6c9232f5cb80bde5d61a5285a334deb78a4cad6804c800dd3a3d6" %} package: name: dicey @@ -14,7 +14,7 @@ source: build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("dicey", max_pin="x.x") }} @@ -22,20 +22,16 @@ requirements: build: - make - {{ compiler('cxx') }} - - cmake >=3.10 + - cmake - autoconf - automake - pkg-config - - clangdev - - llvm-openmp host: - zlib - bzip2 - libdeflate - boost-cpp - htslib - - clangdev - - llvm-openmp run: - zlib - bzip2 diff --git a/recipes/dingii/meta.yaml b/recipes/dingii/meta.yaml new file mode 100644 index 0000000000000..bc78c1938465d --- /dev/null +++ b/recipes/dingii/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "0.0.1" %} +{% set name = "dingII" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/Danderson123/{{ name|lower }}/archive/v{{ version }}.tar.gz + sha256: 60a35ad2b5cf04b50ac0723d3841e903b23e7dbe071f483ebe0afb1192106140 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + entry_points: + - dingII = dingII.__main__:main + run_exports: + - {{ pin_subpackage("dingii", max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.8 + - networkx >=3.1 + +test: + imports: + - dingII + commands: + - dingII --help + +about: + home: "https://gitlab.ub.uni-bielefeld.de/gi/dingiiofficial" + summary: 'Computing the Rearrangement Distance of Natural Genomes.' + license: MIT + license_family: MIT + license_file: LICENSE + dev_url: "https://gitlab.ub.uni-bielefeld.de/gi/dingiiofficial" + doc_url: "https://gitlab.ub.uni-bielefeld.de/gi/dingiiofficial/-/blob/main/README.md" + +extra: + recipe-maintainers: + - leobkmer + identifiers: + - doi:10.48550/arXiv.2001.02139 diff --git a/recipes/diphase/meta.yaml b/recipes/diphase/meta.yaml index c7e671514d4ce..a2c0dfb3380be 100644 --- a/recipes/diphase/meta.yaml +++ b/recipes/diphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "diphase" %} -{% set version = "1.0.0" %} -{% set sha256 = "bd6ae483fb7763eff44935d3a19c7d8df604805e84615ed65566161458b50e77" %} +{% set version = "1.0.3" %} +{% set sha256 = "5e5971c62c66858d8c22a658821bc6fed443ecdad8811c4cd67feea7d518c127" %} package: name: {{ name }} diff --git a/recipes/discosnp/meta.yaml b/recipes/discosnp/meta.yaml index aa63f1e864baf..67923ba1b5953 100644 --- a/recipes/discosnp/meta.yaml +++ b/recipes/discosnp/meta.yaml @@ -10,8 +10,10 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 skip: True # [osx] + run_exports: + - {{ pin_subpackage('discosnp', max_pin="x") }} requirements: build: @@ -38,6 +40,8 @@ about: summary: reference-free small variant caller for short read sequencing data extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:discosnp - doi:10.1093/nar/gkn000 diff --git a/recipes/distle/meta.yaml b/recipes/distle/meta.yaml index 1cfe3807ac8aa..740d308b1d7e0 100644 --- a/recipes/distle/meta.yaml +++ b/recipes/distle/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.1" %} -{% set sha256 = "fd637102b8d305a50e76c3b2e8a88ffaa417a861ec23704c39902e5423a2e20e" %} +{% set version = "0.2.0" %} +{% set sha256 = "8e153099d18c3e7383f1f5a300732136a5161d2cd5bcbe152f03d02830d65175" %} package: name: distle @@ -35,4 +35,4 @@ extra: recipe-maintainers: - khajji - boasvdp - - ids-bioinformatics \ No newline at end of file + - ids-bioinformatics diff --git a/recipes/dna-nn/build.sh b/recipes/dna-nn/build.sh new file mode 100644 index 0000000000000..bfca91f0ebf92 --- /dev/null +++ b/recipes/dna-nn/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +set -x -e + +export CPATH=${PREFIX}/include + +mkdir -p "${PREFIX}/bin" + +make -j"${CPU_COUNT}" + +chmod 0755 dna-brnn +chmod 0755 dna-cnn +chmod 0755 gen-fq +chmod 0755 parse-rm.js + +cp -rf dna-brnn "${PREFIX}/bin" +cp -rf dna-cnn "${PREFIX}/bin" +cp -rf gen-fq "${PREFIX}/bin" +cp -rf parse-rm.js "${PREFIX}/bin" diff --git a/recipes/dna-nn/meta.yaml b/recipes/dna-nn/meta.yaml new file mode 100644 index 0000000000000..66c70ccaea69a --- /dev/null +++ b/recipes/dna-nn/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "0.1" %} +{% set name = "dna-nn" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/lh3/dna-nn/archive/refs/tags/v{{ version }}.tar.gz + sha256: bac26a25ad9e0315351b170bc33ab4e41b7573818fd9527b661f882b96ae0a8a + +build: + number: 1 + run_exports: + - {{ pin_subpackage("dna-nn", max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - zlib # zlib needed in build to build correctly + host: + - zlib + run: + - k8 + +test: + commands: + - echo $(dna-brnn 2>&1) | grep "dna-brnn" + - echo $(dna-cnn 2>&1) | grep "dna-cnn" + - echo $(gen-fq 2>&1) | grep "gen-fq" + - echo $(parse-rm.js 2>&1) | grep "k8 parse-rm" + +about: + home: "https://github.com/lh3/dna-nn" + dev_url: "https://github.com/lh3/dna-nn" + license: Unknown + summary: "Model and predict short DNA sequence features with neural networks." + +extra: + additional-platforms: + - linux-aarch64 + recipe-maintainers: + - smeds diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index ca0ab07f0d1c8..fb13849f5c288 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.8.0" %} +{% set version = "0.8.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 393c70dc355243200b7652810b3349e763de6bfcc07e168e51308c16cde045ea + sha256: 0e27734328a1e200c2181f7c02c6c5ffec0ea773bb5fa15eef3a7b2aeafc188b build: number: 0 diff --git a/recipes/dnaio/meta.yaml b/recipes/dnaio/meta.yaml index 0d5e1798c520f..f6b7feb2ad7c2 100644 --- a/recipes/dnaio/meta.yaml +++ b/recipes/dnaio/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 4786dc63614b9f3011463d9ea9d981723dd38d1091a415a557f71d8c74400f38 build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps -vv" run_exports: - {{ pin_subpackage('dnaio', max_pin="x") }} @@ -39,5 +39,6 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 recipe-maintainers: - marcelm diff --git a/recipes/dockq/meta.yaml b/recipes/dockq/meta.yaml new file mode 100644 index 0000000000000..9c21a4695b948 --- /dev/null +++ b/recipes/dockq/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "DockQ" %} +{% set version = "2.1.3" %} +{% set author = "bjornwallner" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0]|lower }}/{{ name|lower }}/{{ name|lower }}-{{ version }}.tar.gz + sha256: 50c4e2b4bced3bf865b12061ec0b56e23de1383dc70b445441848224f6c72c0d + +build: + entry_points: + - DockQ = DockQ.__main__:main + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python >=3.8 + - setuptools >=68 + - cython + - numpy <2.0 + - pip + run: + - python >=3.8 + - biopython >=1.79 + - networkx + - parallelbar + - {{ pin_compatible('numpy') }} + +test: + imports: + - {{ name }} + commands: + - pip check + - {{ name }} --help + requires: + - pip + +about: + home: https://github.com/{{ author }}/{{ name }} + dev_url: https://github.com/{{ author }}/{{ name }} + doc_url: https://github.com/{{ author }}/{{ name }}#{{ name|lower }} + summary: A Quality Measure for Protein, Nucleic Acids and Small Ligand Docking Modelsc + license: MIT + license_family: MIT + license_file: LICENSE + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - eunos-1128 diff --git a/recipes/dsk/build.sh b/recipes/dsk/build.sh index aa1fe014afa92..f833350da05ec 100644 --- a/recipes/dsk/build.sh +++ b/recipes/dsk/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + if [ `uname` == Darwin ]; then export MACOSX_DEPLOYMENT_TARGET=10.9 fi @@ -22,5 +24,5 @@ cmake .. \ -DCMAKE_PREFIX_PATH=${PREFIX} \ -DCPPUNIT_INCLUDE_DIR=${PREFIX}/include -make -j 2 +make -j ${CPU_COUNT} make install diff --git a/recipes/dsk/meta.yaml b/recipes/dsk/meta.yaml index a7090bf1d4bcb..d9f31a8beb004 100644 --- a/recipes/dsk/meta.yaml +++ b/recipes/dsk/meta.yaml @@ -11,9 +11,11 @@ source: - install_paths.patch build: - number: 4 + number: 5 # Requires clang>=4.5 skip: True # [osx] + run_exports: + - {{ pin_subpackage('dsk', max_pin='x') }} requirements: build: @@ -38,6 +40,8 @@ about: summary: DSK is a k-mer counter for reads or genomes. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:dsk - doi:10.1093/bioinformatics/btt020 diff --git a/recipes/duplex-tools/meta.yaml b/recipes/duplex-tools/meta.yaml index 1dde7f26e9869..e570a25b840e5 100644 --- a/recipes/duplex-tools/meta.yaml +++ b/recipes/duplex-tools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "duplex-tools" %} -{% set version = "0.2.17" %} +{% set version = "0.3.3" %} package: name: "{{ name|lower }}" @@ -7,30 +7,34 @@ package: source: url: "https://pypi.io/packages/source/d/duplex_tools/duplex_tools-{{ version }}.tar.gz" - sha256: afc5af9bdbea9c0aa3d55952cd391beee60185c6deed38a81e9e6b0f1606ab01 + sha256: 883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300 build: number: 0 entry_points: - duplex_tools = duplex_tools:main - script: "{{ PYTHON }} -m pip install . -vv" + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv noarch: python - + run_exports: + - {{ pin_subpackage('duplex-tools', max_pin="x.x") }} + requirements: host: - pip - - python + - python >=3.7 run: + - python >=3.7 - python-edlib + - mappy + - matplotlib-base - more-itertools - natsort - numpy - pandas - parasail-python - - pathlib - - pyfastx + - pod5 + - pyfastx >=0.9.0 - pysam - - python - tqdm test: @@ -41,9 +45,12 @@ test: about: home: "https://github.com/nanoporetech/duplex-tools" - license: MPL-2.0 - license_file: LICENSE.md - summary: "Duplex Tools contains a set of utilities for dealing with ONT Duplex sequencing data" + license: "MPL-2.0" + license_family: OTHER + license_file: "LICENSE.md" + summary: "Duplex Tools contains a set of utilities for dealing with ONT Duplex sequencing data." + dev_url: "https://github.com/nanoporetech/duplex-tools" + doc_url: "https://github.com/nanoporetech/duplex-tools/blob/v{{ version }}/README.md" extra: recipe-maintainers: diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 11e66e5ca8a77..172199dff30e6 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.380.0" %} +{% set version = "0.383.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e3fb70b283a9eda2f861d6b85322841d78b2655cd7de11f1e946643b58de3d4f + sha256: 377af4014a5f27efd6fe9478d0fa9c30ced245947fbd2e2e5713c8a37db598b0 build: number: 0 diff --git a/recipes/dysgu/meta.yaml b/recipes/dysgu/meta.yaml index a1a09caab84af..7b51ba6e19580 100644 --- a/recipes/dysgu/meta.yaml +++ b/recipes/dysgu/meta.yaml @@ -1,6 +1,6 @@ {% set name = "dysgu" %} -{% set version = "1.6.6" %} -{% set sha256hash = "cabc54afc88c8a855f79067bdeddc089d99ec91a4e4fe21fd18f42962d0d6a6d" %} +{% set version = "1.6.7" %} +{% set sha256hash = "918eed7bf70e7033994212c5e3cab65c7c6a8ddd566ecde470241ddd7429fca2" %} package: name: {{ name|lower }} diff --git a/recipes/earlgrey/build.sh b/recipes/earlgrey/build.sh index 5f17a2045b907..f0c29fd0423d2 100644 --- a/recipes/earlgrey/build.sh +++ b/recipes/earlgrey/build.sh @@ -26,10 +26,10 @@ cd ../ && rm -rf SA-SSR/ # Fixes to earlGrey executable sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGrey #remove check that conda environment has a specific name - +sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGreyLibConstruct #remove check that conda environment has a specific name # Fixes sed command for executables so that it works on both linux and macos -sed -i.bak "s|sed -i |sed -i.bak |g" ${PACKAGE_HOME}/earlGrey ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh +sed -i.bak "s|sed -i |sed -i.bak |g" ${PACKAGE_HOME}/earlGrey ${PACKAGE_HOME}/earlGreyLibConstruct ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh # Remove -pa from RepeatClassifier @@ -43,6 +43,7 @@ sed -i.bak 's/-t ${THREADS} / /' ${SCRIPT_DIR}/TEstrainer/TEstrainer # Add SCRIPT_DIR to correct path sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGrey +sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGreyLibConstruct sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/rcMergeRepeat* sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/headSwap.sh sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/autoPie.sh @@ -51,6 +52,7 @@ sed -i.bak "s|INSERT_FILENAME_HERE|${SCRIPT_DIR}/TEstrainer/scripts/|g" ${SCRIPT # Set permissions to files chmod +x ${PACKAGE_HOME}/earlGrey +chmod +x ${PACKAGE_HOME}/earlGreyLibConstruct chmod +x ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh chmod +x ${SCRIPT_DIR}/* > /dev/null 2>&1 chmod +x ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/ltr_finder @@ -76,3 +78,4 @@ echo "unset PERL5LIB" >> "${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}_deactivat # Put earlGrey executable in bin cd ${PREFIX}/bin ln -sf ${PACKAGE_HOME}/earlGrey . +ln -sf ${PACKAGE_HOME}/earlGreyLibConstruct . diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 6403cc72f9d2b..a9772ad58ae11 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.4.0" %} -{% set sha256 = "2557e79c112fdb2e9f1fd96d21394752db0a8004723fe35953d6619c887dcf97" %} +{% set version = "4.5.0" %} +{% set sha256 = "9d0365e5f0ff6df7f81b3ed1019776b2ccc5172dc4ec8ecaf84db1ef958bc671" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('earlgrey', max_pin='x') }} @@ -52,6 +52,7 @@ requirements: - bedtools - emboss - pybedtools + - samtools test: commands: diff --git a/recipes/egglib/meta.yaml b/recipes/egglib/meta.yaml index 459f58ae40dbb..5d52f0a65b5c6 100644 --- a/recipes/egglib/meta.yaml +++ b/recipes/egglib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "egglib" %} -{% set version = "3.3.3" %} +{% set version = "3.3.4" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/EggLib-{{ version }}.zip - sha256: 8f788e1d40243a7e489c71a20581a5e842e0f49bca87096fcee572c087865fc2 + sha256: 685acf514c2b14d3cc4e21e6ca03951599c77b9c0f6530c417cd717d813fafd7 build: - number: 1 + number: 0 skip: True # [osx] script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: diff --git a/recipes/eigensoft/build.sh b/recipes/eigensoft/build.sh index e5d538abac1ba..85a00b34850ed 100644 --- a/recipes/eigensoft/build.sh +++ b/recipes/eigensoft/build.sh @@ -1,6 +1,8 @@ +#!/usr/bin/env bash + set -xeuo pipefail cd src -make all +make -j ${CPU_COUNT} all # Install (makefile install has hard-coded destination, so have to do this manually) mkdir -p $PREFIX/bin diff --git a/recipes/eigensoft/meta.yaml b/recipes/eigensoft/meta.yaml index 346ef87b9d9b4..8f1bc6a86354b 100644 --- a/recipes/eigensoft/meta.yaml +++ b/recipes/eigensoft/meta.yaml @@ -14,7 +14,7 @@ source: - 0003-remove-wrong-cflag.patch # [osx] build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('eigensoft', max_pin='x.x') }} @@ -44,6 +44,9 @@ about: summary: The EIGENSOFT package implements methods for analzing population structure and performing stratification correction extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - biotools:Eigensoft - doi:10.1371/journal.pgen.0020190 diff --git a/recipes/el_gato/meta.yaml b/recipes/el_gato/meta.yaml index 7dc82c6beb55f..0c15f3b4c1530 100644 --- a/recipes/el_gato/meta.yaml +++ b/recipes/el_gato/meta.yaml @@ -1,6 +1,6 @@ {% set name = "el_gato" %} -{% set version = "1.18.2" %} -{% set hash = "328a8399d01594a69a87c11357310efe54c00159949b396f1211d7ce2787040a" %} +{% set version = "1.19.0" %} +{% set hash = "ad390572ce785707b67a00f25978c4032981ac7e6149ddc423443e9189b30e75" %} {% set user = "appliedbinf" %} package: diff --git a/recipes/emu/meta.yaml b/recipes/emu/meta.yaml index ad6bd76d68361..b3c8730ce7056 100644 --- a/recipes/emu/meta.yaml +++ b/recipes/emu/meta.yaml @@ -1,18 +1,21 @@ {% set name = "emu" %} -{% set version = "3.4.5" %} +{% set version = "3.5.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: 'https://gitlab.com/treangenlab/emu/-/archive/v{{version}}/emu-v{{version}}.tar.gz' - sha256: a77a3d362384d8e12bbb5f75dc74eaf0f04faec1e4f69195b9e92bc7c025296e + url: 'https://github.com/treangenlab/emu/archive/refs/tags/v{{version}}.tar.gz' + sha256: 3e26d6f66dfd7e0ff1bc63cefb8a4a08bbed4726b8c0002bf0e34abed7a18ed0 build: noarch: generic number: 0 script: mkdir -p ${PREFIX}/bin && cp emu ${PREFIX}/bin + + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: run: @@ -36,7 +39,7 @@ test: - emu --help about: - home: https://gitlab.com/treangenlab/emu + home: https://github.com/treangenlab/emu license: MIT license_file: LICENSE.txt summary: Emu is a relative abundance estimator for 16s genomic data. diff --git a/recipes/ena-upload-cli/meta.yaml b/recipes/ena-upload-cli/meta.yaml index 2a3213ae200e8..3c6fd85b48c5f 100644 --- a/recipes/ena-upload-cli/meta.yaml +++ b/recipes/ena-upload-cli/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ena-upload-cli" %} -{% set version = "0.7.3" %} +{% set version = "0.7.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/usegalaxy-eu/ena-upload-cli/archive/refs/tags/{{ version }}.tar.gz" - sha256: 9508f63fddb0dc9541f1500e0c4ed064c21ad59ac3e0d2140497475387113745 + sha256: da6b07a681ae6c9ac61ca5b3e7e6fe8a5ed3f0ed7bae64936e19b33dfb2782bc build: number: 0 @@ -26,7 +26,7 @@ requirements: - genshi ==0.7.* - lxml >=4.9.3,<=5.0.0 - pandas >=2.0.3,<=3.0.0 - - pyyaml ==5.* + - pyyaml ==5.3.* - requests >=2.31.0,<=3.0.0 - openpyxl >=3.1.2,<=4.0.0 - jsonschema >=4.19.1 diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index cd4dc94fffa01..8a4af45e09e1a 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "7.3.1" %} -{% set sha256 = "e6dbb93e8b39c81e53ef96afcba0e958869c95a2d1dda83e1a6077a73f9f4cfb" %} +{% set version = "8.0.0" %} +{% set sha256 = "a5f11f651420aac7b801f4ae611814e4e72f91b4ba25376000408675b3ba3050" %} package: name: ena-webin-cli diff --git a/recipes/ensembl-utils/meta.yaml b/recipes/ensembl-utils/meta.yaml index 6c5809c20dfae..6d53d194a3ff8 100644 --- a/recipes/ensembl-utils/meta.yaml +++ b/recipes/ensembl-utils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ensembl-utils" %} -{% set version = "0.4.1" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ensembl_utils-{{ version }}.tar.gz - sha256: 77ec8c4a100df2981f4fb63a9dc13c90c454a8521614c523bfb66f9a273c5d7f + sha256: 85185aba9a3bbf0abbf7e380a25079dfcc3fa913a4ecd37143495625d7604ad7 build: entry_points: diff --git a/recipes/eukfinder/build.sh b/recipes/eukfinder/build.sh new file mode 100755 index 0000000000000..67d7ab942645b --- /dev/null +++ b/recipes/eukfinder/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash +set -ex +mkdir -p ${PREFIX}/bin +# Setup PLAST binaries +cp build/bin/plast $PREFIX/bin/ + +# Build acc2tax +# According to https://bioconda.github.io/contributor/troubleshooting.html +# and https://github.com/bioconda/bioconda-recipes/pull/49360#discussion_r1686187284 +$CC -o acc2tax acc2tax.c +cp acc2tax $PREFIX/bin/ + +chmod +x $PREFIX/bin/plast +chmod +x $PREFIX/bin/acc2tax + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/eukfinder/meta.yaml b/recipes/eukfinder/meta.yaml new file mode 100644 index 0000000000000..5067efc48f607 --- /dev/null +++ b/recipes/eukfinder/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.2.3" %} + +package: + name: eukfinder + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('eukfinder', max_pin="x") }} + +source: + - url: https://github.com/RogerLab/Eukfinder/archive/refs/tags/v{{ version }}.tar.gz + sha256: 8b8235049084e8c7171ce8968b07be25bad9b9979ce1f04cfe4b8690f5641a7d + - url: https://github.com/PLAST-software/plast-library/releases/download/v2.3.2/plastbinary_osx_v2.3.2.tar.gz # [osx] + sha256: 0dbbf88f6e59bb153ff04b5cc80743304d44fc1196de930fd2b56a1061792a6a # [osx] + - url: https://github.com/PLAST-software/plast-library/releases/download/v2.3.2/plastbinary_linux_v2.3.2.tar.gz # [linux] + sha256: d8a3ad66849b6090c41acde71750e3d0c339d6b9b7c6f316c307870d773d86fe # [linux] + - url: https://github.com/Tassadaar/acc2tax/archive/refs/tags/v1.0.tar.gz + sha256: 349fa233c565eaa01ef31b9d3f32fa01a9d9f234ba7e0136e289af837add6979 + +requirements: + build: + - wget + - python >=3.6,<3.7 + - setuptools + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cmake + host: + - python >=3.6,<3.7 + - setuptools + run: + - python >=3.6,<3.7 + - ete3 + - numpy + - pandas + - joblib + - pyqt =5 + - spades + - seqkit + - trimmomatic + - centrifuge + - bowtie2 + + +test: + commands: + - plast -h + - acc2tax --help + - eukfinder --help + - eukfinder read_prep -h + - eukfinder short_seqs -h + - eukfinder long_seqs -h + + +about: + home: https://github.com/RogerLab/Eukfinder + license: MIT + license_file: LICENSE.txt + summary: "Eukfinder is a tool for detecting eukaryotic sequences in metagenomic data." diff --git a/recipes/eukulele/meta.yaml b/recipes/eukulele/meta.yaml index 23dce68e05f3c..24cd50ddf57b4 100644 --- a/recipes/eukulele/meta.yaml +++ b/recipes/eukulele/meta.yaml @@ -1,25 +1,21 @@ -{% set version = "2.0.7" %} -{% set sha256 = "e52ca613c92ef99a6f01e503674b1c35ee26de6c03c4cb58338278e3a348a394" %} +{% set name = "eukulele" %} +{% set version = "2.0.9" %} +{% set sha256 = "575ab81fd5453abbf092543caaf12116ab36cd5451caeb4c87086a93f12e7431" %} package: - name: eukulele - version: 2.0.7 - -build: - number: 0 - noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps" - run_exports: - - {{ pin_subpackage('eukulele', max_pin="2.0.7") }} + name: {{ name }} + version: {{ version }} source: - url: https://github.com/AlexanderLabWHOI/EUKulele/archive/refs/tags/v2.0.7_3.tar.gz + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/EUKulele-{{ version }}.tar.gz sha256: {{ sha256 }} -test: - commands: - - EUKulele --version | grep '{{ version }}' - - EUKulele --help +build: + number: 1 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" + run_exports: + - {{ pin_subpackage('eukulele', max_pin="x") }} requirements: host: @@ -28,21 +24,35 @@ requirements: - pytest-runner run: - python >=3.6 - - numpy ==1.19.5 - - biopython ==1.78 - - pandas ==1.2.0 + - numpy + - biopython + - pandas - seaborn-base - boost-cpp - chardet + - multiprocess - joblib - ujson + - python-coveralls - pyyaml - - matplotlib-base ==3.3.3 - - blast ==2.2.31 - - diamond ==0.9.24 + - matplotlib-base + - pytest-cov + - pytest-xdist + - sphinxcontrib-bibtex ==1.0.0 + - blast + - diamond + - busco >=4.0.4 + +test: + commands: + - EUKulele --version | grep '{{ version }}' + - EUKulele --help about: - home: https://github.com/AlexanderLabWHOI/EUKulele + home: "https://github.com/AlexanderLabWHOI/EUKulele" license: MIT + license_family: MIT license_file: LICENSE - summary: Easy taxonomic annotation for eukaryotic microbes + summary: "Easy taxonomic annotation for eukaryotic microbes." + dev_url: "https://github.com/AlexanderLabWHOI/EUKulele" + doc_url: "https://github.com/AlexanderLabWHOI/EUKulele/blob/{{ version }}/README.md" diff --git a/recipes/eva-sub-cli/build.sh b/recipes/eva-sub-cli/build.sh index aa7198453931d..695dd90715c8c 100644 --- a/recipes/eva-sub-cli/build.sh +++ b/recipes/eva-sub-cli/build.sh @@ -3,11 +3,10 @@ BIOVALIDATOR_VERSION=2.2.1 EVA_SUB_CLI="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}" -mkdir -p ${PREFIX}/bin ${EVA_SUB_CLI} +mkdir -p ${EVA_SUB_CLI} # Install eva-sub-cli $PYTHON -m pip install . -cp bin/* ${PREFIX}/bin echo "Done with eva-sub-cli" cd ${EVA_SUB_CLI} diff --git a/recipes/eva-sub-cli/meta.yaml b/recipes/eva-sub-cli/meta.yaml index 2b2ff86a1b018..2b0ae04c0c9d7 100644 --- a/recipes/eva-sub-cli/meta.yaml +++ b/recipes/eva-sub-cli/meta.yaml @@ -1,5 +1,5 @@ {% set name = "eva-sub-cli" %} -{% set version = "0.3" %} +{% set version = "0.4" %} package: name: {{ name }} @@ -7,11 +7,13 @@ package: source: url: https://github.com/EBIvariation/eva-sub-cli/archive/v{{version}}.tar.gz - sha256: bf5e00ffd7f4a290350011ceb626f818111f8646975e5dd7247910555971e1bd + sha256: be4d4109d9879ad94ccc01a3bd534ff6077775f126977dfb3f2d6fd9cfb251ba build: number: 0 noarch: generic + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -20,7 +22,7 @@ requirements: - nextflow >=21.10.0 - python >=3.8 - nodejs >=10.19.1 - - vcf-validator >=0.9.6 + - vcf-validator >=0.9.7 - ebi-eva-common-pyutils >=0.6.1 - pyyaml - jinja2 @@ -28,11 +30,12 @@ requirements: - requests - jsonschema - unzip + - setuptools-scm run: - nextflow >=21.10.0 - python >=3.8 - nodejs >=10.19.1 - - vcf-validator >=0.9.6 + - vcf-validator >=0.9.7 - ebi-eva-common-pyutils >=0.6.1 - pyyaml - jinja2 diff --git a/recipes/evidencemodeler/meta.yaml b/recipes/evidencemodeler/meta.yaml index f9e47e1f09777..d9a8365861794 100644 --- a/recipes/evidencemodeler/meta.yaml +++ b/recipes/evidencemodeler/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3ee69ad822a35204ff02b670fe047d8b0da250cf9f43ebabbe33ce47f498e668 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('evidencemodeler', max_pin='x') }} @@ -27,6 +27,7 @@ requirements: - perl-carp - perl-uri - perl-dbi + - perl-db_file test: commands: diff --git a/recipes/exomiser-rest-prioritiser/meta.yaml b/recipes/exomiser-rest-prioritiser/meta.yaml index 5f67ff79744ad..f00da2d66df74 100644 --- a/recipes/exomiser-rest-prioritiser/meta.yaml +++ b/recipes/exomiser-rest-prioritiser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "14.0.0" %} -{% set sha256 = "6817537b1e602f533219089fc89d6c1d154e26e61efb05a5de382a56eeba4094" %} +{% set version = "14.0.2" %} +{% set sha256 = "752d46ae3e28aad581fd891d3ad2c1045039d52d52806c9da57e95c42c0beba6" %} package: name: exomiser-rest-prioritiser diff --git a/recipes/expam/meta.yaml b/recipes/expam/meta.yaml index bfae3d6356b7e..b17336bf93486 100644 --- a/recipes/expam/meta.yaml +++ b/recipes/expam/meta.yaml @@ -1,5 +1,5 @@ {% set name = "expam" %} -{% set version = "1.2.2.5" %} +{% set version = "1.4.0.5" %} package: name: "{{ name|lower }}" @@ -7,12 +7,15 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4a102a67da23c37598c0a0778d0caf99d4c6c0ea4286aff7ca0ab360dc5cda09 + sha256: 7b89e363b95e8b04da05a5cc9c5b51ac29988a926e9ca510ca8735faae4a5cfb build: - number: 1 - skip: true # [py < 38] - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + number: 0 + skip: True # [osx] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + entry_points: + - expam=expam.main:main + - expam_limit=expam.sandbox.main:main run_exports: - {{ pin_subpackage('expam', max_pin="x") }} @@ -24,9 +27,9 @@ requirements: - python - cython - numpy >=1.22.0 - - setuptools >=46.4 run: - python + - ete3 - numpy >=1.22.0 - matplotlib-base - multiprocess @@ -47,8 +50,11 @@ about: license_family: BSD license_file: LICENSE summary: "Metagenomic profiling using a reference phylogeny" - doc_url: https://expam.readthedocs.io/en/latest/ + doc_url: https://expam.readthedocs.io/en/latest + dev_url: https://github.com/seansolari/expam extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - seansolari diff --git a/recipes/ezcharts/meta.yaml b/recipes/ezcharts/meta.yaml new file mode 100644 index 0000000000000..d439af6dc504d --- /dev/null +++ b/recipes/ezcharts/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "ezcharts" %} +{% set version = "0.10.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/ezcharts-{{ version }}.tar.gz + sha256: 5357d3104057a14cb05afda3ef252771fcc00ced3200bd25a0195795ed6daae1 + +build: + number: 0 + noarch: python + entry_points: + - ezcharts = ezcharts:cli + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('ezcharts', max_pin="x.x") }} + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - bokeh >=3.1.0,<3.2.dev0 + - dominate + - jinja2 + - libsass + - numpy + - pandas + - pydantic <2.0.0 + - scipy + - seaborn-base >=0.12.0,<0.13.dev0 + - sigfig + - natsort + - pysam + - pymsaviz + - biopython + +test: + imports: + - ezcharts + commands: + - ezcharts --help + +about: + home: "https://github.com/epi2me-labs/ezcharts" + summary: "eCharts plotting API." + license: "BSD-4-Clause" + license_family: BSD + license_file: LICENSE + dev_url: "https://github.com/epi2me-labs/ezcharts" + doc_url: "https://github.com/epi2me-labs/ezcharts/blob/v{{ version }}/README.md" diff --git a/recipes/ezomero/meta.yaml b/recipes/ezomero/meta.yaml index 97d8d21b17bb5..1ea7010c444ed 100644 --- a/recipes/ezomero/meta.yaml +++ b/recipes/ezomero/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.0.1" %} +{% set version = "3.1.0" %} {% set name = "ezomero" %} package: @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 2fc7c85626e013bb993d2da300d870bbfdf395d1574f72af086b12d182eebe95 + sha256: 4b681333d8d56077ac14062dc9109a0d5aad033d5287e14fc8c4c616b129e162 build: noarch: python diff --git a/recipes/f5c/build.sh b/recipes/f5c/build.sh index 89e1f0240816d..838e83b3b3e28 100644 --- a/recipes/f5c/build.sh +++ b/recipes/f5c/build.sh @@ -1,11 +1,14 @@ #!/bin/bash + +set -xe + scripts/install-hts.sh scripts/install-zstd.sh ./configure --enable-localzstd cd slow5lib -make CC=$CC CXX=$CXX +make -j ${CPU_COUNT} CC=$CC CXX=$CXX cd .. export CFLAGS="${CFLAGS} -D__STDC_FORMAT_MACROS" -make CC=$CC CXX=$CXX +make -j ${CPU_COUNT} CC=$CC CXX=$CXX mkdir -p $PREFIX/bin cp f5c $PREFIX/bin/f5c diff --git a/recipes/f5c/meta.yaml b/recipes/f5c/meta.yaml index 7b31342809f0d..307b7c047ae47 100644 --- a/recipes/f5c/meta.yaml +++ b/recipes/f5c/meta.yaml @@ -1,5 +1,5 @@ {% set name = "f5c" %} -{% set version = "1.4" %} +{% set version = "1.5" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/hasindu2008/f5c/releases/download/v{{ version }}/f5c-v{{ version }}-release.tar.gz - sha256: 9336b35caf6486f9fffc791591ef7b40bea9156ecfb1d315fe222b6e9957d632 + sha256: 3354813a0523ae3fead68cc3ec5859fa745576b5dc88758a9de172184fac20ab build: number: 1 @@ -37,3 +37,8 @@ about: license: MIT license_file: LICENSE summary: 'An optimised re-implementation of the call-methylation and eventalign modules in Nanopolish.' + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/falco/build.sh b/recipes/falco/build.sh index fe81a6f4127d6..ad4472c78b36a 100644 --- a/recipes/falco/build.sh +++ b/recipes/falco/build.sh @@ -1,9 +1,13 @@ #!/bin/bash +set -xe + +export M4="$BUILD_PREFIX/bin/m4" + # add Configuration and example files to opt falco=$PREFIX/opt/falco mkdir -p $falco -cp -r ./* $falco +cp -rf ./* $falco #to fix problems with htslib export C_INCLUDE_PATH=$C_INCLUDE_PATH:${PREFIX}/include @@ -11,9 +15,15 @@ export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:${PREFIX}/include export LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib export LD_LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I{PREFIX}/include" + cd $falco -./configure --prefix=$falco --enable-hts -make +autoreconf -if +./configure --prefix=$falco --enable-hts CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" +make -j ${CPU_COUNT} make install for i in $(ls -1 | grep -v Configuration | grep -v bin); do diff --git a/recipes/falco/meta.yaml b/recipes/falco/meta.yaml index 766c20816dbf0..b11966d06a4d1 100644 --- a/recipes/falco/meta.yaml +++ b/recipes/falco/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.2" %} +{% set version = "1.2.4" %} package: name: falco @@ -10,10 +10,9 @@ build: # falco is currently not intended to be stable between minor versions (x.x). - {{ pin_subpackage('falco', max_pin="x.x") }} - source: url: https://github.com/smithlabcode/falco/releases/download/v{{ version }}/falco-{{ version }}.tar.gz - sha256: 09cfb96eb4292ba0ca48713634e9da48fbe07e57a4ae8f24f356583ed6b1028b + sha256: 116c257fbf87bf99083d8e539a51ce74bc5a8d141f99a437a0c23e9d1379096a requirements: build: @@ -21,26 +20,31 @@ requirements: - {{ compiler('cxx') }} - autoconf - automake + - libtool host: - zlib - htslib run: - - zlib - htslib about: - home: https://github.com/smithlabcode/falco + home: 'https://github.com/smithlabcode/falco' license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE summary: | falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads. - doc_url: 'https://falco.readthedocs.io/' + doc_url: 'https://falco.readthedocs.io' + dev_url: 'https://github.com/smithlabcode/falco' test: commands: - falco extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - andrewdavidsmith - guilhermesena1 diff --git a/recipes/fast-edit-distance/meta.yaml b/recipes/fast-edit-distance/meta.yaml index f21cf9685a5c5..a9fa25ffb9240 100644 --- a/recipes/fast-edit-distance/meta.yaml +++ b/recipes/fast-edit-distance/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fast-edit-distance" %} -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: {{ name|lower }} @@ -7,11 +7,11 @@ package: source: url: https://github.com/youyupei/fast_edit_distance/archive/v{{ version }}.tar.gz - sha256: c3f3913381d8a7a5eb96cef5b31bc69fb19c55b653a98525abc0c4922cd07247 + sha256: 71ead99841435bc2e94be5c8ec89ab5797472b0e7924e0b1a171e5ddf4f7e501 build: - number: 1 - script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + number: 0 + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir run_exports: - {{ pin_subpackage('fast-edit-distance', max_pin="x") }} @@ -30,9 +30,15 @@ test: - fast_edit_distance about: - home: https://github.com/youyupei/fast_edit_distance + home: "https://github.com/youyupei/fast_edit_distance" license: MIT license_family: MIT license_file: LICENSE - dev_url: https://github.com/youyupei/fast_edit_distance + dev_url: "https://github.com/youyupei/fast_edit_distance" summary: "A implementation of edit distance with improved runtime." + doc_url: "https://github.com/youyupei/fast_edit_distance/blob/v{{ version }}/README.md" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/fastahack/build.sh b/recipes/fastahack/build.sh index 8ad0bf8e76ef4..a1bc7742e43c0 100644 --- a/recipes/fastahack/build.sh +++ b/recipes/fastahack/build.sh @@ -1,2 +1,6 @@ -make +#!/usr/bin/env bash + +set -xe + +make -j ${CPU_COUNT} make install \ No newline at end of file diff --git a/recipes/fastahack/meta.yaml b/recipes/fastahack/meta.yaml index 2a41dfad0892d..dfb358e4aad19 100644 --- a/recipes/fastahack/meta.yaml +++ b/recipes/fastahack/meta.yaml @@ -1,22 +1,26 @@ +{% set name = "fastahack" %} +{% set version = "1.0.0" %} + + package: - name: fastahack - version: 2016.07.2 + name: {{ name }} + version: {{ version }} source: - url: https://github.com/ekg/fastahack/archive/bbc645f2f7966cb7b44446200c02627c3168b399.zip - md5: d32a9dee44a8da7477631930e92f5095 + url: https://github.com/ekg/fastahack/archive/refs/tags/v{{ version }}.tar.gz + sha256: cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae build: - number: 6 + number: 1 skip: True # [osx] + run_exports: + - {{ pin_subpackage("fastahack", max_pin="x") }} requirements: build: - make - {{ compiler('cxx') }} - run: - test: commands: - fastahack 2>&1 | grep "usage" >/dev/null @@ -26,3 +30,7 @@ about: license: MIT license_file: LICENSE summary: fastahack --- *fast* FASTA file indexing, subsequence and sequence extraction + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/fastani/build.sh b/recipes/fastani/build.sh index 8008be92c6a0a..a52e240621bd5 100644 --- a/recipes/fastani/build.sh +++ b/recipes/fastani/build.sh @@ -7,6 +7,8 @@ export CPP_INCLUDE_PATH=${PREFIX}/include export CPLUS_INCLUDE_PATH=${PREFIX}/include export CXX_INCLUDE_PATH=${PREFIX}/include +export M4=${BUILD_PREFIX}/bin/m4 + mkdir -p $PREFIX/bin ./bootstrap.sh diff --git a/recipes/fastani/meta.yaml b/recipes/fastani/meta.yaml index 82c05c4c98336..eb471a88b27f4 100644 --- a/recipes/fastani/meta.yaml +++ b/recipes/fastani/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('fastani', max_pin="x") }} @@ -49,4 +49,5 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 + - osx-arm64 diff --git a/recipes/fastlin/meta.yaml b/recipes/fastlin/meta.yaml index 48e37b8638cb2..d208f595b3223 100644 --- a/recipes/fastlin/meta.yaml +++ b/recipes/fastlin/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fastlin" %} -{% set version = "0.2.3" %} +{% set version = "0.4.1" %} package: name: {{ name|lower}} @@ -7,7 +7,7 @@ package: source: url: https://github.com/rderelle/fastlin/archive/{{ version }}.tar.gz - sha256: 07c427740b520756d25e435e784e3b3d1cca0d08bcce07c5e213a35c4694ccaf + sha256: 928730bbd2b7c7397b0b69da2e3cc90391f9771bcd33870c7037cc0e4ca1fc4f build: number: 0 @@ -29,3 +29,8 @@ about: license_family: MIT license_file: LICENSE summary: fastlin, ultra-fast MTBC lineage typing + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/fastme/build.sh b/recipes/fastme/build.sh index 2817a50021413..43ffe694346e6 100644 --- a/recipes/fastme/build.sh +++ b/recipes/fastme/build.sh @@ -1,6 +1,9 @@ #!/bin/bash +set -xe + +export M4=${BUILD_PREFIX}/bin/m4 autoreconf -ifv ./configure --prefix=${PREFIX} -make -j4 +make -j ${CPU_COUNT} make install diff --git a/recipes/fastme/meta.yaml b/recipes/fastme/meta.yaml index 04aa30baef6a7..fa70f80f4d49e 100644 --- a/recipes/fastme/meta.yaml +++ b/recipes/fastme/meta.yaml @@ -1,16 +1,18 @@ {% set name = "fastme" %} -{% set version = "2.1.6.1" %} -{% set sha256 = "fae0609576873cb137ad4f63529b3ccba8f747b857c23c7870236aba440076ca" %} +{% set version = "2.1.6.3" %} +{% set sha256 = "d49ff78cca7b76eadf8443efb33f071a7e8a152618ffa3d8e790f167d0a0b176" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} source: - url: https://gite.lirmm.fr/atgc/FastME/-/archive/v2.1.6.1/FastME-v2.1.6.1.tar.gz + url: https://gite.lirmm.fr/atgc/FastME/-/archive/v{{ version }}/FastME-v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: @@ -28,11 +30,16 @@ test: about: home: http://www.atgc-montpellier.fr/fastme/binaries.php summary: a comprehensive, accurate and fast distance-based phylogeny inference program. - license: GPLv3 - license_family: GPL - license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE' + license: GPL-3.0-only + license_family: GPL3 + license_file: LICENSE + dev_url: https://gite.lirmm.fr/atgc/FastME/ + doc_url: http://www.atgc-montpellier.fr/fastme/usersguide.php extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - biotools:fastme - doi:10.1093/molbev/msv150 diff --git a/recipes/fastq-screen/build.sh b/recipes/fastq-screen/build.sh index 9231a3df38e4f..992b6d8c20941 100644 --- a/recipes/fastq-screen/build.sh +++ b/recipes/fastq-screen/build.sh @@ -1,8 +1,9 @@ #!/bin/bash + fastqscreen=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $fastqscreen sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' fastq_screen -cp -r ./* $fastqscreen -rm -f $fastqscreen/fastq_screen.bak +cp -rf ./* $fastqscreen +rm -rf $fastqscreen/fastq_screen.bak mkdir -p $PREFIX/bin -ln -s $fastqscreen/fastq_screen $PREFIX/bin/fastq_screen +ln -sf $fastqscreen/fastq_screen $PREFIX/bin/fastq_screen diff --git a/recipes/fastq-screen/meta.yaml b/recipes/fastq-screen/meta.yaml index 213a3d619d8db..9b5b05615e468 100644 --- a/recipes/fastq-screen/meta.yaml +++ b/recipes/fastq-screen/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.3" %} -{% set sha256 = "002750d78ca50fe0f789e24445e10988e16244f81b4f0189bf2fc4ee8b680be5" %} +{% set version = "0.16.0" %} +{% set sha256 = "4c193cd4755506a1ecb2ae0e325a4d2e47a26ae093786255be46c38a8d8c16ed" %} package: name: fastq-screen @@ -12,9 +12,11 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('fastq-screen', max_pin="x.x") }} requirements: - build: + host: - bowtie - bowtie2 - perl @@ -31,6 +33,8 @@ test: - fastq_screen --version about: - home: 'http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/' - license: GPLv3 - summary: 'FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect' + home: 'https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen' + license: GPL-3.0-or-later + license_family: GPL3 + summary: 'FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.' + dev_url: https://github.com/StevenWingett/FastQ-Screen diff --git a/recipes/fastqc-rs/meta.yaml b/recipes/fastqc-rs/meta.yaml index e7049ad4f89f4..3a05e9698633c 100644 --- a/recipes/fastqc-rs/meta.yaml +++ b/recipes/fastqc-rs/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "0.3.2" %} +{% set version = "0.3.4" %} package: name: fastqc-rs version: {{version}} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('fastqc-rs', max_pin="x.x") }} source: url: https://github.com/fastqc-rs/fastqc-rs/archive/v{{ version }}.tar.gz - sha256: f2dc917e71d3408d88aa2372dc485dc58b5fb0d0af940f9f48fbecb8a34ca78d + sha256: 02b789b7194a56aeb529413462dc693f747847c7e2481a093e2f56d1eeb7e780 requirements: build: - - rust >=1.30 - clangdev - cmake - make - {{ compiler('c') }} - {{ compiler('cxx') }} + - {{ compiler('rust') }} - pkg-config host: - clangdev @@ -36,9 +38,13 @@ test: about: home: https://fastqc-rs.github.io license: MIT - summary: | - A fast quality control tool for FASTQ files written in rust. + license_file: LICENSE + summary: A fast quality control tool for FASTQ files written in rust. + dev_url: https://github.com/fastqc-rs/fastqc-rs extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - fxwiegand diff --git a/recipes/fgpyo/meta.yaml b/recipes/fgpyo/meta.yaml index 63a3a10fe4ea2..69a4df4c53ebc 100644 --- a/recipes/fgpyo/meta.yaml +++ b/recipes/fgpyo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fgpyo" %} -{% set version = "0.5.0" %} +{% set version = "0.7.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/fulcrumgenomics/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 875a189a0db739bd150b677a3b1c5a48489c83bc7da2cc405aee02a137ab7a04 + sha256: 0d0b0d6f2e365c136830e803e4a6d56fe20c6d615a4b857b423f19c51b700bab build: noarch: python diff --git a/recipes/fibertools-rs/build.sh b/recipes/fibertools-rs/build.sh index e73cd0dd01dcb..0c518e5203032 100644 --- a/recipes/fibertools-rs/build.sh +++ b/recipes/fibertools-rs/build.sh @@ -3,12 +3,6 @@ # Set the desitnation for the libtorch files # -# -# TODO: Remove the following export when pinning is updated and we use -# {{ compiler('rust') }} in the recipe. -export \ - CARGO_NET_GIT_FETCH_WITH_CLI=true \ - CARGO_HOME="${BUILD_PREFIX}/.cargo" export BINDGEN_EXTRA_CLANG_ARGS="${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" # diff --git a/recipes/fibertools-rs/build_failure.linux-64.yaml b/recipes/fibertools-rs/build_failure.linux-64.yaml deleted file mode 100644 index 8f5fc2bb460ea..0000000000000 --- a/recipes/fibertools-rs/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b174a9af23ec686e13e6e0fe058d229b43e22e070337f81076130ac3b1c05680 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - INFO (fibertools-rs,lib/libtorch.so): lib/libtorch_cuda_cpp.so found in this package - INFO (fibertools-rs,lib/libtorch.so): lib/libtorch_cpu.so found in this package - INFO (fibertools-rs,lib/libtorch.so): lib/libtorch_cuda_cu.so found in this package - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): lib/libcudnn_ops_infer.so.8 found in this package - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): lib/libcudnn_ops_train.so.8 found in this package - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): lib/libcudnn_cnn_infer.so.8 found in this package - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): lib/libcublas-2854e16e.so.11 found in this package - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): lib/libcublasLt-b015978e.so.11 found in this package - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/librt.so.1 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libdl.so.2 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): Needed DSO lib/libstdc.so.6 found in conda-forge::libstdcxx-ng-12.2.0-h46fd767_19 - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): Needed DSO lib/libgcc_s.so.1 found in conda-forge::libgcc-ng-12.2.0-h65d4601_19 - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libcudnn_cnn_train.so.8): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/ld-linux-x86-64.so.2 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libnvrtc-builtins-fed02928.so.11.6): Needed DSO lib/libstdc.so.6 found in conda-forge::libstdcxx-ng-12.2.0-h46fd767_19 - INFO (fibertools-rs,lib/libnvrtc-builtins-fed02928.so.11.6): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libnvrtc-builtins-fed02928.so.11.6): Needed DSO lib/libgcc_s.so.1 found in conda-forge::libgcc-ng-12.2.0-h65d4601_19 - INFO (fibertools-rs,lib/libnvrtc-builtins-fed02928.so.11.6): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): lib/libtorch_cpu.so found in this package - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): lib/libtorch_cuda.so found in this package - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libdl.so.2 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): lib/libtorch_cuda_cpp.so found in this package - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): lib/libc10_cuda.so found in this package - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): lib/libc10.so found in this package - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): lib/libcublas-2854e16e.so.11 found in this package - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/librt.so.1 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): lib/libtorch_cuda_cu.so found in this package - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): Needed DSO lib/libstdc.so.6 found in conda-forge::libstdcxx-ng-12.2.0-h46fd767_19 - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): Needed DSO lib/libgcc_s.so.1 found in conda-forge::libgcc-ng-12.2.0-h65d4601_19 - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cuda_linalg.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/ld-linux-x86-64.so.2 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cpu.so): lib/libgomp-a34b3233.so.1 found in this package - INFO (fibertools-rs,lib/libtorch_cpu.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cpu.so): lib/libc10.so found in this package - INFO (fibertools-rs,lib/libtorch_cpu.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/librt.so.1 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cpu.so): Needed DSO lib/libgcc_s.so.1 found in conda-forge::libgcc-ng-12.2.0-h65d4601_19 - INFO (fibertools-rs,lib/libtorch_cpu.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libdl.so.2 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cpu.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cpu.so): lib/libcudart-45da57e3.so.11.0 found in this package - INFO (fibertools-rs,lib/libtorch_cpu.so): Needed DSO lib/libstdc.so.6 found in conda-forge::libstdcxx-ng-12.2.0-h46fd767_19 - INFO (fibertools-rs,lib/libtorch_cpu.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - INFO (fibertools-rs,lib/libtorch_cpu.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/ld-linux-x86-64.so.2 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 - WARNING (fibertools-rs): run-exports library package conda-forge::openssl-3.1.1-hd590300_1 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) - WARNING (fibertools-rs): run-exports library package conda-forge::gsl-2.7-he838d99_0 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) - Fixing permissions - INFO :: Time taken to mark (prefix) - 0 replacements in 0 files was 20.91 seconds - Files containing CONDA_PREFIX - ----------------------------- - bin/ft (binary): Patching - TEST START: /opt/conda/conda-bld/linux-64/fibertools-rs-0.1.4-ha48afa3_1.tar.bz2 - Renaming work directory '/opt/conda/conda-bld/fibertools-rs_1685546594028/work' to '/opt/conda/conda-bld/fibertools-rs_1685546594028/work_moved_fibertools-rs-0.1.4-ha48afa3_1_linux-64' - INFO:conda_build.utils:Renaming work directory '/opt/conda/conda-bld/fibertools-rs_1685546594028/work' to '/opt/conda/conda-bld/fibertools-rs_1685546594028/work_moved_fibertools-rs-0.1.4-ha48afa3_1_linux-64' - shutil.move(work)=/opt/conda/conda-bld/fibertools-rs_1685546594028/work, dest=/opt/conda/conda-bld/fibertools-rs_1685546594028/work_moved_fibertools-rs-0.1.4-ha48afa3_1_linux-64) - INFO:conda_build.utils:shutil.move(work)=/opt/conda/conda-bld/fibertools-rs_1685546594028/work, dest=/opt/conda/conda-bld/fibertools-rs_1685546594028/work_moved_fibertools-rs-0.1.4-ha48afa3_1_linux-64) - [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - opt/conda/conda-bl.. 100% - opt/conda/conda-bl.. [2K[1A[2K[1A[2K[0Gopt/conda/conda-bld/linux-64 - opt/conda/conda-bld/noarch - [?25h - ## Package Plan ## - - environment location: /opt/conda/conda-bld/fibertools-rs_1685546594028/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - - - The following NEW packages will be INSTALLED: - - _libgcc_mutex: 0.1-conda_forge conda-forge - _openmp_mutex: 4.5-2_gnu conda-forge - ca-certificates: 2023.5.7-hbcca054_0 conda-forge - cuda-cudart: 12.0.107-h59595ed_5 conda-forge - cuda-cudart_linux-64: 12.0.107-h59595ed_5 conda-forge - cuda-version: 12.0-hffde075_2 conda-forge - fibertools-rs: 0.1.4-ha48afa3_1 local - gsl: 2.7-he838d99_0 conda-forge - libblas: 3.9.0-16_linux64_openblas conda-forge - libcblas: 3.9.0-16_linux64_openblas conda-forge - libgcc-ng: 12.2.0-h65d4601_19 conda-forge - libgfortran-ng: 12.2.0-h69a702a_19 conda-forge - libgfortran5: 12.2.0-h337968e_19 conda-forge - libgomp: 12.2.0-h65d4601_19 conda-forge - libopenblas: 0.3.21-pthreads_h78a6416_3 conda-forge - libstdcxx-ng: 12.2.0-h46fd767_19 conda-forge - openssl: 3.1.1-hd590300_1 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - export PREFIX=/opt/conda/conda-bld/fibertools-rs_1685546594028/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export SRC_DIR=/opt/conda/conda-bld/fibertools-rs_1685546594028/test_tmp - ft help - ft: error while loading shared libraries: libcudart-45da57e3.so.11.0: ELF load command address/offset not properly aligned - Tests failed for fibertools-rs-0.1.4-ha48afa3_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken - WARNING:conda_build.build:Tests failed for fibertools-rs-0.1.4-ha48afa3_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken - TESTS FAILED: fibertools-rs-0.1.4-ha48afa3_1.tar.bz2 -# Last 100 lines of the build log. diff --git a/recipes/fibertools-rs/conda_build_config.yaml b/recipes/fibertools-rs/conda_build_config.yaml deleted file mode 100644 index 08edf02f36afc..0000000000000 --- a/recipes/fibertools-rs/conda_build_config.yaml +++ /dev/null @@ -1 +0,0 @@ -# https://github.com/conda-forge/conda-forge-pinning-feedstock/blob/bd8ecffadbaa19077609ca7649b5ec60452ff83c/recipe/conda_build_config.yaml \ No newline at end of file diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml index 5166a33b6115a..2a13e6f52bfd5 100644 --- a/recipes/fibertools-rs/meta.yaml +++ b/recipes/fibertools-rs/meta.yaml @@ -1,23 +1,20 @@ -{% set version = "0.5.3" %} +{% set version = "0.5.4" %} {% set name = "fibertools-rs" %} {% set build_number = "0" %} package: name: {{ name }} version: {{ version }} - source: url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz - sha256: 62a38ab16a199d9d03a79f7ccf3543d10127635baa7898edc004e636383fadad - + sha256: d0dc8523b9c0f2c2b368fb450d6cf6f45e13fb53bdbbd1847f1bb748fb5af42b build: run_exports: - - {{ pin_subpackage('fibertools-rs', max_pin="x") }} + - {{ pin_subpackage('fibertools-rs', max_pin="x.x") }} number: {{ build_number }} - requirements: build: - {{ compiler('c') }} @@ -25,8 +22,6 @@ requirements: - {{ compiler('rust') }} - make - cmake - - unzip - - curl # all the host and run requirements match those needed for htslib host: - libcurl @@ -35,24 +30,22 @@ requirements: - zlib - libdeflate - openssl # [not osx] + - unzip + - curl run: - - libcurl - - bzip2 - - xz - - zlib - - libdeflate - openssl # [not osx] test: commands: - ft help - about: home: https://github.com/fiberseq/fibertools-rs license: MIT + license_family: MIT summary: Mitchell Vollger's rust tools for fiberseq data. - + dev_url: https://github.com/fiberseq/fibertools-rs + doc_url: https://fiberseq.github.io/fibertools/fibertools.html extra: recipe-maintainers: @@ -60,4 +53,3 @@ extra: additional-platforms: - osx-arm64 # - linux-aarch64 # Dependency issue, see https://github.com/bioconda/bioconda-recipes/pull/48868 - diff --git a/recipes/fiji-omero_ij/meta.yaml b/recipes/fiji-omero_ij/meta.yaml index 5899814ca4d33..fc132d9dea7b0 100644 --- a/recipes/fiji-omero_ij/meta.yaml +++ b/recipes/fiji-omero_ij/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fiji-omero_ij" %} -{% set version = "5.8.4" %} +{% set version = "5.8.6" %} package: name: {{ name | lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/ome/omero-insight/releases/download/v{{ version }}/omero_ij-{{ version }}-all.jar - sha256: 14020e96fd8908907bf6f9747085452d6068b25a1df62546037ba0a3a876aa92 + sha256: d5e512dbc9125f21b904141bddbbe06768f279ac859eb5dd8206f725590617d1 build: number: 0 diff --git a/recipes/fiji-simple_omero_client/meta.yaml b/recipes/fiji-simple_omero_client/meta.yaml index 98f1a97ecd7cd..ae6d29efb6ced 100644 --- a/recipes/fiji-simple_omero_client/meta.yaml +++ b/recipes/fiji-simple_omero_client/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fiji-simple_omero_client" %} -{% set version = "5.18.0" %} +{% set version = "5.19.0" %} package: name: {{ name | lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/GReD-Clermont/simple-omero-client/releases/download/{{ version }}/simple-omero-client-{{ version }}.jar - sha256: 0b70886437e9cf6c2ab1096d6e711c7319b45bac6784ab4aac5fb8ef98e64e61 + sha256: 4d3e592b4d3bd2e9c692cab376d8a1b83ea29ba2a2d56d606ed5de09b5077734 build: number: 0 diff --git a/recipes/fiji/meta.yaml b/recipes/fiji/meta.yaml index 055f596ba2279..32d3dc462697e 100644 --- a/recipes/fiji/meta.yaml +++ b/recipes/fiji/meta.yaml @@ -1,15 +1,16 @@ package: name: fiji - version: 20231211 + version: 20240614 source: - - url: https://downloads.imagej.net/fiji/archive/20231211-1317/fiji-linux64.zip # [linux] - md5: 9292db721a289c13de35dbb882a84c2a # [linux] - - url: https://downloads.imagej.net/fiji/archive/20231211-1317/fiji-macosx.zip # [osx] - md5: 46959cc6a43b7ace2981a9a4a3486e4c # [osx] + - url: https://downloads.imagej.net/fiji/archive/20240614-2117/fiji-linux64.zip # [linux] + md5: 7b210a29f56248252fc5f10eada6e470 # [linux] + - url: https://downloads.imagej.net/fiji/archive/20240614-2117/fiji-macosx.zip # [osx] + md5: f3d107a4569e230770ce7462ee8d94ea # [osx] build: number: 0 + skip: True # [osx] run_exports: - {{ pin_subpackage("fiji", max_pin=None) }} @@ -29,7 +30,7 @@ test: about: home: http://fiji.sc - license: GNU General Public License + license: GPL-3.0-or-later summary: Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. extra: diff --git a/recipes/flexi-formatter/meta.yaml b/recipes/flexi-formatter/meta.yaml new file mode 100644 index 0000000000000..497fd0006fc48 --- /dev/null +++ b/recipes/flexi-formatter/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "flexi-formatter" %} +{% set version = "0.0.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flexi_formatter-{{ version }}.tar.gz + sha256: c3a054fe1b8a3f9ccb307559ef125236d3f6f134dd35be4f3862e8b136ebd8bd + +build: + entry_points: + - flexi_formatter = flexi_formatter.reformat_flexiplex_tags:app + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin='x.x') }} + +requirements: + host: + - python >=3 + - pip + - setuptools + run: + - python >=3 + - typer + - simplesam + - samtools + +test: + imports: + - flexi_formatter + - simplesam + commands: + - flexi_formatter --help + - samtools --help + requires: + - pip + +about: + home: "https://github.com/VIB-CCB-BioIT/flexiplex_tag_formatter" + summary: Moving flexiplex barcode and UMI to bam tags + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - ljwharbers diff --git a/recipes/flumutdb/meta.yaml b/recipes/flumutdb/meta.yaml index 61b8b678f0783..d344a18a237cf 100644 --- a/recipes/flumutdb/meta.yaml +++ b/recipes/flumutdb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flumutdb" %} -{% set version = "6.2" %} +{% set version = "6.3" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flumutdb-{{ version }}.tar.gz - sha256: 7a604b2c2b0eeebf3dcb453b597d012bfed4d768821799c8b6598b2af3caf625 + sha256: a98b7eaf5c821129b8cdb9d740d00d9ecb87f5d6c253112de8105713c0e1a732 build: run_exports: diff --git a/recipes/flye/build_failure.linux-64.yaml b/recipes/flye/build_failure.linux-64.yaml deleted file mode 100644 index a406f2626fdcc..0000000000000 --- a/recipes/flye/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 577df4f0a9db63e97ed56cec147ab74fc83826ef97945bc3489ec47ece2f4725 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Removed build tracker: '/tmp/pip-build-tracker-0s_3_n2n' - - Resource usage statistics from building flye: - Process count: 20 - CPU time: Sys=0:00:08.1, User=0:02:13.1 - Memory: 1.6G - Disk usage: 252.4K - Time elapsed: 0:01:11.0 - - - compiling .pyc files... - number of files: 104 - Warning: rpath /opt/conda/conda-bld/flye_1717795145756/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717795145756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it) - Warning: rpath /opt/conda/conda-bld/flye_1717795145756/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717795145756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it) - Warning: rpath /opt/conda/conda-bld/flye_1717795145756/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717795145756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it) - INFO: sysroot: '/opt/conda/conda-bld/flye_1717795145756/_build_env/x86_64-conda-linux-gnu/sysroot/' files: '['usr/share/zoneinfo/zone.tab', 'usr/share/zoneinfo/tzdata.zi', 'usr/share/zoneinfo/right/Zulu', 'usr/share/zoneinfo/right/WET']' - INFO (flye,bin/flye-minimap2): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-minimap2): Needed DSO lib/libz.so.1 found in conda-forge/linux-64::libzlib==1.2.13=h4ab18f5_6 - INFO (flye,bin/flye-minimap2): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-minimap2): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-modules): Needed DSO lib/libz.so.1 found in conda-forge/linux-64::libzlib==1.2.13=h4ab18f5_6 - INFO (flye,bin/flye-modules): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-64::libstdcxx-ng==13.2.0=hc0a3c3a_7 - INFO (flye,bin/flye-modules): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-modules): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-64::libgcc-ng==13.2.0=h77fa898_7 - INFO (flye,bin/flye-modules): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-modules): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-modules): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/ld-linux-x86-64.so.2 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-samtools): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-samtools): Needed DSO lib/libz.so.1 found in conda-forge/linux-64::libzlib==1.2.13=h4ab18f5_6 - INFO (flye,bin/flye-samtools): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-samtools): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libdl.so.2 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye,bin/flye-samtools): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17 - INFO (flye): Interpreted package 'flye' is interpreted by 'python' - Fixing permissions - Packaged license file/s. - INFO :: Time taken to mark (prefix) - 0 replacements in 0 files was 0.07 seconds - Files containing CONDA_PREFIX - ----------------------------- - bin/flye (text): Patching - TEST START: /opt/conda/conda-bld/linux-64/flye-2.9.4-py312ha1f7cf2_1.tar.bz2 - Renaming work directory '/opt/conda/conda-bld/flye_1717795145756/work' to '/opt/conda/conda-bld/flye_1717795145756/work_moved_flye-2.9.4-py312ha1f7cf2_1_linux-64' - shutil.move(work)=/opt/conda/conda-bld/flye_1717795145756/work, dest=/opt/conda/conda-bld/flye_1717795145756/work_moved_flye-2.9.4-py312ha1f7cf2_1_linux-64) - Reloading output folder (local): ...working... done - Solving environment (_test_env): ...working... done - - ## Package Plan ## - - environment location: /opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - - - The following NEW packages will be INSTALLED: - - _libgcc_mutex: 0.1-conda_forge conda-forge - _openmp_mutex: 4.5-2_gnu conda-forge - bzip2: 1.0.8-hd590300_5 conda-forge - ca-certificates: 2024.6.2-hbcca054_0 conda-forge - flye: 2.9.4-py312ha1f7cf2_1 local - ld_impl_linux-64: 2.40-hf3520f5_2 conda-forge - libexpat: 2.6.2-h59595ed_0 conda-forge - libffi: 3.4.2-h7f98852_5 conda-forge - libgcc-ng: 13.2.0-h77fa898_7 conda-forge - libgomp: 13.2.0-h77fa898_7 conda-forge - libnsl: 2.0.1-hd590300_0 conda-forge - libsqlite: 3.45.3-h2797004_0 conda-forge - libstdcxx-ng: 13.2.0-hc0a3c3a_7 conda-forge - libuuid: 2.38.1-h0b41bf4_0 conda-forge - libxcrypt: 4.4.36-hd590300_1 conda-forge - libzlib: 1.3.1-h4ab18f5_1 conda-forge - ncurses: 6.5-h59595ed_0 conda-forge - openssl: 3.3.1-h4ab18f5_0 conda-forge - pip: 24.0-pyhd8ed1ab_0 conda-forge - python: 3.12.3-hab00c5b_0_cpython conda-forge - python_abi: 3.12-4_cp312 conda-forge - readline: 8.2-h8228510_1 conda-forge - setuptools: 70.0.0-pyhd8ed1ab_0 conda-forge - tk: 8.6.13-noxft_h4845f30_101 conda-forge - tzdata: 2024a-h0c530f3_0 conda-forge - wheel: 0.43.0-pyhd8ed1ab_1 conda-forge - xz: 5.2.6-h166bdaf_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - export PREFIX=/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - export SRC_DIR=/opt/conda/conda-bld/flye_1717795145756/test_tmp - flye -h - grep Assembly - Traceback (most recent call last): - File "/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/flye", line 7, in - from flye.main import main - File "/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/main.py", line 19, in - import flye.polishing.alignment as aln - File "/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/polishing/alignment.py", line 18, in - import flye.utils.fasta_parser as fp - File "/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/utils/fasta_parser.py", line 26, in - from flye.six.moves import range - ModuleNotFoundError: No module named 'flye.six.moves' - WARNING: Tests failed for flye-2.9.4-py312ha1f7cf2_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken - TESTS FAILED: flye-2.9.4-py312ha1f7cf2_1.tar.bz2 -# Last 100 lines of the build log. diff --git a/recipes/flye/build_failure.linux-aarch64.yaml b/recipes/flye/build_failure.linux-aarch64.yaml deleted file mode 100644 index d451186baca31..0000000000000 --- a/recipes/flye/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 577df4f0a9db63e97ed56cec147ab74fc83826ef97945bc3489ec47ece2f4725 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - CPU time: Sys=0:00:04.6, User=0:01:53.3 - Memory: 1.7G - Disk usage: 289.9K - Time elapsed: 0:01:33.1 - - - Packaging flye - Packaging flye-2.9.4-py312h747c3d4_1 - compiling .pyc files... - number of files: 104 - Warning: rpath /opt/conda/conda-bld/flye_1717793573507/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717793573507/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it) - Warning: rpath /opt/conda/conda-bld/flye_1717793573507/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717793573507/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it) - Warning: rpath /opt/conda/conda-bld/flye_1717793573507/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717793573507/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it) - INFO: sysroot: '/opt/conda/conda-bld/flye_1717793573507/_build_env/aarch64-conda-linux-gnu/sysroot/' files: '['usr/share/zoneinfo/zone1970.tab', 'usr/share/zoneinfo/zone.tab', 'usr/share/zoneinfo/tzdata.zi', 'usr/share/zoneinfo/right/Zulu']' - INFO (flye,bin/flye-modules): Needed DSO lib/libz.so.1 found in conda-forge/linux-aarch64::libzlib==1.2.13=h68df207_6 - INFO (flye,bin/flye-modules): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-aarch64::libstdcxx-ng==13.2.0=h3f4de04_7 - INFO (flye,bin/flye-modules): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-modules): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-aarch64::libgcc-ng==13.2.0=he277a41_7 - INFO (flye,bin/flye-modules): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-modules): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-modules): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-minimap2): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-minimap2): Needed DSO lib/libz.so.1 found in conda-forge/linux-aarch64::libzlib==1.2.13=h68df207_6 - INFO (flye,bin/flye-minimap2): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-minimap2): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-minimap2): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-samtools): Needed DSO lib/libz.so.1 found in conda-forge/linux-aarch64::libzlib==1.2.13=h68df207_6 - INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libdl.so.2 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14 - INFO (flye): Interpreted package 'flye' is interpreted by 'python' - Fixing permissions - Packaged license file/s. - INFO :: Time taken to mark (prefix) - 0 replacements in 0 files was 0.13 seconds - Files containing CONDA_PREFIX - ----------------------------- - bin/flye (text): Patching - WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. - TEST START: /opt/conda/conda-bld/linux-aarch64/flye-2.9.4-py312h747c3d4_1.tar.bz2 - Renaming work directory '/opt/conda/conda-bld/flye_1717793573507/work' to '/opt/conda/conda-bld/flye_1717793573507/work_moved_flye-2.9.4-py312h747c3d4_1_linux-aarch64' - shutil.move(work)=/opt/conda/conda-bld/flye_1717793573507/work, dest=/opt/conda/conda-bld/flye_1717793573507/work_moved_flye-2.9.4-py312h747c3d4_1_linux-aarch64) - Reloading output folder (local): ...working... done - Solving environment (_test_env): ...working... done - - ## Package Plan ## - - environment location: /opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - - - The following NEW packages will be INSTALLED: - - _openmp_mutex: 4.5-2_gnu conda-forge - bzip2: 1.0.8-h31becfc_5 conda-forge - ca-certificates: 2024.6.2-hcefe29a_0 conda-forge - flye: 2.9.4-py312h747c3d4_1 local - ld_impl_linux-aarch64: 2.40-h9fc2d93_2 conda-forge - libexpat: 2.6.2-h2f0025b_0 conda-forge - libffi: 3.4.2-h3557bc0_5 conda-forge - libgcc-ng: 13.2.0-he277a41_7 conda-forge - libgomp: 13.2.0-he277a41_7 conda-forge - libnsl: 2.0.1-h31becfc_0 conda-forge - libsqlite: 3.45.3-h194ca79_0 conda-forge - libstdcxx-ng: 13.2.0-h3f4de04_7 conda-forge - libuuid: 2.38.1-hb4cce97_0 conda-forge - libxcrypt: 4.4.36-h31becfc_1 conda-forge - libzlib: 1.3.1-h68df207_1 conda-forge - ncurses: 6.5-h0425590_0 conda-forge - openssl: 3.3.1-h68df207_0 conda-forge - pip: 24.0-pyhd8ed1ab_0 conda-forge - python: 3.12.3-h43d1f9e_0_cpython conda-forge - python_abi: 3.12-4_cp312 conda-forge - readline: 8.2-h8fc344f_1 conda-forge - setuptools: 70.0.0-pyhd8ed1ab_0 conda-forge - tk: 8.6.13-h194ca79_0 conda-forge - tzdata: 2024a-h0c530f3_0 conda-forge - wheel: 0.43.0-pyhd8ed1ab_1 conda-forge - xz: 5.2.6-h9cdd2b7_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - export PREFIX=/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - export SRC_DIR=/opt/conda/conda-bld/flye_1717793573507/test_tmp - flye -h - grep Assembly - Traceback (most recent call last): - File "/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/flye", line 7, in - from flye.main import main - File "/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/main.py", line 19, in - import flye.polishing.alignment as aln - File "/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/polishing/alignment.py", line 18, in - import flye.utils.fasta_parser as fp - File "/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/utils/fasta_parser.py", line 26, in - from flye.six.moves import range - ModuleNotFoundError: No module named 'flye.six.moves' - WARNING: Tests failed for flye-2.9.4-py312h747c3d4_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken - TESTS FAILED: flye-2.9.4-py312h747c3d4_1.tar.bz2 -# Last 100 lines of the build log. diff --git a/recipes/flye/build_failure.osx-64.yaml b/recipes/flye/build_failure.osx-64.yaml deleted file mode 100644 index 453ba051fb8e3..0000000000000 --- a/recipes/flye/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 577df4f0a9db63e97ed56cec147ab74fc83826ef97945bc3489ec47ece2f4725 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - make: 4.3-h22f3db7_1 conda-forge - openssl: 3.3.1-h87427d6_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.6-h915ae27_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: 2.9.4_197a2dfe39.tar.gz - Downloading https://github.com/fenderglass/Flye/archive/2.9.4.tar.gz - Success - checking file Makefile - patching file Makefile - /opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/python: No module named pip - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/flye/0001-Makefile-aarch64.patch - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/flye/0001-Makefile-aarch64.patch with args: - ['-Np1', '-i', '/tmp/tmpfu1zkvqb/0001-Makefile-aarch64.patch.native', '--binary'] - Patch analysis gives: - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - [[ RA-MD1LOVE ]] - [[ 0001-Makefile-aarch64.patch ]] - - Key: - - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/work/conda_build.sh']' returned non-zero exit status 1. - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/flye-2.9.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/flye-2.9.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/flye-2.9.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/flye-2.9.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -# Last 100 lines of the build log. diff --git a/recipes/flye/meta.yaml b/recipes/flye/meta.yaml index 4cc8f7c9eb91a..74f66f83a7c9b 100644 --- a/recipes/flye/meta.yaml +++ b/recipes/flye/meta.yaml @@ -1,6 +1,6 @@ {% set name = "flye" %} -{% set version = "2.9.4" %} -{% set sha256 = "197a2dfe39fc324a39d8e1901af4f539609159c4a64a578ec8e60f73f5ea4696" %} +{% set version = "2.9.5" %} +{% set sha256 = "7b384266d83b1e66bcaf82d49d35ac6c587bad9146e8f3b752a220291f6b1a6f" %} package: name: {{ name }} @@ -13,8 +13,7 @@ source: - 0001-Makefile-aarch64.patch build: - number: 2 - skip: True # [py > 311] + number: 1 entry_points: - flye = flye.main:main run_exports: @@ -30,6 +29,7 @@ requirements: - zlib run: - python + - setuptools # [osx and arm64] test: commands: diff --git a/recipes/fqtk/build.sh b/recipes/fqtk/build.sh index 403679dd60ea7..9a2b15637fd93 100644 --- a/recipes/fqtk/build.sh +++ b/recipes/fqtk/build.sh @@ -1,11 +1,7 @@ #!/bin/bash -e -# TODO: Remove the following export when pinning is updated and we use -# {{ compiler('rust') }} in the recipe. -export \ - CARGO_NET_GIT_FETCH_WITH_CLI=true \ - CARGO_HOME="${BUILD_PREFIX}/.cargo" - export BINDGEN_EXTRA_CLANG_ARGS="${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --no-track --verbose --root "${PREFIX}" --path . diff --git a/recipes/fqtk/meta.yaml b/recipes/fqtk/meta.yaml index dce25b0d49c3e..575e3f00fb789 100644 --- a/recipes/fqtk/meta.yaml +++ b/recipes/fqtk/meta.yaml @@ -1,38 +1,44 @@ {% set name = "fqtk" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name }} version: {{ version }} -build: - number: 0 - source: url: https://github.com/fulcrumgenomics/{{ name }}/archive/v{{ version }}.tar.gz - sha256: b03c993e5705d2e764ee696559ed31002b04f036ad103e64c18659aa309cbc6b + sha256: f64598b7493b2c87fe8b17330c137c98eb66e352f3648809e4128ea25f300a2e + +build: + number: 1 + run_exports: + - {{ pin_subpackage('fqtk', max_pin="x.x") }} requirements: build: - {{ compiler('cxx') }} - - rust >=1.60 + - {{ compiler('rust') }} - pkg-config - make - cmake - host: - run: test: commands: - fqtk --help about: - home: https://github.com/fulcrumgenomics/{{ name }} + home: "https://github.com/fulcrumgenomics/{{ name }}" license: MIT + license_family: MIT license_file: LICENSE - summary: A toolkit for working with FASTQ files. + summary: "A toolkit for working with FASTQ files." + dev_url: "https://github.com/fulcrumgenomics/{{ name }}" + doc_url: "https://github.com/fulcrumgenomics/fqtk/blob/v{{ version }}/README.md" extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - NatPRoach - nh13 diff --git a/recipes/fraposa-pgsc/meta.yaml b/recipes/fraposa-pgsc/meta.yaml index 5babab25225b0..111722c775d10 100644 --- a/recipes/fraposa-pgsc/meta.yaml +++ b/recipes/fraposa-pgsc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fraposa-pgsc" %} -{% set version = "1.0.0" %} +{% set version = "1.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/fraposa_pgsc-{{ version }}.tar.gz - sha256: a21ce6c8d90752f23d3694dbbd69060a7dabaeb6ac29d0ecc27c0435b7fce0a7 + sha256: 227fd14a7b82859597dd484828de74c7ab8f22d08ea51a7dc7cf6ca1a4827033 build: entry_points: diff --git a/recipes/freebayes/0001-make-meson-build-conda-friendly.patch b/recipes/freebayes/0001-make-meson-build-conda-friendly.patch index 98067c888dcb8..320213ecdd109 100644 --- a/recipes/freebayes/0001-make-meson-build-conda-friendly.patch +++ b/recipes/freebayes/0001-make-meson-build-conda-friendly.patch @@ -1,39 +1,23 @@ -From 62630d76f804c930753b0215ed09a33a02e1347e Mon Sep 17 00:00:00 2001 -From: Lightning Auriga -Date: Sat, 7 Oct 2023 12:25:42 -0400 -Subject: [PATCH 1/2] make meson build conda friendly - ---- - meson.build | 58 +++++++++-------------------------------------------- - 1 file changed, 9 insertions(+), 49 deletions(-) - diff --git a/meson.build b/meson.build -index 2a91caf..66b8016 100644 +index 9d727f9..9288fbb 100644 --- a/meson.build +++ b/meson.build -@@ -15,7 +15,7 @@ - # meson build -Dstatic=true -Dprefer_system_deps=false --buildtype release +@@ -23,14 +23,10 @@ static_build = get_option('static') - project('freebayes', ['cpp', 'c'], -- version : '1.3.6', -+ version : '1.3.7', - default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3']) - static_build = get_option('static') + cc = meson.get_compiler('cpp') -@@ -24,21 +24,16 @@ cc = meson.get_compiler('cpp') - zlib_dep = dependency('zlib', static: static_build) +-# fastahack_dep = cc.find_library('libfastahack') lzma_dep = dependency('liblzma', static: static_build) - thread_dep = dependency('threads', static: static_build) + seqlib_dep = dependency('libseqlib', static: static_build, required: false) + # smithwaterman_dep = cc.find_library('libsmithwaterman') -tabixpp_dep = cc.find_library('tabixpp', required: false, static: static_build) + thread_dep = dependency('threads', static: static_build) +-vcflib_dep = cc.find_library('libvcflib') +-wfa2lib_dep = cc.find_library('libwfa2') + zlib_dep = dependency('zlib', static: static_build) # to compile htslib use - # meson build -Dprefer_system_deps=false - # otherwise it tries to pick up the local system libs - if get_option('prefer_system_deps') - htslib_dep = dependency('htslib', static: static_build, required: false) -- tabixpp_dep = cc.find_library('tabixpp', static: static_build, required: false) -- vcflib_dep = dependency('libvcflib', static: static_build, required: false) - seqlib_dep = dependency('libseqlib', static: static_build, required: false) +@@ -41,8 +37,6 @@ if get_option('prefer_system_deps') else # uses the local git submodules htslib_dep = dependency('', required : false) @@ -42,15 +26,13 @@ index 2a91caf..66b8016 100644 seqlib_dep = dependency('', required : false) endif -@@ -99,50 +94,15 @@ if not htslib_dep.found() +@@ -123,47 +114,16 @@ if not htslib_dep.found() htslib_dep = declare_dependency(link_with : htslib_lib, include_directories : htslib_inc) else - htslib_inc = [] -+ htslib_inc = [get_option('prefix') + '/include'] -+ htslib_lib = [get_option('prefix') + '/lib'] - endif - +-endif +- - -if not tabixpp_dep.found() - tabixpp_inc = include_directories('contrib/vcflib/contrib/tabixpp/') @@ -63,8 +45,13 @@ index 2a91caf..66b8016 100644 - include_directories : tabixpp_inc) -else - tabixpp_inc = [] --endif ++ htslib_inc = [get_option('prefix') + '/include'] ++ htslib_lib = [get_option('prefix') + '/lib'] + endif + +-vcflib_inc = include_directories() - +-# optionally build from source. As we unbundled just check out the vcflib repo in contrib. -if not vcflib_dep.found() - vcflib_inc = include_directories( - 'contrib/vcflib/src', @@ -78,12 +65,6 @@ index 2a91caf..66b8016 100644 - 'contrib/vcflib/src/allele.cpp', - 'contrib/vcflib/src/cigar.cpp', - 'contrib/vcflib/src/split.cpp', -- 'contrib/vcflib/contrib/fastahack/Fasta.cpp', -- 'contrib/vcflib/contrib/smithwaterman/SmithWatermanGotoh.cpp', -- 'contrib/vcflib/contrib/smithwaterman/disorder.cpp', -- 'contrib/vcflib/contrib/smithwaterman/Repeats.cpp', -- 'contrib/vcflib/contrib/smithwaterman/LeftAlign.cpp', -- 'contrib/vcflib/contrib/smithwaterman/IndelAllele.cpp', - ) - vcflib_lib = static_library('custom_vcflib', - vcflib_src, @@ -97,10 +78,11 @@ index 2a91caf..66b8016 100644 +vcflib_inc = [get_option('prefix') + '/include'] +vcflib_lib = [get_option('prefix') + '/lib'] +vcflib_dep = [] ++wfa2lib_dep = [] if not seqlib_dep.found() -@@ -227,7 +187,7 @@ freebayes_lib = static_library( +@@ -248,11 +208,11 @@ freebayes_lib = static_library( if static_build link_arguments = '-static' else @@ -109,6 +91,7 @@ index 2a91caf..66b8016 100644 endif executable('freebayes', --- -2.41.0 - + [freebayes_src,multichoose_src,fastahack_src,smithwaterman_src], + include_directories : [multichoose_inc, fastahack_inc, smithwaterman_inc, incdir], + cpp_args : extra_cpp_args, + link_args: link_arguments, diff --git a/recipes/freebayes/0002-fix-intervaltree-include-path.patch b/recipes/freebayes/0002-fix-intervaltree-include-path.patch index ad42bf6a166ac..45d1820b05fd7 100644 --- a/recipes/freebayes/0002-fix-intervaltree-include-path.patch +++ b/recipes/freebayes/0002-fix-intervaltree-include-path.patch @@ -9,31 +9,30 @@ Subject: [PATCH 2/2] fix intervaltree include path 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/BedReader.cpp b/src/BedReader.cpp -index 9dd79c7..ea79235 100644 +index dabd0af..ea79235 100644 --- a/src/BedReader.cpp +++ b/src/BedReader.cpp @@ -11,7 +11,7 @@ #include "Utility.h" #include "BedReader.h" #include "Logging.h" --#include "../intervaltree/IntervalTree.h" +-#include +#include "IntervalTree.h" using namespace std; diff --git a/src/BedReader.h b/src/BedReader.h -index 03abb3f..8777d53 100644 +index 5a44f29..8777d53 100644 --- a/src/BedReader.h +++ b/src/BedReader.h @@ -9,7 +9,7 @@ #include #include #include --#include "../intervaltree/IntervalTree.h" +-#include +#include "IntervalTree.h" #include "split.h" using namespace std; -- 2.41.0 - diff --git a/recipes/freebayes/0003-meson-macos.patch b/recipes/freebayes/0003-meson-macos.patch index 47e1176d8d7ad..9091480e20d24 100644 --- a/recipes/freebayes/0003-meson-macos.patch +++ b/recipes/freebayes/0003-meson-macos.patch @@ -1,13 +1,13 @@ diff --git a/meson.build b/meson.build -index 66b8016..bf0bf10 100644 +index 7fb0625..e0983af 100644 --- a/meson.build +++ b/meson.build @@ -16,7 +16,7 @@ project('freebayes', ['cpp', 'c'], - version : '1.3.7', + version : '1.3.8', - default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3']) + default_options : ['warning_level=1', 'cpp_std=c++14', 'optimization=3']) static_build = get_option('static') - cc = meson.get_compiler('cpp') + # used by Debian: add_global_arguments('-D_GLIBCXX_ASSERTIONS=1', language : 'cpp') diff --git a/recipes/freebayes/build.sh b/recipes/freebayes/build.sh index a090a95414a3a..8032f54a79517 100644 --- a/recipes/freebayes/build.sh +++ b/recipes/freebayes/build.sh @@ -1,19 +1,33 @@ #!/bin/bash -mkdir build mkdir -p ${PREFIX}/bin -CXX="${CXX}" CC="${CC}" meson setup --buildtype release --prefix "${PREFIX}" \ - --strip --prefer-static -Dprefer_system_deps=true build/ +cd freebayes +mkdir build + +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I{PREFIX}/include" + +CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" meson setup --buildtype release \ + --prefix "${PREFIX}" --strip \ + --includedir "${PREFIX}/include" \ + --libdir "${PREFIX}/lib" build/ cd build ninja -v ninja -v install -##Copy scripts over ## This will likely need to be removed with an updated build -cp -n ../scripts/*.py $PREFIX/bin -cp -n ../scripts/*.sh $PREFIX/bin -cp -n ../scripts/*.pl $PREFIX/bin +## Copy scripts over to ${PREFIX}/bin ## +chmod 0755 ../scripts/*.py +chmod 0755 ../scripts/*.sh +chmod 0755 ../scripts/*.pl +cp -nf ../scripts/*.py ${PREFIX}/bin +cp -nf ../scripts/*.sh ${PREFIX}/bin +cp -nf ../scripts/*.pl ${PREFIX}/bin -cp -n ../scripts/freebayes-parallel $PREFIX/bin +chmod 0755 ${PREFIX}/bin/freebayes +chmod 0755 ../scripts/freebayes-parallel +cp -nf ../scripts/freebayes-parallel ${PREFIX}/bin diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index f10c0fa32a4b2..5381e2fb554f3 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -1,17 +1,27 @@ {% set name = "freebayes" %} -{% set version = "1.3.7" %} +{% set version = "1.3.8" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/freebayes/freebayes/archive/refs/tags/v{{ version }}.tar.gz - sha256: 89c2202aaa82925bc6a49e04df593e5ef3b1547b3b514efcbd490a54d8ad200b - patches: - - 0001-make-meson-build-conda-friendly.patch - - 0002-fix-intervaltree-include-path.patch - - 0003-meson-macos.patch # [osx] + - folder: freebayes + url: https://github.com/freebayes/freebayes/archive/refs/tags/v{{ version }}.tar.gz + sha256: d1c24b1d1b35277e7403cd67063557998218a105c916b01a745e7704715fce67 + patches: + - 0001-make-meson-build-conda-friendly.patch + - 0002-fix-intervaltree-include-path.patch + - 0003-meson-macos.patch # [osx] + - folder: freebayes/contrib/smithwaterman + url: https://github.com/ekg/smithwaterman/archive/2610e259611ae4cde8f03c72499d28f03f6d38a7.tar.gz + sha256: 8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8 + - folder: freebayes/contrib/multichoose + url: https://github.com/vcflib/multichoose/archive/255192edd49cfe36557f7f4f0d2d6ee1c702ffbb.tar.gz + sha256: 0045051ee85d36435582151830efe0eefb466be0ec9aedbbc4465dca30d22102 + - folder: freebayes/contrib/fastahack + url: https://github.com/ekg/fastahack/archive/refs/tags/v1.0.0.tar.gz + sha256: cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae build: number: 2 @@ -33,12 +43,13 @@ requirements: - vcflib - simde - zlib + - wfa2-lib run: - parallel - samtools - tabixpp - vcflib - - zlib + - wfa2-lib test: commands: @@ -46,12 +57,13 @@ test: - freebayes-parallel about: - home: https://github.com/freebayes/freebayes + home: "https://github.com/freebayes/freebayes" license: MIT - license_file: LICENSE + license_file: "freebayes/LICENSE" license_family: MIT - summary: Bayesian haplotype-based polymorphism discovery and genotyping - dev_url: https://github.com/freebayes/freebayes + summary: "Bayesian haplotype-based polymorphism discovery and genotyping." + dev_url: "https://github.com/freebayes/freebayes" + doc_url: "https://github.com/freebayes/freebayes/blob/v{{ version }}/README.md" extra: additional-platforms: @@ -59,5 +71,6 @@ extra: identifiers: - biotools:freebayes - usegalaxy-eu:freebayes + - doi:10.48550/arXiv.1207.3907 recipe-maintainers: - jpuritz diff --git a/recipes/fwdpy11/meta.yaml b/recipes/fwdpy11/meta.yaml index 6729780e4e7e6..848cd1006671e 100644 --- a/recipes/fwdpy11/meta.yaml +++ b/recipes/fwdpy11/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fwdpy11" %} -{% set version = "0.24.0" %} +{% set version = "0.24.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/fwdpy11-{{ version }}.tar.gz - sha256: 1b7b0ad6a78ccb43ebc1d5dee43ae6542dc254543aad6aad3462165204afe3a0 + sha256: d0d0d3b9b504d47bd23cfedab39bc4978d2fb21a73e8645140a8c25e211e5800 build: skip: True # [py < 39 or py > 312] diff --git a/recipes/galah/meta.yaml b/recipes/galah/meta.yaml index f90f03562e182..be438161e898a 100644 --- a/recipes/galah/meta.yaml +++ b/recipes/galah/meta.yaml @@ -1,13 +1,13 @@ -{% set version = "0.4.0" %} +{% set version = "0.4.2" %} {% set name = "galah" %} -{% set sha256 = "9b40cc805df15461e5b07fd3108663cc92d286030c17fefe5a33716b5b8fa10a" %} +{% set sha256 = "6908d5038925032e8e2a2b2533bb5b1cb7ad2b51a89fe144b34bb57677ee287a" %} package: name: {{ name }} version: {{ version }} build: - number: 1 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage('galah', max_pin="x.x") }} diff --git a/recipes/galaxy-data/meta.yaml b/recipes/galaxy-data/meta.yaml index 12aa8245714e8..c8e6406f0d915 100644 --- a/recipes/galaxy-data/meta.yaml +++ b/recipes/galaxy-data/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "24.1.1" %} -{% set sha256 = "be4d1ba81589cc5e6d4fb38829c1770483cff6c380b7647aa80b7bc90737f573" %} +{% set version = "24.1.2" %} +{% set sha256 = "d75e5e9e954773c683cb54a655da0c9733f1c6b0f6e691fedb6a1edc6e4aede2" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index f5c2829d09ef4..83a3987023337 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "24.1.1" %} -{% set sha256 = "d3c23617eed928515fd492fd97588790b1c095fdd298b5f5584307f34846c4ca" %} +{% set version = "24.1.2" %} +{% set sha256 = "39f25b6f9a2f48625bf21fe0021e90768f598db1113867960420afc5988a4e70" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index ed250a556cf83..0581ff15a3a22 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "24.1.1" %} -{% set sha256 = "0a38e7fedc5c9300507d441c17d745957e1c8a0c65d1b7efde62361bf024eff1" %} +{% set version = "24.1.2" %} +{% set sha256 = "1079e628fb89125792781e9a62711e8281f3cd34eff0cd5ce8ed452d6c06cb3e" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: diff --git a/recipes/galaxy-schema/meta.yaml b/recipes/galaxy-schema/meta.yaml index f89975a11c2c7..2cb94358c1d1f 100644 --- a/recipes/galaxy-schema/meta.yaml +++ b/recipes/galaxy-schema/meta.yaml @@ -1,6 +1,6 @@ {% set name = "galaxy-schema" %} -{% set version = "24.1.1" %} -{% set sha256 = "622c65bf1f7fc0cfb5cf6ee844e819a7ceff2b929aca5894848761b3a7df84fa" %} +{% set version = "24.1.2" %} +{% set sha256 = "526d9c7e211da145f4169272a69b4a512304110da3dd9df61d0d305991db5309" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: diff --git a/recipes/galaxy_sequence_utils/meta.yaml b/recipes/galaxy_sequence_utils/meta.yaml index 5e9efa7fccb47..944a77c94f3a7 100644 --- a/recipes/galaxy_sequence_utils/meta.yaml +++ b/recipes/galaxy_sequence_utils/meta.yaml @@ -18,7 +18,7 @@ source: build: noarch: python - number: 1 + number: 2 preserve_egg_dir: True run_exports: -{{ pin_subpackage(name, max_pin="x") }} @@ -40,12 +40,13 @@ build: requirements: host: - - python + # uses the imp module which has been deprecated in 3.12 + - python <3.12 - setuptools - six run: - - python + - python <3.12 - six test: diff --git a/recipes/gappa/build.sh b/recipes/gappa/build.sh index 2456a7bb675f9..8686b9ce267bb 100644 --- a/recipes/gappa/build.sh +++ b/recipes/gappa/build.sh @@ -8,5 +8,5 @@ make -j ${CPU_COUNT} mkdir -p $PREFIX/bin +chmod 0755 bin/gappa cp bin/gappa $PREFIX/bin - diff --git a/recipes/gappa/meta.yaml b/recipes/gappa/meta.yaml index e1be51a506d49..968f366e34297 100644 --- a/recipes/gappa/meta.yaml +++ b/recipes/gappa/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.8.5" build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('gappa', max_pin='x.x') }} @@ -17,9 +17,11 @@ requirements: - {{ compiler('cxx') }} - cmake host: - - llvm-openmp # [osx] + - libgomp # [linux] + - llvm-openmp # [osx] - zlib run: + - libgomp # [linux] - llvm-openmp # [osx] test: @@ -29,6 +31,7 @@ test: about: home: https://github.com/lczech/gappa license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE.txt summary: Genesis Applications for Phylogenetic Placement Analysis description: | @@ -42,6 +45,7 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - doi:10.1093/bioinformatics/btaa070 - doi:10.3389/fbinf.2022.871393 diff --git a/recipes/gapseq/meta.yaml b/recipes/gapseq/meta.yaml index b62b67d0b8755..c1275e49f6191 100644 --- a/recipes/gapseq/meta.yaml +++ b/recipes/gapseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2" %} +{% set version = "1.3.1" %} package: name: gapseq @@ -6,7 +6,7 @@ package: source: url: https://github.com/jotech/gapseq/archive/refs/tags/v{{ version}}.tar.gz - sha256: 061799f8e0406662450dd3d8d61d824220670fb23231895deecd490a5cbdf7cf + sha256: 8702d9bc844c04aa06fba083bd81bdf4585bfbb581b890052ba5af378a85a2c6 build: number: 0 diff --git a/recipes/gbintk/meta.yaml b/recipes/gbintk/meta.yaml new file mode 100644 index 0000000000000..55b527d6a6173 --- /dev/null +++ b/recipes/gbintk/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "gbintk" %} +{% set version = "1.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/metagentools/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" + sha256: 9e0784a6ecf826631dd6c8a84f24d4f0df9c80d2800c5615094fb99750326b3c + +build: + number: 1 + noarch: false + entry_points: + - gbintk = gbintk.cli:main + script: + - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('gbintk', max_pin="x.x") }} + +requirements: + host: + - pip + - python >=3.7,<3.11 + - flit-core + run: + - python >=3.7,<3.11 + - click + - pkg-config + - python-igraph + - cairo + - cairocffi + - cogent3 + - networkx + - tqdm + - scipy + - numpy + - pandas + - tabulate + - fraggenescan + - hmmer + - graphbin + - graphbin2 + - metacoag >=1.2.1 + +test: + commands: + - gbintk --help + +about: + home: "https://github.com/metagentools/gbintk" + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: "GraphBin-Tk: assembly graph-based metagenomic binning toolkit" + description: | + GraphBin-Tk is a toolkit that combines assembly graph-based metagenomic bin-refinement and binning techniques GraphBin, GraphBin2 and MetaCoAG. + doc_url: "https://gbintk.readthedocs.io/" + dev_url: "https://github.com/metagentools/gbintk" + +extra: + skip-lints: + - should_be_noarch_generic + recipe-maintainers: + - Vini2 diff --git a/recipes/gdc-client/meta.yaml b/recipes/gdc-client/meta.yaml index 5c06114381bf7..22e25c0ab7aa4 100644 --- a/recipes/gdc-client/meta.yaml +++ b/recipes/gdc-client/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gdc-client" %} -{% set version = "2.0" %} +{% set version = "2.3" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/NCI-GDC/gdc-client/archive/{{ version }}.tar.gz - sha256: 4d81ab9d3a8efca2091691310cb1ef0511b7049fde375f146974f8d7d028fa20 + sha256: c4617516d84572135ee21b3b0bbaf4a5d360dcfe752ef70ba89c156ab64d1870 build: number: 0 diff --git a/recipes/gempipe/meta.yaml b/recipes/gempipe/meta.yaml index 80aaf1acc33f4..53866de36f064 100755 --- a/recipes/gempipe/meta.yaml +++ b/recipes/gempipe/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.33.4" %} +{% set version = "1.35.3" %} package: name: "gempipe" @@ -7,14 +7,14 @@ package: source: url: https://github.com/lazzarigioele/gempipe/archive/v{{ version }}.tar.gz - sha256: ff9a7f7ab4faa2ac1ed0e77d3e9051034f6f5a98dea347bebdb978727ccb73ea + sha256: 98652ae059cb2ef582e3ec7d1d4c217ff3c061fcbc758acf0bc1a1e8616a18c0 build: - number: 0 # Build number, increment this when making new builds of the same version + number: 0 noarch: python script: - - {{ PYTHON }} -m pip install . -vv --no-deps # Script to run for building the package + - {{ PYTHON }} -m pip install . -vv --no-deps entry_points: - gempipe = gempipe:main run_exports: @@ -45,6 +45,9 @@ requirements: - blast >=2.12.0 - diamond >=2.0.15 - eggnog-mapper >=2.1.7 + - matplotlib-base >=3.7.0 + - seaborn >=0.13.0 + test: @@ -52,6 +55,9 @@ test: - gempipe commands: - gempipe --help + - gempipe recon --help + - gempipe derive --help + - gempipe autopilot --help about: diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml index dd588c788987b..3e73bdf53321c 100644 --- a/recipes/gencove/meta.yaml +++ b/recipes/gencove/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gencove" %} -{% set version = "2.18.3" %} -{% set sha256 = "e4762be0bc238bbe13c98daa1e4eead1a5a14d65b6651650238784adf8c093f2" %} +{% set version = "2.21.0" %} +{% set sha256 = "805be8b0c0f3e8d189bca16a805649e9594d455c0fa183ecd856ee3208287258" %} package: name: {{ name }} diff --git a/recipes/genmod/meta.yaml b/recipes/genmod/meta.yaml index 4b226e225aa97..4bf3f662ad0da 100644 --- a/recipes/genmod/meta.yaml +++ b/recipes/genmod/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genmod" %} -{% set version = "3.8.2" %} +{% set version = "3.8.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 72921cce29fd8d6b99eea76921a0a71d3846abcb92bcb02dafd24886ab9264a3 + sha256: 97a411f3f014557cf57aed9cc18e55e097ab7c54b191eb7995c10dd97d4bdeaf build: number: 0 diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index 206a6bcb905ee..b51cf838f00c0 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -10,13 +10,13 @@ source: sha256: 631599f9fea8ea8d07bdc9334e0fc328aed1274968da78f6f5854c0146022233 build: - number: 1 + number: 2 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - genomad=genomad.cli:cli run_exports: - - {{ pin_subpackage("genomad", max_pin="x") }} + - {{ pin_subpackage("genomad", max_pin=None) }} requirements: host: diff --git a/recipes/genomedata/meta.yaml b/recipes/genomedata/meta.yaml index e2eebeb0d54df..12a66928b7dc5 100644 --- a/recipes/genomedata/meta.yaml +++ b/recipes/genomedata/meta.yaml @@ -1,6 +1,6 @@ {% set name = "genomedata" %} -{% set version = "1.7.2" %} -{% set sha256 = "588efabd6a163af059e945aa6c638b9e9129ab46f27c4a35baafdbfb5f7edbbd" %} +{% set version = "1.7.3" %} +{% set sha256 = "308a2110ec14659f4a9e40d1515e5d9c95ebf808923f0cfbbe5cff4e7a8cce3c" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: build: skip: True # [osx or py < 39] - number: 2 + number: 1 entry_points: - genomedata-close-data = genomedata._close_data:main - genomedata-erase-data = genomedata._erase_data:main @@ -45,7 +45,7 @@ requirements: - hdf5 - pytables >=3.4.3 - pybigwig - - path.py + - path - textinput - bedtools - ucsc-bigwigtobedgraph >=377 diff --git a/recipes/genomepy/meta.yaml b/recipes/genomepy/meta.yaml index f82088f838ea9..be6715605d58e 100644 --- a/recipes/genomepy/meta.yaml +++ b/recipes/genomepy/meta.yaml @@ -9,7 +9,7 @@ source: sha256: c550e32fbafd67ae4ce3792356459fd6658de70ab8820a735a8a815238643be9 build: - number: 1 + number: 2 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv run_exports: @@ -30,7 +30,7 @@ requirements: - filelock >=3.5 - loguru - mygene - - mysql-connector-python + - mysql-connector-python <=8.4.0 - norns >=0.1.6 - numpy - pandas diff --git a/recipes/genomic_address_service/meta.yaml b/recipes/genomic_address_service/meta.yaml index 6eea935428e20..4e65403116784 100644 --- a/recipes/genomic_address_service/meta.yaml +++ b/recipes/genomic_address_service/meta.yaml @@ -1,6 +1,6 @@ {% set name = "genomic_address_service" %} -{% set version = "0.1.1" %} -{% set sha256 = "5aa088e063190561f09c8d5f66f54af5a2c7561e2ad24eaf41055e56331b2954" %} +{% set version = "0.1.2" %} +{% set sha256 = "c338cdca4d23730dc78725226d9ef2853b7aa63e3fc130359fab75cd2df3d34a" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage("genomic_address_service", max_pin="x.x") }} diff --git a/recipes/geofetch/meta.yaml b/recipes/geofetch/meta.yaml index bddae8d83699a..fcbc65091e017 100644 --- a/recipes/geofetch/meta.yaml +++ b/recipes/geofetch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "geofetch" %} -{% set version = "0.12.6" %} +{% set version = "0.12.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7ce07c05bad3f18b6f44b79579342604c2b56890e1dec293373b462bf06690b6 + sha256: c7820852dcb5a619a510616b0ca80f402a6a2a60f95d081ea7e174b387ec3e36 build: number: 0 diff --git a/recipes/get_homologues/meta.yaml b/recipes/get_homologues/meta.yaml index 989cdb036468d..0528198c7538b 100644 --- a/recipes/get_homologues/meta.yaml +++ b/recipes/get_homologues/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.6.3" %} -{% set sha256 = "b2f35bffae497ac764159a4786af820573c436a43ccd67b7ded8ac7e8d4a1a6f" %} +{% set version = "3.7.1" %} +{% set sha256 = "eeb9361695cafc35a1b92b29b647874713f85641218b1de5cddca551d334fe9d" %} package: name: get_homologues diff --git a/recipes/gfastats/build.sh b/recipes/gfastats/build.sh index ebc40b05e0827..541d146c1fbcd 100644 --- a/recipes/gfastats/build.sh +++ b/recipes/gfastats/build.sh @@ -1,9 +1,11 @@ #!/bin/sh +set -xe + export LIBRARY_PATH="${PREFIX}/lib:$LIBRARY_PATH" export CXXFLAGS="-g -Wall -I$PREFIX/include -O3 -I$SRC_DIR/include -I$SRC_DIR/include/zlib -std=gnu++14 -lstdc++" -make -j CXX=$CXX +make -j ${CPU_COUNT} CXX=$CXX mkdir -p $PREFIX/bin/ cp build/bin/gfastats $PREFIX/bin/ diff --git a/recipes/gfastats/meta.yaml b/recipes/gfastats/meta.yaml index e8744f927e173..a7158f50509c9 100644 --- a/recipes/gfastats/meta.yaml +++ b/recipes/gfastats/meta.yaml @@ -1,16 +1,18 @@ {% set name = "gfastats" %} -{% set version = "1.3.6" %} +{% set version = "1.3.7" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/vgl-hub/gfastats/releases/download/v{{ version }}/{{ name }}.v{{ version }}.tar.gz - sha256: 9f48bafeca028fa00aa862724857bdfe3d2d44c9509280c094d06f91ea648f66 + git_url: https://github.com/vgl-hub/gfastats.git + git_tag: v{{ version }} build: - number: 3 + number: 1 + run_exports: + - {{ pin_subpackage('gfastats', max_pin="x") }} requirements: build: @@ -30,9 +32,15 @@ about: summary: The swiss army knife for genome assembly extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - biotools:gfastats - usegalaxy-eu:gfastats container: # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly extended-base: true + skip-lints: + - uses_vcs_url + - missing_hash \ No newline at end of file diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml index 85619dbaf4cc2..f06207b8c5c82 100644 --- a/recipes/gget/meta.yaml +++ b/recipes/gget/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gget" %} -{% set version = "0.28.6" %} -{% set sha256 = "4cbc60e967a30d79878525cbae64871bf1f7c764427a689a7f55e52720b01f82" %} +{% set version = "0.29.0" %} +{% set sha256 = "5af54af941477bead501d66a0509a8bcf672ba637ef0750bb3faef79959512e3" %} package: name: "{{ name|lower }}" @@ -21,26 +21,26 @@ build: requirements: host: - - python >=3.6 + - python >=3.7 - pip - bs4 - requests >=2.22.0 - pandas >=1.0.0 - ipython - - mysql-connector-python >=8.0.5,<=8.0.29 + - mysql-connector-python >=8.0.32 - matplotlib-base - tqdm - ipywidgets - lxml - numpy >=1.17.2 run: - - python >=3.6 + - python >=3.7 - numpy >=1.17.2 - pandas >=1.0.0 - requests >=2.22.0 - ipython - matplotlib-base - - mysql-connector-python >=8.0.5,<=8.0.29 + - mysql-connector-python >=8.0.32 - bs4 >=4.10.0 - ipywidgets - tqdm @@ -60,10 +60,10 @@ test: about: home: "https://github.com/pachterlab/gget" - license: BSD-2-Clause + license: "BSD-2-Clause" license_family: BSD license_file: LICENSE - summary: "gget enables efficient querying of genomic databases" + summary: "gget enables efficient querying of genomic databases." description: | gget enables efficient querying of genomic databases, such as Ensembl, UniProt, NCBI, directly into a Python or terminal programming environment. It was @@ -75,3 +75,5 @@ extra: recipe-maintainers: - nh13 - lauraluebbert + identifiers: + - doi:10.1093/bioinformatics/btac836 diff --git a/recipes/giatools/meta.yaml b/recipes/giatools/meta.yaml index c3ef78906c776..569685efd8a6a 100644 --- a/recipes/giatools/meta.yaml +++ b/recipes/giatools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "giatools" %} -{% set version = "0.1.2" %} +{% set version = "0.3.1" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/BMCV/giatools/archive/refs/tags/{{ version }}.zip" - sha256: a16291b3f3d1868559e8a87d9656a254da9f438e0dcd178ea331b707df3d8f1f + sha256: 3c763086a656514219a9b81fbfe2c4ac1c58a91c58345d18ebd028c44e2eb080 build: number: 0 diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index 759a24c161362..511ba6f6917ca 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -1,5 +1,6 @@ #!/bin/bash -euo +export M4="${BUILD_PREFIX}/bin/m4" export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" @@ -11,7 +12,7 @@ export LC_ALL=en_US.UTF-8 if [ "$(uname)" == "Darwin" ]; then # for Mac OSX export LDFLAGS="${LDFLAGS} -headerpad_max_install_names" - export CFLAGS="${CFLAGS} -m64" + export CFLAGS="${CFLAGS} -m64 -Wno-implicit-function-declaration -Wdeprecated-non-prototype" export LC_ALL=C fi @@ -22,6 +23,9 @@ case $(uname -m) in aarch64) SIMD_LEVEL="arm" ;; + arm64) + SIMD_LEVEL="arm" + ;; *) SIMD_LEVEL="none" ;; diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index e8c298171af19..71ff7f70c033b 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2024.05.20" %} -{% set sha256 = "a3e434ace5943595be983ad213a4d05d5c86287f13ca50d938e8bcb1b17f4087" %} +{% set version = "2024.09.18" %} +{% set sha256 = "00d28c1a8c95295c8edd006cc0d1b5154cabe185de1f5a5dd8ccdb01fab38a18" %} package: name: {{ name|lower }} @@ -14,6 +14,7 @@ source: build: number: 0 + skip: True # [osx and x86_64] run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} diff --git a/recipes/gmap/single_quote_paths.patch b/recipes/gmap/single_quote_paths.patch index eb91cc0d478f1..d84b680d54a59 100644 --- a/recipes/gmap/single_quote_paths.patch +++ b/recipes/gmap/single_quote_paths.patch @@ -35,7 +35,7 @@ --- a/util/gmap_build.pl.in 2020-06-01 02:24:13.000000000 +0200 +++ b/util/gmap_build.pl.in 2020-06-18 12:50:12.031880110 +0200 -@@ -14,7 +14,7 @@ +@@ -14,7 +14,7 @@ use Getopt::Long; Getopt::Long::Configure(qw(no_auto_abbrev no_ignore_case_always)); # Default values @@ -44,15 +44,14 @@ my $sampling = 3; my $sleeptime = 2; -@@ -92,7 +92,7 @@ - print STDERR "Writing files under $user_gmapdb\n"; - $gmapdb = $user_gmapdb; +@@ -99,7 +99,7 @@ if (defined($user_genomedb)) { + print STDERR "Writing genome files under $user_genomedb\n"; + $genomedb = $user_genomedb; } else { -- $gmapdb = "@GMAPDB@"; -+ $gmapdb = '@GMAPDB@'; - print STDERR "Destination directory not defined with -D flag, so writing files under $gmapdb\n"; - } - +- $genomedb = "@GMAPDB@"; ++ $genomedb = '@GMAPDB@'; + print STDERR "Destination directory for genome not defined with -D flag, so writing files under $genomedb\n"; + } --- a/util/gmap_cat.pl.in 2020-04-22 20:17:57.000000000 +0200 diff --git a/recipes/gmwi2/meta.yaml b/recipes/gmwi2/meta.yaml index 1a93956e3f40b..f869ede61ffd9 100644 --- a/recipes/gmwi2/meta.yaml +++ b/recipes/gmwi2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gmwi2" %} -{% set version = "1.5" %} +{% set version = "1.6" %} package: name: "{{ name }}" @@ -14,7 +14,7 @@ build: source: url: https://github.com/danielchang2002/GMWI2/archive/{{version}}.tar.gz - sha256: de63741ecc88c3d13b4b259a495e938d9b026950e9ff100b6e465f8e0c38a419 + sha256: 0751b5030a8ce51cea924393872ff128d4c76444b980bc41b23b83a310c125b0 requirements: host: @@ -37,7 +37,6 @@ test: commands: - metaphlan --version - gmwi2 --version - - repair.sh --version - fastqc --version - bowtie2 --version - samtools --version diff --git a/recipes/gofasta/meta.yaml b/recipes/gofasta/meta.yaml index 64a8626a53d44..0064cbdb824bc 100644 --- a/recipes/gofasta/meta.yaml +++ b/recipes/gofasta/meta.yaml @@ -13,7 +13,7 @@ requirements: - {{ compiler('go-nocgo') }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('gofasta', max_pin="x") }} script: @@ -32,4 +32,5 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 + - osx-arm64 diff --git a/recipes/graphbin/meta.yaml b/recipes/graphbin/meta.yaml index 38193911b89b9..9f7a0c6dd5008 100644 --- a/recipes/graphbin/meta.yaml +++ b/recipes/graphbin/meta.yaml @@ -1,28 +1,32 @@ {% set name = "GraphBin" %} -{% set version = "1.7.1" %} +{% set version = "1.7.4" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://github.com/metagentools/{{ name }}/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz" - sha256: 605de80cd132c349ffd0dffbece4cd265f120df19d9258a79cfea1e73276fa6c + url: "https://github.com/metagentools/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" + sha256: b1c7080aa61535fb3112e4fe3aae186b346a0074eec6e93650564a3b349cc69c build: number: 0 noarch: python + entry_points: + - graphbin = graphbin.cli:main script: - - "{{ PYTHON }} -m pip install . -vv" + - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('graphbin', max_pin="x") }} requirements: host: - pip - - python + - python >=3.7,<3.11 - flit-core run: - cairocffi - - python >=3.7.1,<3.11 + - python >=3.7,<3.11 - python-igraph - tqdm - click @@ -35,6 +39,7 @@ test: about: home: "https://github.com/Vini2/GraphBin" license: BSD-3 + license_family: BSD license_file: LICENSE summary: "GraphBin: Refined binning of metagenomic contigs using assembly graphs" description: | diff --git a/recipes/graphbin2/meta.yaml b/recipes/graphbin2/meta.yaml index e1976a97ce5e1..e1f542ba39620 100644 --- a/recipes/graphbin2/meta.yaml +++ b/recipes/graphbin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "GraphBin2" %} -{% set version = "1.3.1" %} +{% set version = "1.3.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/metagentools/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 4086cc93980a4c964da2b9d0ae84eaf3aa4a6b9c01aa23b2c2d965bf85cef5f2 + sha256: 03ab89dbb6d26c9b414ff808598c295cf22fd3af22816a5c9fada94104a79686 build: number: 0 diff --git a/recipes/graphmap/build.sh b/recipes/graphmap/build.sh index 84d5270b03c2f..8d0b68e45a2ef 100644 --- a/recipes/graphmap/build.sh +++ b/recipes/graphmap/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + export CPP_INCLUDE_PATH=${PREFIX}/include export CPLUS_INCLUDE_PATH=${PREFIX}/include export CXX_INCLUDE_PATH=${PREFIX}/include @@ -10,10 +12,10 @@ mkdir -p $PREFIX/bin make modules if [ "$(uname)" == "Darwin" ]; then echo "Installing GraphMap for OSX." - make mac GCC=$CXX GCC_MAC=$CXX + make -j ${CPU_COUNT} mac GCC=$CXX GCC_MAC=$CXX cp bin/Mac/graphmap $PREFIX/bin/graphmap2 else echo "Installing GraphMap for UNIX/Linux." - make GCC=$CXX LD_FLAGS="$LDFLAGS -static-libgcc -static-libstdc++ -m64 -ffreestanding" + make -j ${CPU_COUNT} GCC=$CXX LD_FLAGS="$LDFLAGS -static-libgcc -static-libstdc++ -ffreestanding" cp bin/Linux-x64/graphmap2 $PREFIX/bin fi diff --git a/recipes/graphmap/graphmap2-aarch64.patch b/recipes/graphmap/graphmap2-aarch64.patch new file mode 100644 index 0000000000000..48899e5c02618 --- /dev/null +++ b/recipes/graphmap/graphmap2-aarch64.patch @@ -0,0 +1,9034 @@ +diff --git c/Makefile i/Makefile +index b709f1c..ac14179 100755 +--- c/Makefile ++++ i/Makefile +@@ -44,12 +44,12 @@ CC_LIBS = -static-libgcc -static-libstdc++ -D__cplusplus=201103L + # INCLUDE = -I"./src/" -I"/usr/include/" -I"src/libs/seqan-library-1.4.2/include" + INCLUDE = -I"./src/" -I"/usr/include/" -I"$(CODEBASE)/seqlib/src/libs/seqan-library-2.0.1/include" -I"$(CODEBASE)/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" $(CODEBASE_SRC_FOLDERS) + +-CC_FLAGS_DEBUG = -O3 -g -rdynamic -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native +-CC_FLAGS_RELEASE = -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread # -march=native +-CC_FLAGS_EXTCIGAR = -DRELEASE_VERSION -DUSE_EXTENDED_CIGAR_FORMAT -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native +-CC_FLAGS_NOT_RELEASE = -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native +-CC_FLAGS_NOT_RELEASE_EXT = -g -O3 -DUSE_EXTENDED_CIGAR_FORMAT -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native +-LD_FLAGS = -static-libgcc -static-libstdc++ -m64 -ffreestanding ++CC_FLAGS_DEBUG = -O3 -g -rdynamic -c -fmessage-length=0 -ffreestanding -fopenmp -std=c++11 -Werror=return-type -pthread -march=native ++CC_FLAGS_RELEASE = -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -std=c++11 -Werror=return-type -pthread # -march=native ++CC_FLAGS_EXTCIGAR = -DRELEASE_VERSION -DUSE_EXTENDED_CIGAR_FORMAT -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -std=c++11 -Werror=return-type -pthread -march=native ++CC_FLAGS_NOT_RELEASE = -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native ++CC_FLAGS_NOT_RELEASE_EXT = -g -O3 -DUSE_EXTENDED_CIGAR_FORMAT -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native ++LD_FLAGS = -static-libgcc -static-libstdc++ -ffreestanding + # LD_LIBS = -lpthread -lgomp -lm -lz -ldivsufsort64 + LD_LIBS = -lpthread -lgomp -lm -lz + +diff --git c/src/ksw2/ksw2_extd2_sse.cc i/src/ksw2/ksw2_extd2_sse.cc +index 56cd8cd..85da803 100644 +--- c/src/ksw2/ksw2_extd2_sse.cc ++++ i/src/ksw2/ksw2_extd2_sse.cc +@@ -3,13 +3,25 @@ + #include + #include "ksw2.h" + +-#ifdef __SSE2__ +-#include ++#ifdef __x86_64__ ++ #ifdef __SSE2__ ++ #include ++ #define KSW_EXTD2_SSE_SUPPORTED 1 ++ #endif // __SSE2__ + +-#ifdef __SSE4_1__ +-#include +-#endif ++ #ifdef __SSE4_1__ ++ #include ++ #endif ++#else ++ #define SSE2NEON_PRECISE_MINMAX 1 ++ #define SSE2NEON_PRECISE_DIV 1 ++ #define SSE2NEON_PRECISE_SQRT 1 ++ #define SSE2NEON_PRECISE_DP 1 ++ #include "sse2neon.h" ++ #define KSW_EXTD2_SSE_SUPPORTED 1 ++#endif //__x86_64__ + ++#ifdef KSW_EXTD2_SSE_SUPPORTED + void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, + int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int flag, ksw_extz_t *ez) + { +@@ -371,4 +383,4 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin + kfree(km, mem2); kfree(km, off); + } + } +-#endif // __SSE2__ ++#endif // KSW_EXTD2_SSE_SUPPORTED +diff --git c/src/ksw2/ksw2_exts2_sse.cc i/src/ksw2/ksw2_exts2_sse.cc +index 6decd2d..3191355 100644 +--- c/src/ksw2/ksw2_exts2_sse.cc ++++ i/src/ksw2/ksw2_exts2_sse.cc +@@ -3,13 +3,25 @@ + #include + #include "ksw2.h" + +-#ifdef __SSE2__ +-#include ++#ifdef __x86_64__ ++ #ifdef __SSE2__ ++ #include ++ #define KSW_EXTS2_SSE_SUPPORTED 1 ++ #endif // __SSE2__ + +-#ifdef __SSE4_1__ +-#include +-#endif ++ #ifdef __SSE4_1__ ++ #include ++ #endif ++#else ++ #define SSE2NEON_PRECISE_MINMAX 1 ++ #define SSE2NEON_PRECISE_DIV 1 ++ #define SSE2NEON_PRECISE_SQRT 1 ++ #define SSE2NEON_PRECISE_DP 1 ++ #include "sse2neon.h" ++ #define KSW_EXTS2_SSE_SUPPORTED 1 ++#endif //__x86_64__ + ++#ifdef KSW_EXTS2_SSE_SUPPORTED + void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, + int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez) + { +@@ -354,4 +366,4 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin + kfree(km, mem2); kfree(km, off); + } + } +-#endif // __SSE2__ ++#endif // KSW_EXTS2_SSE_SUPPORTED +diff --git c/src/ksw2/ksw2_extz2_sse.cc i/src/ksw2/ksw2_extz2_sse.cc +index f21f184..6df4b64 100644 +--- c/src/ksw2/ksw2_extz2_sse.cc ++++ i/src/ksw2/ksw2_extz2_sse.cc +@@ -2,13 +2,26 @@ + #include + #include "ksw2.h" + +-#ifdef __SSE2__ +-#include + +-#ifdef __SSE4_1__ +-#include +-#endif ++#ifdef __x86_64__ ++ #ifdef __SSE2__ ++ #include ++ #define KSW_EXTZ2_SSE_SUPPORTED 1 ++ #endif // __SSE2__ ++ ++ #ifdef __SSE4_1__ ++ #include ++ #endif ++#else ++ #define SSE2NEON_PRECISE_MINMAX 1 ++ #define SSE2NEON_PRECISE_DIV 1 ++ #define SSE2NEON_PRECISE_SQRT 1 ++ #define SSE2NEON_PRECISE_DP 1 ++ #include "sse2neon.h" ++ #define KSW_EXTZ2_SSE_SUPPORTED 1 ++#endif //__x86_64__ + ++#ifdef KSW_EXTZ2_SSE_SUPPORTED + void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez) + { + #define __dp_code_block1 \ +@@ -284,4 +297,4 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin + kfree(km, mem2); kfree(km, off); + } + } +-#endif // __SSE2__ ++#endif // KSW_EXTZ2_SSE_SUPPORTED +diff --git c/src/ksw2/ksw2_ll_sse.cc i/src/ksw2/ksw2_ll_sse.cc +index 6e13049..e2d49bf 100644 +--- c/src/ksw2/ksw2_ll_sse.cc ++++ i/src/ksw2/ksw2_ll_sse.cc +@@ -1,16 +1,26 @@ + #include + #include + #include +-#include + #include "ksw2.h" + ++#ifdef __x86_64__ ++ #include ++ ++#else ++ #define SSE2NEON_PRECISE_MINMAX 1 ++ #define SSE2NEON_PRECISE_DIV 1 ++ #define SSE2NEON_PRECISE_SQRT 1 ++ #define SSE2NEON_PRECISE_DP 1 ++ #include "sse2neon.h" ++#endif //__x86_64__ ++ + #ifdef __GNUC__ + #define LIKELY(x) __builtin_expect((x),1) + #define UNLIKELY(x) __builtin_expect((x),0) + #else + #define LIKELY(x) (x) + #define UNLIKELY(x) (x) +-#endif ++#endif // __GNUC__ + + typedef struct { + int qlen, slen; +diff --git c/src/sse2neon.h i/src/sse2neon.h +new file mode 100644 +index 0000000..44d26af +--- /dev/null ++++ i/src/sse2neon.h +@@ -0,0 +1,8848 @@ ++#ifndef SSE2NEON_H ++#define SSE2NEON_H ++ ++// This header file provides a simple API translation layer ++// between SSE intrinsics to their corresponding Arm/Aarch64 NEON versions ++// ++// This header file does not yet translate all of the SSE intrinsics. ++// ++// Contributors to this work are: ++// John W. Ratcliff ++// Brandon Rowlett ++// Ken Fast ++// Eric van Beurden ++// Alexander Potylitsin ++// Hasindu Gamaarachchi ++// Jim Huang ++// Mark Cheng ++// Malcolm James MacLeod ++// Devin Hussey (easyaspi314) ++// Sebastian Pop ++// Developer Ecosystem Engineering ++// Danila Kutenin ++// François Turban (JishinMaster) ++// Pei-Hsuan Hung ++// Yang-Hao Yuan ++// Syoyo Fujita ++// Brecht Van Lommel ++ ++/* ++ * sse2neon is freely redistributable under the MIT License. ++ * ++ * Permission is hereby granted, free of charge, to any person obtaining a copy ++ * of this software and associated documentation files (the "Software"), to deal ++ * in the Software without restriction, including without limitation the rights ++ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell ++ * copies of the Software, and to permit persons to whom the Software is ++ * furnished to do so, subject to the following conditions: ++ * ++ * The above copyright notice and this permission notice shall be included in ++ * all copies or substantial portions of the Software. ++ * ++ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR ++ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, ++ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE ++ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER ++ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, ++ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE ++ * SOFTWARE. ++ */ ++ ++/* Tunable configurations */ ++ ++/* Enable precise implementation of math operations ++ * This would slow down the computation a bit, but gives consistent result with ++ * x86 SSE. (e.g. would solve a hole or NaN pixel in the rendering result) ++ */ ++/* _mm_min|max_ps|ss|pd|sd */ ++#ifndef SSE2NEON_PRECISE_MINMAX ++#define SSE2NEON_PRECISE_MINMAX (0) ++#endif ++/* _mm_rcp_ps and _mm_div_ps */ ++#ifndef SSE2NEON_PRECISE_DIV ++#define SSE2NEON_PRECISE_DIV (0) ++#endif ++/* _mm_sqrt_ps and _mm_rsqrt_ps */ ++#ifndef SSE2NEON_PRECISE_SQRT ++#define SSE2NEON_PRECISE_SQRT (0) ++#endif ++/* _mm_dp_pd */ ++#ifndef SSE2NEON_PRECISE_DP ++#define SSE2NEON_PRECISE_DP (0) ++#endif ++ ++/* compiler specific definitions */ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma push_macro("FORCE_INLINE") ++#pragma push_macro("ALIGN_STRUCT") ++#define FORCE_INLINE static inline __attribute__((always_inline)) ++#define ALIGN_STRUCT(x) __attribute__((aligned(x))) ++#define _sse2neon_likely(x) __builtin_expect(!!(x), 1) ++#define _sse2neon_unlikely(x) __builtin_expect(!!(x), 0) ++#else /* non-GNU / non-clang compilers */ ++#warning "Macro name collisions may happen with unsupported compiler." ++#ifndef FORCE_INLINE ++#define FORCE_INLINE static inline ++#endif ++#ifndef ALIGN_STRUCT ++#define ALIGN_STRUCT(x) __declspec(align(x)) ++#endif ++#define _sse2neon_likely(x) (x) ++#define _sse2neon_unlikely(x) (x) ++#endif ++ ++/* C language does not allow initializing a variable with a function call. */ ++#ifdef __cplusplus ++#define _sse2neon_const static const ++#else ++#define _sse2neon_const const ++#endif ++ ++#include ++#include ++ ++/* Architecture-specific build options */ ++/* FIXME: #pragma GCC push_options is only available on GCC */ ++#if defined(__GNUC__) ++#if defined(__arm__) && __ARM_ARCH == 7 ++/* According to ARM C Language Extensions Architecture specification, ++ * __ARM_NEON is defined to a value indicating the Advanced SIMD (NEON) ++ * architecture supported. ++ */ ++#if !defined(__ARM_NEON) || !defined(__ARM_NEON__) ++#error "You must enable NEON instructions (e.g. -mfpu=neon) to use SSE2NEON." ++#endif ++#if !defined(__clang__) ++#pragma GCC push_options ++#pragma GCC target("fpu=neon") ++#endif ++#elif defined(__aarch64__) ++#if !defined(__clang__) ++#pragma GCC push_options ++#pragma GCC target("+simd") ++#endif ++#elif __ARM_ARCH == 8 ++#if !defined(__ARM_NEON) || !defined(__ARM_NEON__) ++#error \ ++ "You must enable NEON instructions (e.g. -mfpu=neon-fp-armv8) to use SSE2NEON." ++#endif ++#if !defined(__clang__) ++#pragma GCC push_options ++#endif ++#else ++#error "Unsupported target. Must be either ARMv7-A+NEON or ARMv8-A." ++#endif ++#endif ++ ++#include ++#if !defined(__aarch64__) && (__ARM_ARCH == 8) ++#if defined __has_include && __has_include() ++#include ++#endif ++#endif ++ ++/* Rounding functions require either Aarch64 instructions or libm failback */ ++#if !defined(__aarch64__) ++#include ++#endif ++ ++/* On ARMv7, some registers, such as PMUSERENR and PMCCNTR, are read-only ++ * or even not accessible in user mode. ++ * To write or access to these registers in user mode, ++ * we have to perform syscall instead. ++ */ ++#if !defined(__aarch64__) ++#include ++#endif ++ ++/* "__has_builtin" can be used to query support for built-in functions ++ * provided by gcc/clang and other compilers that support it. ++ */ ++#ifndef __has_builtin /* GCC prior to 10 or non-clang compilers */ ++/* Compatibility with gcc <= 9 */ ++#if defined(__GNUC__) && (__GNUC__ <= 9) ++#define __has_builtin(x) HAS##x ++#define HAS__builtin_popcount 1 ++#define HAS__builtin_popcountll 1 ++#else ++#define __has_builtin(x) 0 ++#endif ++#endif ++ ++/** ++ * MACRO for shuffle parameter for _mm_shuffle_ps(). ++ * Argument fp3 is a digit[0123] that represents the fp from argument "b" ++ * of mm_shuffle_ps that will be placed in fp3 of result. fp2 is the same ++ * for fp2 in result. fp1 is a digit[0123] that represents the fp from ++ * argument "a" of mm_shuffle_ps that will be places in fp1 of result. ++ * fp0 is the same for fp0 of result. ++ */ ++#define _MM_SHUFFLE(fp3, fp2, fp1, fp0) \ ++ (((fp3) << 6) | ((fp2) << 4) | ((fp1) << 2) | ((fp0))) ++ ++/* Rounding mode macros. */ ++#define _MM_FROUND_TO_NEAREST_INT 0x00 ++#define _MM_FROUND_TO_NEG_INF 0x01 ++#define _MM_FROUND_TO_POS_INF 0x02 ++#define _MM_FROUND_TO_ZERO 0x03 ++#define _MM_FROUND_CUR_DIRECTION 0x04 ++#define _MM_FROUND_NO_EXC 0x08 ++#define _MM_FROUND_RAISE_EXC 0x00 ++#define _MM_FROUND_NINT (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_FLOOR (_MM_FROUND_TO_NEG_INF | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_CEIL (_MM_FROUND_TO_POS_INF | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_TRUNC (_MM_FROUND_TO_ZERO | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_RINT (_MM_FROUND_CUR_DIRECTION | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_NEARBYINT (_MM_FROUND_CUR_DIRECTION | _MM_FROUND_NO_EXC) ++#define _MM_ROUND_NEAREST 0x0000 ++#define _MM_ROUND_DOWN 0x2000 ++#define _MM_ROUND_UP 0x4000 ++#define _MM_ROUND_TOWARD_ZERO 0x6000 ++/* Flush zero mode macros. */ ++#define _MM_FLUSH_ZERO_MASK 0x8000 ++#define _MM_FLUSH_ZERO_ON 0x8000 ++#define _MM_FLUSH_ZERO_OFF 0x0000 ++/* Denormals are zeros mode macros. */ ++#define _MM_DENORMALS_ZERO_MASK 0x0040 ++#define _MM_DENORMALS_ZERO_ON 0x0040 ++#define _MM_DENORMALS_ZERO_OFF 0x0000 ++ ++/* indicate immediate constant argument in a given range */ ++#define __constrange(a, b) const ++ ++/* A few intrinsics accept traditional data types like ints or floats, but ++ * most operate on data types that are specific to SSE. ++ * If a vector type ends in d, it contains doubles, and if it does not have ++ * a suffix, it contains floats. An integer vector type can contain any type ++ * of integer, from chars to shorts to unsigned long longs. ++ */ ++typedef int64x1_t __m64; ++typedef float32x4_t __m128; /* 128-bit vector containing 4 floats */ ++// On ARM 32-bit architecture, the float64x2_t is not supported. ++// The data type __m128d should be represented in a different way for related ++// intrinsic conversion. ++#if defined(__aarch64__) ++typedef float64x2_t __m128d; /* 128-bit vector containing 2 doubles */ ++#else ++typedef float32x4_t __m128d; ++#endif ++typedef int64x2_t __m128i; /* 128-bit vector containing integers */ ++ ++// __int64 is defined in the Intrinsics Guide which maps to different datatype ++// in different data model ++#if !(defined(_WIN32) || defined(_WIN64) || defined(__int64)) ++#if (defined(__x86_64__) || defined(__i386__)) ++#define __int64 long long ++#else ++#define __int64 int64_t ++#endif ++#endif ++ ++/* type-safe casting between types */ ++ ++#define vreinterpretq_m128_f16(x) vreinterpretq_f32_f16(x) ++#define vreinterpretq_m128_f32(x) (x) ++#define vreinterpretq_m128_f64(x) vreinterpretq_f32_f64(x) ++ ++#define vreinterpretq_m128_u8(x) vreinterpretq_f32_u8(x) ++#define vreinterpretq_m128_u16(x) vreinterpretq_f32_u16(x) ++#define vreinterpretq_m128_u32(x) vreinterpretq_f32_u32(x) ++#define vreinterpretq_m128_u64(x) vreinterpretq_f32_u64(x) ++ ++#define vreinterpretq_m128_s8(x) vreinterpretq_f32_s8(x) ++#define vreinterpretq_m128_s16(x) vreinterpretq_f32_s16(x) ++#define vreinterpretq_m128_s32(x) vreinterpretq_f32_s32(x) ++#define vreinterpretq_m128_s64(x) vreinterpretq_f32_s64(x) ++ ++#define vreinterpretq_f16_m128(x) vreinterpretq_f16_f32(x) ++#define vreinterpretq_f32_m128(x) (x) ++#define vreinterpretq_f64_m128(x) vreinterpretq_f64_f32(x) ++ ++#define vreinterpretq_u8_m128(x) vreinterpretq_u8_f32(x) ++#define vreinterpretq_u16_m128(x) vreinterpretq_u16_f32(x) ++#define vreinterpretq_u32_m128(x) vreinterpretq_u32_f32(x) ++#define vreinterpretq_u64_m128(x) vreinterpretq_u64_f32(x) ++ ++#define vreinterpretq_s8_m128(x) vreinterpretq_s8_f32(x) ++#define vreinterpretq_s16_m128(x) vreinterpretq_s16_f32(x) ++#define vreinterpretq_s32_m128(x) vreinterpretq_s32_f32(x) ++#define vreinterpretq_s64_m128(x) vreinterpretq_s64_f32(x) ++ ++#define vreinterpretq_m128i_s8(x) vreinterpretq_s64_s8(x) ++#define vreinterpretq_m128i_s16(x) vreinterpretq_s64_s16(x) ++#define vreinterpretq_m128i_s32(x) vreinterpretq_s64_s32(x) ++#define vreinterpretq_m128i_s64(x) (x) ++ ++#define vreinterpretq_m128i_u8(x) vreinterpretq_s64_u8(x) ++#define vreinterpretq_m128i_u16(x) vreinterpretq_s64_u16(x) ++#define vreinterpretq_m128i_u32(x) vreinterpretq_s64_u32(x) ++#define vreinterpretq_m128i_u64(x) vreinterpretq_s64_u64(x) ++ ++#define vreinterpretq_f32_m128i(x) vreinterpretq_f32_s64(x) ++#define vreinterpretq_f64_m128i(x) vreinterpretq_f64_s64(x) ++ ++#define vreinterpretq_s8_m128i(x) vreinterpretq_s8_s64(x) ++#define vreinterpretq_s16_m128i(x) vreinterpretq_s16_s64(x) ++#define vreinterpretq_s32_m128i(x) vreinterpretq_s32_s64(x) ++#define vreinterpretq_s64_m128i(x) (x) ++ ++#define vreinterpretq_u8_m128i(x) vreinterpretq_u8_s64(x) ++#define vreinterpretq_u16_m128i(x) vreinterpretq_u16_s64(x) ++#define vreinterpretq_u32_m128i(x) vreinterpretq_u32_s64(x) ++#define vreinterpretq_u64_m128i(x) vreinterpretq_u64_s64(x) ++ ++#define vreinterpret_m64_s8(x) vreinterpret_s64_s8(x) ++#define vreinterpret_m64_s16(x) vreinterpret_s64_s16(x) ++#define vreinterpret_m64_s32(x) vreinterpret_s64_s32(x) ++#define vreinterpret_m64_s64(x) (x) ++ ++#define vreinterpret_m64_u8(x) vreinterpret_s64_u8(x) ++#define vreinterpret_m64_u16(x) vreinterpret_s64_u16(x) ++#define vreinterpret_m64_u32(x) vreinterpret_s64_u32(x) ++#define vreinterpret_m64_u64(x) vreinterpret_s64_u64(x) ++ ++#define vreinterpret_m64_f16(x) vreinterpret_s64_f16(x) ++#define vreinterpret_m64_f32(x) vreinterpret_s64_f32(x) ++#define vreinterpret_m64_f64(x) vreinterpret_s64_f64(x) ++ ++#define vreinterpret_u8_m64(x) vreinterpret_u8_s64(x) ++#define vreinterpret_u16_m64(x) vreinterpret_u16_s64(x) ++#define vreinterpret_u32_m64(x) vreinterpret_u32_s64(x) ++#define vreinterpret_u64_m64(x) vreinterpret_u64_s64(x) ++ ++#define vreinterpret_s8_m64(x) vreinterpret_s8_s64(x) ++#define vreinterpret_s16_m64(x) vreinterpret_s16_s64(x) ++#define vreinterpret_s32_m64(x) vreinterpret_s32_s64(x) ++#define vreinterpret_s64_m64(x) (x) ++ ++#define vreinterpret_f32_m64(x) vreinterpret_f32_s64(x) ++ ++#if defined(__aarch64__) ++#define vreinterpretq_m128d_s32(x) vreinterpretq_f64_s32(x) ++#define vreinterpretq_m128d_s64(x) vreinterpretq_f64_s64(x) ++ ++#define vreinterpretq_m128d_u64(x) vreinterpretq_f64_u64(x) ++ ++#define vreinterpretq_m128d_f32(x) vreinterpretq_f64_f32(x) ++#define vreinterpretq_m128d_f64(x) (x) ++ ++#define vreinterpretq_s64_m128d(x) vreinterpretq_s64_f64(x) ++ ++#define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f64(x) ++#define vreinterpretq_u64_m128d(x) vreinterpretq_u64_f64(x) ++ ++#define vreinterpretq_f64_m128d(x) (x) ++#define vreinterpretq_f32_m128d(x) vreinterpretq_f32_f64(x) ++#else ++#define vreinterpretq_m128d_s32(x) vreinterpretq_f32_s32(x) ++#define vreinterpretq_m128d_s64(x) vreinterpretq_f32_s64(x) ++ ++#define vreinterpretq_m128d_u32(x) vreinterpretq_f32_u32(x) ++#define vreinterpretq_m128d_u64(x) vreinterpretq_f32_u64(x) ++ ++#define vreinterpretq_m128d_f32(x) (x) ++ ++#define vreinterpretq_s64_m128d(x) vreinterpretq_s64_f32(x) ++ ++#define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f32(x) ++#define vreinterpretq_u64_m128d(x) vreinterpretq_u64_f32(x) ++ ++#define vreinterpretq_f32_m128d(x) (x) ++#endif ++ ++// A struct is defined in this header file called 'SIMDVec' which can be used ++// by applications which attempt to access the contents of an __m128 struct ++// directly. It is important to note that accessing the __m128 struct directly ++// is bad coding practice by Microsoft: @see: ++// https://docs.microsoft.com/en-us/cpp/cpp/m128 ++// ++// However, some legacy source code may try to access the contents of an __m128 ++// struct directly so the developer can use the SIMDVec as an alias for it. Any ++// casting must be done manually by the developer, as you cannot cast or ++// otherwise alias the base NEON data type for intrinsic operations. ++// ++// union intended to allow direct access to an __m128 variable using the names ++// that the MSVC compiler provides. This union should really only be used when ++// trying to access the members of the vector as integer values. GCC/clang ++// allow native access to the float members through a simple array access ++// operator (in C since 4.6, in C++ since 4.8). ++// ++// Ideally direct accesses to SIMD vectors should not be used since it can cause ++// a performance hit. If it really is needed however, the original __m128 ++// variable can be aliased with a pointer to this union and used to access ++// individual components. The use of this union should be hidden behind a macro ++// that is used throughout the codebase to access the members instead of always ++// declaring this type of variable. ++typedef union ALIGN_STRUCT(16) SIMDVec { ++ float m128_f32[4]; // as floats - DON'T USE. Added for convenience. ++ int8_t m128_i8[16]; // as signed 8-bit integers. ++ int16_t m128_i16[8]; // as signed 16-bit integers. ++ int32_t m128_i32[4]; // as signed 32-bit integers. ++ int64_t m128_i64[2]; // as signed 64-bit integers. ++ uint8_t m128_u8[16]; // as unsigned 8-bit integers. ++ uint16_t m128_u16[8]; // as unsigned 16-bit integers. ++ uint32_t m128_u32[4]; // as unsigned 32-bit integers. ++ uint64_t m128_u64[2]; // as unsigned 64-bit integers. ++} SIMDVec; ++ ++// casting using SIMDVec ++#define vreinterpretq_nth_u64_m128i(x, n) (((SIMDVec *) &x)->m128_u64[n]) ++#define vreinterpretq_nth_u32_m128i(x, n) (((SIMDVec *) &x)->m128_u32[n]) ++#define vreinterpretq_nth_u8_m128i(x, n) (((SIMDVec *) &x)->m128_u8[n]) ++ ++/* SSE macros */ ++#define _MM_GET_FLUSH_ZERO_MODE _sse2neon_mm_get_flush_zero_mode ++#define _MM_SET_FLUSH_ZERO_MODE _sse2neon_mm_set_flush_zero_mode ++#define _MM_GET_DENORMALS_ZERO_MODE _sse2neon_mm_get_denormals_zero_mode ++#define _MM_SET_DENORMALS_ZERO_MODE _sse2neon_mm_set_denormals_zero_mode ++ ++// Function declaration ++// SSE ++FORCE_INLINE unsigned int _MM_GET_ROUNDING_MODE(); ++FORCE_INLINE __m128 _mm_move_ss(__m128, __m128); ++FORCE_INLINE __m128 _mm_or_ps(__m128, __m128); ++FORCE_INLINE __m128 _mm_set_ps1(float); ++FORCE_INLINE __m128 _mm_setzero_ps(void); ++// SSE2 ++FORCE_INLINE __m128i _mm_and_si128(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_castps_si128(__m128); ++FORCE_INLINE __m128i _mm_cmpeq_epi32(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_cvtps_epi32(__m128); ++FORCE_INLINE __m128d _mm_move_sd(__m128d, __m128d); ++FORCE_INLINE __m128i _mm_or_si128(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_set_epi32(int, int, int, int); ++FORCE_INLINE __m128i _mm_set_epi64x(int64_t, int64_t); ++FORCE_INLINE __m128d _mm_set_pd(double, double); ++FORCE_INLINE __m128i _mm_set1_epi32(int); ++FORCE_INLINE __m128i _mm_setzero_si128(); ++// SSE4.1 ++FORCE_INLINE __m128d _mm_ceil_pd(__m128d); ++FORCE_INLINE __m128 _mm_ceil_ps(__m128); ++FORCE_INLINE __m128d _mm_floor_pd(__m128d); ++FORCE_INLINE __m128 _mm_floor_ps(__m128); ++FORCE_INLINE __m128d _mm_round_pd(__m128d, int); ++FORCE_INLINE __m128 _mm_round_ps(__m128, int); ++// SSE4.2 ++FORCE_INLINE uint32_t _mm_crc32_u8(uint32_t, uint8_t); ++ ++/* Backwards compatibility for compilers with lack of specific type support */ ++ ++// Older gcc does not define vld1q_u8_x4 type ++#if defined(__GNUC__) && !defined(__clang__) && \ ++ ((__GNUC__ <= 11 && defined(__arm__)) || \ ++ (__GNUC__ == 10 && __GNUC_MINOR__ < 3 && defined(__aarch64__)) || \ ++ (__GNUC__ <= 9 && defined(__aarch64__))) ++FORCE_INLINE uint8x16x4_t _sse2neon_vld1q_u8_x4(const uint8_t *p) ++{ ++ uint8x16x4_t ret; ++ ret.val[0] = vld1q_u8(p + 0); ++ ret.val[1] = vld1q_u8(p + 16); ++ ret.val[2] = vld1q_u8(p + 32); ++ ret.val[3] = vld1q_u8(p + 48); ++ return ret; ++} ++#else ++// Wraps vld1q_u8_x4 ++FORCE_INLINE uint8x16x4_t _sse2neon_vld1q_u8_x4(const uint8_t *p) ++{ ++ return vld1q_u8_x4(p); ++} ++#endif ++ ++/* Function Naming Conventions ++ * The naming convention of SSE intrinsics is straightforward. A generic SSE ++ * intrinsic function is given as follows: ++ * _mm__ ++ * ++ * The parts of this format are given as follows: ++ * 1. describes the operation performed by the intrinsic ++ * 2. identifies the data type of the function's primary arguments ++ * ++ * This last part, , is a little complicated. It identifies the ++ * content of the input values, and can be set to any of the following values: ++ * + ps - vectors contain floats (ps stands for packed single-precision) ++ * + pd - vectors cantain doubles (pd stands for packed double-precision) ++ * + epi8/epi16/epi32/epi64 - vectors contain 8-bit/16-bit/32-bit/64-bit ++ * signed integers ++ * + epu8/epu16/epu32/epu64 - vectors contain 8-bit/16-bit/32-bit/64-bit ++ * unsigned integers ++ * + si128 - unspecified 128-bit vector or 256-bit vector ++ * + m128/m128i/m128d - identifies input vector types when they are different ++ * than the type of the returned vector ++ * ++ * For example, _mm_setzero_ps. The _mm implies that the function returns ++ * a 128-bit vector. The _ps at the end implies that the argument vectors ++ * contain floats. ++ * ++ * A complete example: Byte Shuffle - pshufb (_mm_shuffle_epi8) ++ * // Set packed 16-bit integers. 128 bits, 8 short, per 16 bits ++ * __m128i v_in = _mm_setr_epi16(1, 2, 3, 4, 5, 6, 7, 8); ++ * // Set packed 8-bit integers ++ * // 128 bits, 16 chars, per 8 bits ++ * __m128i v_perm = _mm_setr_epi8(1, 0, 2, 3, 8, 9, 10, 11, ++ * 4, 5, 12, 13, 6, 7, 14, 15); ++ * // Shuffle packed 8-bit integers ++ * __m128i v_out = _mm_shuffle_epi8(v_in, v_perm); // pshufb ++ * ++ * Data (Number, Binary, Byte Index): ++ +------+------+-------------+------+------+-------------+ ++ | 1 | 2 | 3 | 4 | Number ++ +------+------+------+------+------+------+------+------+ ++ | 0000 | 0001 | 0000 | 0010 | 0000 | 0011 | 0000 | 0100 | Binary ++ +------+------+------+------+------+------+------+------+ ++ | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | Index ++ +------+------+------+------+------+------+------+------+ ++ ++ +------+------+------+------+------+------+------+------+ ++ | 5 | 6 | 7 | 8 | Number ++ +------+------+------+------+------+------+------+------+ ++ | 0000 | 0101 | 0000 | 0110 | 0000 | 0111 | 0000 | 1000 | Binary ++ +------+------+------+------+------+------+------+------+ ++ | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | Index ++ +------+------+------+------+------+------+------+------+ ++ * Index (Byte Index): ++ +------+------+------+------+------+------+------+------+ ++ | 1 | 0 | 2 | 3 | 8 | 9 | 10 | 11 | ++ +------+------+------+------+------+------+------+------+ ++ ++ +------+------+------+------+------+------+------+------+ ++ | 4 | 5 | 12 | 13 | 6 | 7 | 14 | 15 | ++ +------+------+------+------+------+------+------+------+ ++ * Result: ++ +------+------+------+------+------+------+------+------+ ++ | 1 | 0 | 2 | 3 | 8 | 9 | 10 | 11 | Index ++ +------+------+------+------+------+------+------+------+ ++ | 0001 | 0000 | 0000 | 0010 | 0000 | 0101 | 0000 | 0110 | Binary ++ +------+------+------+------+------+------+------+------+ ++ | 256 | 2 | 5 | 6 | Number ++ +------+------+------+------+------+------+------+------+ ++ ++ +------+------+------+------+------+------+------+------+ ++ | 4 | 5 | 12 | 13 | 6 | 7 | 14 | 15 | Index ++ +------+------+------+------+------+------+------+------+ ++ | 0000 | 0011 | 0000 | 0111 | 0000 | 0100 | 0000 | 1000 | Binary ++ +------+------+------+------+------+------+------+------+ ++ | 3 | 7 | 4 | 8 | Number ++ +------+------+------+------+------+------+-------------+ ++ */ ++ ++/* Constants for use with _mm_prefetch. */ ++enum _mm_hint { ++ _MM_HINT_NTA = 0, /* load data to L1 and L2 cache, mark it as NTA */ ++ _MM_HINT_T0 = 1, /* load data to L1 and L2 cache */ ++ _MM_HINT_T1 = 2, /* load data to L2 cache only */ ++ _MM_HINT_T2 = 3, /* load data to L2 cache only, mark it as NTA */ ++ _MM_HINT_ENTA = 4, /* exclusive version of _MM_HINT_NTA */ ++ _MM_HINT_ET0 = 5, /* exclusive version of _MM_HINT_T0 */ ++ _MM_HINT_ET1 = 6, /* exclusive version of _MM_HINT_T1 */ ++ _MM_HINT_ET2 = 7 /* exclusive version of _MM_HINT_T2 */ ++}; ++ ++// The bit field mapping to the FPCR(floating-point control register) ++typedef struct { ++ uint16_t res0; ++ uint8_t res1 : 6; ++ uint8_t bit22 : 1; ++ uint8_t bit23 : 1; ++ uint8_t bit24 : 1; ++ uint8_t res2 : 7; ++#if defined(__aarch64__) ++ uint32_t res3; ++#endif ++} fpcr_bitfield; ++ ++// Takes the upper 64 bits of a and places it in the low end of the result ++// Takes the lower 64 bits of b and places it into the high end of the result. ++FORCE_INLINE __m128 _mm_shuffle_ps_1032(__m128 a, __m128 b) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a32, b10)); ++} ++ ++// takes the lower two 32-bit values from a and swaps them and places in high ++// end of result takes the higher two 32 bit values from b and swaps them and ++// places in low end of result. ++FORCE_INLINE __m128 _mm_shuffle_ps_2301(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b23 = vrev64_f32(vget_high_f32(vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b23)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0321(__m128 a, __m128 b) ++{ ++ float32x2_t a21 = vget_high_f32( ++ vextq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 3)); ++ float32x2_t b03 = vget_low_f32( ++ vextq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b), 3)); ++ return vreinterpretq_m128_f32(vcombine_f32(a21, b03)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2103(__m128 a, __m128 b) ++{ ++ float32x2_t a03 = vget_low_f32( ++ vextq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 3)); ++ float32x2_t b21 = vget_high_f32( ++ vextq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b), 3)); ++ return vreinterpretq_m128_f32(vcombine_f32(a03, b21)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1010(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b10)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1001(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b10)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0101(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b01)); ++} ++ ++// keeps the low 64 bits of b in the low and puts the high 64 bits of a in the ++// high ++FORCE_INLINE __m128 _mm_shuffle_ps_3210(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b32)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0011(__m128 a, __m128 b) ++{ ++ float32x2_t a11 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(a)), 1); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a11, b00)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0022(__m128 a, __m128 b) ++{ ++ float32x2_t a22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a22, b00)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2200(__m128 a, __m128 b) ++{ ++ float32x2_t a00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t b22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a00, b22)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_3202(__m128 a, __m128 b) ++{ ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ float32x2_t a22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t a02 = vset_lane_f32(a0, a22, 1); /* TODO: use vzip ?*/ ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a02, b32)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1133(__m128 a, __m128 b) ++{ ++ float32x2_t a33 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 1); ++ float32x2_t b11 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a33, b11)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2010(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32_t b2 = vgetq_lane_f32(vreinterpretq_f32_m128(b), 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b20)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2001(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32_t b2 = vgetq_lane_f32(b, 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b20)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2032(__m128 a, __m128 b) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32_t b2 = vgetq_lane_f32(b, 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a32, b20)); ++} ++ ++// Kahan summation for accurate summation of floating-point numbers. ++// http://blog.zachbjornson.com/2019/08/11/fast-float-summation.html ++FORCE_INLINE void _sse2neon_kadd_f32(float *sum, float *c, float y) ++{ ++ y -= *c; ++ float t = *sum + y; ++ *c = (t - *sum) - y; ++ *sum = t; ++} ++ ++#if defined(__ARM_FEATURE_CRYPTO) && \ ++ (defined(__aarch64__) || __has_builtin(__builtin_arm_crypto_vmullp64)) ++// Wraps vmull_p64 ++FORCE_INLINE uint64x2_t _sse2neon_vmull_p64(uint64x1_t _a, uint64x1_t _b) ++{ ++ poly64_t a = vget_lane_p64(vreinterpret_p64_u64(_a), 0); ++ poly64_t b = vget_lane_p64(vreinterpret_p64_u64(_b), 0); ++ return vreinterpretq_u64_p128(vmull_p64(a, b)); ++} ++#else // ARMv7 polyfill ++// ARMv7/some A64 lacks vmull_p64, but it has vmull_p8. ++// ++// vmull_p8 calculates 8 8-bit->16-bit polynomial multiplies, but we need a ++// 64-bit->128-bit polynomial multiply. ++// ++// It needs some work and is somewhat slow, but it is still faster than all ++// known scalar methods. ++// ++// Algorithm adapted to C from ++// https://www.workofard.com/2017/07/ghash-for-low-end-cores/, which is adapted ++// from "Fast Software Polynomial Multiplication on ARM Processors Using the ++// NEON Engine" by Danilo Camara, Conrado Gouvea, Julio Lopez and Ricardo Dahab ++// (https://hal.inria.fr/hal-01506572) ++static uint64x2_t _sse2neon_vmull_p64(uint64x1_t _a, uint64x1_t _b) ++{ ++ poly8x8_t a = vreinterpret_p8_u64(_a); ++ poly8x8_t b = vreinterpret_p8_u64(_b); ++ ++ // Masks ++ uint8x16_t k48_32 = vcombine_u8(vcreate_u8(0x0000ffffffffffff), ++ vcreate_u8(0x00000000ffffffff)); ++ uint8x16_t k16_00 = vcombine_u8(vcreate_u8(0x000000000000ffff), ++ vcreate_u8(0x0000000000000000)); ++ ++ // Do the multiplies, rotating with vext to get all combinations ++ uint8x16_t d = vreinterpretq_u8_p16(vmull_p8(a, b)); // D = A0 * B0 ++ uint8x16_t e = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 1))); // E = A0 * B1 ++ uint8x16_t f = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 1), b)); // F = A1 * B0 ++ uint8x16_t g = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 2))); // G = A0 * B2 ++ uint8x16_t h = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 2), b)); // H = A2 * B0 ++ uint8x16_t i = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 3))); // I = A0 * B3 ++ uint8x16_t j = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 3), b)); // J = A3 * B0 ++ uint8x16_t k = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 4))); // L = A0 * B4 ++ ++ // Add cross products ++ uint8x16_t l = veorq_u8(e, f); // L = E + F ++ uint8x16_t m = veorq_u8(g, h); // M = G + H ++ uint8x16_t n = veorq_u8(i, j); // N = I + J ++ ++ // Interleave. Using vzip1 and vzip2 prevents Clang from emitting TBL ++ // instructions. ++#if defined(__aarch64__) ++ uint8x16_t lm_p0 = vreinterpretq_u8_u64( ++ vzip1q_u64(vreinterpretq_u64_u8(l), vreinterpretq_u64_u8(m))); ++ uint8x16_t lm_p1 = vreinterpretq_u8_u64( ++ vzip2q_u64(vreinterpretq_u64_u8(l), vreinterpretq_u64_u8(m))); ++ uint8x16_t nk_p0 = vreinterpretq_u8_u64( ++ vzip1q_u64(vreinterpretq_u64_u8(n), vreinterpretq_u64_u8(k))); ++ uint8x16_t nk_p1 = vreinterpretq_u8_u64( ++ vzip2q_u64(vreinterpretq_u64_u8(n), vreinterpretq_u64_u8(k))); ++#else ++ uint8x16_t lm_p0 = vcombine_u8(vget_low_u8(l), vget_low_u8(m)); ++ uint8x16_t lm_p1 = vcombine_u8(vget_high_u8(l), vget_high_u8(m)); ++ uint8x16_t nk_p0 = vcombine_u8(vget_low_u8(n), vget_low_u8(k)); ++ uint8x16_t nk_p1 = vcombine_u8(vget_high_u8(n), vget_high_u8(k)); ++#endif ++ // t0 = (L) (P0 + P1) << 8 ++ // t1 = (M) (P2 + P3) << 16 ++ uint8x16_t t0t1_tmp = veorq_u8(lm_p0, lm_p1); ++ uint8x16_t t0t1_h = vandq_u8(lm_p1, k48_32); ++ uint8x16_t t0t1_l = veorq_u8(t0t1_tmp, t0t1_h); ++ ++ // t2 = (N) (P4 + P5) << 24 ++ // t3 = (K) (P6 + P7) << 32 ++ uint8x16_t t2t3_tmp = veorq_u8(nk_p0, nk_p1); ++ uint8x16_t t2t3_h = vandq_u8(nk_p1, k16_00); ++ uint8x16_t t2t3_l = veorq_u8(t2t3_tmp, t2t3_h); ++ ++ // De-interleave ++#if defined(__aarch64__) ++ uint8x16_t t0 = vreinterpretq_u8_u64( ++ vuzp1q_u64(vreinterpretq_u64_u8(t0t1_l), vreinterpretq_u64_u8(t0t1_h))); ++ uint8x16_t t1 = vreinterpretq_u8_u64( ++ vuzp2q_u64(vreinterpretq_u64_u8(t0t1_l), vreinterpretq_u64_u8(t0t1_h))); ++ uint8x16_t t2 = vreinterpretq_u8_u64( ++ vuzp1q_u64(vreinterpretq_u64_u8(t2t3_l), vreinterpretq_u64_u8(t2t3_h))); ++ uint8x16_t t3 = vreinterpretq_u8_u64( ++ vuzp2q_u64(vreinterpretq_u64_u8(t2t3_l), vreinterpretq_u64_u8(t2t3_h))); ++#else ++ uint8x16_t t1 = vcombine_u8(vget_high_u8(t0t1_l), vget_high_u8(t0t1_h)); ++ uint8x16_t t0 = vcombine_u8(vget_low_u8(t0t1_l), vget_low_u8(t0t1_h)); ++ uint8x16_t t3 = vcombine_u8(vget_high_u8(t2t3_l), vget_high_u8(t2t3_h)); ++ uint8x16_t t2 = vcombine_u8(vget_low_u8(t2t3_l), vget_low_u8(t2t3_h)); ++#endif ++ // Shift the cross products ++ uint8x16_t t0_shift = vextq_u8(t0, t0, 15); // t0 << 8 ++ uint8x16_t t1_shift = vextq_u8(t1, t1, 14); // t1 << 16 ++ uint8x16_t t2_shift = vextq_u8(t2, t2, 13); // t2 << 24 ++ uint8x16_t t3_shift = vextq_u8(t3, t3, 12); // t3 << 32 ++ ++ // Accumulate the products ++ uint8x16_t cross1 = veorq_u8(t0_shift, t1_shift); ++ uint8x16_t cross2 = veorq_u8(t2_shift, t3_shift); ++ uint8x16_t mix = veorq_u8(d, cross1); ++ uint8x16_t r = veorq_u8(mix, cross2); ++ return vreinterpretq_u64_u8(r); ++} ++#endif // ARMv7 polyfill ++ ++// C equivalent: ++// __m128i _mm_shuffle_epi32_default(__m128i a, ++// __constrange(0, 255) int imm) { ++// __m128i ret; ++// ret[0] = a[imm & 0x3]; ret[1] = a[(imm >> 2) & 0x3]; ++// ret[2] = a[(imm >> 4) & 0x03]; ret[3] = a[(imm >> 6) & 0x03]; ++// return ret; ++// } ++#define _mm_shuffle_epi32_default(a, imm) \ ++ __extension__({ \ ++ int32x4_t ret; \ ++ ret = vmovq_n_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm) & (0x3))); \ ++ ret = vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 2) & 0x3), \ ++ ret, 1); \ ++ ret = vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 4) & 0x3), \ ++ ret, 2); \ ++ ret = vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 6) & 0x3), \ ++ ret, 3); \ ++ vreinterpretq_m128i_s32(ret); \ ++ }) ++ ++// Takes the upper 64 bits of a and places it in the low end of the result ++// Takes the lower 64 bits of a and places it into the high end of the result. ++FORCE_INLINE __m128i _mm_shuffle_epi_1032(__m128i a) ++{ ++ int32x2_t a32 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a32, a10)); ++} ++ ++// takes the lower two 32-bit values from a and swaps them and places in low end ++// of result takes the higher two 32 bit values from a and swaps them and places ++// in high end of result. ++FORCE_INLINE __m128i _mm_shuffle_epi_2301(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ int32x2_t a23 = vrev64_s32(vget_high_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a23)); ++} ++ ++// rotates the least significant 32 bits into the most significant 32 bits, and ++// shifts the rest down ++FORCE_INLINE __m128i _mm_shuffle_epi_0321(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vextq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(a), 1)); ++} ++ ++// rotates the most significant 32 bits into the least significant 32 bits, and ++// shifts the rest up ++FORCE_INLINE __m128i _mm_shuffle_epi_2103(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vextq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(a), 3)); ++} ++ ++// gets the lower 64 bits of a, and places it in the upper 64 bits ++// gets the lower 64 bits of a and places it in the lower 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_1010(__m128i a) ++{ ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a10, a10)); ++} ++ ++// gets the lower 64 bits of a, swaps the 0 and 1 elements, and places it in the ++// lower 64 bits gets the lower 64 bits of a, and places it in the upper 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_1001(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a10)); ++} ++ ++// gets the lower 64 bits of a, swaps the 0 and 1 elements and places it in the ++// upper 64 bits gets the lower 64 bits of a, swaps the 0 and 1 elements, and ++// places it in the lower 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_0101(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a01)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_2211(__m128i a) ++{ ++ int32x2_t a11 = vdup_lane_s32(vget_low_s32(vreinterpretq_s32_m128i(a)), 1); ++ int32x2_t a22 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 0); ++ return vreinterpretq_m128i_s32(vcombine_s32(a11, a22)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_0122(__m128i a) ++{ ++ int32x2_t a22 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 0); ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a22, a01)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_3332(__m128i a) ++{ ++ int32x2_t a32 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t a33 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 1); ++ return vreinterpretq_m128i_s32(vcombine_s32(a32, a33)); ++} ++ ++// FORCE_INLINE __m128i _mm_shuffle_epi32_splat(__m128i a, __constrange(0,255) ++// int imm) ++#if defined(__aarch64__) ++#define _mm_shuffle_epi32_splat(a, imm) \ ++ __extension__({ \ ++ vreinterpretq_m128i_s32( \ ++ vdupq_laneq_s32(vreinterpretq_s32_m128i(a), (imm))); \ ++ }) ++#else ++#define _mm_shuffle_epi32_splat(a, imm) \ ++ __extension__({ \ ++ vreinterpretq_m128i_s32( \ ++ vdupq_n_s32(vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm)))); \ ++ }) ++#endif ++ ++// NEON does not support a general purpose permute intrinsic ++// Selects four specific single-precision, floating-point values from a and b, ++// based on the mask i. ++// ++// C equivalent: ++// __m128 _mm_shuffle_ps_default(__m128 a, __m128 b, ++// __constrange(0, 255) int imm) { ++// __m128 ret; ++// ret[0] = a[imm & 0x3]; ret[1] = a[(imm >> 2) & 0x3]; ++// ret[2] = b[(imm >> 4) & 0x03]; ret[3] = b[(imm >> 6) & 0x03]; ++// return ret; ++// } ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/5f0858x0(v=vs.100).aspx ++#define _mm_shuffle_ps_default(a, b, imm) \ ++ __extension__({ \ ++ float32x4_t ret; \ ++ ret = vmovq_n_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(a), (imm) & (0x3))); \ ++ ret = vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(a), ((imm) >> 2) & 0x3), \ ++ ret, 1); \ ++ ret = vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(b), ((imm) >> 4) & 0x3), \ ++ ret, 2); \ ++ ret = vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(b), ((imm) >> 6) & 0x3), \ ++ ret, 3); \ ++ vreinterpretq_m128_f32(ret); \ ++ }) ++ ++// Shuffles the lower 4 signed or unsigned 16-bit integers in a as specified ++// by imm. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/y41dkk37(v=vs.100) ++// FORCE_INLINE __m128i _mm_shufflelo_epi16_function(__m128i a, ++// __constrange(0,255) int ++// imm) ++#define _mm_shufflelo_epi16_function(a, imm) \ ++ __extension__({ \ ++ int16x8_t ret = vreinterpretq_s16_m128i(a); \ ++ int16x4_t lowBits = vget_low_s16(ret); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, (imm) & (0x3)), ret, 0); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 2) & 0x3), ret, \ ++ 1); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 4) & 0x3), ret, \ ++ 2); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 6) & 0x3), ret, \ ++ 3); \ ++ vreinterpretq_m128i_s16(ret); \ ++ }) ++ ++// Shuffles the upper 4 signed or unsigned 16-bit integers in a as specified ++// by imm. ++// https://msdn.microsoft.com/en-us/library/13ywktbs(v=vs.100).aspx ++// FORCE_INLINE __m128i _mm_shufflehi_epi16_function(__m128i a, ++// __constrange(0,255) int ++// imm) ++#define _mm_shufflehi_epi16_function(a, imm) \ ++ __extension__({ \ ++ int16x8_t ret = vreinterpretq_s16_m128i(a); \ ++ int16x4_t highBits = vget_high_s16(ret); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, (imm) & (0x3)), ret, 4); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 2) & 0x3), ret, \ ++ 5); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 4) & 0x3), ret, \ ++ 6); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 6) & 0x3), ret, \ ++ 7); \ ++ vreinterpretq_m128i_s16(ret); \ ++ }) ++ ++/* MMX */ ++ ++//_mm_empty is a no-op on arm ++FORCE_INLINE void _mm_empty(void) {} ++ ++/* SSE */ ++ ++// Adds the four single-precision, floating-point values of a and b. ++// ++// r0 := a0 + b0 ++// r1 := a1 + b1 ++// r2 := a2 + b2 ++// r3 := a3 + b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/c9848chc(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_add_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vaddq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// adds the scalar single-precision floating point values of a and b. ++// https://msdn.microsoft.com/en-us/library/be94x2y6(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_add_ss(__m128 a, __m128 b) ++{ ++ float32_t b0 = vgetq_lane_f32(vreinterpretq_f32_m128(b), 0); ++ float32x4_t value = vsetq_lane_f32(b0, vdupq_n_f32(0), 0); ++ // the upper values in the result must be the remnants of . ++ return vreinterpretq_m128_f32(vaddq_f32(a, value)); ++} ++ ++// Computes the bitwise AND of the four single-precision, floating-point values ++// of a and b. ++// ++// r0 := a0 & b0 ++// r1 := a1 & b1 ++// r2 := a2 & b2 ++// r3 := a3 & b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/73ck1xc5(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_and_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vandq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Computes the bitwise AND-NOT of the four single-precision, floating-point ++// values of a and b. ++// ++// r0 := ~a0 & b0 ++// r1 := ~a1 & b1 ++// r2 := ~a2 & b2 ++// r3 := ~a3 & b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/68h7wd02(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_andnot_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vbicq_s32(vreinterpretq_s32_m128(b), ++ vreinterpretq_s32_m128(a))); // *NOTE* argument swap ++} ++ ++// Average packed unsigned 16-bit integers in a and b, and store the results in ++// dst. ++// ++// FOR j := 0 to 3 ++// i := j*16 ++// dst[i+15:i] := (a[i+15:i] + b[i+15:i] + 1) >> 1 ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_avg_pu16 ++FORCE_INLINE __m64 _mm_avg_pu16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u16( ++ vrhadd_u16(vreinterpret_u16_m64(a), vreinterpret_u16_m64(b))); ++} ++ ++// Average packed unsigned 8-bit integers in a and b, and store the results in ++// dst. ++// ++// FOR j := 0 to 7 ++// i := j*8 ++// dst[i+7:i] := (a[i+7:i] + b[i+7:i] + 1) >> 1 ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_avg_pu8 ++FORCE_INLINE __m64 _mm_avg_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vrhadd_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Compares for equality. ++// https://msdn.microsoft.com/en-us/library/vstudio/36aectz5(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmpeq_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for equality. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/k423z28e(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpeq_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpeq_ps(a, b)); ++} ++ ++// Compares for greater than or equal. ++// https://msdn.microsoft.com/en-us/library/vstudio/fs813y2t(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmpge_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for greater than or equal. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/kesh3ddc(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpge_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpge_ps(a, b)); ++} ++ ++// Compares for greater than. ++// ++// r0 := (a0 > b0) ? 0xffffffff : 0x0 ++// r1 := (a1 > b1) ? 0xffffffff : 0x0 ++// r2 := (a2 > b2) ? 0xffffffff : 0x0 ++// r3 := (a3 > b3) ? 0xffffffff : 0x0 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/11dy102s(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmpgt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for greater than. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/1xyyyy9e(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpgt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpgt_ps(a, b)); ++} ++ ++// Compares for less than or equal. ++// ++// r0 := (a0 <= b0) ? 0xffffffff : 0x0 ++// r1 := (a1 <= b1) ? 0xffffffff : 0x0 ++// r2 := (a2 <= b2) ? 0xffffffff : 0x0 ++// r3 := (a3 <= b3) ? 0xffffffff : 0x0 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/1s75w83z(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmple_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for less than or equal. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/a7x0hbhw(v=vs.100) ++FORCE_INLINE __m128 _mm_cmple_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmple_ps(a, b)); ++} ++ ++// Compares for less than ++// https://msdn.microsoft.com/en-us/library/vstudio/f330yhc8(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmplt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for less than ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/fy94wye7(v=vs.100) ++FORCE_INLINE __m128 _mm_cmplt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmplt_ps(a, b)); ++} ++ ++// Compares for inequality. ++// https://msdn.microsoft.com/en-us/library/sf44thbx(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmpneq_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compares for inequality. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/ekya8fh4(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpneq_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpneq_ps(a, b)); ++} ++ ++// Compares for not greater than or equal. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/wsexys62(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpnge_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compares for not greater than or equal. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/fk2y80s8(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpnge_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnge_ps(a, b)); ++} ++ ++// Compares for not greater than. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/d0xh7w0s(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpngt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compares for not greater than. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/z7x9ydwh(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpngt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpngt_ps(a, b)); ++} ++ ++// Compares for not less than or equal. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/6a330kxw(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpnle_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compares for not less than or equal. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/z7x9ydwh(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpnle_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnle_ps(a, b)); ++} ++ ++// Compares for not less than. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/4686bbdw(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpnlt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compares for not less than. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/56b9z2wf(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpnlt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnlt_ps(a, b)); ++} ++ ++// Compares the four 32-bit floats in a and b to check if any values are NaN. ++// Ordered compare between each value returns true for "orderable" and false for ++// "not orderable" (NaN). ++// https://msdn.microsoft.com/en-us/library/vstudio/0h9w00fx(v=vs.100).aspx see ++// also: ++// http://stackoverflow.com/questions/8627331/what-does-ordered-unordered-comparison-mean ++// http://stackoverflow.com/questions/29349621/neon-isnanval-intrinsics ++FORCE_INLINE __m128 _mm_cmpord_ps(__m128 a, __m128 b) ++{ ++ // Note: NEON does not have ordered compare builtin ++ // Need to compare a eq a and b eq b to check for NaN ++ // Do AND of results to get final ++ uint32x4_t ceqaa = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t ceqbb = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_u32(vandq_u32(ceqaa, ceqbb)); ++} ++ ++// Compares for ordered. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/343t62da(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpord_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpord_ps(a, b)); ++} ++ ++// Compares for unordered. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/khy6fk1t(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpunord_ps(__m128 a, __m128 b) ++{ ++ uint32x4_t f32a = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t f32b = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_u32(vmvnq_u32(vandq_u32(f32a, f32b))); ++} ++ ++// Compares for unordered. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/2as2387b(v=vs.100) ++FORCE_INLINE __m128 _mm_cmpunord_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpunord_ps(a, b)); ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using an equality operation. : ++// https://msdn.microsoft.com/en-us/library/93yx2h2b(v=vs.100).aspx ++FORCE_INLINE int _mm_comieq_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_eq_b = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_eq_b, 0) & 0x1; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using a greater than or equal operation. : ++// https://msdn.microsoft.com/en-us/library/8t80des6(v=vs.100).aspx ++FORCE_INLINE int _mm_comige_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_ge_b = ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_ge_b, 0) & 0x1; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using a greater than operation. : ++// https://msdn.microsoft.com/en-us/library/b0738e0t(v=vs.100).aspx ++FORCE_INLINE int _mm_comigt_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_gt_b = ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_gt_b, 0) & 0x1; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using a less than or equal operation. : ++// https://msdn.microsoft.com/en-us/library/1w4t7c57(v=vs.90).aspx ++FORCE_INLINE int _mm_comile_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_le_b = ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_le_b, 0) & 0x1; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using a less than operation. : ++// https://msdn.microsoft.com/en-us/library/2kwe606b(v=vs.90).aspx Important ++// note!! The documentation on MSDN is incorrect! If either of the values is a ++// NAN the docs say you will get a one, but in fact, it will return a zero!! ++FORCE_INLINE int _mm_comilt_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_lt_b = ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_lt_b, 0) & 0x1; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using an inequality operation. : ++// https://msdn.microsoft.com/en-us/library/bafh5e0a(v=vs.90).aspx ++FORCE_INLINE int _mm_comineq_ss(__m128 a, __m128 b) ++{ ++ return !_mm_comieq_ss(a, b); ++} ++ ++// Convert packed signed 32-bit integers in b to packed single-precision ++// (32-bit) floating-point elements, store the results in the lower 2 elements ++// of dst, and copy the upper 2 packed elements from a to the upper elements of ++// dst. ++// ++// dst[31:0] := Convert_Int32_To_FP32(b[31:0]) ++// dst[63:32] := Convert_Int32_To_FP32(b[63:32]) ++// dst[95:64] := a[95:64] ++// dst[127:96] := a[127:96] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvt_pi2ps ++FORCE_INLINE __m128 _mm_cvt_pi2ps(__m128 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vcvt_f32_s32(vreinterpret_s32_m64(b)), ++ vget_high_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := 32*j ++// dst[i+31:i] := Convert_FP32_To_Int32(a[i+31:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvt_ps2pi ++FORCE_INLINE __m64 _mm_cvt_ps2pi(__m128 a) ++{ ++#if defined(__aarch64__) || defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpret_m64_s32( ++ vget_low_s32(vcvtnq_s32_f32(vrndiq_f32(vreinterpretq_f32_m128(a))))); ++#else ++ return vreinterpret_m64_s32(vcvt_s32_f32(vget_low_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION))))); ++#endif ++} ++ ++// Convert the signed 32-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// ++// dst[31:0] := Convert_Int32_To_FP32(b[31:0]) ++// dst[127:32] := a[127:32] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvt_si2ss ++FORCE_INLINE __m128 _mm_cvt_si2ss(__m128 a, int b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32((float) b, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvt_ss2si ++FORCE_INLINE int _mm_cvt_ss2si(__m128 a) ++{ ++#if defined(__aarch64__) || defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vgetq_lane_s32(vcvtnq_s32_f32(vrndiq_f32(vreinterpretq_f32_m128(a))), ++ 0); ++#else ++ float32_t data = vgetq_lane_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION)), 0); ++ return (int32_t) data; ++#endif ++} ++ ++// Convert packed 16-bit integers in a to packed single-precision (32-bit) ++// floating-point elements, and store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*16 ++// m := j*32 ++// dst[m+31:m] := Convert_Int16_To_FP32(a[i+15:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpi16_ps ++FORCE_INLINE __m128 _mm_cvtpi16_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_s32(vmovl_s16(vreinterpret_s16_m64(a)))); ++} ++ ++// Convert packed 32-bit integers in b to packed single-precision (32-bit) ++// floating-point elements, store the results in the lower 2 elements of dst, ++// and copy the upper 2 packed elements from a to the upper elements of dst. ++// ++// dst[31:0] := Convert_Int32_To_FP32(b[31:0]) ++// dst[63:32] := Convert_Int32_To_FP32(b[63:32]) ++// dst[95:64] := a[95:64] ++// dst[127:96] := a[127:96] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpi32_ps ++FORCE_INLINE __m128 _mm_cvtpi32_ps(__m128 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vcvt_f32_s32(vreinterpret_s32_m64(b)), ++ vget_high_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert packed signed 32-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, store the results in the lower 2 elements ++// of dst, then convert the packed signed 32-bit integers in b to ++// single-precision (32-bit) floating-point element, and store the results in ++// the upper 2 elements of dst. ++// ++// dst[31:0] := Convert_Int32_To_FP32(a[31:0]) ++// dst[63:32] := Convert_Int32_To_FP32(a[63:32]) ++// dst[95:64] := Convert_Int32_To_FP32(b[31:0]) ++// dst[127:96] := Convert_Int32_To_FP32(b[63:32]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpi32x2_ps ++FORCE_INLINE __m128 _mm_cvtpi32x2_ps(__m64 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32( ++ vcombine_s32(vreinterpret_s32_m64(a), vreinterpret_s32_m64(b)))); ++} ++ ++// Convert the lower packed 8-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, and store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*8 ++// m := j*32 ++// dst[m+31:m] := Convert_Int8_To_FP32(a[i+7:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpi8_ps ++FORCE_INLINE __m128 _mm_cvtpi8_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32( ++ vmovl_s16(vget_low_s16(vmovl_s8(vreinterpret_s8_m64(a)))))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 16-bit integers, and store the results in dst. Note: this intrinsic ++// will generate 0x7FFF, rather than 0x8000, for input values between 0x7FFF and ++// 0x7FFFFFFF. ++// ++// FOR j := 0 to 3 ++// i := 16*j ++// k := 32*j ++// IF a[k+31:k] >= FP32(0x7FFF) && a[k+31:k] <= FP32(0x7FFFFFFF) ++// dst[i+15:i] := 0x7FFF ++// ELSE ++// dst[i+15:i] := Convert_FP32_To_Int16(a[k+31:k]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtps_pi16 ++FORCE_INLINE __m64 _mm_cvtps_pi16(__m128 a) ++{ ++ const __m128 i16Min = _mm_set_ps1((float) INT16_MIN); ++ const __m128 i16Max = _mm_set_ps1((float) INT16_MAX); ++ const __m128 i32Max = _mm_set_ps1((float) INT32_MAX); ++ const __m128i maxMask = _mm_castps_si128( ++ _mm_and_ps(_mm_cmpge_ps(a, i16Max), _mm_cmple_ps(a, i32Max))); ++ const __m128i betweenMask = _mm_castps_si128( ++ _mm_and_ps(_mm_cmpgt_ps(a, i16Min), _mm_cmplt_ps(a, i16Max))); ++ const __m128i minMask = _mm_cmpeq_epi32(_mm_or_si128(maxMask, betweenMask), ++ _mm_setzero_si128()); ++ __m128i max = _mm_and_si128(maxMask, _mm_set1_epi32(INT16_MAX)); ++ __m128i min = _mm_and_si128(minMask, _mm_set1_epi32(INT16_MIN)); ++ __m128i cvt = _mm_and_si128(betweenMask, _mm_cvtps_epi32(a)); ++ __m128i res32 = _mm_or_si128(_mm_or_si128(max, min), cvt); ++ return vreinterpret_m64_s16(vmovn_s32(vreinterpretq_s32_m128i(res32))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := 32*j ++// dst[i+31:i] := Convert_FP32_To_Int32(a[i+31:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtps_pi32 ++#define _mm_cvtps_pi32(a) _mm_cvt_ps2pi(a) ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 8-bit integers, and store the results in lower 4 elements of dst. ++// Note: this intrinsic will generate 0x7F, rather than 0x80, for input values ++// between 0x7F and 0x7FFFFFFF. ++// ++// FOR j := 0 to 3 ++// i := 8*j ++// k := 32*j ++// IF a[k+31:k] >= FP32(0x7F) && a[k+31:k] <= FP32(0x7FFFFFFF) ++// dst[i+7:i] := 0x7F ++// ELSE ++// dst[i+7:i] := Convert_FP32_To_Int8(a[k+31:k]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtps_pi8 ++FORCE_INLINE __m64 _mm_cvtps_pi8(__m128 a) ++{ ++ const __m128 i8Min = _mm_set_ps1((float) INT8_MIN); ++ const __m128 i8Max = _mm_set_ps1((float) INT8_MAX); ++ const __m128 i32Max = _mm_set_ps1((float) INT32_MAX); ++ const __m128i maxMask = _mm_castps_si128( ++ _mm_and_ps(_mm_cmpge_ps(a, i8Max), _mm_cmple_ps(a, i32Max))); ++ const __m128i betweenMask = _mm_castps_si128( ++ _mm_and_ps(_mm_cmpgt_ps(a, i8Min), _mm_cmplt_ps(a, i8Max))); ++ const __m128i minMask = _mm_cmpeq_epi32(_mm_or_si128(maxMask, betweenMask), ++ _mm_setzero_si128()); ++ __m128i max = _mm_and_si128(maxMask, _mm_set1_epi32(INT8_MAX)); ++ __m128i min = _mm_and_si128(minMask, _mm_set1_epi32(INT8_MIN)); ++ __m128i cvt = _mm_and_si128(betweenMask, _mm_cvtps_epi32(a)); ++ __m128i res32 = _mm_or_si128(_mm_or_si128(max, min), cvt); ++ int16x4_t res16 = vmovn_s32(vreinterpretq_s32_m128i(res32)); ++ int8x8_t res8 = vmovn_s16(vcombine_s16(res16, res16)); ++ static const uint32_t bitMask[2] = {0xFFFFFFFF, 0}; ++ int8x8_t mask = vreinterpret_s8_u32(vld1_u32(bitMask)); ++ ++ return vreinterpret_m64_s8(vorr_s8(vand_s8(mask, res8), vdup_n_s8(0))); ++} ++ ++// Convert packed unsigned 16-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, and store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*16 ++// m := j*32 ++// dst[m+31:m] := Convert_UInt16_To_FP32(a[i+15:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpu16_ps ++FORCE_INLINE __m128 _mm_cvtpu16_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_u32(vmovl_u16(vreinterpret_u16_m64(a)))); ++} ++ ++// Convert the lower packed unsigned 8-bit integers in a to packed ++// single-precision (32-bit) floating-point elements, and store the results in ++// dst. ++// ++// FOR j := 0 to 3 ++// i := j*8 ++// m := j*32 ++// dst[m+31:m] := Convert_UInt8_To_FP32(a[i+7:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpu8_ps ++FORCE_INLINE __m128 _mm_cvtpu8_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_u32( ++ vmovl_u16(vget_low_u16(vmovl_u8(vreinterpret_u8_m64(a)))))); ++} ++ ++// Convert the signed 32-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// ++// dst[31:0] := Convert_Int32_To_FP32(b[31:0]) ++// dst[127:32] := a[127:32] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi32_ss ++#define _mm_cvtsi32_ss(a, b) _mm_cvt_si2ss(a, b) ++ ++// Convert the signed 64-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// ++// dst[31:0] := Convert_Int64_To_FP32(b[63:0]) ++// dst[127:32] := a[127:32] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi64_ss ++FORCE_INLINE __m128 _mm_cvtsi64_ss(__m128 a, int64_t b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32((float) b, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Copy the lower single-precision (32-bit) floating-point element of a to dst. ++// ++// dst[31:0] := a[31:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtss_f32 ++FORCE_INLINE float _mm_cvtss_f32(__m128 a) ++{ ++ return vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// ++// dst[31:0] := Convert_FP32_To_Int32(a[31:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtss_si32 ++#define _mm_cvtss_si32(a) _mm_cvt_ss2si(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// ++// dst[63:0] := Convert_FP32_To_Int64(a[31:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtss_si64 ++FORCE_INLINE int64_t _mm_cvtss_si64(__m128 a) ++{ ++#if defined(__aarch64__) || defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return (int64_t) vgetq_lane_f32(vrndiq_f32(vreinterpretq_f32_m128(a)), 0); ++#else ++ float32_t data = vgetq_lane_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION)), 0); ++ return (int64_t) data; ++#endif ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := 32*j ++// dst[i+31:i] := Convert_FP32_To_Int32_Truncate(a[i+31:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtt_ps2pi ++FORCE_INLINE __m64 _mm_cvtt_ps2pi(__m128 a) ++{ ++ return vreinterpret_m64_s32( ++ vget_low_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// ++// dst[31:0] := Convert_FP32_To_Int32_Truncate(a[31:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtt_ss2si ++FORCE_INLINE int _mm_cvtt_ss2si(__m128 a) ++{ ++ return vgetq_lane_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a)), 0); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := 32*j ++// dst[i+31:i] := Convert_FP32_To_Int32_Truncate(a[i+31:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvttps_pi32 ++#define _mm_cvttps_pi32(a) _mm_cvtt_ps2pi(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// ++// dst[31:0] := Convert_FP32_To_Int32_Truncate(a[31:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvttss_si32 ++#define _mm_cvttss_si32(a) _mm_cvtt_ss2si(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// ++// dst[63:0] := Convert_FP32_To_Int64_Truncate(a[31:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvttss_si64 ++FORCE_INLINE int64_t _mm_cvttss_si64(__m128 a) ++{ ++ return (int64_t) vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++} ++ ++// Divides the four single-precision, floating-point values of a and b. ++// ++// r0 := a0 / b0 ++// r1 := a1 / b1 ++// r2 := a2 / b2 ++// r3 := a3 / b3 ++// ++// https://msdn.microsoft.com/en-us/library/edaw8147(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_div_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) && !SSE2NEON_PRECISE_DIV ++ return vreinterpretq_m128_f32( ++ vdivq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x4_t recip = vrecpeq_f32(vreinterpretq_f32_m128(b)); ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(b))); ++#if SSE2NEON_PRECISE_DIV ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(b))); ++#endif ++ return vreinterpretq_m128_f32(vmulq_f32(vreinterpretq_f32_m128(a), recip)); ++#endif ++} ++ ++// Divides the scalar single-precision floating point value of a by b. ++// https://msdn.microsoft.com/en-us/library/4y73xa49(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_div_ss(__m128 a, __m128 b) ++{ ++ float32_t value = ++ vgetq_lane_f32(vreinterpretq_f32_m128(_mm_div_ps(a, b)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Extract a 16-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_extract_pi16 ++#define _mm_extract_pi16(a, imm) \ ++ (int32_t) vget_lane_u16(vreinterpret_u16_m64(a), (imm)) ++ ++// Free aligned memory that was allocated with _mm_malloc. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_free ++FORCE_INLINE void _mm_free(void *addr) ++{ ++ free(addr); ++} ++ ++// Macro: Get the flush zero bits from the MXCSR control and status register. ++// The flush zero may contain any of the following flags: _MM_FLUSH_ZERO_ON or ++// _MM_FLUSH_ZERO_OFF ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_MM_GET_FLUSH_ZERO_MODE ++FORCE_INLINE unsigned int _sse2neon_mm_get_flush_zero_mode() ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("mrs %0, FPCR" : "=r"(r.value)); /* read */ ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ return r.field.bit24 ? _MM_FLUSH_ZERO_ON : _MM_FLUSH_ZERO_OFF; ++} ++ ++// Macro: Get the rounding mode bits from the MXCSR control and status register. ++// The rounding mode may contain any of the following flags: _MM_ROUND_NEAREST, ++// _MM_ROUND_DOWN, _MM_ROUND_UP, _MM_ROUND_TOWARD_ZERO ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_MM_GET_ROUNDING_MODE ++FORCE_INLINE unsigned int _MM_GET_ROUNDING_MODE() ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("mrs %0, FPCR" : "=r"(r.value)); /* read */ ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ if (r.field.bit22) { ++ return r.field.bit23 ? _MM_ROUND_TOWARD_ZERO : _MM_ROUND_UP; ++ } else { ++ return r.field.bit23 ? _MM_ROUND_DOWN : _MM_ROUND_NEAREST; ++ } ++} ++ ++// Copy a to dst, and insert the 16-bit integer i into dst at the location ++// specified by imm8. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_insert_pi16 ++#define _mm_insert_pi16(a, b, imm) \ ++ __extension__({ \ ++ vreinterpret_m64_s16( \ ++ vset_lane_s16((b), vreinterpret_s16_m64(a), (imm))); \ ++ }) ++ ++// Loads four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/vstudio/zzd50xxt(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_load_ps(const float *p) ++{ ++ return vreinterpretq_m128_f32(vld1q_f32(p)); ++} ++ ++// Load a single-precision (32-bit) floating-point element from memory into all ++// elements of dst. ++// ++// dst[31:0] := MEM[mem_addr+31:mem_addr] ++// dst[63:32] := MEM[mem_addr+31:mem_addr] ++// dst[95:64] := MEM[mem_addr+31:mem_addr] ++// dst[127:96] := MEM[mem_addr+31:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_load_ps1 ++#define _mm_load_ps1 _mm_load1_ps ++ ++// Loads an single - precision, floating - point value into the low word and ++// clears the upper three words. ++// https://msdn.microsoft.com/en-us/library/548bb9h4%28v=vs.90%29.aspx ++FORCE_INLINE __m128 _mm_load_ss(const float *p) ++{ ++ return vreinterpretq_m128_f32(vsetq_lane_f32(*p, vdupq_n_f32(0), 0)); ++} ++ ++// Loads a single single-precision, floating-point value, copying it into all ++// four words ++// https://msdn.microsoft.com/en-us/library/vstudio/5cdkf716(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_load1_ps(const float *p) ++{ ++ return vreinterpretq_m128_f32(vld1q_dup_f32(p)); ++} ++ ++// Sets the upper two single-precision, floating-point values with 64 ++// bits of data loaded from the address p; the lower two values are passed ++// through from a. ++// ++// r0 := a0 ++// r1 := a1 ++// r2 := *p0 ++// r3 := *p1 ++// ++// https://msdn.microsoft.com/en-us/library/w92wta0x(v%3dvs.100).aspx ++FORCE_INLINE __m128 _mm_loadh_pi(__m128 a, __m64 const *p) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vget_low_f32(a), vld1_f32((const float32_t *) p))); ++} ++ ++// Sets the lower two single-precision, floating-point values with 64 ++// bits of data loaded from the address p; the upper two values are passed ++// through from a. ++// ++// Return Value ++// r0 := *p0 ++// r1 := *p1 ++// r2 := a2 ++// r3 := a3 ++// ++// https://msdn.microsoft.com/en-us/library/s57cyak2(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_loadl_pi(__m128 a, __m64 const *p) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vld1_f32((const float32_t *) p), vget_high_f32(a))); ++} ++ ++// Load 4 single-precision (32-bit) floating-point elements from memory into dst ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// ++// dst[31:0] := MEM[mem_addr+127:mem_addr+96] ++// dst[63:32] := MEM[mem_addr+95:mem_addr+64] ++// dst[95:64] := MEM[mem_addr+63:mem_addr+32] ++// dst[127:96] := MEM[mem_addr+31:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadr_ps ++FORCE_INLINE __m128 _mm_loadr_ps(const float *p) ++{ ++ float32x4_t v = vrev64q_f32(vld1q_f32(p)); ++ return vreinterpretq_m128_f32(vextq_f32(v, v, 2)); ++} ++ ++// Loads four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/x1b16s7z%28v=vs.90%29.aspx ++FORCE_INLINE __m128 _mm_loadu_ps(const float *p) ++{ ++ // for neon, alignment doesn't matter, so _mm_load_ps and _mm_loadu_ps are ++ // equivalent for neon ++ return vreinterpretq_m128_f32(vld1q_f32(p)); ++} ++ ++// Load unaligned 16-bit integer from memory into the first element of dst. ++// ++// dst[15:0] := MEM[mem_addr+15:mem_addr] ++// dst[MAX:16] := 0 ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadu_si16 ++FORCE_INLINE __m128i _mm_loadu_si16(const void *p) ++{ ++ return vreinterpretq_m128i_s16( ++ vsetq_lane_s16(*(const int16_t *) p, vdupq_n_s16(0), 0)); ++} ++ ++// Load unaligned 64-bit integer from memory into the first element of dst. ++// ++// dst[63:0] := MEM[mem_addr+63:mem_addr] ++// dst[MAX:64] := 0 ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadu_si64 ++FORCE_INLINE __m128i _mm_loadu_si64(const void *p) ++{ ++ return vreinterpretq_m128i_s64( ++ vcombine_s64(vld1_s64((const int64_t *) p), vdup_n_s64(0))); ++} ++ ++// Allocate aligned blocks of memory. ++// https://software.intel.com/en-us/ ++// cpp-compiler-developer-guide-and-reference-allocating-and-freeing-aligned-memory-blocks ++FORCE_INLINE void *_mm_malloc(size_t size, size_t align) ++{ ++ void *ptr; ++ if (align == 1) ++ return malloc(size); ++ if (align == 2 || (sizeof(void *) == 8 && align == 4)) ++ align = sizeof(void *); ++ if (!posix_memalign(&ptr, align, size)) ++ return ptr; ++ return NULL; ++} ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_maskmove_si64 ++FORCE_INLINE void _mm_maskmove_si64(__m64 a, __m64 mask, char *mem_addr) ++{ ++ int8x8_t shr_mask = vshr_n_s8(vreinterpret_s8_m64(mask), 7); ++ __m128 b = _mm_load_ps((const float *) mem_addr); ++ int8x8_t masked = ++ vbsl_s8(vreinterpret_u8_s8(shr_mask), vreinterpret_s8_m64(a), ++ vreinterpret_s8_u64(vget_low_u64(vreinterpretq_u64_m128(b)))); ++ vst1_s8((int8_t *) mem_addr, masked); ++} ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_maskmovq ++#define _m_maskmovq(a, mask, mem_addr) _mm_maskmove_si64(a, mask, mem_addr) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// ++// FOR j := 0 to 3 ++// i := j*16 ++// dst[i+15:i] := MAX(a[i+15:i], b[i+15:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_max_pi16 ++FORCE_INLINE __m64 _mm_max_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vmax_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Computes the maximums of the four single-precision, floating-point values of ++// a and b. ++// https://msdn.microsoft.com/en-us/library/vstudio/ff5d607a(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_max_ps(__m128 a, __m128 b) ++{ ++#if SSE2NEON_PRECISE_MINMAX ++ float32x4_t _a = vreinterpretq_f32_m128(a); ++ float32x4_t _b = vreinterpretq_f32_m128(b); ++ return vreinterpretq_m128_f32(vbslq_f32(vcgtq_f32(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128_f32( ++ vmaxq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#endif ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// ++// FOR j := 0 to 7 ++// i := j*8 ++// dst[i+7:i] := MAX(a[i+7:i], b[i+7:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_max_pu8 ++FORCE_INLINE __m64 _mm_max_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vmax_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Computes the maximum of the two lower scalar single-precision floating point ++// values of a and b. ++// https://msdn.microsoft.com/en-us/library/s6db5esz(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_max_ss(__m128 a, __m128 b) ++{ ++ float32_t value = vgetq_lane_f32(_mm_max_ps(a, b), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Compare packed signed 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// ++// FOR j := 0 to 3 ++// i := j*16 ++// dst[i+15:i] := MIN(a[i+15:i], b[i+15:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_min_pi16 ++FORCE_INLINE __m64 _mm_min_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vmin_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Computes the minima of the four single-precision, floating-point values of a ++// and b. ++// https://msdn.microsoft.com/en-us/library/vstudio/wh13kadz(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_min_ps(__m128 a, __m128 b) ++{ ++#if SSE2NEON_PRECISE_MINMAX ++ float32x4_t _a = vreinterpretq_f32_m128(a); ++ float32x4_t _b = vreinterpretq_f32_m128(b); ++ return vreinterpretq_m128_f32(vbslq_f32(vcltq_f32(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128_f32( ++ vminq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#endif ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// ++// FOR j := 0 to 7 ++// i := j*8 ++// dst[i+7:i] := MIN(a[i+7:i], b[i+7:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_min_pu8 ++FORCE_INLINE __m64 _mm_min_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vmin_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Computes the minimum of the two lower scalar single-precision floating point ++// values of a and b. ++// https://msdn.microsoft.com/en-us/library/0a9y7xaa(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_min_ss(__m128 a, __m128 b) ++{ ++ float32_t value = vgetq_lane_f32(_mm_min_ps(a, b), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Sets the low word to the single-precision, floating-point value of b ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/35hdzazd(v=vs.100) ++FORCE_INLINE __m128 _mm_move_ss(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(vgetq_lane_f32(vreinterpretq_f32_m128(b), 0), ++ vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Moves the upper two values of B into the lower two values of A. ++// ++// r3 := a3 ++// r2 := a2 ++// r1 := b3 ++// r0 := b2 ++FORCE_INLINE __m128 _mm_movehl_ps(__m128 __A, __m128 __B) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(__A)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(__B)); ++ return vreinterpretq_m128_f32(vcombine_f32(b32, a32)); ++} ++ ++// Moves the lower two values of B into the upper two values of A. ++// ++// r3 := b1 ++// r2 := b0 ++// r1 := a1 ++// r0 := a0 ++FORCE_INLINE __m128 _mm_movelh_ps(__m128 __A, __m128 __B) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(__A)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(__B)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b10)); ++} ++ ++// Create mask from the most significant bit of each 8-bit element in a, and ++// store the result in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_movemask_pi8 ++FORCE_INLINE int _mm_movemask_pi8(__m64 a) ++{ ++ uint8x8_t input = vreinterpret_u8_m64(a); ++#if defined(__aarch64__) ++ static const int8x8_t shift = {0, 1, 2, 3, 4, 5, 6, 7}; ++ uint8x8_t tmp = vshr_n_u8(input, 7); ++ return vaddv_u8(vshl_u8(tmp, shift)); ++#else ++ // Refer the implementation of `_mm_movemask_epi8` ++ uint16x4_t high_bits = vreinterpret_u16_u8(vshr_n_u8(input, 7)); ++ uint32x2_t paired16 = ++ vreinterpret_u32_u16(vsra_n_u16(high_bits, high_bits, 7)); ++ uint8x8_t paired32 = ++ vreinterpret_u8_u32(vsra_n_u32(paired16, paired16, 14)); ++ return vget_lane_u8(paired32, 0) | ((int) vget_lane_u8(paired32, 4) << 4); ++#endif ++} ++ ++// NEON does not provide this method ++// Creates a 4-bit mask from the most significant bits of the four ++// single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/vstudio/4490ys29(v=vs.100).aspx ++FORCE_INLINE int _mm_movemask_ps(__m128 a) ++{ ++ uint32x4_t input = vreinterpretq_u32_m128(a); ++#if defined(__aarch64__) ++ static const int32x4_t shift = {0, 1, 2, 3}; ++ uint32x4_t tmp = vshrq_n_u32(input, 31); ++ return vaddvq_u32(vshlq_u32(tmp, shift)); ++#else ++ // Uses the exact same method as _mm_movemask_epi8, see that for details. ++ // Shift out everything but the sign bits with a 32-bit unsigned shift ++ // right. ++ uint64x2_t high_bits = vreinterpretq_u64_u32(vshrq_n_u32(input, 31)); ++ // Merge the two pairs together with a 64-bit unsigned shift right + add. ++ uint8x16_t paired = ++ vreinterpretq_u8_u64(vsraq_n_u64(high_bits, high_bits, 31)); ++ // Extract the result. ++ return vgetq_lane_u8(paired, 0) | (vgetq_lane_u8(paired, 8) << 2); ++#endif ++} ++ ++// Multiplies the four single-precision, floating-point values of a and b. ++// ++// r0 := a0 * b0 ++// r1 := a1 * b1 ++// r2 := a2 * b2 ++// r3 := a3 * b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/22kbk6t9(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_mul_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vmulq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Multiply the lower single-precision (32-bit) floating-point element in a and ++// b, store the result in the lower element of dst, and copy the upper 3 packed ++// elements from a to the upper elements of dst. ++// ++// dst[31:0] := a[31:0] * b[31:0] ++// dst[127:32] := a[127:32] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_mul_ss ++FORCE_INLINE __m128 _mm_mul_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_mul_ps(a, b)); ++} ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_mulhi_pu16 ++FORCE_INLINE __m64 _mm_mulhi_pu16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u16(vshrn_n_u32( ++ vmull_u16(vreinterpret_u16_m64(a), vreinterpret_u16_m64(b)), 16)); ++} ++ ++// Computes the bitwise OR of the four single-precision, floating-point values ++// of a and b. ++// https://msdn.microsoft.com/en-us/library/vstudio/7ctdsyy0(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_or_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vorrq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Average packed unsigned 8-bit integers in a and b, and store the results in ++// dst. ++// ++// FOR j := 0 to 7 ++// i := j*8 ++// dst[i+7:i] := (a[i+7:i] + b[i+7:i] + 1) >> 1 ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pavgb ++#define _m_pavgb(a, b) _mm_avg_pu8(a, b) ++ ++// Average packed unsigned 16-bit integers in a and b, and store the results in ++// dst. ++// ++// FOR j := 0 to 3 ++// i := j*16 ++// dst[i+15:i] := (a[i+15:i] + b[i+15:i] + 1) >> 1 ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pavgw ++#define _m_pavgw(a, b) _mm_avg_pu16(a, b) ++ ++// Extract a 16-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pextrw ++#define _m_pextrw(a, imm) _mm_extract_pi16(a, imm) ++ ++// Copy a to dst, and insert the 16-bit integer i into dst at the location ++// specified by imm8. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=m_pinsrw ++#define _m_pinsrw(a, i, imm) _mm_insert_pi16(a, i, imm) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pmaxsw ++#define _m_pmaxsw(a, b) _mm_max_pi16(a, b) ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pmaxub ++#define _m_pmaxub(a, b) _mm_max_pu8(a, b) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pminsw ++#define _m_pminsw(a, b) _mm_min_pi16(a, b) ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pminub ++#define _m_pminub(a, b) _mm_min_pu8(a, b) ++ ++// Create mask from the most significant bit of each 8-bit element in a, and ++// store the result in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pmovmskb ++#define _m_pmovmskb(a) _mm_movemask_pi8(a) ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pmulhuw ++#define _m_pmulhuw(a, b) _mm_mulhi_pu16(a, b) ++ ++// Loads one cache line of data from address p to a location closer to the ++// processor. https://msdn.microsoft.com/en-us/library/84szxsww(v=vs.100).aspx ++FORCE_INLINE void _mm_prefetch(const void *p, int i) ++{ ++ (void) i; ++ __builtin_prefetch(p); ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce four ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=m_psadbw ++#define _m_psadbw(a, b) _mm_sad_pu8(a, b) ++ ++// Shuffle 16-bit integers in a using the control in imm8, and store the results ++// in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_m_pshufw ++#define _m_pshufw(a, imm) _mm_shuffle_pi16(a, imm) ++ ++// Compute the approximate reciprocal of packed single-precision (32-bit) ++// floating-point elements in a, and store the results in dst. The maximum ++// relative error for this approximation is less than 1.5*2^-12. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_rcp_ps ++FORCE_INLINE __m128 _mm_rcp_ps(__m128 in) ++{ ++ float32x4_t recip = vrecpeq_f32(vreinterpretq_f32_m128(in)); ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(in))); ++#if SSE2NEON_PRECISE_DIV ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(in))); ++#endif ++ return vreinterpretq_m128_f32(recip); ++} ++ ++// Compute the approximate reciprocal of the lower single-precision (32-bit) ++// floating-point element in a, store the result in the lower element of dst, ++// and copy the upper 3 packed elements from a to the upper elements of dst. The ++// maximum relative error for this approximation is less than 1.5*2^-12. ++// ++// dst[31:0] := (1.0 / a[31:0]) ++// dst[127:32] := a[127:32] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_rcp_ss ++FORCE_INLINE __m128 _mm_rcp_ss(__m128 a) ++{ ++ return _mm_move_ss(a, _mm_rcp_ps(a)); ++} ++ ++// Computes the approximations of the reciprocal square roots of the four ++// single-precision floating point values of in. ++// The current precision is 1% error. ++// https://msdn.microsoft.com/en-us/library/22hfsh53(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_rsqrt_ps(__m128 in) ++{ ++ float32x4_t out = vrsqrteq_f32(vreinterpretq_f32_m128(in)); ++#if SSE2NEON_PRECISE_SQRT ++ // Additional Netwon-Raphson iteration for accuracy ++ out = vmulq_f32( ++ out, vrsqrtsq_f32(vmulq_f32(vreinterpretq_f32_m128(in), out), out)); ++ out = vmulq_f32( ++ out, vrsqrtsq_f32(vmulq_f32(vreinterpretq_f32_m128(in), out), out)); ++#endif ++ return vreinterpretq_m128_f32(out); ++} ++ ++// Compute the approximate reciprocal square root of the lower single-precision ++// (32-bit) floating-point element in a, store the result in the lower element ++// of dst, and copy the upper 3 packed elements from a to the upper elements of ++// dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_rsqrt_ss ++FORCE_INLINE __m128 _mm_rsqrt_ss(__m128 in) ++{ ++ return vsetq_lane_f32(vgetq_lane_f32(_mm_rsqrt_ps(in), 0), in, 0); ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce four ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sad_pu8 ++FORCE_INLINE __m64 _mm_sad_pu8(__m64 a, __m64 b) ++{ ++ uint64x1_t t = vpaddl_u32(vpaddl_u16( ++ vpaddl_u8(vabd_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))))); ++ return vreinterpret_m64_u16( ++ vset_lane_u16(vget_lane_u64(t, 0), vdup_n_u16(0), 0)); ++} ++ ++// Macro: Set the flush zero bits of the MXCSR control and status register to ++// the value in unsigned 32-bit integer a. The flush zero may contain any of the ++// following flags: _MM_FLUSH_ZERO_ON or _MM_FLUSH_ZERO_OFF ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_MM_SET_FLUSH_ZERO_MODE ++FORCE_INLINE void _sse2neon_mm_set_flush_zero_mode(unsigned int flag) ++{ ++ // AArch32 Advanced SIMD arithmetic always uses the Flush-to-zero setting, ++ // regardless of the value of the FZ bit. ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("mrs %0, FPCR" : "=r"(r.value)); /* read */ ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ r.field.bit24 = (flag & _MM_FLUSH_ZERO_MASK) == _MM_FLUSH_ZERO_ON; ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("msr FPCR, %0" ::"r"(r)); /* write */ ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Sets the four single-precision, floating-point values to the four inputs. ++// https://msdn.microsoft.com/en-us/library/vstudio/afh0zf75(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_set_ps(float w, float z, float y, float x) ++{ ++ float ALIGN_STRUCT(16) data[4] = {x, y, z, w}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Sets the four single-precision, floating-point values to w. ++// https://msdn.microsoft.com/en-us/library/vstudio/2x1se8ha(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_set_ps1(float _w) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(_w)); ++} ++ ++// Macro: Set the rounding mode bits of the MXCSR control and status register to ++// the value in unsigned 32-bit integer a. The rounding mode may contain any of ++// the following flags: _MM_ROUND_NEAREST, _MM_ROUND_DOWN, _MM_ROUND_UP, ++// _MM_ROUND_TOWARD_ZERO ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_MM_SET_ROUNDING_MODE ++FORCE_INLINE void _MM_SET_ROUNDING_MODE(int rounding) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("mrs %0, FPCR" : "=r"(r.value)); /* read */ ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ switch (rounding) { ++ case _MM_ROUND_TOWARD_ZERO: ++ r.field.bit22 = 1; ++ r.field.bit23 = 1; ++ break; ++ case _MM_ROUND_DOWN: ++ r.field.bit22 = 0; ++ r.field.bit23 = 1; ++ break; ++ case _MM_ROUND_UP: ++ r.field.bit22 = 1; ++ r.field.bit23 = 0; ++ break; ++ default: //_MM_ROUND_NEAREST ++ r.field.bit22 = 0; ++ r.field.bit23 = 0; ++ } ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("msr FPCR, %0" ::"r"(r)); /* write */ ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Copy single-precision (32-bit) floating-point element a to the lower element ++// of dst, and zero the upper 3 elements. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_set_ss ++FORCE_INLINE __m128 _mm_set_ss(float a) ++{ ++ float ALIGN_STRUCT(16) data[4] = {a, 0, 0, 0}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Sets the four single-precision, floating-point values to w. ++// ++// r0 := r1 := r2 := r3 := w ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/2x1se8ha(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_set1_ps(float _w) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(_w)); ++} ++ ++// FIXME: _mm_setcsr() implementation supports changing the rounding mode only. ++FORCE_INLINE void _mm_setcsr(unsigned int a) ++{ ++ _MM_SET_ROUNDING_MODE(a); ++} ++ ++// FIXME: _mm_getcsr() implementation supports reading the rounding mode only. ++FORCE_INLINE unsigned int _mm_getcsr() ++{ ++ return _MM_GET_ROUNDING_MODE(); ++} ++ ++// Sets the four single-precision, floating-point values to the four inputs in ++// reverse order. ++// https://msdn.microsoft.com/en-us/library/vstudio/d2172ct3(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_setr_ps(float w, float z, float y, float x) ++{ ++ float ALIGN_STRUCT(16) data[4] = {w, z, y, x}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Clears the four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/vstudio/tk1t2tbz(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_setzero_ps(void) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(0)); ++} ++ ++// Shuffle 16-bit integers in a using the control in imm8, and store the results ++// in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_shuffle_pi16 ++#if __has_builtin(__builtin_shufflevector) ++#define _mm_shuffle_pi16(a, imm) \ ++ __extension__({ \ ++ vreinterpret_m64_s16(__builtin_shufflevector( \ ++ vreinterpret_s16_m64(a), vreinterpret_s16_m64(a), (imm & 0x3), \ ++ ((imm >> 2) & 0x3), ((imm >> 4) & 0x3), ((imm >> 6) & 0x3))); \ ++ }) ++#else ++#define _mm_shuffle_pi16(a, imm) \ ++ __extension__({ \ ++ int16x4_t ret; \ ++ ret = \ ++ vmov_n_s16(vget_lane_s16(vreinterpret_s16_m64(a), (imm) & (0x3))); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(a), ((imm) >> 2) & 0x3), ret, \ ++ 1); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(a), ((imm) >> 4) & 0x3), ret, \ ++ 2); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(a), ((imm) >> 6) & 0x3), ret, \ ++ 3); \ ++ vreinterpret_m64_s16(ret); \ ++ }) ++#endif ++ ++// Guarantees that every preceding store is globally visible before any ++// subsequent store. ++// https://msdn.microsoft.com/en-us/library/5h2w73d1%28v=vs.90%29.aspx ++FORCE_INLINE void _mm_sfence(void) ++{ ++ __sync_synchronize(); ++} ++ ++// FORCE_INLINE __m128 _mm_shuffle_ps(__m128 a, __m128 b, __constrange(0,255) ++// int imm) ++#if __has_builtin(__builtin_shufflevector) ++#define _mm_shuffle_ps(a, b, imm) \ ++ __extension__({ \ ++ float32x4_t _input1 = vreinterpretq_f32_m128(a); \ ++ float32x4_t _input2 = vreinterpretq_f32_m128(b); \ ++ float32x4_t _shuf = __builtin_shufflevector( \ ++ _input1, _input2, (imm) & (0x3), ((imm) >> 2) & 0x3, \ ++ (((imm) >> 4) & 0x3) + 4, (((imm) >> 6) & 0x3) + 4); \ ++ vreinterpretq_m128_f32(_shuf); \ ++ }) ++#else // generic ++#define _mm_shuffle_ps(a, b, imm) \ ++ __extension__({ \ ++ __m128 ret; \ ++ switch (imm) { \ ++ case _MM_SHUFFLE(1, 0, 3, 2): \ ++ ret = _mm_shuffle_ps_1032((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 3, 0, 1): \ ++ ret = _mm_shuffle_ps_2301((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 3, 2, 1): \ ++ ret = _mm_shuffle_ps_0321((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 1, 0, 3): \ ++ ret = _mm_shuffle_ps_2103((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 1, 0): \ ++ ret = _mm_movelh_ps((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 0, 1): \ ++ ret = _mm_shuffle_ps_1001((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 0, 1): \ ++ ret = _mm_shuffle_ps_0101((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 1, 0): \ ++ ret = _mm_shuffle_ps_3210((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 1, 1): \ ++ ret = _mm_shuffle_ps_0011((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 2, 2): \ ++ ret = _mm_shuffle_ps_0022((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 0, 0): \ ++ ret = _mm_shuffle_ps_2200((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 0, 2): \ ++ ret = _mm_shuffle_ps_3202((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 3, 2): \ ++ ret = _mm_movehl_ps((b), (a)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 1, 3, 3): \ ++ ret = _mm_shuffle_ps_1133((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 1, 0): \ ++ ret = _mm_shuffle_ps_2010((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 0, 1): \ ++ ret = _mm_shuffle_ps_2001((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 3, 2): \ ++ ret = _mm_shuffle_ps_2032((a), (b)); \ ++ break; \ ++ default: \ ++ ret = _mm_shuffle_ps_default((a), (b), (imm)); \ ++ break; \ ++ } \ ++ ret; \ ++ }) ++#endif ++ ++// Computes the approximations of square roots of the four single-precision, ++// floating-point values of a. First computes reciprocal square roots and then ++// reciprocals of the four values. ++// ++// r0 := sqrt(a0) ++// r1 := sqrt(a1) ++// r2 := sqrt(a2) ++// r3 := sqrt(a3) ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/8z67bwwk(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_sqrt_ps(__m128 in) ++{ ++#if SSE2NEON_PRECISE_SQRT ++ float32x4_t recip = vrsqrteq_f32(vreinterpretq_f32_m128(in)); ++ ++ // Test for vrsqrteq_f32(0) -> positive infinity case. ++ // Change to zero, so that s * 1/sqrt(s) result is zero too. ++ const uint32x4_t pos_inf = vdupq_n_u32(0x7F800000); ++ const uint32x4_t div_by_zero = ++ vceqq_u32(pos_inf, vreinterpretq_u32_f32(recip)); ++ recip = vreinterpretq_f32_u32( ++ vandq_u32(vmvnq_u32(div_by_zero), vreinterpretq_u32_f32(recip))); ++ ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32( ++ vrsqrtsq_f32(vmulq_f32(recip, recip), vreinterpretq_f32_m128(in)), ++ recip); ++ recip = vmulq_f32( ++ vrsqrtsq_f32(vmulq_f32(recip, recip), vreinterpretq_f32_m128(in)), ++ recip); ++ ++ // sqrt(s) = s * 1/sqrt(s) ++ return vreinterpretq_m128_f32(vmulq_f32(vreinterpretq_f32_m128(in), recip)); ++#elif defined(__aarch64__) ++ return vreinterpretq_m128_f32(vsqrtq_f32(vreinterpretq_f32_m128(in))); ++#else ++ float32x4_t recipsq = vrsqrteq_f32(vreinterpretq_f32_m128(in)); ++ float32x4_t sq = vrecpeq_f32(recipsq); ++ return vreinterpretq_m128_f32(sq); ++#endif ++} ++ ++// Computes the approximation of the square root of the scalar single-precision ++// floating point value of in. ++// https://msdn.microsoft.com/en-us/library/ahfsc22d(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_sqrt_ss(__m128 in) ++{ ++ float32_t value = ++ vgetq_lane_f32(vreinterpretq_f32_m128(_mm_sqrt_ps(in)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(in), 0)); ++} ++ ++// Stores four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/vstudio/s3h4ay6y(v=vs.100).aspx ++FORCE_INLINE void _mm_store_ps(float *p, __m128 a) ++{ ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++} ++ ++// Store the lower single-precision (32-bit) floating-point element from a into ++// 4 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// ++// MEM[mem_addr+31:mem_addr] := a[31:0] ++// MEM[mem_addr+63:mem_addr+32] := a[31:0] ++// MEM[mem_addr+95:mem_addr+64] := a[31:0] ++// MEM[mem_addr+127:mem_addr+96] := a[31:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_store_ps1 ++FORCE_INLINE void _mm_store_ps1(float *p, __m128 a) ++{ ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ vst1q_f32(p, vdupq_n_f32(a0)); ++} ++ ++// Stores the lower single - precision, floating - point value. ++// https://msdn.microsoft.com/en-us/library/tzz10fbx(v=vs.100).aspx ++FORCE_INLINE void _mm_store_ss(float *p, __m128 a) ++{ ++ vst1q_lane_f32(p, vreinterpretq_f32_m128(a), 0); ++} ++ ++// Store the lower single-precision (32-bit) floating-point element from a into ++// 4 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// ++// MEM[mem_addr+31:mem_addr] := a[31:0] ++// MEM[mem_addr+63:mem_addr+32] := a[31:0] ++// MEM[mem_addr+95:mem_addr+64] := a[31:0] ++// MEM[mem_addr+127:mem_addr+96] := a[31:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_store1_ps ++#define _mm_store1_ps _mm_store_ps1 ++ ++// Stores the upper two single-precision, floating-point values of a to the ++// address p. ++// ++// *p0 := a2 ++// *p1 := a3 ++// ++// https://msdn.microsoft.com/en-us/library/a7525fs8(v%3dvs.90).aspx ++FORCE_INLINE void _mm_storeh_pi(__m64 *p, __m128 a) ++{ ++ *p = vreinterpret_m64_f32(vget_high_f32(a)); ++} ++ ++// Stores the lower two single-precision floating point values of a to the ++// address p. ++// ++// *p0 := a0 ++// *p1 := a1 ++// ++// https://msdn.microsoft.com/en-us/library/h54t98ks(v=vs.90).aspx ++FORCE_INLINE void _mm_storel_pi(__m64 *p, __m128 a) ++{ ++ *p = vreinterpret_m64_f32(vget_low_f32(a)); ++} ++ ++// Store 4 single-precision (32-bit) floating-point elements from a into memory ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// ++// MEM[mem_addr+31:mem_addr] := a[127:96] ++// MEM[mem_addr+63:mem_addr+32] := a[95:64] ++// MEM[mem_addr+95:mem_addr+64] := a[63:32] ++// MEM[mem_addr+127:mem_addr+96] := a[31:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storer_ps ++FORCE_INLINE void _mm_storer_ps(float *p, __m128 a) ++{ ++ float32x4_t tmp = vrev64q_f32(vreinterpretq_f32_m128(a)); ++ float32x4_t rev = vextq_f32(tmp, tmp, 2); ++ vst1q_f32(p, rev); ++} ++ ++// Stores four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/44e30x22(v=vs.100).aspx ++FORCE_INLINE void _mm_storeu_ps(float *p, __m128 a) ++{ ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++} ++ ++// Stores 16-bits of integer data a at the address p. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storeu_si16 ++FORCE_INLINE void _mm_storeu_si16(void *p, __m128i a) ++{ ++ vst1q_lane_s16((int16_t *) p, vreinterpretq_s16_m128i(a), 0); ++} ++ ++// Stores 64-bits of integer data a at the address p. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storeu_si64 ++FORCE_INLINE void _mm_storeu_si64(void *p, __m128i a) ++{ ++ vst1q_lane_s64((int64_t *) p, vreinterpretq_s64_m128i(a), 0); ++} ++ ++// Store 64-bits of integer data from a into memory using a non-temporal memory ++// hint. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_stream_pi ++FORCE_INLINE void _mm_stream_pi(__m64 *p, __m64 a) ++{ ++ vst1_s64((int64_t *) p, vreinterpret_s64_m64(a)); ++} ++ ++// Store 128-bits (composed of 4 packed single-precision (32-bit) floating- ++// point elements) from a into memory using a non-temporal memory hint. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_stream_ps ++FORCE_INLINE void _mm_stream_ps(float *p, __m128 a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, (float32x4_t *) p); ++#else ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++#endif ++} ++ ++// Subtracts the four single-precision, floating-point values of a and b. ++// ++// r0 := a0 - b0 ++// r1 := a1 - b1 ++// r2 := a2 - b2 ++// r3 := a3 - b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/1zad2k61(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_sub_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vsubq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Subtract the lower single-precision (32-bit) floating-point element in b from ++// the lower single-precision (32-bit) floating-point element in a, store the ++// result in the lower element of dst, and copy the upper 3 packed elements from ++// a to the upper elements of dst. ++// ++// dst[31:0] := a[31:0] - b[31:0] ++// dst[127:32] := a[127:32] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sub_ss ++FORCE_INLINE __m128 _mm_sub_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_sub_ps(a, b)); ++} ++ ++// Macro: Transpose the 4x4 matrix formed by the 4 rows of single-precision ++// (32-bit) floating-point elements in row0, row1, row2, and row3, and store the ++// transposed matrix in these vectors (row0 now contains column 0, etc.). ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=MM_TRANSPOSE4_PS ++#define _MM_TRANSPOSE4_PS(row0, row1, row2, row3) \ ++ do { \ ++ float32x4x2_t ROW01 = vtrnq_f32(row0, row1); \ ++ float32x4x2_t ROW23 = vtrnq_f32(row2, row3); \ ++ row0 = vcombine_f32(vget_low_f32(ROW01.val[0]), \ ++ vget_low_f32(ROW23.val[0])); \ ++ row1 = vcombine_f32(vget_low_f32(ROW01.val[1]), \ ++ vget_low_f32(ROW23.val[1])); \ ++ row2 = vcombine_f32(vget_high_f32(ROW01.val[0]), \ ++ vget_high_f32(ROW23.val[0])); \ ++ row3 = vcombine_f32(vget_high_f32(ROW01.val[1]), \ ++ vget_high_f32(ROW23.val[1])); \ ++ } while (0) ++ ++// according to the documentation, these intrinsics behave the same as the ++// non-'u' versions. We'll just alias them here. ++#define _mm_ucomieq_ss _mm_comieq_ss ++#define _mm_ucomige_ss _mm_comige_ss ++#define _mm_ucomigt_ss _mm_comigt_ss ++#define _mm_ucomile_ss _mm_comile_ss ++#define _mm_ucomilt_ss _mm_comilt_ss ++#define _mm_ucomineq_ss _mm_comineq_ss ++ ++// Return vector of type __m128i with undefined elements. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=mm_undefined_si128 ++FORCE_INLINE __m128i _mm_undefined_si128(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128i a; ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Return vector of type __m128 with undefined elements. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_undefined_ps ++FORCE_INLINE __m128 _mm_undefined_ps(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128 a; ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Selects and interleaves the upper two single-precision, floating-point values ++// from a and b. ++// ++// r0 := a2 ++// r1 := b2 ++// r2 := a3 ++// r3 := b3 ++// ++// https://msdn.microsoft.com/en-us/library/skccxx7d%28v=vs.90%29.aspx ++FORCE_INLINE __m128 _mm_unpackhi_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128_f32( ++ vzip2q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a1 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b1 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ float32x2x2_t result = vzip_f32(a1, b1); ++ return vreinterpretq_m128_f32(vcombine_f32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Selects and interleaves the lower two single-precision, floating-point values ++// from a and b. ++// ++// r0 := a0 ++// r1 := b0 ++// r2 := a1 ++// r3 := b1 ++// ++// https://msdn.microsoft.com/en-us/library/25st103b%28v=vs.90%29.aspx ++FORCE_INLINE __m128 _mm_unpacklo_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128_f32( ++ vzip1q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a1 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b1 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ float32x2x2_t result = vzip_f32(a1, b1); ++ return vreinterpretq_m128_f32(vcombine_f32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Computes bitwise EXOR (exclusive-or) of the four single-precision, ++// floating-point values of a and b. ++// https://msdn.microsoft.com/en-us/library/ss6k3wk8(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_xor_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ veorq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++/* SSE2 */ ++ ++// Adds the 8 signed or unsigned 16-bit integers in a to the 8 signed or ++// unsigned 16-bit integers in b. ++// https://msdn.microsoft.com/en-us/library/fceha5k4(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_add_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vaddq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Adds the 4 signed or unsigned 32-bit integers in a to the 4 signed or ++// unsigned 32-bit integers in b. ++// ++// r0 := a0 + b0 ++// r1 := a1 + b1 ++// r2 := a2 + b2 ++// r3 := a3 + b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/09xs4fkk(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_add_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vaddq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Adds the 4 signed or unsigned 64-bit integers in a to the 4 signed or ++// unsigned 32-bit integers in b. ++// https://msdn.microsoft.com/en-us/library/vstudio/09xs4fkk(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_add_epi64(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s64( ++ vaddq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++} ++ ++// Adds the 16 signed or unsigned 8-bit integers in a to the 16 signed or ++// unsigned 8-bit integers in b. ++// https://technet.microsoft.com/en-us/subscriptions/yc7tcyzs(v=vs.90) ++FORCE_INLINE __m128i _mm_add_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vaddq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Add packed double-precision (64-bit) floating-point elements in a and b, and ++// store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_add_pd ++FORCE_INLINE __m128d _mm_add_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vaddq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] + db[0]; ++ c[1] = da[1] + db[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Add the lower double-precision (64-bit) floating-point element in a and b, ++// store the result in the lower element of dst, and copy the upper element from ++// a to the upper element of dst. ++// ++// dst[63:0] := a[63:0] + b[63:0] ++// dst[127:64] := a[127:64] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_add_sd ++FORCE_INLINE __m128d _mm_add_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_add_pd(a, b)); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] + db[0]; ++ c[1] = da[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Add 64-bit integers a and b, and store the result in dst. ++// ++// dst[63:0] := a[63:0] + b[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_add_si64 ++FORCE_INLINE __m64 _mm_add_si64(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s64( ++ vadd_s64(vreinterpret_s64_m64(a), vreinterpret_s64_m64(b))); ++} ++ ++// Adds the 8 signed 16-bit integers in a to the 8 signed 16-bit integers in b ++// and saturates. ++// ++// r0 := SignedSaturate(a0 + b0) ++// r1 := SignedSaturate(a1 + b1) ++// ... ++// r7 := SignedSaturate(a7 + b7) ++// ++// https://msdn.microsoft.com/en-us/library/1a306ef8(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_adds_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vqaddq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Add packed signed 8-bit integers in a and b using saturation, and store the ++// results in dst. ++// ++// FOR j := 0 to 15 ++// i := j*8 ++// dst[i+7:i] := Saturate8( a[i+7:i] + b[i+7:i] ) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_adds_epi8 ++FORCE_INLINE __m128i _mm_adds_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vqaddq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Add packed unsigned 16-bit integers in a and b using saturation, and store ++// the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_adds_epu16 ++FORCE_INLINE __m128i _mm_adds_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vqaddq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Adds the 16 unsigned 8-bit integers in a to the 16 unsigned 8-bit integers in ++// b and saturates.. ++// https://msdn.microsoft.com/en-us/library/9hahyddy(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_adds_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vqaddq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compute the bitwise AND of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// dst[i+63:i] := a[i+63:i] AND b[i+63:i] ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_and_pd ++FORCE_INLINE __m128d _mm_and_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ vandq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Computes the bitwise AND of the 128-bit value in a and the 128-bit value in ++// b. ++// ++// r := a & b ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/6d1txsa8(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_and_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vandq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compute the bitwise NOT of packed double-precision (64-bit) floating-point ++// elements in a and then AND with b, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// dst[i+63:i] := ((NOT a[i+63:i]) AND b[i+63:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_andnot_pd ++FORCE_INLINE __m128d _mm_andnot_pd(__m128d a, __m128d b) ++{ ++ // *NOTE* argument swap ++ return vreinterpretq_m128d_s64( ++ vbicq_s64(vreinterpretq_s64_m128d(b), vreinterpretq_s64_m128d(a))); ++} ++ ++// Computes the bitwise AND of the 128-bit value in b and the bitwise NOT of the ++// 128-bit value in a. ++// ++// r := (~a) & b ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/1beaceh8(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_andnot_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vbicq_s32(vreinterpretq_s32_m128i(b), ++ vreinterpretq_s32_m128i(a))); // *NOTE* argument swap ++} ++ ++// Computes the average of the 8 unsigned 16-bit integers in a and the 8 ++// unsigned 16-bit integers in b and rounds. ++// ++// r0 := (a0 + b0) / 2 ++// r1 := (a1 + b1) / 2 ++// ... ++// r7 := (a7 + b7) / 2 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/y13ca3c8(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_avg_epu16(__m128i a, __m128i b) ++{ ++ return (__m128i) vrhaddq_u16(vreinterpretq_u16_m128i(a), ++ vreinterpretq_u16_m128i(b)); ++} ++ ++// Computes the average of the 16 unsigned 8-bit integers in a and the 16 ++// unsigned 8-bit integers in b and rounds. ++// ++// r0 := (a0 + b0) / 2 ++// r1 := (a1 + b1) / 2 ++// ... ++// r15 := (a15 + b15) / 2 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/8zwh554a(v%3dvs.90).aspx ++FORCE_INLINE __m128i _mm_avg_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vrhaddq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Shift a left by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_bslli_si128 ++#define _mm_bslli_si128(a, imm) _mm_slli_si128(a, imm) ++ ++// Shift a right by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_bsrli_si128 ++#define _mm_bsrli_si128(a, imm) _mm_srli_si128(a, imm) ++ ++// Cast vector of type __m128d to type __m128. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_castpd_ps ++FORCE_INLINE __m128 _mm_castpd_ps(__m128d a) ++{ ++ return vreinterpretq_m128_s64(vreinterpretq_s64_m128d(a)); ++} ++ ++// Cast vector of type __m128d to type __m128i. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_castpd_si128 ++FORCE_INLINE __m128i _mm_castpd_si128(__m128d a) ++{ ++ return vreinterpretq_m128i_s64(vreinterpretq_s64_m128d(a)); ++} ++ ++// Cast vector of type __m128 to type __m128d. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_castps_pd ++FORCE_INLINE __m128d _mm_castps_pd(__m128 a) ++{ ++ return vreinterpretq_m128d_s32(vreinterpretq_s32_m128(a)); ++} ++ ++// Applies a type cast to reinterpret four 32-bit floating point values passed ++// in as a 128-bit parameter as packed 32-bit integers. ++// https://msdn.microsoft.com/en-us/library/bb514099.aspx ++FORCE_INLINE __m128i _mm_castps_si128(__m128 a) ++{ ++ return vreinterpretq_m128i_s32(vreinterpretq_s32_m128(a)); ++} ++ ++// Cast vector of type __m128i to type __m128d. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_castsi128_pd ++FORCE_INLINE __m128d _mm_castsi128_pd(__m128i a) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vreinterpretq_f64_m128i(a)); ++#else ++ return vreinterpretq_m128d_f32(vreinterpretq_f32_m128i(a)); ++#endif ++} ++ ++// Applies a type cast to reinterpret four 32-bit integers passed in as a ++// 128-bit parameter as packed 32-bit floating point values. ++// https://msdn.microsoft.com/en-us/library/bb514029.aspx ++FORCE_INLINE __m128 _mm_castsi128_ps(__m128i a) ++{ ++ return vreinterpretq_m128_s32(vreinterpretq_s32_m128i(a)); ++} ++ ++// Cache line containing p is flushed and invalidated from all caches in the ++// coherency domain. : ++// https://msdn.microsoft.com/en-us/library/ba08y07y(v=vs.100).aspx ++FORCE_INLINE void _mm_clflush(void const *p) ++{ ++ (void) p; ++ // no corollary for Neon? ++} ++ ++// Compares the 8 signed or unsigned 16-bit integers in a and the 8 signed or ++// unsigned 16-bit integers in b for equality. ++// https://msdn.microsoft.com/en-us/library/2ay060te(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmpeq_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vceqq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed 32-bit integers in a and b for equality, and store the results ++// in dst ++FORCE_INLINE __m128i _mm_cmpeq_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vceqq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compares the 16 signed or unsigned 8-bit integers in a and the 16 signed or ++// unsigned 8-bit integers in b for equality. ++// https://msdn.microsoft.com/en-us/library/windows/desktop/bz5xk21a(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_cmpeq_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vceqq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for equality, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpeq_pd ++FORCE_INLINE __m128d _mm_cmpeq_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64( ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128d_u32(vandq_u32(cmp, swapped)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for equality, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpeq_sd ++FORCE_INLINE __m128d _mm_cmpeq_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpeq_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for greater-than-or-equal, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpge_pd ++FORCE_INLINE __m128d _mm_cmpge_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64( ++ vcgeq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) >= (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (*(double *) &a1) >= (*(double *) &b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for greater-than-or-equal, store the result in the lower element of dst, ++// and copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpge_sd ++FORCE_INLINE __m128d _mm_cmpge_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_cmpge_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) >= (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compares the 8 signed 16-bit integers in a and the 8 signed 16-bit integers ++// in b for greater than. ++// ++// r0 := (a0 > b0) ? 0xffff : 0x0 ++// r1 := (a1 > b1) ? 0xffff : 0x0 ++// ... ++// r7 := (a7 > b7) ? 0xffff : 0x0 ++// ++// https://technet.microsoft.com/en-us/library/xd43yfsa(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmpgt_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcgtq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compares the 4 signed 32-bit integers in a and the 4 signed 32-bit integers ++// in b for greater than. ++// https://msdn.microsoft.com/en-us/library/vstudio/1s9f2z0y(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmpgt_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vcgtq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compares the 16 signed 8-bit integers in a and the 16 signed 8-bit integers ++// in b for greater than. ++// ++// r0 := (a0 > b0) ? 0xff : 0x0 ++// r1 := (a1 > b1) ? 0xff : 0x0 ++// ... ++// r15 := (a15 > b15) ? 0xff : 0x0 ++// ++// https://msdn.microsoft.com/zh-tw/library/wf45zt2b(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmpgt_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcgtq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for greater-than, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpgt_pd ++FORCE_INLINE __m128d _mm_cmpgt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64( ++ vcgtq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) > (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (*(double *) &a1) > (*(double *) &b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for greater-than, store the result in the lower element of dst, and copy ++// the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpgt_sd ++FORCE_INLINE __m128d _mm_cmpgt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_cmpgt_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) > (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for less-than-or-equal, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmple_pd ++FORCE_INLINE __m128d _mm_cmple_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64( ++ vcleq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) <= (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (*(double *) &a1) <= (*(double *) &b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for less-than-or-equal, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmple_sd ++FORCE_INLINE __m128d _mm_cmple_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_cmple_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) <= (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compares the 8 signed 16-bit integers in a and the 8 signed 16-bit integers ++// in b for less than. ++// ++// r0 := (a0 < b0) ? 0xffff : 0x0 ++// r1 := (a1 < b1) ? 0xffff : 0x0 ++// ... ++// r7 := (a7 < b7) ? 0xffff : 0x0 ++// ++// https://technet.microsoft.com/en-us/library/t863edb2(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmplt_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcltq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++ ++// Compares the 4 signed 32-bit integers in a and the 4 signed 32-bit integers ++// in b for less than. ++// https://msdn.microsoft.com/en-us/library/vstudio/4ak0bf5d(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmplt_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vcltq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compares the 16 signed 8-bit integers in a and the 16 signed 8-bit integers ++// in b for lesser than. ++// https://msdn.microsoft.com/en-us/library/windows/desktop/9s46csht(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_cmplt_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcltq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for less-than, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmplt_pd ++FORCE_INLINE __m128d _mm_cmplt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64( ++ vcltq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) < (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (*(double *) &a1) < (*(double *) &b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for less-than, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmplt_sd ++FORCE_INLINE __m128d _mm_cmplt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_cmplt_pd(a, b)); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) < (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-equal, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpneq_pd ++FORCE_INLINE __m128d _mm_cmpneq_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_s32(vmvnq_s32(vreinterpretq_s32_u64( ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))))); ++#else ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128d_u32(vmvnq_u32(vandq_u32(cmp, swapped))); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-equal, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpneq_sd ++FORCE_INLINE __m128d _mm_cmpneq_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpneq_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-greater-than-or-equal, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpnge_pd ++FORCE_INLINE __m128d _mm_cmpnge_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcgeq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ++ !((*(double *) &a0) >= (*(double *) &b0)) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = ++ !((*(double *) &a1) >= (*(double *) &b1)) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-greater-than-or-equal, store the result in the lower element of ++// dst, and copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpnge_sd ++FORCE_INLINE __m128d _mm_cmpnge_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnge_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-greater-than, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_cmpngt_pd ++FORCE_INLINE __m128d _mm_cmpngt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcgtq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ++ !((*(double *) &a0) > (*(double *) &b0)) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = ++ !((*(double *) &a1) > (*(double *) &b1)) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-greater-than, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpngt_sd ++FORCE_INLINE __m128d _mm_cmpngt_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpngt_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-less-than-or-equal, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpnle_pd ++FORCE_INLINE __m128d _mm_cmpnle_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcleq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ++ !((*(double *) &a0) <= (*(double *) &b0)) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = ++ !((*(double *) &a1) <= (*(double *) &b1)) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-less-than-or-equal, store the result in the lower element of dst, ++// and copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpnle_sd ++FORCE_INLINE __m128d _mm_cmpnle_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnle_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-less-than, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpnlt_pd ++FORCE_INLINE __m128d _mm_cmpnlt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcltq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ++ !((*(double *) &a0) < (*(double *) &b0)) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = ++ !((*(double *) &a1) < (*(double *) &b1)) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-less-than, store the result in the lower element of dst, and copy ++// the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpnlt_sd ++FORCE_INLINE __m128d _mm_cmpnlt_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnlt_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// to see if neither is NaN, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpord_pd ++FORCE_INLINE __m128d _mm_cmpord_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ // Excluding NaNs, any two floating point numbers can be compared. ++ uint64x2_t not_nan_a = ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(a)); ++ uint64x2_t not_nan_b = ++ vceqq_f64(vreinterpretq_f64_m128d(b), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_u64(vandq_u64(not_nan_a, not_nan_b)); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ((*(double *) &a0) == (*(double *) &a0) && ++ (*(double *) &b0) == (*(double *) &b0)) ++ ? ~UINT64_C(0) ++ : UINT64_C(0); ++ d[1] = ((*(double *) &a1) == (*(double *) &a1) && ++ (*(double *) &b1) == (*(double *) &b1)) ++ ? ~UINT64_C(0) ++ : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b to see if neither is NaN, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpord_sd ++FORCE_INLINE __m128d _mm_cmpord_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_cmpord_pd(a, b)); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t d[2]; ++ d[0] = ((*(double *) &a0) == (*(double *) &a0) && ++ (*(double *) &b0) == (*(double *) &b0)) ++ ? ~UINT64_C(0) ++ : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// to see if either is NaN, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpunord_pd ++FORCE_INLINE __m128d _mm_cmpunord_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ // Two NaNs are not equal in comparison operation. ++ uint64x2_t not_nan_a = ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(a)); ++ uint64x2_t not_nan_b = ++ vceqq_f64(vreinterpretq_f64_m128d(b), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_s32( ++ vmvnq_s32(vreinterpretq_s32_u64(vandq_u64(not_nan_a, not_nan_b)))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ((*(double *) &a0) == (*(double *) &a0) && ++ (*(double *) &b0) == (*(double *) &b0)) ++ ? UINT64_C(0) ++ : ~UINT64_C(0); ++ d[1] = ((*(double *) &a1) == (*(double *) &a1) && ++ (*(double *) &b1) == (*(double *) &b1)) ++ ? UINT64_C(0) ++ : ~UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b to see if either is NaN, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cmpunord_sd ++FORCE_INLINE __m128d _mm_cmpunord_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_cmpunord_pd(a, b)); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t d[2]; ++ d[0] = ((*(double *) &a0) == (*(double *) &a0) && ++ (*(double *) &b0) == (*(double *) &b0)) ++ ? UINT64_C(0) ++ : ~UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for greater-than-or-equal, and return the boolean result (0 or 1). ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_comige_sd ++FORCE_INLINE int _mm_comige_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vgetq_lane_u64(vcgeq_f64(a, b), 0) & 0x1; ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ ++ return (*(double *) &a0 >= *(double *) &b0); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for greater-than, and return the boolean result (0 or 1). ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_comigt_sd ++FORCE_INLINE int _mm_comigt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vgetq_lane_u64(vcgtq_f64(a, b), 0) & 0x1; ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ ++ return (*(double *) &a0 > *(double *) &b0); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for less-than-or-equal, and return the boolean result (0 or 1). ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_comile_sd ++FORCE_INLINE int _mm_comile_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vgetq_lane_u64(vcleq_f64(a, b), 0) & 0x1; ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ ++ return (*(double *) &a0 <= *(double *) &b0); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for less-than, and return the boolean result (0 or 1). ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_comilt_sd ++FORCE_INLINE int _mm_comilt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vgetq_lane_u64(vcltq_f64(a, b), 0) & 0x1; ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ ++ return (*(double *) &a0 < *(double *) &b0); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for equality, and return the boolean result (0 or 1). ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_comieq_sd ++FORCE_INLINE int _mm_comieq_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vgetq_lane_u64(vceqq_f64(a, b), 0) & 0x1; ++#else ++ uint32x4_t a_not_nan = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(a)); ++ uint32x4_t b_not_nan = ++ vceqq_u32(vreinterpretq_u32_m128d(b), vreinterpretq_u32_m128d(b)); ++ uint32x4_t a_and_b_not_nan = vandq_u32(a_not_nan, b_not_nan); ++ uint32x4_t a_eq_b = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint64x2_t and_results = vandq_u64(vreinterpretq_u64_u32(a_and_b_not_nan), ++ vreinterpretq_u64_u32(a_eq_b)); ++ return vgetq_lane_u64(and_results, 0) & 0x1; ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for not-equal, and return the boolean result (0 or 1). ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_comineq_sd ++FORCE_INLINE int _mm_comineq_sd(__m128d a, __m128d b) ++{ ++ return !_mm_comieq_sd(a, b); ++} ++ ++// Convert packed signed 32-bit integers in a to packed double-precision ++// (64-bit) floating-point elements, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*32 ++// m := j*64 ++// dst[m+63:m] := Convert_Int32_To_FP64(a[i+31:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtepi32_pd ++FORCE_INLINE __m128d _mm_cvtepi32_pd(__m128i a) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vcvtq_f64_s64(vmovl_s32(vget_low_s32(vreinterpretq_s32_m128i(a))))); ++#else ++ double a0 = (double) vgetq_lane_s32(vreinterpretq_s32_m128i(a), 0); ++ double a1 = (double) vgetq_lane_s32(vreinterpretq_s32_m128i(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Converts the four signed 32-bit integer values of a to single-precision, ++// floating-point values ++// https://msdn.microsoft.com/en-us/library/vstudio/36bwxcx5(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cvtepi32_ps(__m128i a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32(vreinterpretq_s32_m128i(a))); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := 32*j ++// k := 64*j ++// dst[i+31:i] := Convert_FP64_To_Int32(a[k+63:k]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpd_epi32 ++FORCE_INLINE __m128i _mm_cvtpd_epi32(__m128d a) ++{ ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double d0 = ((double *) &rnd)[0]; ++ double d1 = ((double *) &rnd)[1]; ++ return _mm_set_epi32(0, 0, (int32_t) d1, (int32_t) d0); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := 32*j ++// k := 64*j ++// dst[i+31:i] := Convert_FP64_To_Int32(a[k+63:k]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpd_pi32 ++FORCE_INLINE __m64 _mm_cvtpd_pi32(__m128d a) ++{ ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double d0 = ((double *) &rnd)[0]; ++ double d1 = ((double *) &rnd)[1]; ++ int32_t ALIGN_STRUCT(16) data[2] = {(int32_t) d0, (int32_t) d1}; ++ return vreinterpret_m64_s32(vld1_s32(data)); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed single-precision (32-bit) floating-point elements, and store the ++// results in dst. ++// ++// FOR j := 0 to 1 ++// i := 32*j ++// k := 64*j ++// dst[i+31:i] := Convert_FP64_To_FP32(a[k+64:k]) ++// ENDFOR ++// dst[127:64] := 0 ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpd_ps ++FORCE_INLINE __m128 _mm_cvtpd_ps(__m128d a) ++{ ++#if defined(__aarch64__) ++ float32x2_t tmp = vcvt_f32_f64(vreinterpretq_f64_m128d(a)); ++ return vreinterpretq_m128_f32(vcombine_f32(tmp, vdup_n_f32(0))); ++#else ++ float a0 = (float) ((double *) &a)[0]; ++ float a1 = (float) ((double *) &a)[1]; ++ return _mm_set_ps(0, 0, a1, a0); ++#endif ++} ++ ++// Convert packed signed 32-bit integers in a to packed double-precision ++// (64-bit) floating-point elements, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*32 ++// m := j*64 ++// dst[m+63:m] := Convert_Int32_To_FP64(a[i+31:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtpi32_pd ++FORCE_INLINE __m128d _mm_cvtpi32_pd(__m64 a) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vcvtq_f64_s64(vmovl_s32(vreinterpret_s32_m64(a)))); ++#else ++ double a0 = (double) vget_lane_s32(vreinterpret_s32_m64(a), 0); ++ double a1 = (double) vget_lane_s32(vreinterpret_s32_m64(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Converts the four single-precision, floating-point values of a to signed ++// 32-bit integer values. ++// ++// r0 := (int) a0 ++// r1 := (int) a1 ++// r2 := (int) a2 ++// r3 := (int) a3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/xdc42k5e(v=vs.100).aspx ++// *NOTE*. The default rounding mode on SSE is 'round to even', which ARMv7-A ++// does not support! It is supported on ARMv8-A however. ++FORCE_INLINE __m128i _mm_cvtps_epi32(__m128 a) ++{ ++#if defined(__aarch64__) || defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ switch (_MM_GET_ROUNDING_MODE()) { ++ case _MM_ROUND_NEAREST: ++ return vreinterpretq_m128i_s32(vcvtnq_s32_f32(a)); ++ case _MM_ROUND_DOWN: ++ return vreinterpretq_m128i_s32(vcvtmq_s32_f32(a)); ++ case _MM_ROUND_UP: ++ return vreinterpretq_m128i_s32(vcvtpq_s32_f32(a)); ++ default: // _MM_ROUND_TOWARD_ZERO ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(a)); ++ } ++#else ++ float *f = (float *) &a; ++ switch (_MM_GET_ROUNDING_MODE()) { ++ case _MM_ROUND_NEAREST: { ++ uint32x4_t signmask = vdupq_n_u32(0x80000000); ++ float32x4_t half = vbslq_f32(signmask, vreinterpretq_f32_m128(a), ++ vdupq_n_f32(0.5f)); /* +/- 0.5 */ ++ int32x4_t r_normal = vcvtq_s32_f32(vaddq_f32( ++ vreinterpretq_f32_m128(a), half)); /* round to integer: [a + 0.5]*/ ++ int32x4_t r_trunc = vcvtq_s32_f32( ++ vreinterpretq_f32_m128(a)); /* truncate to integer: [a] */ ++ int32x4_t plusone = vreinterpretq_s32_u32(vshrq_n_u32( ++ vreinterpretq_u32_s32(vnegq_s32(r_trunc)), 31)); /* 1 or 0 */ ++ int32x4_t r_even = vbicq_s32(vaddq_s32(r_trunc, plusone), ++ vdupq_n_s32(1)); /* ([a] + {0,1}) & ~1 */ ++ float32x4_t delta = vsubq_f32( ++ vreinterpretq_f32_m128(a), ++ vcvtq_f32_s32(r_trunc)); /* compute delta: delta = (a - [a]) */ ++ uint32x4_t is_delta_half = ++ vceqq_f32(delta, half); /* delta == +/- 0.5 */ ++ return vreinterpretq_m128i_s32( ++ vbslq_s32(is_delta_half, r_even, r_normal)); ++ } ++ case _MM_ROUND_DOWN: ++ return _mm_set_epi32(floorf(f[3]), floorf(f[2]), floorf(f[1]), ++ floorf(f[0])); ++ case _MM_ROUND_UP: ++ return _mm_set_epi32(ceilf(f[3]), ceilf(f[2]), ceilf(f[1]), ++ ceilf(f[0])); ++ default: // _MM_ROUND_TOWARD_ZERO ++ return _mm_set_epi32((int32_t) f[3], (int32_t) f[2], (int32_t) f[1], ++ (int32_t) f[0]); ++ } ++#endif ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed double-precision (64-bit) floating-point elements, and store the ++// results in dst. ++// ++// FOR j := 0 to 1 ++// i := 64*j ++// k := 32*j ++// dst[i+63:i] := Convert_FP32_To_FP64(a[k+31:k]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtps_pd ++FORCE_INLINE __m128d _mm_cvtps_pd(__m128 a) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vcvt_f64_f32(vget_low_f32(vreinterpretq_f32_m128(a)))); ++#else ++ double a0 = (double) vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ double a1 = (double) vgetq_lane_f32(vreinterpretq_f32_m128(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Copy the lower double-precision (64-bit) floating-point element of a to dst. ++// ++// dst[63:0] := a[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsd_f64 ++FORCE_INLINE double _mm_cvtsd_f64(__m128d a) ++{ ++#if defined(__aarch64__) ++ return (double) vgetq_lane_f64(vreinterpretq_f64_m128d(a), 0); ++#else ++ return ((double *) &a)[0]; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// ++// dst[31:0] := Convert_FP64_To_Int32(a[63:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsd_si32 ++FORCE_INLINE int32_t _mm_cvtsd_si32(__m128d a) ++{ ++#if defined(__aarch64__) ++ return (int32_t) vgetq_lane_f64(vrndiq_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double ret = ((double *) &rnd)[0]; ++ return (int32_t) ret; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// ++// dst[63:0] := Convert_FP64_To_Int64(a[63:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsd_si64 ++FORCE_INLINE int64_t _mm_cvtsd_si64(__m128d a) ++{ ++#if defined(__aarch64__) ++ return (int64_t) vgetq_lane_f64(vrndiq_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double ret = ((double *) &rnd)[0]; ++ return (int64_t) ret; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// ++// dst[63:0] := Convert_FP64_To_Int64(a[63:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsd_si64x ++#define _mm_cvtsd_si64x _mm_cvtsd_si64 ++ ++// Convert the lower double-precision (64-bit) floating-point element in b to a ++// single-precision (32-bit) floating-point element, store the result in the ++// lower element of dst, and copy the upper 3 packed elements from a to the ++// upper elements of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsd_ss ++FORCE_INLINE __m128 _mm_cvtsd_ss(__m128 a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128_f32(vsetq_lane_f32( ++ vget_lane_f32(vcvt_f32_f64(vreinterpretq_f64_m128d(b)), 0), ++ vreinterpretq_f32_m128(a), 0)); ++#else ++ return vreinterpretq_m128_f32(vsetq_lane_f32((float) ((double *) &b)[0], ++ vreinterpretq_f32_m128(a), 0)); ++#endif ++} ++ ++// Copy the lower 32-bit integer in a to dst. ++// ++// dst[31:0] := a[31:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi128_si32 ++FORCE_INLINE int _mm_cvtsi128_si32(__m128i a) ++{ ++ return vgetq_lane_s32(vreinterpretq_s32_m128i(a), 0); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// ++// dst[63:0] := a[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi128_si64 ++FORCE_INLINE int64_t _mm_cvtsi128_si64(__m128i a) ++{ ++ return vgetq_lane_s64(vreinterpretq_s64_m128i(a), 0); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi128_si64x ++#define _mm_cvtsi128_si64x(a) _mm_cvtsi128_si64(a) ++ ++// Convert the signed 32-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi32_sd ++FORCE_INLINE __m128d _mm_cvtsi32_sd(__m128d a, int32_t b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64((double) b, vreinterpretq_f64_m128d(a), 0)); ++#else ++ double bf = (double) b; ++ return vreinterpretq_m128d_s64( ++ vsetq_lane_s64(*(int64_t *) &bf, vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// ++// dst[63:0] := a[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi128_si64x ++#define _mm_cvtsi128_si64x(a) _mm_cvtsi128_si64(a) ++ ++// Moves 32-bit integer a to the least significant 32 bits of an __m128 object, ++// zero extending the upper bits. ++// ++// r0 := a ++// r1 := 0x0 ++// r2 := 0x0 ++// r3 := 0x0 ++// ++// https://msdn.microsoft.com/en-us/library/ct3539ha%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_cvtsi32_si128(int a) ++{ ++ return vreinterpretq_m128i_s32(vsetq_lane_s32(a, vdupq_n_s32(0), 0)); ++} ++ ++// Convert the signed 64-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi64_sd ++FORCE_INLINE __m128d _mm_cvtsi64_sd(__m128d a, int64_t b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64((double) b, vreinterpretq_f64_m128d(a), 0)); ++#else ++ double bf = (double) b; ++ return vreinterpretq_m128d_s64( ++ vsetq_lane_s64(*(int64_t *) &bf, vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Moves 64-bit integer a to the least significant 64 bits of an __m128 object, ++// zero extending the upper bits. ++// ++// r0 := a ++// r1 := 0x0 ++FORCE_INLINE __m128i _mm_cvtsi64_si128(int64_t a) ++{ ++ return vreinterpretq_m128i_s64(vsetq_lane_s64(a, vdupq_n_s64(0), 0)); ++} ++ ++// Copy 64-bit integer a to the lower element of dst, and zero the upper ++// element. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi64x_si128 ++#define _mm_cvtsi64x_si128(a) _mm_cvtsi64_si128(a) ++ ++// Convert the signed 64-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi64x_sd ++#define _mm_cvtsi64x_sd(a, b) _mm_cvtsi64_sd(a, b) ++ ++// Convert the lower single-precision (32-bit) floating-point element in b to a ++// double-precision (64-bit) floating-point element, store the result in the ++// lower element of dst, and copy the upper element from a to the upper element ++// of dst. ++// ++// dst[63:0] := Convert_FP32_To_FP64(b[31:0]) ++// dst[127:64] := a[127:64] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtss_sd ++FORCE_INLINE __m128d _mm_cvtss_sd(__m128d a, __m128 b) ++{ ++ double d = (double) vgetq_lane_f32(vreinterpretq_f32_m128(b), 0); ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64(d, vreinterpretq_f64_m128d(a), 0)); ++#else ++ return vreinterpretq_m128d_s64( ++ vsetq_lane_s64(*(int64_t *) &d, vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvttpd_epi32 ++FORCE_INLINE __m128i _mm_cvttpd_epi32(__m128d a) ++{ ++ double a0 = ((double *) &a)[0]; ++ double a1 = ((double *) &a)[1]; ++ return _mm_set_epi32(0, 0, (int32_t) a1, (int32_t) a0); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvttpd_pi32 ++FORCE_INLINE __m64 _mm_cvttpd_pi32(__m128d a) ++{ ++ double a0 = ((double *) &a)[0]; ++ double a1 = ((double *) &a)[1]; ++ int32_t ALIGN_STRUCT(16) data[2] = {(int32_t) a0, (int32_t) a1}; ++ return vreinterpret_m64_s32(vld1_s32(data)); ++} ++ ++// Converts the four single-precision, floating-point values of a to signed ++// 32-bit integer values using truncate. ++// https://msdn.microsoft.com/en-us/library/vstudio/1h005y6x(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cvttps_epi32(__m128 a) ++{ ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a))); ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// ++// dst[63:0] := Convert_FP64_To_Int32_Truncate(a[63:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvttsd_si32 ++FORCE_INLINE int32_t _mm_cvttsd_si32(__m128d a) ++{ ++ double ret = *((double *) &a); ++ return (int32_t) ret; ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// ++// dst[63:0] := Convert_FP64_To_Int64_Truncate(a[63:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvttsd_si64 ++FORCE_INLINE int64_t _mm_cvttsd_si64(__m128d a) ++{ ++#if defined(__aarch64__) ++ return vgetq_lane_s64(vcvtq_s64_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ double ret = *((double *) &a); ++ return (int64_t) ret; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// ++// dst[63:0] := Convert_FP64_To_Int64_Truncate(a[63:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvttsd_si64x ++#define _mm_cvttsd_si64x(a) _mm_cvttsd_si64(a) ++ ++// Divide packed double-precision (64-bit) floating-point elements in a by ++// packed elements in b, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := 64*j ++// dst[i+63:i] := a[i+63:i] / b[i+63:i] ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_div_pd ++FORCE_INLINE __m128d _mm_div_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vdivq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] / db[0]; ++ c[1] = da[1] / db[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Divide the lower double-precision (64-bit) floating-point element in a by the ++// lower double-precision (64-bit) floating-point element in b, store the result ++// in the lower element of dst, and copy the upper element from a to the upper ++// element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_div_sd ++FORCE_INLINE __m128d _mm_div_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ float64x2_t tmp = ++ vdivq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64(vgetq_lane_f64(vreinterpretq_f64_m128d(a), 1), tmp, 1)); ++#else ++ return _mm_move_sd(a, _mm_div_pd(a, b)); ++#endif ++} ++ ++// Extracts the selected signed or unsigned 16-bit integer from a and zero ++// extends. ++// https://msdn.microsoft.com/en-us/library/6dceta0c(v=vs.100).aspx ++// FORCE_INLINE int _mm_extract_epi16(__m128i a, __constrange(0,8) int imm) ++#define _mm_extract_epi16(a, imm) \ ++ vgetq_lane_u16(vreinterpretq_u16_m128i(a), (imm)) ++ ++// Inserts the least significant 16 bits of b into the selected 16-bit integer ++// of a. ++// https://msdn.microsoft.com/en-us/library/kaze8hz1%28v=vs.100%29.aspx ++// FORCE_INLINE __m128i _mm_insert_epi16(__m128i a, int b, ++// __constrange(0,8) int imm) ++#define _mm_insert_epi16(a, b, imm) \ ++ __extension__({ \ ++ vreinterpretq_m128i_s16( \ ++ vsetq_lane_s16((b), vreinterpretq_s16_m128i(a), (imm))); \ ++ }) ++ ++// Loads two double-precision from 16-byte aligned memory, floating-point ++// values. ++// ++// dst[127:0] := MEM[mem_addr+127:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_load_pd ++FORCE_INLINE __m128d _mm_load_pd(const double *p) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vld1q_f64(p)); ++#else ++ const float *fp = (const float *) p; ++ float ALIGN_STRUCT(16) data[4] = {fp[0], fp[1], fp[2], fp[3]}; ++ return vreinterpretq_m128d_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// ++// dst[63:0] := MEM[mem_addr+63:mem_addr] ++// dst[127:64] := MEM[mem_addr+63:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_load_pd1 ++#define _mm_load_pd1 _mm_load1_pd ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// lower of dst, and zero the upper element. mem_addr does not need to be ++// aligned on any particular boundary. ++// ++// dst[63:0] := MEM[mem_addr+63:mem_addr] ++// dst[127:64] := 0 ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_load_sd ++FORCE_INLINE __m128d _mm_load_sd(const double *p) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vsetq_lane_f64(*p, vdupq_n_f64(0), 0)); ++#else ++ const float *fp = (const float *) p; ++ float ALIGN_STRUCT(16) data[4] = {fp[0], fp[1], 0, 0}; ++ return vreinterpretq_m128d_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Loads 128-bit value. : ++// https://msdn.microsoft.com/en-us/library/atzzad1h(v=vs.80).aspx ++FORCE_INLINE __m128i _mm_load_si128(const __m128i *p) ++{ ++ return vreinterpretq_m128i_s32(vld1q_s32((const int32_t *) p)); ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// ++// dst[63:0] := MEM[mem_addr+63:mem_addr] ++// dst[127:64] := MEM[mem_addr+63:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_load1_pd ++FORCE_INLINE __m128d _mm_load1_pd(const double *p) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vld1q_dup_f64(p)); ++#else ++ return vreinterpretq_m128d_s64(vdupq_n_s64(*(const int64_t *) p)); ++#endif ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// upper element of dst, and copy the lower element from a to dst. mem_addr does ++// not need to be aligned on any particular boundary. ++// ++// dst[63:0] := a[63:0] ++// dst[127:64] := MEM[mem_addr+63:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadh_pd ++FORCE_INLINE __m128d _mm_loadh_pd(__m128d a, const double *p) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vcombine_f64(vget_low_f64(vreinterpretq_f64_m128d(a)), vld1_f64(p))); ++#else ++ return vreinterpretq_m128d_f32(vcombine_f32( ++ vget_low_f32(vreinterpretq_f32_m128d(a)), vld1_f32((const float *) p))); ++#endif ++} ++ ++// Load 64-bit integer from memory into the first element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadl_epi64 ++FORCE_INLINE __m128i _mm_loadl_epi64(__m128i const *p) ++{ ++ /* Load the lower 64 bits of the value pointed to by p into the ++ * lower 64 bits of the result, zeroing the upper 64 bits of the result. ++ */ ++ return vreinterpretq_m128i_s32( ++ vcombine_s32(vld1_s32((int32_t const *) p), vcreate_s32(0))); ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// lower element of dst, and copy the upper element from a to dst. mem_addr does ++// not need to be aligned on any particular boundary. ++// ++// dst[63:0] := MEM[mem_addr+63:mem_addr] ++// dst[127:64] := a[127:64] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadl_pd ++FORCE_INLINE __m128d _mm_loadl_pd(__m128d a, const double *p) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vcombine_f64(vld1_f64(p), vget_high_f64(vreinterpretq_f64_m128d(a)))); ++#else ++ return vreinterpretq_m128d_f32( ++ vcombine_f32(vld1_f32((const float *) p), ++ vget_high_f32(vreinterpretq_f32_m128d(a)))); ++#endif ++} ++ ++// Load 2 double-precision (64-bit) floating-point elements from memory into dst ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// ++// dst[63:0] := MEM[mem_addr+127:mem_addr+64] ++// dst[127:64] := MEM[mem_addr+63:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadr_pd ++FORCE_INLINE __m128d _mm_loadr_pd(const double *p) ++{ ++#if defined(__aarch64__) ++ float64x2_t v = vld1q_f64(p); ++ return vreinterpretq_m128d_f64(vextq_f64(v, v, 1)); ++#else ++ int64x2_t v = vld1q_s64((const int64_t *) p); ++ return vreinterpretq_m128d_s64(vextq_s64(v, v, 1)); ++#endif ++} ++ ++// Loads two double-precision from unaligned memory, floating-point values. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadu_pd ++FORCE_INLINE __m128d _mm_loadu_pd(const double *p) ++{ ++ return _mm_load_pd(p); ++} ++ ++// Loads 128-bit value. : ++// https://msdn.microsoft.com/zh-cn/library/f4k12ae8(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_loadu_si128(const __m128i *p) ++{ ++ return vreinterpretq_m128i_s32(vld1q_s32((const int32_t *) p)); ++} ++ ++// Load unaligned 32-bit integer from memory into the first element of dst. ++// ++// dst[31:0] := MEM[mem_addr+31:mem_addr] ++// dst[MAX:32] := 0 ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loadu_si32 ++FORCE_INLINE __m128i _mm_loadu_si32(const void *p) ++{ ++ return vreinterpretq_m128i_s32( ++ vsetq_lane_s32(*(const int32_t *) p, vdupq_n_s32(0), 0)); ++} ++ ++// Multiplies the 8 signed 16-bit integers from a by the 8 signed 16-bit ++// integers from b. ++// ++// r0 := (a0 * b0) + (a1 * b1) ++// r1 := (a2 * b2) + (a3 * b3) ++// r2 := (a4 * b4) + (a5 * b5) ++// r3 := (a6 * b6) + (a7 * b7) ++// https://msdn.microsoft.com/en-us/library/yht36sa6(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_madd_epi16(__m128i a, __m128i b) ++{ ++ int32x4_t low = vmull_s16(vget_low_s16(vreinterpretq_s16_m128i(a)), ++ vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int32x4_t high = vmull_s16(vget_high_s16(vreinterpretq_s16_m128i(a)), ++ vget_high_s16(vreinterpretq_s16_m128i(b))); ++ ++ int32x2_t low_sum = vpadd_s32(vget_low_s32(low), vget_high_s32(low)); ++ int32x2_t high_sum = vpadd_s32(vget_low_s32(high), vget_high_s32(high)); ++ ++ return vreinterpretq_m128i_s32(vcombine_s32(low_sum, high_sum)); ++} ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. mem_addr does not need to be aligned ++// on any particular boundary. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_maskmoveu_si128 ++FORCE_INLINE void _mm_maskmoveu_si128(__m128i a, __m128i mask, char *mem_addr) ++{ ++ int8x16_t shr_mask = vshrq_n_s8(vreinterpretq_s8_m128i(mask), 7); ++ __m128 b = _mm_load_ps((const float *) mem_addr); ++ int8x16_t masked = ++ vbslq_s8(vreinterpretq_u8_s8(shr_mask), vreinterpretq_s8_m128i(a), ++ vreinterpretq_s8_m128(b)); ++ vst1q_s8((int8_t *) mem_addr, masked); ++} ++ ++// Computes the pairwise maxima of the 8 signed 16-bit integers from a and the 8 ++// signed 16-bit integers from b. ++// https://msdn.microsoft.com/en-us/LIBRary/3x060h7c(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_max_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vmaxq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Computes the pairwise maxima of the 16 unsigned 8-bit integers from a and the ++// 16 unsigned 8-bit integers from b. ++// https://msdn.microsoft.com/en-us/library/st6634za(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_max_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vmaxq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b, ++// and store packed maximum values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_max_pd ++FORCE_INLINE __m128d _mm_max_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++#if SSE2NEON_PRECISE_MINMAX ++ float64x2_t _a = vreinterpretq_f64_m128d(a); ++ float64x2_t _b = vreinterpretq_f64_m128d(b); ++ return vreinterpretq_m128d_f64(vbslq_f64(vcgtq_f64(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128d_f64( ++ vmaxq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#endif ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) > (*(double *) &b0) ? a0 : b0; ++ d[1] = (*(double *) &a1) > (*(double *) &b1) ? a1 : b1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b, store the maximum value in the lower element of dst, and copy the upper ++// element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_max_sd ++FORCE_INLINE __m128d _mm_max_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_max_pd(a, b)); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2] = {da[0] > db[0] ? da[0] : db[0], da[1]}; ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) c)); ++#endif ++} ++ ++// Computes the pairwise minima of the 8 signed 16-bit integers from a and the 8 ++// signed 16-bit integers from b. ++// https://msdn.microsoft.com/en-us/library/vstudio/6te997ew(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_min_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vminq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Computes the pairwise minima of the 16 unsigned 8-bit integers from a and the ++// 16 unsigned 8-bit integers from b. ++// https://msdn.microsoft.com/ko-kr/library/17k8cf58(v=vs.100).aspxx ++FORCE_INLINE __m128i _mm_min_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vminq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b, ++// and store packed minimum values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_min_pd ++FORCE_INLINE __m128d _mm_min_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++#if SSE2NEON_PRECISE_MINMAX ++ float64x2_t _a = vreinterpretq_f64_m128d(a); ++ float64x2_t _b = vreinterpretq_f64_m128d(b); ++ return vreinterpretq_m128d_f64(vbslq_f64(vcltq_f64(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128d_f64( ++ vminq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#endif ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) < (*(double *) &b0) ? a0 : b0; ++ d[1] = (*(double *) &a1) < (*(double *) &b1) ? a1 : b1; ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b, store the minimum value in the lower element of dst, and copy the upper ++// element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_min_sd ++FORCE_INLINE __m128d _mm_min_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_min_pd(a, b)); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2] = {da[0] < db[0] ? da[0] : db[0], da[1]}; ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) c)); ++#endif ++} ++ ++// Copy the lower 64-bit integer in a to the lower element of dst, and zero the ++// upper element. ++// ++// dst[63:0] := a[63:0] ++// dst[127:64] := 0 ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_move_epi64 ++FORCE_INLINE __m128i _mm_move_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_s64( ++ vsetq_lane_s64(0, vreinterpretq_s64_m128i(a), 1)); ++} ++ ++// Move the lower double-precision (64-bit) floating-point element from b to the ++// lower element of dst, and copy the upper element from a to the upper element ++// of dst. ++// ++// dst[63:0] := b[63:0] ++// dst[127:64] := a[127:64] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_move_sd ++FORCE_INLINE __m128d _mm_move_sd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_f32( ++ vcombine_f32(vget_low_f32(vreinterpretq_f32_m128d(b)), ++ vget_high_f32(vreinterpretq_f32_m128d(a)))); ++} ++ ++// NEON does not provide a version of this function. ++// Creates a 16-bit mask from the most significant bits of the 16 signed or ++// unsigned 8-bit integers in a and zero extends the upper bits. ++// https://msdn.microsoft.com/en-us/library/vstudio/s090c8fk(v=vs.100).aspx ++FORCE_INLINE int _mm_movemask_epi8(__m128i a) ++{ ++ // Use increasingly wide shifts+adds to collect the sign bits ++ // together. ++ // Since the widening shifts would be rather confusing to follow in little ++ // endian, everything will be illustrated in big endian order instead. This ++ // has a different result - the bits would actually be reversed on a big ++ // endian machine. ++ ++ // Starting input (only half the elements are shown): ++ // 89 ff 1d c0 00 10 99 33 ++ uint8x16_t input = vreinterpretq_u8_m128i(a); ++ ++ // Shift out everything but the sign bits with an unsigned shift right. ++ // ++ // Bytes of the vector:: ++ // 89 ff 1d c0 00 10 99 33 ++ // \ \ \ \ \ \ \ \ high_bits = (uint16x4_t)(input >> 7) ++ // | | | | | | | | ++ // 01 01 00 01 00 00 01 00 ++ // ++ // Bits of first important lane(s): ++ // 10001001 (89) ++ // \______ ++ // | ++ // 00000001 (01) ++ uint16x8_t high_bits = vreinterpretq_u16_u8(vshrq_n_u8(input, 7)); ++ ++ // Merge the even lanes together with a 16-bit unsigned shift right + add. ++ // 'xx' represents garbage data which will be ignored in the final result. ++ // In the important bytes, the add functions like a binary OR. ++ // ++ // 01 01 00 01 00 00 01 00 ++ // \_ | \_ | \_ | \_ | paired16 = (uint32x4_t)(input + (input >> 7)) ++ // \| \| \| \| ++ // xx 03 xx 01 xx 00 xx 02 ++ // ++ // 00000001 00000001 (01 01) ++ // \_______ | ++ // \| ++ // xxxxxxxx xxxxxx11 (xx 03) ++ uint32x4_t paired16 = ++ vreinterpretq_u32_u16(vsraq_n_u16(high_bits, high_bits, 7)); ++ ++ // Repeat with a wider 32-bit shift + add. ++ // xx 03 xx 01 xx 00 xx 02 ++ // \____ | \____ | paired32 = (uint64x1_t)(paired16 + (paired16 >> ++ // 14)) ++ // \| \| ++ // xx xx xx 0d xx xx xx 02 ++ // ++ // 00000011 00000001 (03 01) ++ // \\_____ || ++ // '----.\|| ++ // xxxxxxxx xxxx1101 (xx 0d) ++ uint64x2_t paired32 = ++ vreinterpretq_u64_u32(vsraq_n_u32(paired16, paired16, 14)); ++ ++ // Last, an even wider 64-bit shift + add to get our result in the low 8 bit ++ // lanes. xx xx xx 0d xx xx xx 02 ++ // \_________ | paired64 = (uint8x8_t)(paired32 + (paired32 >> ++ // 28)) ++ // \| ++ // xx xx xx xx xx xx xx d2 ++ // ++ // 00001101 00000010 (0d 02) ++ // \ \___ | | ++ // '---. \| | ++ // xxxxxxxx 11010010 (xx d2) ++ uint8x16_t paired64 = ++ vreinterpretq_u8_u64(vsraq_n_u64(paired32, paired32, 28)); ++ ++ // Extract the low 8 bits from each 64-bit lane with 2 8-bit extracts. ++ // xx xx xx xx xx xx xx d2 ++ // || return paired64[0] ++ // d2 ++ // Note: Little endian would return the correct value 4b (01001011) instead. ++ return vgetq_lane_u8(paired64, 0) | ((int) vgetq_lane_u8(paired64, 8) << 8); ++} ++ ++// Set each bit of mask dst based on the most significant bit of the ++// corresponding packed double-precision (64-bit) floating-point element in a. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_movemask_pd ++FORCE_INLINE int _mm_movemask_pd(__m128d a) ++{ ++ uint64x2_t input = vreinterpretq_u64_m128d(a); ++ uint64x2_t high_bits = vshrq_n_u64(input, 63); ++ return vgetq_lane_u64(high_bits, 0) | (vgetq_lane_u64(high_bits, 1) << 1); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// ++// dst[63:0] := a[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_movepi64_pi64 ++FORCE_INLINE __m64 _mm_movepi64_pi64(__m128i a) ++{ ++ return vreinterpret_m64_s64(vget_low_s64(vreinterpretq_s64_m128i(a))); ++} ++ ++// Copy the 64-bit integer a to the lower element of dst, and zero the upper ++// element. ++// ++// dst[63:0] := a[63:0] ++// dst[127:64] := 0 ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_movpi64_epi64 ++FORCE_INLINE __m128i _mm_movpi64_epi64(__m64 a) ++{ ++ return vreinterpretq_m128i_s64( ++ vcombine_s64(vreinterpret_s64_m64(a), vdup_n_s64(0))); ++} ++ ++// Multiply the low unsigned 32-bit integers from each packed 64-bit element in ++// a and b, and store the unsigned 64-bit results in dst. ++// ++// r0 := (a0 & 0xFFFFFFFF) * (b0 & 0xFFFFFFFF) ++// r1 := (a2 & 0xFFFFFFFF) * (b2 & 0xFFFFFFFF) ++FORCE_INLINE __m128i _mm_mul_epu32(__m128i a, __m128i b) ++{ ++ // vmull_u32 upcasts instead of masking, so we downcast. ++ uint32x2_t a_lo = vmovn_u64(vreinterpretq_u64_m128i(a)); ++ uint32x2_t b_lo = vmovn_u64(vreinterpretq_u64_m128i(b)); ++ return vreinterpretq_m128i_u64(vmull_u32(a_lo, b_lo)); ++} ++ ++// Multiply packed double-precision (64-bit) floating-point elements in a and b, ++// and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_mul_pd ++FORCE_INLINE __m128d _mm_mul_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vmulq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] * db[0]; ++ c[1] = da[1] * db[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Multiply the lower double-precision (64-bit) floating-point element in a and ++// b, store the result in the lower element of dst, and copy the upper element ++// from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=mm_mul_sd ++FORCE_INLINE __m128d _mm_mul_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_mul_pd(a, b)); ++} ++ ++// Multiply the low unsigned 32-bit integers from a and b, and store the ++// unsigned 64-bit result in dst. ++// ++// dst[63:0] := a[31:0] * b[31:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_mul_su32 ++FORCE_INLINE __m64 _mm_mul_su32(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u64(vget_low_u64( ++ vmull_u32(vreinterpret_u32_m64(a), vreinterpret_u32_m64(b)))); ++} ++ ++// Multiplies the 8 signed 16-bit integers from a by the 8 signed 16-bit ++// integers from b. ++// ++// r0 := (a0 * b0)[31:16] ++// r1 := (a1 * b1)[31:16] ++// ... ++// r7 := (a7 * b7)[31:16] ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/59hddw1d(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_mulhi_epi16(__m128i a, __m128i b) ++{ ++ /* FIXME: issue with large values because of result saturation */ ++ // int16x8_t ret = vqdmulhq_s16(vreinterpretq_s16_m128i(a), ++ // vreinterpretq_s16_m128i(b)); /* =2*a*b */ return ++ // vreinterpretq_m128i_s16(vshrq_n_s16(ret, 1)); ++ int16x4_t a3210 = vget_low_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b3210 = vget_low_s16(vreinterpretq_s16_m128i(b)); ++ int32x4_t ab3210 = vmull_s16(a3210, b3210); /* 3333222211110000 */ ++ int16x4_t a7654 = vget_high_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b7654 = vget_high_s16(vreinterpretq_s16_m128i(b)); ++ int32x4_t ab7654 = vmull_s16(a7654, b7654); /* 7777666655554444 */ ++ uint16x8x2_t r = ++ vuzpq_u16(vreinterpretq_u16_s32(ab3210), vreinterpretq_u16_s32(ab7654)); ++ return vreinterpretq_m128i_u16(r.val[1]); ++} ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_mulhi_epu16 ++FORCE_INLINE __m128i _mm_mulhi_epu16(__m128i a, __m128i b) ++{ ++ uint16x4_t a3210 = vget_low_u16(vreinterpretq_u16_m128i(a)); ++ uint16x4_t b3210 = vget_low_u16(vreinterpretq_u16_m128i(b)); ++ uint32x4_t ab3210 = vmull_u16(a3210, b3210); ++#if defined(__aarch64__) ++ uint32x4_t ab7654 = ++ vmull_high_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b)); ++ uint16x8_t r = vuzp2q_u16(vreinterpretq_u16_u32(ab3210), ++ vreinterpretq_u16_u32(ab7654)); ++ return vreinterpretq_m128i_u16(r); ++#else ++ uint16x4_t a7654 = vget_high_u16(vreinterpretq_u16_m128i(a)); ++ uint16x4_t b7654 = vget_high_u16(vreinterpretq_u16_m128i(b)); ++ uint32x4_t ab7654 = vmull_u16(a7654, b7654); ++ uint16x8x2_t r = ++ vuzpq_u16(vreinterpretq_u16_u32(ab3210), vreinterpretq_u16_u32(ab7654)); ++ return vreinterpretq_m128i_u16(r.val[1]); ++#endif ++} ++ ++// Multiplies the 8 signed or unsigned 16-bit integers from a by the 8 signed or ++// unsigned 16-bit integers from b. ++// ++// r0 := (a0 * b0)[15:0] ++// r1 := (a1 * b1)[15:0] ++// ... ++// r7 := (a7 * b7)[15:0] ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/9ks1472s(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_mullo_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vmulq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compute the bitwise OR of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=mm_or_pd ++FORCE_INLINE __m128d _mm_or_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ vorrq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Computes the bitwise OR of the 128-bit value in a and the 128-bit value in b. ++// ++// r := a | b ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/ew8ty0db(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_or_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vorrq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Packs the 16 signed 16-bit integers from a and b into 8-bit integers and ++// saturates. ++// https://msdn.microsoft.com/en-us/library/k4y4f7w5%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_packs_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vcombine_s8(vqmovn_s16(vreinterpretq_s16_m128i(a)), ++ vqmovn_s16(vreinterpretq_s16_m128i(b)))); ++} ++ ++// Packs the 8 signed 32-bit integers from a and b into signed 16-bit integers ++// and saturates. ++// ++// r0 := SignedSaturate(a0) ++// r1 := SignedSaturate(a1) ++// r2 := SignedSaturate(a2) ++// r3 := SignedSaturate(a3) ++// r4 := SignedSaturate(b0) ++// r5 := SignedSaturate(b1) ++// r6 := SignedSaturate(b2) ++// r7 := SignedSaturate(b3) ++// ++// https://msdn.microsoft.com/en-us/library/393t56f9%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_packs_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vqmovn_s32(vreinterpretq_s32_m128i(a)), ++ vqmovn_s32(vreinterpretq_s32_m128i(b)))); ++} ++ ++// Packs the 16 signed 16 - bit integers from a and b into 8 - bit unsigned ++// integers and saturates. ++// ++// r0 := UnsignedSaturate(a0) ++// r1 := UnsignedSaturate(a1) ++// ... ++// r7 := UnsignedSaturate(a7) ++// r8 := UnsignedSaturate(b0) ++// r9 := UnsignedSaturate(b1) ++// ... ++// r15 := UnsignedSaturate(b7) ++// ++// https://msdn.microsoft.com/en-us/library/07ad1wx4(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_packus_epi16(const __m128i a, const __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcombine_u8(vqmovun_s16(vreinterpretq_s16_m128i(a)), ++ vqmovun_s16(vreinterpretq_s16_m128i(b)))); ++} ++ ++// Pause the processor. This is typically used in spin-wait loops and depending ++// on the x86 processor typical values are in the 40-100 cycle range. The ++// 'yield' instruction isn't a good fit because it's effectively a nop on most ++// Arm cores. Experience with several databases has shown has shown an 'isb' is ++// a reasonable approximation. ++FORCE_INLINE void _mm_pause() ++{ ++ __asm__ __volatile__("isb\n"); ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce two ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of 64-bit elements in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sad_epu8 ++FORCE_INLINE __m128i _mm_sad_epu8(__m128i a, __m128i b) ++{ ++ uint16x8_t t = vpaddlq_u8(vabdq_u8((uint8x16_t) a, (uint8x16_t) b)); ++ return vreinterpretq_m128i_u64(vpaddlq_u32(vpaddlq_u16(t))); ++} ++ ++// Sets the 8 signed 16-bit integer values. ++// https://msdn.microsoft.com/en-au/library/3e0fek84(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_set_epi16(short i7, ++ short i6, ++ short i5, ++ short i4, ++ short i3, ++ short i2, ++ short i1, ++ short i0) ++{ ++ int16_t ALIGN_STRUCT(16) data[8] = {i0, i1, i2, i3, i4, i5, i6, i7}; ++ return vreinterpretq_m128i_s16(vld1q_s16(data)); ++} ++ ++// Sets the 4 signed 32-bit integer values. ++// https://msdn.microsoft.com/en-us/library/vstudio/019beekt(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_set_epi32(int i3, int i2, int i1, int i0) ++{ ++ int32_t ALIGN_STRUCT(16) data[4] = {i0, i1, i2, i3}; ++ return vreinterpretq_m128i_s32(vld1q_s32(data)); ++} ++ ++// Returns the __m128i structure with its two 64-bit integer values ++// initialized to the values of the two 64-bit integers passed in. ++// https://msdn.microsoft.com/en-us/library/dk2sdw0h(v=vs.120).aspx ++FORCE_INLINE __m128i _mm_set_epi64(__m64 i1, __m64 i2) ++{ ++ return _mm_set_epi64x((int64_t) i1, (int64_t) i2); ++} ++ ++// Returns the __m128i structure with its two 64-bit integer values ++// initialized to the values of the two 64-bit integers passed in. ++// https://msdn.microsoft.com/en-us/library/dk2sdw0h(v=vs.120).aspx ++FORCE_INLINE __m128i _mm_set_epi64x(int64_t i1, int64_t i2) ++{ ++ return vreinterpretq_m128i_s64( ++ vcombine_s64(vcreate_s64(i2), vcreate_s64(i1))); ++} ++ ++// Sets the 16 signed 8-bit integer values. ++// https://msdn.microsoft.com/en-us/library/x0cx8zd3(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_set_epi8(signed char b15, ++ signed char b14, ++ signed char b13, ++ signed char b12, ++ signed char b11, ++ signed char b10, ++ signed char b9, ++ signed char b8, ++ signed char b7, ++ signed char b6, ++ signed char b5, ++ signed char b4, ++ signed char b3, ++ signed char b2, ++ signed char b1, ++ signed char b0) ++{ ++ int8_t ALIGN_STRUCT(16) ++ data[16] = {(int8_t) b0, (int8_t) b1, (int8_t) b2, (int8_t) b3, ++ (int8_t) b4, (int8_t) b5, (int8_t) b6, (int8_t) b7, ++ (int8_t) b8, (int8_t) b9, (int8_t) b10, (int8_t) b11, ++ (int8_t) b12, (int8_t) b13, (int8_t) b14, (int8_t) b15}; ++ return (__m128i) vld1q_s8(data); ++} ++ ++// Set packed double-precision (64-bit) floating-point elements in dst with the ++// supplied values. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_set_pd ++FORCE_INLINE __m128d _mm_set_pd(double e1, double e0) ++{ ++ double ALIGN_STRUCT(16) data[2] = {e0, e1}; ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vld1q_f64((float64_t *) data)); ++#else ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) data)); ++#endif ++} ++ ++// Broadcast double-precision (64-bit) floating-point value a to all elements of ++// dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_set_pd1 ++#define _mm_set_pd1 _mm_set1_pd ++ ++// Copy double-precision (64-bit) floating-point element a to the lower element ++// of dst, and zero the upper element. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_set_sd ++FORCE_INLINE __m128d _mm_set_sd(double a) ++{ ++ return _mm_set_pd(0, a); ++} ++ ++// Sets the 8 signed 16-bit integer values to w. ++// ++// r0 := w ++// r1 := w ++// ... ++// r7 := w ++// ++// https://msdn.microsoft.com/en-us/library/k0ya3x0e(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_set1_epi16(short w) ++{ ++ return vreinterpretq_m128i_s16(vdupq_n_s16(w)); ++} ++ ++// Sets the 4 signed 32-bit integer values to i. ++// ++// r0 := i ++// r1 := i ++// r2 := i ++// r3 := I ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/h4xscxat(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_set1_epi32(int _i) ++{ ++ return vreinterpretq_m128i_s32(vdupq_n_s32(_i)); ++} ++ ++// Sets the 2 signed 64-bit integer values to i. ++// https://docs.microsoft.com/en-us/previous-versions/visualstudio/visual-studio-2010/whtfzhzk(v=vs.100) ++FORCE_INLINE __m128i _mm_set1_epi64(__m64 _i) ++{ ++ return vreinterpretq_m128i_s64(vdupq_n_s64((int64_t) _i)); ++} ++ ++// Sets the 2 signed 64-bit integer values to i. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_set1_epi64x ++FORCE_INLINE __m128i _mm_set1_epi64x(int64_t _i) ++{ ++ return vreinterpretq_m128i_s64(vdupq_n_s64(_i)); ++} ++ ++// Sets the 16 signed 8-bit integer values to b. ++// ++// r0 := b ++// r1 := b ++// ... ++// r15 := b ++// ++// https://msdn.microsoft.com/en-us/library/6e14xhyf(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_set1_epi8(signed char w) ++{ ++ return vreinterpretq_m128i_s8(vdupq_n_s8(w)); ++} ++ ++// Broadcast double-precision (64-bit) floating-point value a to all elements of ++// dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_set1_pd ++FORCE_INLINE __m128d _mm_set1_pd(double d) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vdupq_n_f64(d)); ++#else ++ return vreinterpretq_m128d_s64(vdupq_n_s64(*(int64_t *) &d)); ++#endif ++} ++ ++// Sets the 8 signed 16-bit integer values in reverse order. ++// ++// Return Value ++// r0 := w0 ++// r1 := w1 ++// ... ++// r7 := w7 ++FORCE_INLINE __m128i _mm_setr_epi16(short w0, ++ short w1, ++ short w2, ++ short w3, ++ short w4, ++ short w5, ++ short w6, ++ short w7) ++{ ++ int16_t ALIGN_STRUCT(16) data[8] = {w0, w1, w2, w3, w4, w5, w6, w7}; ++ return vreinterpretq_m128i_s16(vld1q_s16((int16_t *) data)); ++} ++ ++// Sets the 4 signed 32-bit integer values in reverse order ++// https://technet.microsoft.com/en-us/library/security/27yb3ee5(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_setr_epi32(int i3, int i2, int i1, int i0) ++{ ++ int32_t ALIGN_STRUCT(16) data[4] = {i3, i2, i1, i0}; ++ return vreinterpretq_m128i_s32(vld1q_s32(data)); ++} ++ ++// Set packed 64-bit integers in dst with the supplied values in reverse order. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_setr_epi64 ++FORCE_INLINE __m128i _mm_setr_epi64(__m64 e1, __m64 e0) ++{ ++ return vreinterpretq_m128i_s64(vcombine_s64(e1, e0)); ++} ++ ++// Sets the 16 signed 8-bit integer values in reverse order. ++// https://msdn.microsoft.com/en-us/library/2khb9c7k(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_setr_epi8(signed char b0, ++ signed char b1, ++ signed char b2, ++ signed char b3, ++ signed char b4, ++ signed char b5, ++ signed char b6, ++ signed char b7, ++ signed char b8, ++ signed char b9, ++ signed char b10, ++ signed char b11, ++ signed char b12, ++ signed char b13, ++ signed char b14, ++ signed char b15) ++{ ++ int8_t ALIGN_STRUCT(16) ++ data[16] = {(int8_t) b0, (int8_t) b1, (int8_t) b2, (int8_t) b3, ++ (int8_t) b4, (int8_t) b5, (int8_t) b6, (int8_t) b7, ++ (int8_t) b8, (int8_t) b9, (int8_t) b10, (int8_t) b11, ++ (int8_t) b12, (int8_t) b13, (int8_t) b14, (int8_t) b15}; ++ return (__m128i) vld1q_s8(data); ++} ++ ++// Set packed double-precision (64-bit) floating-point elements in dst with the ++// supplied values in reverse order. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_setr_pd ++FORCE_INLINE __m128d _mm_setr_pd(double e1, double e0) ++{ ++ return _mm_set_pd(e0, e1); ++} ++ ++// Return vector of type __m128d with all elements set to zero. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_setzero_pd ++FORCE_INLINE __m128d _mm_setzero_pd(void) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vdupq_n_f64(0)); ++#else ++ return vreinterpretq_m128d_f32(vdupq_n_f32(0)); ++#endif ++} ++ ++// Sets the 128-bit value to zero ++// https://msdn.microsoft.com/en-us/library/vstudio/ys7dw0kh(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_setzero_si128(void) ++{ ++ return vreinterpretq_m128i_s32(vdupq_n_s32(0)); ++} ++ ++// Shuffles the 4 signed or unsigned 32-bit integers in a as specified by imm. ++// https://msdn.microsoft.com/en-us/library/56f67xbk%28v=vs.90%29.aspx ++// FORCE_INLINE __m128i _mm_shuffle_epi32(__m128i a, ++// __constrange(0,255) int imm) ++#if __has_builtin(__builtin_shufflevector) ++#define _mm_shuffle_epi32(a, imm) \ ++ __extension__({ \ ++ int32x4_t _input = vreinterpretq_s32_m128i(a); \ ++ int32x4_t _shuf = __builtin_shufflevector( \ ++ _input, _input, (imm) & (0x3), ((imm) >> 2) & 0x3, \ ++ ((imm) >> 4) & 0x3, ((imm) >> 6) & 0x3); \ ++ vreinterpretq_m128i_s32(_shuf); \ ++ }) ++#else // generic ++#define _mm_shuffle_epi32(a, imm) \ ++ __extension__({ \ ++ __m128i ret; \ ++ switch (imm) { \ ++ case _MM_SHUFFLE(1, 0, 3, 2): \ ++ ret = _mm_shuffle_epi_1032((a)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 3, 0, 1): \ ++ ret = _mm_shuffle_epi_2301((a)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 3, 2, 1): \ ++ ret = _mm_shuffle_epi_0321((a)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 1, 0, 3): \ ++ ret = _mm_shuffle_epi_2103((a)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 1, 0): \ ++ ret = _mm_shuffle_epi_1010((a)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 0, 1): \ ++ ret = _mm_shuffle_epi_1001((a)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 0, 1): \ ++ ret = _mm_shuffle_epi_0101((a)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 1, 1): \ ++ ret = _mm_shuffle_epi_2211((a)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 2, 2): \ ++ ret = _mm_shuffle_epi_0122((a)); \ ++ break; \ ++ case _MM_SHUFFLE(3, 3, 3, 2): \ ++ ret = _mm_shuffle_epi_3332((a)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 0, 0): \ ++ ret = _mm_shuffle_epi32_splat((a), 0); \ ++ break; \ ++ case _MM_SHUFFLE(1, 1, 1, 1): \ ++ ret = _mm_shuffle_epi32_splat((a), 1); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 2, 2): \ ++ ret = _mm_shuffle_epi32_splat((a), 2); \ ++ break; \ ++ case _MM_SHUFFLE(3, 3, 3, 3): \ ++ ret = _mm_shuffle_epi32_splat((a), 3); \ ++ break; \ ++ default: \ ++ ret = _mm_shuffle_epi32_default((a), (imm)); \ ++ break; \ ++ } \ ++ ret; \ ++ }) ++#endif ++ ++// Shuffle double-precision (64-bit) floating-point elements using the control ++// in imm8, and store the results in dst. ++// ++// dst[63:0] := (imm8[0] == 0) ? a[63:0] : a[127:64] ++// dst[127:64] := (imm8[1] == 0) ? b[63:0] : b[127:64] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_shuffle_pd ++#if __has_builtin(__builtin_shufflevector) ++#define _mm_shuffle_pd(a, b, imm8) \ ++ vreinterpretq_m128d_s64(__builtin_shufflevector( \ ++ vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b), imm8 & 0x1, \ ++ ((imm8 & 0x2) >> 1) + 2)) ++#else ++#define _mm_shuffle_pd(a, b, imm8) \ ++ _mm_castsi128_pd(_mm_set_epi64x( \ ++ vgetq_lane_s64(vreinterpretq_s64_m128d(b), (imm8 & 0x2) >> 1), \ ++ vgetq_lane_s64(vreinterpretq_s64_m128d(a), imm8 & 0x1))) ++#endif ++ ++// FORCE_INLINE __m128i _mm_shufflehi_epi16(__m128i a, ++// __constrange(0,255) int imm) ++#if __has_builtin(__builtin_shufflevector) ++#define _mm_shufflehi_epi16(a, imm) \ ++ __extension__({ \ ++ int16x8_t _input = vreinterpretq_s16_m128i(a); \ ++ int16x8_t _shuf = __builtin_shufflevector( \ ++ _input, _input, 0, 1, 2, 3, ((imm) & (0x3)) + 4, \ ++ (((imm) >> 2) & 0x3) + 4, (((imm) >> 4) & 0x3) + 4, \ ++ (((imm) >> 6) & 0x3) + 4); \ ++ vreinterpretq_m128i_s16(_shuf); \ ++ }) ++#else // generic ++#define _mm_shufflehi_epi16(a, imm) _mm_shufflehi_epi16_function((a), (imm)) ++#endif ++ ++// FORCE_INLINE __m128i _mm_shufflelo_epi16(__m128i a, ++// __constrange(0,255) int imm) ++#if __has_builtin(__builtin_shufflevector) ++#define _mm_shufflelo_epi16(a, imm) \ ++ __extension__({ \ ++ int16x8_t _input = vreinterpretq_s16_m128i(a); \ ++ int16x8_t _shuf = __builtin_shufflevector( \ ++ _input, _input, ((imm) & (0x3)), (((imm) >> 2) & 0x3), \ ++ (((imm) >> 4) & 0x3), (((imm) >> 6) & 0x3), 4, 5, 6, 7); \ ++ vreinterpretq_m128i_s16(_shuf); \ ++ }) ++#else // generic ++#define _mm_shufflelo_epi16(a, imm) _mm_shufflelo_epi16_function((a), (imm)) ++#endif ++ ++// Shift packed 16-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// IF count[63:0] > 15 ++// dst[i+15:i] := 0 ++// ELSE ++// dst[i+15:i] := ZeroExtend16(a[i+15:i] << count[63:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sll_epi16 ++FORCE_INLINE __m128i _mm_sll_epi16(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_setzero_si128(); ++ ++ int16x8_t vc = vdupq_n_s16((int16_t) c); ++ return vreinterpretq_m128i_s16(vshlq_s16(vreinterpretq_s16_m128i(a), vc)); ++} ++ ++// Shift packed 32-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*32 ++// IF count[63:0] > 31 ++// dst[i+31:i] := 0 ++// ELSE ++// dst[i+31:i] := ZeroExtend32(a[i+31:i] << count[63:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sll_epi32 ++FORCE_INLINE __m128i _mm_sll_epi32(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_setzero_si128(); ++ ++ int32x4_t vc = vdupq_n_s32((int32_t) c); ++ return vreinterpretq_m128i_s32(vshlq_s32(vreinterpretq_s32_m128i(a), vc)); ++} ++ ++// Shift packed 64-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// IF count[63:0] > 63 ++// dst[i+63:i] := 0 ++// ELSE ++// dst[i+63:i] := ZeroExtend64(a[i+63:i] << count[63:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sll_epi64 ++FORCE_INLINE __m128i _mm_sll_epi64(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~63)) ++ return _mm_setzero_si128(); ++ ++ int64x2_t vc = vdupq_n_s64((int64_t) c); ++ return vreinterpretq_m128i_s64(vshlq_s64(vreinterpretq_s64_m128i(a), vc)); ++} ++ ++// Shift packed 16-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// IF imm8[7:0] > 15 ++// dst[i+15:i] := 0 ++// ELSE ++// dst[i+15:i] := ZeroExtend16(a[i+15:i] << imm8[7:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_slli_epi16 ++FORCE_INLINE __m128i _mm_slli_epi16(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~15)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s16( ++ vshlq_s16(vreinterpretq_s16_m128i(a), vdupq_n_s16(imm))); ++} ++ ++// Shift packed 32-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*32 ++// IF imm8[7:0] > 31 ++// dst[i+31:i] := 0 ++// ELSE ++// dst[i+31:i] := ZeroExtend32(a[i+31:i] << imm8[7:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_slli_epi32 ++FORCE_INLINE __m128i _mm_slli_epi32(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~31)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s32( ++ vshlq_s32(vreinterpretq_s32_m128i(a), vdupq_n_s32(imm))); ++} ++ ++// Shift packed 64-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// IF imm8[7:0] > 63 ++// dst[i+63:i] := 0 ++// ELSE ++// dst[i+63:i] := ZeroExtend64(a[i+63:i] << imm8[7:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_slli_epi64 ++FORCE_INLINE __m128i _mm_slli_epi64(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~63)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s64( ++ vshlq_s64(vreinterpretq_s64_m128i(a), vdupq_n_s64(imm))); ++} ++ ++// Shift a left by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// ++// tmp := imm8[7:0] ++// IF tmp > 15 ++// tmp := 16 ++// FI ++// dst[127:0] := a[127:0] << (tmp*8) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_slli_si128 ++FORCE_INLINE __m128i _mm_slli_si128(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~15)) ++ return _mm_setzero_si128(); ++ uint8x16_t tmp[2] = {vdupq_n_u8(0), vreinterpretq_u8_m128i(a)}; ++ return vreinterpretq_m128i_u8( ++ vld1q_u8(((uint8_t const *) tmp) + (16 - imm))); ++} ++ ++// Compute the square root of packed double-precision (64-bit) floating-point ++// elements in a, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sqrt_pd ++FORCE_INLINE __m128d _mm_sqrt_pd(__m128d a) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vsqrtq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double a0 = sqrt(((double *) &a)[0]); ++ double a1 = sqrt(((double *) &a)[1]); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Compute the square root of the lower double-precision (64-bit) floating-point ++// element in b, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sqrt_sd ++FORCE_INLINE __m128d _mm_sqrt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return _mm_move_sd(a, _mm_sqrt_pd(b)); ++#else ++ return _mm_set_pd(((double *) &a)[1], sqrt(((double *) &b)[0])); ++#endif ++} ++ ++// Shift packed 16-bit integers in a right by count while shifting in sign bits, ++// and store the results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// IF count[63:0] > 15 ++// dst[i+15:i] := (a[i+15] ? 0xFFFF : 0x0) ++// ELSE ++// dst[i+15:i] := SignExtend16(a[i+15:i] >> count[63:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sra_epi16 ++FORCE_INLINE __m128i _mm_sra_epi16(__m128i a, __m128i count) ++{ ++ int64_t c = (int64_t) vget_low_s64((int64x2_t) count); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_cmplt_epi16(a, _mm_setzero_si128()); ++ return vreinterpretq_m128i_s16(vshlq_s16((int16x8_t) a, vdupq_n_s16(-c))); ++} ++ ++// Shift packed 32-bit integers in a right by count while shifting in sign bits, ++// and store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*32 ++// IF count[63:0] > 31 ++// dst[i+31:i] := (a[i+31] ? 0xFFFFFFFF : 0x0) ++// ELSE ++// dst[i+31:i] := SignExtend32(a[i+31:i] >> count[63:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sra_epi32 ++FORCE_INLINE __m128i _mm_sra_epi32(__m128i a, __m128i count) ++{ ++ int64_t c = (int64_t) vget_low_s64((int64x2_t) count); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_cmplt_epi32(a, _mm_setzero_si128()); ++ return vreinterpretq_m128i_s32(vshlq_s32((int32x4_t) a, vdupq_n_s32(-c))); ++} ++ ++// Shift packed 16-bit integers in a right by imm8 while shifting in sign ++// bits, and store the results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// IF imm8[7:0] > 15 ++// dst[i+15:i] := (a[i+15] ? 0xFFFF : 0x0) ++// ELSE ++// dst[i+15:i] := SignExtend16(a[i+15:i] >> imm8[7:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srai_epi16 ++FORCE_INLINE __m128i _mm_srai_epi16(__m128i a, int imm) ++{ ++ const int count = (imm & ~15) ? 15 : imm; ++ return (__m128i) vshlq_s16((int16x8_t) a, vdupq_n_s16(-count)); ++} ++ ++// Shift packed 32-bit integers in a right by imm8 while shifting in sign bits, ++// and store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*32 ++// IF imm8[7:0] > 31 ++// dst[i+31:i] := (a[i+31] ? 0xFFFFFFFF : 0x0) ++// ELSE ++// dst[i+31:i] := SignExtend32(a[i+31:i] >> imm8[7:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srai_epi32 ++// FORCE_INLINE __m128i _mm_srai_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_srai_epi32(a, imm) \ ++ __extension__({ \ ++ __m128i ret; \ ++ if (_sse2neon_unlikely((imm) == 0)) { \ ++ ret = a; \ ++ } else if (_sse2neon_likely(0 < (imm) && (imm) < 32)) { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshlq_s32(vreinterpretq_s32_m128i(a), vdupq_n_s32(-(imm)))); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshrq_n_s32(vreinterpretq_s32_m128i(a), 31)); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shift packed 16-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// IF count[63:0] > 15 ++// dst[i+15:i] := 0 ++// ELSE ++// dst[i+15:i] := ZeroExtend16(a[i+15:i] >> count[63:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srl_epi16 ++FORCE_INLINE __m128i _mm_srl_epi16(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_setzero_si128(); ++ ++ int16x8_t vc = vdupq_n_s16(-(int16_t) c); ++ return vreinterpretq_m128i_u16(vshlq_u16(vreinterpretq_u16_m128i(a), vc)); ++} ++ ++// Shift packed 32-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*32 ++// IF count[63:0] > 31 ++// dst[i+31:i] := 0 ++// ELSE ++// dst[i+31:i] := ZeroExtend32(a[i+31:i] >> count[63:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srl_epi32 ++FORCE_INLINE __m128i _mm_srl_epi32(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_setzero_si128(); ++ ++ int32x4_t vc = vdupq_n_s32(-(int32_t) c); ++ return vreinterpretq_m128i_u32(vshlq_u32(vreinterpretq_u32_m128i(a), vc)); ++} ++ ++// Shift packed 64-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// IF count[63:0] > 63 ++// dst[i+63:i] := 0 ++// ELSE ++// dst[i+63:i] := ZeroExtend64(a[i+63:i] >> count[63:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srl_epi64 ++FORCE_INLINE __m128i _mm_srl_epi64(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~63)) ++ return _mm_setzero_si128(); ++ ++ int64x2_t vc = vdupq_n_s64(-(int64_t) c); ++ return vreinterpretq_m128i_u64(vshlq_u64(vreinterpretq_u64_m128i(a), vc)); ++} ++ ++// Shift packed 16-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// IF imm8[7:0] > 15 ++// dst[i+15:i] := 0 ++// ELSE ++// dst[i+15:i] := ZeroExtend16(a[i+15:i] >> imm8[7:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srli_epi16 ++#define _mm_srli_epi16(a, imm) \ ++ __extension__({ \ ++ __m128i ret; \ ++ if (_sse2neon_unlikely((imm) & ~15)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u16( \ ++ vshlq_u16(vreinterpretq_u16_m128i(a), vdupq_n_s16(-(imm)))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shift packed 32-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*32 ++// IF imm8[7:0] > 31 ++// dst[i+31:i] := 0 ++// ELSE ++// dst[i+31:i] := ZeroExtend32(a[i+31:i] >> imm8[7:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srli_epi32 ++// FORCE_INLINE __m128i _mm_srli_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_srli_epi32(a, imm) \ ++ __extension__({ \ ++ __m128i ret; \ ++ if (_sse2neon_unlikely((imm) & ~31)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u32( \ ++ vshlq_u32(vreinterpretq_u32_m128i(a), vdupq_n_s32(-(imm)))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shift packed 64-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// IF imm8[7:0] > 63 ++// dst[i+63:i] := 0 ++// ELSE ++// dst[i+63:i] := ZeroExtend64(a[i+63:i] >> imm8[7:0]) ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srli_epi64 ++#define _mm_srli_epi64(a, imm) \ ++ __extension__({ \ ++ __m128i ret; \ ++ if (_sse2neon_unlikely((imm) & ~63)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u64( \ ++ vshlq_u64(vreinterpretq_u64_m128i(a), vdupq_n_s64(-(imm)))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shift a right by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// ++// tmp := imm8[7:0] ++// IF tmp > 15 ++// tmp := 16 ++// FI ++// dst[127:0] := a[127:0] >> (tmp*8) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_srli_si128 ++FORCE_INLINE __m128i _mm_srli_si128(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~15)) ++ return _mm_setzero_si128(); ++ uint8x16_t tmp[2] = {vreinterpretq_u8_m128i(a), vdupq_n_u8(0)}; ++ return vreinterpretq_m128i_u8(vld1q_u8(((uint8_t const *) tmp) + imm)); ++} ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory. mem_addr must be aligned on a 16-byte boundary ++// or a general-protection exception may be generated. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_store_pd ++FORCE_INLINE void _mm_store_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) ++ vst1q_f64((float64_t *) mem_addr, vreinterpretq_f64_m128d(a)); ++#else ++ vst1q_f32((float32_t *) mem_addr, vreinterpretq_f32_m128d(a)); ++#endif ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// 2 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_store_pd1 ++FORCE_INLINE void _mm_store_pd1(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) ++ float64x1_t a_low = vget_low_f64(vreinterpretq_f64_m128d(a)); ++ vst1q_f64((float64_t *) mem_addr, ++ vreinterpretq_f64_m128d(vcombine_f64(a_low, a_low))); ++#else ++ float32x2_t a_low = vget_low_f32(vreinterpretq_f32_m128d(a)); ++ vst1q_f32((float32_t *) mem_addr, ++ vreinterpretq_f32_m128d(vcombine_f32(a_low, a_low))); ++#endif ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// memory. mem_addr does not need to be aligned on any particular boundary. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=mm_store_sd ++FORCE_INLINE void _mm_store_sd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) ++ vst1_f64((float64_t *) mem_addr, vget_low_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_u64((uint64_t *) mem_addr, vget_low_u64(vreinterpretq_u64_m128d(a))); ++#endif ++} ++ ++// Stores four 32-bit integer values as (as a __m128i value) at the address p. ++// https://msdn.microsoft.com/en-us/library/vstudio/edk11s13(v=vs.100).aspx ++FORCE_INLINE void _mm_store_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, vreinterpretq_s32_m128i(a)); ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// 2 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#expand=9,526,5601&text=_mm_store1_pd ++#define _mm_store1_pd _mm_store_pd1 ++ ++// Store the upper double-precision (64-bit) floating-point element from a into ++// memory. ++// ++// MEM[mem_addr+63:mem_addr] := a[127:64] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storeh_pd ++FORCE_INLINE void _mm_storeh_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) ++ vst1_f64((float64_t *) mem_addr, vget_high_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_f32((float32_t *) mem_addr, vget_high_f32(vreinterpretq_f32_m128d(a))); ++#endif ++} ++ ++// Reads the lower 64 bits of b and stores them into the lower 64 bits of a. ++// https://msdn.microsoft.com/en-us/library/hhwf428f%28v=vs.90%29.aspx ++FORCE_INLINE void _mm_storel_epi64(__m128i *a, __m128i b) ++{ ++ vst1_u64((uint64_t *) a, vget_low_u64(vreinterpretq_u64_m128i(b))); ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// memory. ++// ++// MEM[mem_addr+63:mem_addr] := a[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storel_pd ++FORCE_INLINE void _mm_storel_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) ++ vst1_f64((float64_t *) mem_addr, vget_low_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_f32((float32_t *) mem_addr, vget_low_f32(vreinterpretq_f32_m128d(a))); ++#endif ++} ++ ++// Store 2 double-precision (64-bit) floating-point elements from a into memory ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// ++// MEM[mem_addr+63:mem_addr] := a[127:64] ++// MEM[mem_addr+127:mem_addr+64] := a[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storer_pd ++FORCE_INLINE void _mm_storer_pd(double *mem_addr, __m128d a) ++{ ++ float32x4_t f = vreinterpretq_f32_m128d(a); ++ _mm_store_pd(mem_addr, vreinterpretq_m128d_f32(vextq_f32(f, f, 2))); ++} ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory. mem_addr does not need to be aligned on any ++// particular boundary. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storeu_pd ++FORCE_INLINE void _mm_storeu_pd(double *mem_addr, __m128d a) ++{ ++ _mm_store_pd(mem_addr, a); ++} ++ ++// Stores 128-bits of integer data a at the address p. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storeu_si128 ++FORCE_INLINE void _mm_storeu_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, vreinterpretq_s32_m128i(a)); ++} ++ ++// Stores 32-bits of integer data a at the address p. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_storeu_si32 ++FORCE_INLINE void _mm_storeu_si32(void *p, __m128i a) ++{ ++ vst1q_lane_s32((int32_t *) p, vreinterpretq_s32_m128i(a), 0); ++} ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory using a non-temporal memory hint. mem_addr must ++// be aligned on a 16-byte boundary or a general-protection exception may be ++// generated. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_stream_pd ++FORCE_INLINE void _mm_stream_pd(double *p, __m128d a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, (float32x4_t *) p); ++#elif defined(__aarch64__) ++ vst1q_f64(p, vreinterpretq_f64_m128d(a)); ++#else ++ vst1q_s64((int64_t *) p, vreinterpretq_s64_m128d(a)); ++#endif ++} ++ ++// Stores the data in a to the address p without polluting the caches. If the ++// cache line containing address p is already in the cache, the cache will be ++// updated. ++// https://msdn.microsoft.com/en-us/library/ba08y07y%28v=vs.90%29.aspx ++FORCE_INLINE void _mm_stream_si128(__m128i *p, __m128i a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, p); ++#else ++ vst1q_s64((int64_t *) p, vreinterpretq_s64_m128i(a)); ++#endif ++} ++ ++// Store 32-bit integer a into memory using a non-temporal hint to minimize ++// cache pollution. If the cache line containing address mem_addr is already in ++// the cache, the cache will be updated. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_stream_si32 ++FORCE_INLINE void _mm_stream_si32(int *p, int a) ++{ ++ vst1q_lane_s32((int32_t *) p, vdupq_n_s32(a), 0); ++} ++ ++// Store 64-bit integer a into memory using a non-temporal hint to minimize ++// cache pollution. If the cache line containing address mem_addr is already in ++// the cache, the cache will be updated. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_stream_si64 ++FORCE_INLINE void _mm_stream_si64(__int64 *p, __int64 a) ++{ ++ vst1_s64((int64_t *) p, vdup_n_s64((int64_t) a)); ++} ++ ++// Subtract packed 16-bit integers in b from packed 16-bit integers in a, and ++// store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sub_epi16 ++FORCE_INLINE __m128i _mm_sub_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vsubq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Subtracts the 4 signed or unsigned 32-bit integers of b from the 4 signed or ++// unsigned 32-bit integers of a. ++// ++// r0 := a0 - b0 ++// r1 := a1 - b1 ++// r2 := a2 - b2 ++// r3 := a3 - b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/fhh866h0(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_sub_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vsubq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Subtract 2 packed 64-bit integers in b from 2 packed 64-bit integers in a, ++// and store the results in dst. ++// r0 := a0 - b0 ++// r1 := a1 - b1 ++FORCE_INLINE __m128i _mm_sub_epi64(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s64( ++ vsubq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++} ++ ++// Subtract packed 8-bit integers in b from packed 8-bit integers in a, and ++// store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sub_epi8 ++FORCE_INLINE __m128i _mm_sub_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vsubq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Subtract packed double-precision (64-bit) floating-point elements in b from ++// packed double-precision (64-bit) floating-point elements in a, and store the ++// results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// dst[i+63:i] := a[i+63:i] - b[i+63:i] ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=mm_sub_pd ++FORCE_INLINE __m128d _mm_sub_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vsubq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] - db[0]; ++ c[1] = da[1] - db[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Subtract the lower double-precision (64-bit) floating-point element in b from ++// the lower double-precision (64-bit) floating-point element in a, store the ++// result in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sub_sd ++FORCE_INLINE __m128d _mm_sub_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_sub_pd(a, b)); ++} ++ ++// Subtract 64-bit integer b from 64-bit integer a, and store the result in dst. ++// ++// dst[63:0] := a[63:0] - b[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sub_si64 ++FORCE_INLINE __m64 _mm_sub_si64(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s64( ++ vsub_s64(vreinterpret_s64_m64(a), vreinterpret_s64_m64(b))); ++} ++ ++// Subtracts the 8 signed 16-bit integers of b from the 8 signed 16-bit integers ++// of a and saturates. ++// ++// r0 := SignedSaturate(a0 - b0) ++// r1 := SignedSaturate(a1 - b1) ++// ... ++// r7 := SignedSaturate(a7 - b7) ++// ++// https://technet.microsoft.com/en-us/subscriptions/3247z5b8(v=vs.90) ++FORCE_INLINE __m128i _mm_subs_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vqsubq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Subtracts the 16 signed 8-bit integers of b from the 16 signed 8-bit integers ++// of a and saturates. ++// ++// r0 := SignedSaturate(a0 - b0) ++// r1 := SignedSaturate(a1 - b1) ++// ... ++// r15 := SignedSaturate(a15 - b15) ++// ++// https://technet.microsoft.com/en-us/subscriptions/by7kzks1(v=vs.90) ++FORCE_INLINE __m128i _mm_subs_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vqsubq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Subtracts the 8 unsigned 16-bit integers of bfrom the 8 unsigned 16-bit ++// integers of a and saturates.. ++// https://technet.microsoft.com/en-us/subscriptions/index/f44y0s19(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_subs_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vqsubq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Subtracts the 16 unsigned 8-bit integers of b from the 16 unsigned 8-bit ++// integers of a and saturates. ++// ++// r0 := UnsignedSaturate(a0 - b0) ++// r1 := UnsignedSaturate(a1 - b1) ++// ... ++// r15 := UnsignedSaturate(a15 - b15) ++// ++// https://technet.microsoft.com/en-us/subscriptions/yadkxc18(v=vs.90) ++FORCE_INLINE __m128i _mm_subs_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vqsubq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++#define _mm_ucomieq_sd _mm_comieq_sd ++#define _mm_ucomige_sd _mm_comige_sd ++#define _mm_ucomigt_sd _mm_comigt_sd ++#define _mm_ucomile_sd _mm_comile_sd ++#define _mm_ucomilt_sd _mm_comilt_sd ++#define _mm_ucomineq_sd _mm_comineq_sd ++ ++// Return vector of type __m128d with undefined elements. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_undefined_pd ++FORCE_INLINE __m128d _mm_undefined_pd(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128d a; ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Interleaves the upper 4 signed or unsigned 16-bit integers in a with the ++// upper 4 signed or unsigned 16-bit integers in b. ++// ++// r0 := a4 ++// r1 := b4 ++// r2 := a5 ++// r3 := b5 ++// r4 := a6 ++// r5 := b6 ++// r6 := a7 ++// r7 := b7 ++// ++// https://msdn.microsoft.com/en-us/library/03196cz7(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_unpackhi_epi16(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s16( ++ vzip2q_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++#else ++ int16x4_t a1 = vget_high_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b1 = vget_high_s16(vreinterpretq_s16_m128i(b)); ++ int16x4x2_t result = vzip_s16(a1, b1); ++ return vreinterpretq_m128i_s16(vcombine_s16(result.val[0], result.val[1])); ++#endif ++} ++ ++// Interleaves the upper 2 signed or unsigned 32-bit integers in a with the ++// upper 2 signed or unsigned 32-bit integers in b. ++// https://msdn.microsoft.com/en-us/library/65sa7cbs(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_unpackhi_epi32(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s32( ++ vzip2q_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++#else ++ int32x2_t a1 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t b1 = vget_high_s32(vreinterpretq_s32_m128i(b)); ++ int32x2x2_t result = vzip_s32(a1, b1); ++ return vreinterpretq_m128i_s32(vcombine_s32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Interleaves the upper signed or unsigned 64-bit integer in a with the ++// upper signed or unsigned 64-bit integer in b. ++// ++// r0 := a1 ++// r1 := b1 ++FORCE_INLINE __m128i _mm_unpackhi_epi64(__m128i a, __m128i b) ++{ ++ int64x1_t a_h = vget_high_s64(vreinterpretq_s64_m128i(a)); ++ int64x1_t b_h = vget_high_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vcombine_s64(a_h, b_h)); ++} ++ ++// Interleaves the upper 8 signed or unsigned 8-bit integers in a with the upper ++// 8 signed or unsigned 8-bit integers in b. ++// ++// r0 := a8 ++// r1 := b8 ++// r2 := a9 ++// r3 := b9 ++// ... ++// r14 := a15 ++// r15 := b15 ++// ++// https://msdn.microsoft.com/en-us/library/t5h7783k(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_unpackhi_epi8(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s8( ++ vzip2q_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++#else ++ int8x8_t a1 = ++ vreinterpret_s8_s16(vget_high_s16(vreinterpretq_s16_m128i(a))); ++ int8x8_t b1 = ++ vreinterpret_s8_s16(vget_high_s16(vreinterpretq_s16_m128i(b))); ++ int8x8x2_t result = vzip_s8(a1, b1); ++ return vreinterpretq_m128i_s8(vcombine_s8(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave double-precision (64-bit) floating-point elements from ++// the high half of a and b, and store the results in dst. ++// ++// DEFINE INTERLEAVE_HIGH_QWORDS(src1[127:0], src2[127:0]) { ++// dst[63:0] := src1[127:64] ++// dst[127:64] := src2[127:64] ++// RETURN dst[127:0] ++// } ++// dst[127:0] := INTERLEAVE_HIGH_QWORDS(a[127:0], b[127:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_unpackhi_pd ++FORCE_INLINE __m128d _mm_unpackhi_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vzip2q_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ return vreinterpretq_m128d_s64( ++ vcombine_s64(vget_high_s64(vreinterpretq_s64_m128d(a)), ++ vget_high_s64(vreinterpretq_s64_m128d(b)))); ++#endif ++} ++ ++// Interleaves the lower 4 signed or unsigned 16-bit integers in a with the ++// lower 4 signed or unsigned 16-bit integers in b. ++// ++// r0 := a0 ++// r1 := b0 ++// r2 := a1 ++// r3 := b1 ++// r4 := a2 ++// r5 := b2 ++// r6 := a3 ++// r7 := b3 ++// ++// https://msdn.microsoft.com/en-us/library/btxb17bw%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_unpacklo_epi16(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s16( ++ vzip1q_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++#else ++ int16x4_t a1 = vget_low_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b1 = vget_low_s16(vreinterpretq_s16_m128i(b)); ++ int16x4x2_t result = vzip_s16(a1, b1); ++ return vreinterpretq_m128i_s16(vcombine_s16(result.val[0], result.val[1])); ++#endif ++} ++ ++// Interleaves the lower 2 signed or unsigned 32 - bit integers in a with the ++// lower 2 signed or unsigned 32 - bit integers in b. ++// ++// r0 := a0 ++// r1 := b0 ++// r2 := a1 ++// r3 := b1 ++// ++// https://msdn.microsoft.com/en-us/library/x8atst9d(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_unpacklo_epi32(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s32( ++ vzip1q_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++#else ++ int32x2_t a1 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t b1 = vget_low_s32(vreinterpretq_s32_m128i(b)); ++ int32x2x2_t result = vzip_s32(a1, b1); ++ return vreinterpretq_m128i_s32(vcombine_s32(result.val[0], result.val[1])); ++#endif ++} ++ ++FORCE_INLINE __m128i _mm_unpacklo_epi64(__m128i a, __m128i b) ++{ ++ int64x1_t a_l = vget_low_s64(vreinterpretq_s64_m128i(a)); ++ int64x1_t b_l = vget_low_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vcombine_s64(a_l, b_l)); ++} ++ ++// Interleaves the lower 8 signed or unsigned 8-bit integers in a with the lower ++// 8 signed or unsigned 8-bit integers in b. ++// ++// r0 := a0 ++// r1 := b0 ++// r2 := a1 ++// r3 := b1 ++// ... ++// r14 := a7 ++// r15 := b7 ++// ++// https://msdn.microsoft.com/en-us/library/xf7k860c%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_unpacklo_epi8(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s8( ++ vzip1q_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++#else ++ int8x8_t a1 = vreinterpret_s8_s16(vget_low_s16(vreinterpretq_s16_m128i(a))); ++ int8x8_t b1 = vreinterpret_s8_s16(vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int8x8x2_t result = vzip_s8(a1, b1); ++ return vreinterpretq_m128i_s8(vcombine_s8(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave double-precision (64-bit) floating-point elements from ++// the low half of a and b, and store the results in dst. ++// ++// DEFINE INTERLEAVE_QWORDS(src1[127:0], src2[127:0]) { ++// dst[63:0] := src1[63:0] ++// dst[127:64] := src2[63:0] ++// RETURN dst[127:0] ++// } ++// dst[127:0] := INTERLEAVE_QWORDS(a[127:0], b[127:0]) ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_unpacklo_pd ++FORCE_INLINE __m128d _mm_unpacklo_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vzip1q_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ return vreinterpretq_m128d_s64( ++ vcombine_s64(vget_low_s64(vreinterpretq_s64_m128d(a)), ++ vget_low_s64(vreinterpretq_s64_m128d(b)))); ++#endif ++} ++ ++// Compute the bitwise XOR of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// dst[i+63:i] := a[i+63:i] XOR b[i+63:i] ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_xor_pd ++FORCE_INLINE __m128d _mm_xor_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ veorq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Computes the bitwise XOR of the 128-bit value in a and the 128-bit value in ++// b. https://msdn.microsoft.com/en-us/library/fzt08www(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_xor_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ veorq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++/* SSE3 */ ++ ++// Alternatively add and subtract packed double-precision (64-bit) ++// floating-point elements in a to/from packed elements in b, and store the ++// results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*64 ++// IF ((j & 1) == 0) ++// dst[i+63:i] := a[i+63:i] - b[i+63:i] ++// ELSE ++// dst[i+63:i] := a[i+63:i] + b[i+63:i] ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_addsub_pd ++FORCE_INLINE __m128d _mm_addsub_pd(__m128d a, __m128d b) ++{ ++ _sse2neon_const __m128d mask = _mm_set_pd(1.0f, -1.0f); ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vfmaq_f64(vreinterpretq_f64_m128d(a), ++ vreinterpretq_f64_m128d(b), ++ vreinterpretq_f64_m128d(mask))); ++#else ++ return _mm_add_pd(_mm_mul_pd(b, mask), a); ++#endif ++} ++ ++// Alternatively add and subtract packed single-precision (32-bit) ++// floating-point elements in a to/from packed elements in b, and store the ++// results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=addsub_ps ++FORCE_INLINE __m128 _mm_addsub_ps(__m128 a, __m128 b) ++{ ++ _sse2neon_const __m128 mask = _mm_setr_ps(-1.0f, 1.0f, -1.0f, 1.0f); ++#if defined(__aarch64__) || defined(__ARM_FEATURE_FMA) /* VFPv4+ */ ++ return vreinterpretq_m128_f32(vfmaq_f32(vreinterpretq_f32_m128(a), ++ vreinterpretq_f32_m128(mask), ++ vreinterpretq_f32_m128(b))); ++#else ++ return _mm_add_ps(_mm_mul_ps(b, mask), a); ++#endif ++} ++ ++// Horizontally add adjacent pairs of double-precision (64-bit) floating-point ++// elements in a and b, and pack the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hadd_pd ++FORCE_INLINE __m128d _mm_hadd_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vpaddq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[] = {da[0] + da[1], db[0] + db[1]}; ++ return vreinterpretq_m128d_u64(vld1q_u64((uint64_t *) c)); ++#endif ++} ++ ++// Computes pairwise add of each argument as single-precision, floating-point ++// values a and b. ++// https://msdn.microsoft.com/en-us/library/yd9wecaa.aspx ++FORCE_INLINE __m128 _mm_hadd_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128_f32( ++ vpaddq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vpadd_f32(a10, a32), vpadd_f32(b10, b32))); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of double-precision (64-bit) ++// floating-point elements in a and b, and pack the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hsub_pd ++FORCE_INLINE __m128d _mm_hsub_pd(__m128d _a, __m128d _b) ++{ ++#if defined(__aarch64__) ++ float64x2_t a = vreinterpretq_f64_m128d(_a); ++ float64x2_t b = vreinterpretq_f64_m128d(_b); ++ return vreinterpretq_m128d_f64( ++ vsubq_f64(vuzp1q_f64(a, b), vuzp2q_f64(a, b))); ++#else ++ double *da = (double *) &_a; ++ double *db = (double *) &_b; ++ double c[] = {da[0] - da[1], db[0] - db[1]}; ++ return vreinterpretq_m128d_u64(vld1q_u64((uint64_t *) c)); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of single-precision (32-bit) ++// floating-point elements in a and b, and pack the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hsub_ps ++FORCE_INLINE __m128 _mm_hsub_ps(__m128 _a, __m128 _b) ++{ ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++#if defined(__aarch64__) ++ return vreinterpretq_m128_f32( ++ vsubq_f32(vuzp1q_f32(a, b), vuzp2q_f32(a, b))); ++#else ++ float32x4x2_t c = vuzpq_f32(a, b); ++ return vreinterpretq_m128_f32(vsubq_f32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Load 128-bits of integer data from unaligned memory into dst. This intrinsic ++// may perform better than _mm_loadu_si128 when the data crosses a cache line ++// boundary. ++// ++// dst[127:0] := MEM[mem_addr+127:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_lddqu_si128 ++#define _mm_lddqu_si128 _mm_loadu_si128 ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// ++// dst[63:0] := MEM[mem_addr+63:mem_addr] ++// dst[127:64] := MEM[mem_addr+63:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_loaddup_pd ++#define _mm_loaddup_pd _mm_load1_pd ++ ++// Duplicate the low double-precision (64-bit) floating-point element from a, ++// and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_movedup_pd ++FORCE_INLINE __m128d _mm_movedup_pd(__m128d a) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64( ++ vdupq_laneq_f64(vreinterpretq_f64_m128d(a), 0)); ++#else ++ return vreinterpretq_m128d_u64( ++ vdupq_n_u64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0))); ++#endif ++} ++ ++// Duplicate odd-indexed single-precision (32-bit) floating-point elements ++// from a, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_movehdup_ps ++FORCE_INLINE __m128 _mm_movehdup_ps(__m128 a) ++{ ++#if __has_builtin(__builtin_shufflevector) ++ return vreinterpretq_m128_f32(__builtin_shufflevector( ++ vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 1, 1, 3, 3)); ++#else ++ float32_t a1 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 1); ++ float32_t a3 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 3); ++ float ALIGN_STRUCT(16) data[4] = {a1, a1, a3, a3}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Duplicate even-indexed single-precision (32-bit) floating-point elements ++// from a, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_moveldup_ps ++FORCE_INLINE __m128 _mm_moveldup_ps(__m128 a) ++{ ++#if __has_builtin(__builtin_shufflevector) ++ return vreinterpretq_m128_f32(__builtin_shufflevector( ++ vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 0, 0, 2, 2)); ++#else ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ float32_t a2 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 2); ++ float ALIGN_STRUCT(16) data[4] = {a0, a0, a2, a2}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++#endif ++} ++ ++/* SSSE3 */ ++ ++// Compute the absolute value of packed signed 16-bit integers in a, and store ++// the unsigned results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// dst[i+15:i] := ABS(a[i+15:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_abs_epi16 ++FORCE_INLINE __m128i _mm_abs_epi16(__m128i a) ++{ ++ return vreinterpretq_m128i_s16(vabsq_s16(vreinterpretq_s16_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 32-bit integers in a, and store ++// the unsigned results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*32 ++// dst[i+31:i] := ABS(a[i+31:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_abs_epi32 ++FORCE_INLINE __m128i _mm_abs_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_s32(vabsq_s32(vreinterpretq_s32_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 8-bit integers in a, and store ++// the unsigned results in dst. ++// ++// FOR j := 0 to 15 ++// i := j*8 ++// dst[i+7:i] := ABS(a[i+7:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_abs_epi8 ++FORCE_INLINE __m128i _mm_abs_epi8(__m128i a) ++{ ++ return vreinterpretq_m128i_s8(vabsq_s8(vreinterpretq_s8_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 16-bit integers in a, and store ++// the unsigned results in dst. ++// ++// FOR j := 0 to 3 ++// i := j*16 ++// dst[i+15:i] := ABS(a[i+15:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_abs_pi16 ++FORCE_INLINE __m64 _mm_abs_pi16(__m64 a) ++{ ++ return vreinterpret_m64_s16(vabs_s16(vreinterpret_s16_m64(a))); ++} ++ ++// Compute the absolute value of packed signed 32-bit integers in a, and store ++// the unsigned results in dst. ++// ++// FOR j := 0 to 1 ++// i := j*32 ++// dst[i+31:i] := ABS(a[i+31:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_abs_pi32 ++FORCE_INLINE __m64 _mm_abs_pi32(__m64 a) ++{ ++ return vreinterpret_m64_s32(vabs_s32(vreinterpret_s32_m64(a))); ++} ++ ++// Compute the absolute value of packed signed 8-bit integers in a, and store ++// the unsigned results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*8 ++// dst[i+7:i] := ABS(a[i+7:i]) ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_abs_pi8 ++FORCE_INLINE __m64 _mm_abs_pi8(__m64 a) ++{ ++ return vreinterpret_m64_s8(vabs_s8(vreinterpret_s8_m64(a))); ++} ++ ++// Concatenate 16-byte blocks in a and b into a 32-byte temporary result, shift ++// the result right by imm8 bytes, and store the low 16 bytes in dst. ++// ++// tmp[255:0] := ((a[127:0] << 128)[255:0] OR b[127:0]) >> (imm8*8) ++// dst[127:0] := tmp[127:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_alignr_epi8 ++FORCE_INLINE __m128i _mm_alignr_epi8(__m128i a, __m128i b, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~31)) ++ return _mm_setzero_si128(); ++ int idx; ++ uint8x16_t tmp[2]; ++ if (imm >= 16) { ++ idx = imm - 16; ++ tmp[0] = vreinterpretq_u8_m128i(a); ++ tmp[1] = vdupq_n_u8(0); ++ } else { ++ idx = imm; ++ tmp[0] = vreinterpretq_u8_m128i(b); ++ tmp[1] = vreinterpretq_u8_m128i(a); ++ } ++ return vreinterpretq_m128i_u8(vld1q_u8(((uint8_t const *) tmp) + idx)); ++} ++ ++// Concatenate 8-byte blocks in a and b into a 16-byte temporary result, shift ++// the result right by imm8 bytes, and store the low 8 bytes in dst. ++// ++// tmp[127:0] := ((a[63:0] << 64)[127:0] OR b[63:0]) >> (imm8*8) ++// dst[63:0] := tmp[63:0] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_alignr_pi8 ++#define _mm_alignr_pi8(a, b, imm) \ ++ __extension__({ \ ++ __m64 ret; \ ++ if (_sse2neon_unlikely((imm) >= 16)) { \ ++ ret = vreinterpret_m64_s8(vdup_n_s8(0)); \ ++ } else { \ ++ uint8x8_t tmp_low, tmp_high; \ ++ if ((imm) >= 8) { \ ++ const int idx = (imm) -8; \ ++ tmp_low = vreinterpret_u8_m64(a); \ ++ tmp_high = vdup_n_u8(0); \ ++ ret = vreinterpret_m64_u8(vext_u8(tmp_low, tmp_high, idx)); \ ++ } else { \ ++ const int idx = (imm); \ ++ tmp_low = vreinterpret_u8_m64(b); \ ++ tmp_high = vreinterpret_u8_m64(a); \ ++ ret = vreinterpret_m64_u8(vext_u8(tmp_low, tmp_high, idx)); \ ++ } \ ++ } \ ++ ret; \ ++ }) ++ ++// Computes pairwise add of each argument as a 16-bit signed or unsigned integer ++// values a and b. ++FORCE_INLINE __m128i _mm_hadd_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s16(vpaddq_s16(a, b)); ++#else ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vpadd_s16(vget_low_s16(a), vget_high_s16(a)), ++ vpadd_s16(vget_low_s16(b), vget_high_s16(b)))); ++#endif ++} ++ ++// Computes pairwise add of each argument as a 32-bit signed or unsigned integer ++// values a and b. ++FORCE_INLINE __m128i _mm_hadd_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++ return vreinterpretq_m128i_s32( ++ vcombine_s32(vpadd_s32(vget_low_s32(a), vget_high_s32(a)), ++ vpadd_s32(vget_low_s32(b), vget_high_s32(b)))); ++} ++ ++// Horizontally add adjacent pairs of 16-bit integers in a and b, and pack the ++// signed 16-bit results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hadd_pi16 ++FORCE_INLINE __m64 _mm_hadd_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vpadd_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Horizontally add adjacent pairs of 32-bit integers in a and b, and pack the ++// signed 32-bit results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hadd_pi32 ++FORCE_INLINE __m64 _mm_hadd_pi32(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s32( ++ vpadd_s32(vreinterpret_s32_m64(a), vreinterpret_s32_m64(b))); ++} ++ ++// Computes saturated pairwise sub of each argument as a 16-bit signed ++// integer values a and b. ++FORCE_INLINE __m128i _mm_hadds_epi16(__m128i _a, __m128i _b) ++{ ++#if defined(__aarch64__) ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ return vreinterpretq_s64_s16( ++ vqaddq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++ // Interleave using vshrn/vmovn ++ // [a0|a2|a4|a6|b0|b2|b4|b6] ++ // [a1|a3|a5|a7|b1|b3|b5|b7] ++ int16x8_t ab0246 = vcombine_s16(vmovn_s32(a), vmovn_s32(b)); ++ int16x8_t ab1357 = vcombine_s16(vshrn_n_s32(a, 16), vshrn_n_s32(b, 16)); ++ // Saturated add ++ return vreinterpretq_m128i_s16(vqaddq_s16(ab0246, ab1357)); ++#endif ++} ++ ++// Horizontally add adjacent pairs of signed 16-bit integers in a and b using ++// saturation, and pack the signed 16-bit results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hadds_pi16 ++FORCE_INLINE __m64 _mm_hadds_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) ++ return vreinterpret_s64_s16(vqadd_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t res = vuzp_s16(a, b); ++ return vreinterpret_s64_s16(vqadd_s16(res.val[0], res.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 16-bit integers in a and b, and pack ++// the signed 16-bit results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hsub_epi16 ++FORCE_INLINE __m128i _mm_hsub_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s16( ++ vsubq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int16x8x2_t c = vuzpq_s16(a, b); ++ return vreinterpretq_m128i_s16(vsubq_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 32-bit integers in a and b, and pack ++// the signed 32-bit results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hsub_epi32 ++FORCE_INLINE __m128i _mm_hsub_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s32( ++ vsubq_s32(vuzp1q_s32(a, b), vuzp2q_s32(a, b))); ++#else ++ int32x4x2_t c = vuzpq_s32(a, b); ++ return vreinterpretq_m128i_s32(vsubq_s32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 16-bit integers in a and b, and pack ++// the signed 16-bit results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hsub_pi16 ++FORCE_INLINE __m64 _mm_hsub_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) ++ return vreinterpret_m64_s16(vsub_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t c = vuzp_s16(a, b); ++ return vreinterpret_m64_s16(vsub_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 32-bit integers in a and b, and pack ++// the signed 32-bit results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=mm_hsub_pi32 ++FORCE_INLINE __m64 _mm_hsub_pi32(__m64 _a, __m64 _b) ++{ ++ int32x2_t a = vreinterpret_s32_m64(_a); ++ int32x2_t b = vreinterpret_s32_m64(_b); ++#if defined(__aarch64__) ++ return vreinterpret_m64_s32(vsub_s32(vuzp1_s32(a, b), vuzp2_s32(a, b))); ++#else ++ int32x2x2_t c = vuzp_s32(a, b); ++ return vreinterpret_m64_s32(vsub_s32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Computes saturated pairwise difference of each argument as a 16-bit signed ++// integer values a and b. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hsubs_epi16 ++FORCE_INLINE __m128i _mm_hsubs_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s16( ++ vqsubq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int16x8x2_t c = vuzpq_s16(a, b); ++ return vreinterpretq_m128i_s16(vqsubq_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of signed 16-bit integers in a and b ++// using saturation, and pack the signed 16-bit results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_hsubs_pi16 ++FORCE_INLINE __m64 _mm_hsubs_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) ++ return vreinterpret_m64_s16(vqsub_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t c = vuzp_s16(a, b); ++ return vreinterpret_m64_s16(vqsub_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Vertically multiply each unsigned 8-bit integer from a with the corresponding ++// signed 8-bit integer from b, producing intermediate signed 16-bit integers. ++// Horizontally add adjacent pairs of intermediate signed 16-bit integers, ++// and pack the saturated results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// dst[i+15:i] := Saturate_To_Int16( a[i+15:i+8]*b[i+15:i+8] + ++// a[i+7:i]*b[i+7:i] ) ++// ENDFOR ++FORCE_INLINE __m128i _mm_maddubs_epi16(__m128i _a, __m128i _b) ++{ ++#if defined(__aarch64__) ++ uint8x16_t a = vreinterpretq_u8_m128i(_a); ++ int8x16_t b = vreinterpretq_s8_m128i(_b); ++ int16x8_t tl = vmulq_s16(vreinterpretq_s16_u16(vmovl_u8(vget_low_u8(a))), ++ vmovl_s8(vget_low_s8(b))); ++ int16x8_t th = vmulq_s16(vreinterpretq_s16_u16(vmovl_u8(vget_high_u8(a))), ++ vmovl_s8(vget_high_s8(b))); ++ return vreinterpretq_m128i_s16( ++ vqaddq_s16(vuzp1q_s16(tl, th), vuzp2q_s16(tl, th))); ++#else ++ // This would be much simpler if x86 would choose to zero extend OR sign ++ // extend, not both. This could probably be optimized better. ++ uint16x8_t a = vreinterpretq_u16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ ++ // Zero extend a ++ int16x8_t a_odd = vreinterpretq_s16_u16(vshrq_n_u16(a, 8)); ++ int16x8_t a_even = vreinterpretq_s16_u16(vbicq_u16(a, vdupq_n_u16(0xff00))); ++ ++ // Sign extend by shifting left then shifting right. ++ int16x8_t b_even = vshrq_n_s16(vshlq_n_s16(b, 8), 8); ++ int16x8_t b_odd = vshrq_n_s16(b, 8); ++ ++ // multiply ++ int16x8_t prod1 = vmulq_s16(a_even, b_even); ++ int16x8_t prod2 = vmulq_s16(a_odd, b_odd); ++ ++ // saturated add ++ return vreinterpretq_m128i_s16(vqaddq_s16(prod1, prod2)); ++#endif ++} ++ ++// Vertically multiply each unsigned 8-bit integer from a with the corresponding ++// signed 8-bit integer from b, producing intermediate signed 16-bit integers. ++// Horizontally add adjacent pairs of intermediate signed 16-bit integers, and ++// pack the saturated results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_maddubs_pi16 ++FORCE_INLINE __m64 _mm_maddubs_pi16(__m64 _a, __m64 _b) ++{ ++ uint16x4_t a = vreinterpret_u16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++ ++ // Zero extend a ++ int16x4_t a_odd = vreinterpret_s16_u16(vshr_n_u16(a, 8)); ++ int16x4_t a_even = vreinterpret_s16_u16(vand_u16(a, vdup_n_u16(0xff))); ++ ++ // Sign extend by shifting left then shifting right. ++ int16x4_t b_even = vshr_n_s16(vshl_n_s16(b, 8), 8); ++ int16x4_t b_odd = vshr_n_s16(b, 8); ++ ++ // multiply ++ int16x4_t prod1 = vmul_s16(a_even, b_even); ++ int16x4_t prod2 = vmul_s16(a_odd, b_odd); ++ ++ // saturated add ++ return vreinterpret_m64_s16(vqadd_s16(prod1, prod2)); ++} ++ ++// Multiply packed signed 16-bit integers in a and b, producing intermediate ++// signed 32-bit integers. Shift right by 15 bits while rounding up, and store ++// the packed 16-bit integers in dst. ++// ++// r0 := Round(((int32_t)a0 * (int32_t)b0) >> 15) ++// r1 := Round(((int32_t)a1 * (int32_t)b1) >> 15) ++// r2 := Round(((int32_t)a2 * (int32_t)b2) >> 15) ++// ... ++// r7 := Round(((int32_t)a7 * (int32_t)b7) >> 15) ++FORCE_INLINE __m128i _mm_mulhrs_epi16(__m128i a, __m128i b) ++{ ++ // Has issues due to saturation ++ // return vreinterpretq_m128i_s16(vqrdmulhq_s16(a, b)); ++ ++ // Multiply ++ int32x4_t mul_lo = vmull_s16(vget_low_s16(vreinterpretq_s16_m128i(a)), ++ vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int32x4_t mul_hi = vmull_s16(vget_high_s16(vreinterpretq_s16_m128i(a)), ++ vget_high_s16(vreinterpretq_s16_m128i(b))); ++ ++ // Rounding narrowing shift right ++ // narrow = (int16_t)((mul + 16384) >> 15); ++ int16x4_t narrow_lo = vrshrn_n_s32(mul_lo, 15); ++ int16x4_t narrow_hi = vrshrn_n_s32(mul_hi, 15); ++ ++ // Join together ++ return vreinterpretq_m128i_s16(vcombine_s16(narrow_lo, narrow_hi)); ++} ++ ++// Multiply packed signed 16-bit integers in a and b, producing intermediate ++// signed 32-bit integers. Truncate each intermediate integer to the 18 most ++// significant bits, round by adding 1, and store bits [16:1] to dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_mulhrs_pi16 ++FORCE_INLINE __m64 _mm_mulhrs_pi16(__m64 a, __m64 b) ++{ ++ int32x4_t mul_extend = ++ vmull_s16((vreinterpret_s16_m64(a)), (vreinterpret_s16_m64(b))); ++ ++ // Rounding narrowing shift right ++ return vreinterpret_m64_s16(vrshrn_n_s32(mul_extend, 15)); ++} ++ ++// Shuffle packed 8-bit integers in a according to shuffle control mask in the ++// corresponding 8-bit element of b, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_shuffle_epi8 ++FORCE_INLINE __m128i _mm_shuffle_epi8(__m128i a, __m128i b) ++{ ++ int8x16_t tbl = vreinterpretq_s8_m128i(a); // input a ++ uint8x16_t idx = vreinterpretq_u8_m128i(b); // input b ++ uint8x16_t idx_masked = ++ vandq_u8(idx, vdupq_n_u8(0x8F)); // avoid using meaningless bits ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_s8(vqtbl1q_s8(tbl, idx_masked)); ++#elif defined(__GNUC__) ++ int8x16_t ret; ++ // %e and %f represent the even and odd D registers ++ // respectively. ++ __asm__ __volatile__( ++ "vtbl.8 %e[ret], {%e[tbl], %f[tbl]}, %e[idx]\n" ++ "vtbl.8 %f[ret], {%e[tbl], %f[tbl]}, %f[idx]\n" ++ : [ret] "=&w"(ret) ++ : [tbl] "w"(tbl), [idx] "w"(idx_masked)); ++ return vreinterpretq_m128i_s8(ret); ++#else ++ // use this line if testing on aarch64 ++ int8x8x2_t a_split = {vget_low_s8(tbl), vget_high_s8(tbl)}; ++ return vreinterpretq_m128i_s8( ++ vcombine_s8(vtbl2_s8(a_split, vget_low_u8(idx_masked)), ++ vtbl2_s8(a_split, vget_high_u8(idx_masked)))); ++#endif ++} ++ ++// Shuffle packed 8-bit integers in a according to shuffle control mask in the ++// corresponding 8-bit element of b, and store the results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*8 ++// IF b[i+7] == 1 ++// dst[i+7:i] := 0 ++// ELSE ++// index[2:0] := b[i+2:i] ++// dst[i+7:i] := a[index*8+7:index*8] ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_shuffle_pi8 ++FORCE_INLINE __m64 _mm_shuffle_pi8(__m64 a, __m64 b) ++{ ++ const int8x8_t controlMask = ++ vand_s8(vreinterpret_s8_m64(b), vdup_n_s8((int8_t) (0x1 << 7 | 0x07))); ++ int8x8_t res = vtbl1_s8(vreinterpret_s8_m64(a), controlMask); ++ return vreinterpret_m64_s8(res); ++} ++ ++// Negate packed 16-bit integers in a when the corresponding signed ++// 16-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// ++// for i in 0..7 ++// if b[i] < 0 ++// r[i] := -a[i] ++// else if b[i] == 0 ++// r[i] := 0 ++// else ++// r[i] := a[i] ++// fi ++// done ++FORCE_INLINE __m128i _mm_sign_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFF : 0 ++ uint16x8_t ltMask = vreinterpretq_u16_s16(vshrq_n_s16(b, 15)); ++ // (b == 0) ? 0xFFFF : 0 ++#if defined(__aarch64__) ++ int16x8_t zeroMask = vreinterpretq_s16_u16(vceqzq_s16(b)); ++#else ++ int16x8_t zeroMask = vreinterpretq_s16_u16(vceqq_s16(b, vdupq_n_s16(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s16(a) equals to negative ++ // 'a') based on ltMask ++ int16x8_t masked = vbslq_s16(ltMask, vnegq_s16(a), a); ++ // res = masked & (~zeroMask) ++ int16x8_t res = vbicq_s16(masked, zeroMask); ++ return vreinterpretq_m128i_s16(res); ++} ++ ++// Negate packed 32-bit integers in a when the corresponding signed ++// 32-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// ++// for i in 0..3 ++// if b[i] < 0 ++// r[i] := -a[i] ++// else if b[i] == 0 ++// r[i] := 0 ++// else ++// r[i] := a[i] ++// fi ++// done ++FORCE_INLINE __m128i _mm_sign_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFFFFFF : 0 ++ uint32x4_t ltMask = vreinterpretq_u32_s32(vshrq_n_s32(b, 31)); ++ ++ // (b == 0) ? 0xFFFFFFFF : 0 ++#if defined(__aarch64__) ++ int32x4_t zeroMask = vreinterpretq_s32_u32(vceqzq_s32(b)); ++#else ++ int32x4_t zeroMask = vreinterpretq_s32_u32(vceqq_s32(b, vdupq_n_s32(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s32(a) equals to negative ++ // 'a') based on ltMask ++ int32x4_t masked = vbslq_s32(ltMask, vnegq_s32(a), a); ++ // res = masked & (~zeroMask) ++ int32x4_t res = vbicq_s32(masked, zeroMask); ++ return vreinterpretq_m128i_s32(res); ++} ++ ++// Negate packed 8-bit integers in a when the corresponding signed ++// 8-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// ++// for i in 0..15 ++// if b[i] < 0 ++// r[i] := -a[i] ++// else if b[i] == 0 ++// r[i] := 0 ++// else ++// r[i] := a[i] ++// fi ++// done ++FORCE_INLINE __m128i _mm_sign_epi8(__m128i _a, __m128i _b) ++{ ++ int8x16_t a = vreinterpretq_s8_m128i(_a); ++ int8x16_t b = vreinterpretq_s8_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFF : 0 ++ uint8x16_t ltMask = vreinterpretq_u8_s8(vshrq_n_s8(b, 7)); ++ ++ // (b == 0) ? 0xFF : 0 ++#if defined(__aarch64__) ++ int8x16_t zeroMask = vreinterpretq_s8_u8(vceqzq_s8(b)); ++#else ++ int8x16_t zeroMask = vreinterpretq_s8_u8(vceqq_s8(b, vdupq_n_s8(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s8(a) return negative 'a') ++ // based on ltMask ++ int8x16_t masked = vbslq_s8(ltMask, vnegq_s8(a), a); ++ // res = masked & (~zeroMask) ++ int8x16_t res = vbicq_s8(masked, zeroMask); ++ ++ return vreinterpretq_m128i_s8(res); ++} ++ ++// Negate packed 16-bit integers in a when the corresponding signed 16-bit ++// integer in b is negative, and store the results in dst. Element in dst are ++// zeroed out when the corresponding element in b is zero. ++// ++// FOR j := 0 to 3 ++// i := j*16 ++// IF b[i+15:i] < 0 ++// dst[i+15:i] := -(a[i+15:i]) ++// ELSE IF b[i+15:i] == 0 ++// dst[i+15:i] := 0 ++// ELSE ++// dst[i+15:i] := a[i+15:i] ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sign_pi16 ++FORCE_INLINE __m64 _mm_sign_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFF : 0 ++ uint16x4_t ltMask = vreinterpret_u16_s16(vshr_n_s16(b, 15)); ++ ++ // (b == 0) ? 0xFFFF : 0 ++#if defined(__aarch64__) ++ int16x4_t zeroMask = vreinterpret_s16_u16(vceqz_s16(b)); ++#else ++ int16x4_t zeroMask = vreinterpret_s16_u16(vceq_s16(b, vdup_n_s16(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s16(a) return negative 'a') ++ // based on ltMask ++ int16x4_t masked = vbsl_s16(ltMask, vneg_s16(a), a); ++ // res = masked & (~zeroMask) ++ int16x4_t res = vbic_s16(masked, zeroMask); ++ ++ return vreinterpret_m64_s16(res); ++} ++ ++// Negate packed 32-bit integers in a when the corresponding signed 32-bit ++// integer in b is negative, and store the results in dst. Element in dst are ++// zeroed out when the corresponding element in b is zero. ++// ++// FOR j := 0 to 1 ++// i := j*32 ++// IF b[i+31:i] < 0 ++// dst[i+31:i] := -(a[i+31:i]) ++// ELSE IF b[i+31:i] == 0 ++// dst[i+31:i] := 0 ++// ELSE ++// dst[i+31:i] := a[i+31:i] ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sign_pi32 ++FORCE_INLINE __m64 _mm_sign_pi32(__m64 _a, __m64 _b) ++{ ++ int32x2_t a = vreinterpret_s32_m64(_a); ++ int32x2_t b = vreinterpret_s32_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFFFFFF : 0 ++ uint32x2_t ltMask = vreinterpret_u32_s32(vshr_n_s32(b, 31)); ++ ++ // (b == 0) ? 0xFFFFFFFF : 0 ++#if defined(__aarch64__) ++ int32x2_t zeroMask = vreinterpret_s32_u32(vceqz_s32(b)); ++#else ++ int32x2_t zeroMask = vreinterpret_s32_u32(vceq_s32(b, vdup_n_s32(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s32(a) return negative 'a') ++ // based on ltMask ++ int32x2_t masked = vbsl_s32(ltMask, vneg_s32(a), a); ++ // res = masked & (~zeroMask) ++ int32x2_t res = vbic_s32(masked, zeroMask); ++ ++ return vreinterpret_m64_s32(res); ++} ++ ++// Negate packed 8-bit integers in a when the corresponding signed 8-bit integer ++// in b is negative, and store the results in dst. Element in dst are zeroed out ++// when the corresponding element in b is zero. ++// ++// FOR j := 0 to 7 ++// i := j*8 ++// IF b[i+7:i] < 0 ++// dst[i+7:i] := -(a[i+7:i]) ++// ELSE IF b[i+7:i] == 0 ++// dst[i+7:i] := 0 ++// ELSE ++// dst[i+7:i] := a[i+7:i] ++// FI ++// ENDFOR ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_sign_pi8 ++FORCE_INLINE __m64 _mm_sign_pi8(__m64 _a, __m64 _b) ++{ ++ int8x8_t a = vreinterpret_s8_m64(_a); ++ int8x8_t b = vreinterpret_s8_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFF : 0 ++ uint8x8_t ltMask = vreinterpret_u8_s8(vshr_n_s8(b, 7)); ++ ++ // (b == 0) ? 0xFF : 0 ++#if defined(__aarch64__) ++ int8x8_t zeroMask = vreinterpret_s8_u8(vceqz_s8(b)); ++#else ++ int8x8_t zeroMask = vreinterpret_s8_u8(vceq_s8(b, vdup_n_s8(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s8(a) return negative 'a') ++ // based on ltMask ++ int8x8_t masked = vbsl_s8(ltMask, vneg_s8(a), a); ++ // res = masked & (~zeroMask) ++ int8x8_t res = vbic_s8(masked, zeroMask); ++ ++ return vreinterpret_m64_s8(res); ++} ++ ++/* SSE4.1 */ ++ ++// Blend packed 16-bit integers from a and b using control mask imm8, and store ++// the results in dst. ++// ++// FOR j := 0 to 7 ++// i := j*16 ++// IF imm8[j] ++// dst[i+15:i] := b[i+15:i] ++// ELSE ++// dst[i+15:i] := a[i+15:i] ++// FI ++// ENDFOR ++// FORCE_INLINE __m128i _mm_blend_epi16(__m128i a, __m128i b, ++// __constrange(0,255) int imm) ++#define _mm_blend_epi16(a, b, imm) \ ++ __extension__({ \ ++ const uint16_t _mask[8] = {((imm) & (1 << 0)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 1)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 2)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 3)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 4)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 5)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 6)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 7)) ? (uint16_t) -1 : 0x0}; \ ++ uint16x8_t _mask_vec = vld1q_u16(_mask); \ ++ uint16x8_t _a = vreinterpretq_u16_m128i(a); \ ++ uint16x8_t _b = vreinterpretq_u16_m128i(b); \ ++ vreinterpretq_m128i_u16(vbslq_u16(_mask_vec, _b, _a)); \ ++ }) ++ ++// Blend packed double-precision (64-bit) floating-point elements from a and b ++// using control mask imm8, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_blend_pd ++#define _mm_blend_pd(a, b, imm) \ ++ __extension__({ \ ++ const uint64_t _mask[2] = { \ ++ ((imm) & (1 << 0)) ? ~UINT64_C(0) : UINT64_C(0), \ ++ ((imm) & (1 << 1)) ? ~UINT64_C(0) : UINT64_C(0)}; \ ++ uint64x2_t _mask_vec = vld1q_u64(_mask); \ ++ uint64x2_t _a = vreinterpretq_u64_m128d(a); \ ++ uint64x2_t _b = vreinterpretq_u64_m128d(b); \ ++ vreinterpretq_m128d_u64(vbslq_u64(_mask_vec, _b, _a)); \ ++ }) ++ ++// Blend packed single-precision (32-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_blend_ps ++FORCE_INLINE __m128 _mm_blend_ps(__m128 _a, __m128 _b, const char imm8) ++{ ++ const uint32_t ALIGN_STRUCT(16) ++ data[4] = {((imm8) & (1 << 0)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 1)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 2)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 3)) ? UINT32_MAX : 0}; ++ uint32x4_t mask = vld1q_u32(data); ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++ return vreinterpretq_m128_f32(vbslq_f32(mask, b, a)); ++} ++ ++// Blend packed 8-bit integers from a and b using mask, and store the results in ++// dst. ++// ++// FOR j := 0 to 15 ++// i := j*8 ++// IF mask[i+7] ++// dst[i+7:i] := b[i+7:i] ++// ELSE ++// dst[i+7:i] := a[i+7:i] ++// FI ++// ENDFOR ++FORCE_INLINE __m128i _mm_blendv_epi8(__m128i _a, __m128i _b, __m128i _mask) ++{ ++ // Use a signed shift right to create a mask with the sign bit ++ uint8x16_t mask = ++ vreinterpretq_u8_s8(vshrq_n_s8(vreinterpretq_s8_m128i(_mask), 7)); ++ uint8x16_t a = vreinterpretq_u8_m128i(_a); ++ uint8x16_t b = vreinterpretq_u8_m128i(_b); ++ return vreinterpretq_m128i_u8(vbslq_u8(mask, b, a)); ++} ++ ++// Blend packed double-precision (64-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_blendv_pd ++FORCE_INLINE __m128d _mm_blendv_pd(__m128d _a, __m128d _b, __m128d _mask) ++{ ++ uint64x2_t mask = ++ vreinterpretq_u64_s64(vshrq_n_s64(vreinterpretq_s64_m128d(_mask), 63)); ++#if defined(__aarch64__) ++ float64x2_t a = vreinterpretq_f64_m128d(_a); ++ float64x2_t b = vreinterpretq_f64_m128d(_b); ++ return vreinterpretq_m128d_f64(vbslq_f64(mask, b, a)); ++#else ++ uint64x2_t a = vreinterpretq_u64_m128d(_a); ++ uint64x2_t b = vreinterpretq_u64_m128d(_b); ++ return vreinterpretq_m128d_u64(vbslq_u64(mask, b, a)); ++#endif ++} ++ ++// Blend packed single-precision (32-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_blendv_ps ++FORCE_INLINE __m128 _mm_blendv_ps(__m128 _a, __m128 _b, __m128 _mask) ++{ ++ // Use a signed shift right to create a mask with the sign bit ++ uint32x4_t mask = ++ vreinterpretq_u32_s32(vshrq_n_s32(vreinterpretq_s32_m128(_mask), 31)); ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++ return vreinterpretq_m128_f32(vbslq_f32(mask, b, a)); ++} ++ ++// Round the packed double-precision (64-bit) floating-point elements in a up ++// to an integer value, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_ceil_pd ++FORCE_INLINE __m128d _mm_ceil_pd(__m128d a) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vrndpq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double *f = (double *) &a; ++ return _mm_set_pd(ceil(f[1]), ceil(f[0])); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a up to ++// an integer value, and store the results as packed single-precision ++// floating-point elements in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_ceil_ps ++FORCE_INLINE __m128 _mm_ceil_ps(__m128 a) ++{ ++#if defined(__aarch64__) || defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpretq_m128_f32(vrndpq_f32(vreinterpretq_f32_m128(a))); ++#else ++ float *f = (float *) &a; ++ return _mm_set_ps(ceilf(f[3]), ceilf(f[2]), ceilf(f[1]), ceilf(f[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b up to ++// an integer value, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_ceil_sd ++FORCE_INLINE __m128d _mm_ceil_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_ceil_pd(b)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b up to ++// an integer value, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. ++// ++// dst[31:0] := CEIL(b[31:0]) ++// dst[127:32] := a[127:32] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_ceil_ss ++FORCE_INLINE __m128 _mm_ceil_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_ceil_ps(b)); ++} ++ ++// Compare packed 64-bit integers in a and b for equality, and store the results ++// in dst ++FORCE_INLINE __m128i _mm_cmpeq_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_u64( ++ vceqq_u64(vreinterpretq_u64_m128i(a), vreinterpretq_u64_m128i(b))); ++#else ++ // ARMv7 lacks vceqq_u64 ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128i_u32(vandq_u32(cmp, swapped)); ++#endif ++} ++ ++// Converts the four signed 16-bit integers in the lower 64 bits to four signed ++// 32-bit integers. ++FORCE_INLINE __m128i _mm_cvtepi16_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vmovl_s16(vget_low_s16(vreinterpretq_s16_m128i(a)))); ++} ++ ++// Converts the two signed 16-bit integers in the lower 32 bits two signed ++// 32-bit integers. ++FORCE_INLINE __m128i _mm_cvtepi16_epi64(__m128i a) ++{ ++ int16x8_t s16x8 = vreinterpretq_s16_m128i(a); /* xxxx xxxx xxxx 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000x 000x 000B 000A */ ++ int64x2_t s64x2 = vmovl_s32(vget_low_s32(s32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_s64(s64x2); ++} ++ ++// Converts the two signed 32-bit integers in the lower 64 bits to two signed ++// 64-bit integers. ++FORCE_INLINE __m128i _mm_cvtepi32_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_s64( ++ vmovl_s32(vget_low_s32(vreinterpretq_s32_m128i(a)))); ++} ++ ++// Converts the four unsigned 8-bit integers in the lower 16 bits to four ++// unsigned 32-bit integers. ++FORCE_INLINE __m128i _mm_cvtepi8_epi16(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ return vreinterpretq_m128i_s16(s16x8); ++} ++ ++// Converts the four unsigned 8-bit integers in the lower 32 bits to four ++// unsigned 32-bit integers. ++FORCE_INLINE __m128i _mm_cvtepi8_epi32(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000D 000C 000B 000A */ ++ return vreinterpretq_m128i_s32(s32x4); ++} ++ ++// Converts the two signed 8-bit integers in the lower 32 bits to four ++// signed 64-bit integers. ++FORCE_INLINE __m128i _mm_cvtepi8_epi64(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx xxBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0x0x 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000x 000x 000B 000A */ ++ int64x2_t s64x2 = vmovl_s32(vget_low_s32(s32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_s64(s64x2); ++} ++ ++// Converts the four unsigned 16-bit integers in the lower 64 bits to four ++// unsigned 32-bit integers. ++FORCE_INLINE __m128i _mm_cvtepu16_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_u32( ++ vmovl_u16(vget_low_u16(vreinterpretq_u16_m128i(a)))); ++} ++ ++// Converts the two unsigned 16-bit integers in the lower 32 bits to two ++// unsigned 64-bit integers. ++FORCE_INLINE __m128i _mm_cvtepu16_epi64(__m128i a) ++{ ++ uint16x8_t u16x8 = vreinterpretq_u16_m128i(a); /* xxxx xxxx xxxx 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000x 000x 000B 000A */ ++ uint64x2_t u64x2 = vmovl_u32(vget_low_u32(u32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_u64(u64x2); ++} ++ ++// Converts the two unsigned 32-bit integers in the lower 64 bits to two ++// unsigned 64-bit integers. ++FORCE_INLINE __m128i _mm_cvtepu32_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_u64( ++ vmovl_u32(vget_low_u32(vreinterpretq_u32_m128i(a)))); ++} ++ ++// Zero extend packed unsigned 8-bit integers in a to packed 16-bit integers, ++// and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtepu8_epi16 ++FORCE_INLINE __m128i _mm_cvtepu8_epi16(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx HGFE DCBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0H0G 0F0E 0D0C 0B0A */ ++ return vreinterpretq_m128i_u16(u16x8); ++} ++ ++// Converts the four unsigned 8-bit integers in the lower 32 bits to four ++// unsigned 32-bit integers. ++// https://msdn.microsoft.com/en-us/library/bb531467%28v=vs.100%29.aspx ++FORCE_INLINE __m128i _mm_cvtepu8_epi32(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000D 000C 000B 000A */ ++ return vreinterpretq_m128i_u32(u32x4); ++} ++ ++// Converts the two unsigned 8-bit integers in the lower 16 bits to two ++// unsigned 64-bit integers. ++FORCE_INLINE __m128i _mm_cvtepu8_epi64(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx xxxx xxBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0x0x 0x0x 0x0x 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000x 000x 000B 000A */ ++ uint64x2_t u64x2 = vmovl_u32(vget_low_u32(u32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_u64(u64x2); ++} ++ ++// Conditionally multiply the packed double-precision (64-bit) floating-point ++// elements in a and b using the high 4 bits in imm8, sum the four products, and ++// conditionally store the sum in dst using the low 4 bits of imm8. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_dp_pd ++FORCE_INLINE __m128d _mm_dp_pd(__m128d a, __m128d b, const int imm) ++{ ++ // Generate mask value from constant immediate bit value ++ const int64_t bit0Mask = imm & 0x01 ? UINT64_MAX : 0; ++ const int64_t bit1Mask = imm & 0x02 ? UINT64_MAX : 0; ++#if !SSE2NEON_PRECISE_DP ++ const int64_t bit4Mask = imm & 0x10 ? UINT64_MAX : 0; ++ const int64_t bit5Mask = imm & 0x20 ? UINT64_MAX : 0; ++#endif ++ // Conditional multiplication ++#if !SSE2NEON_PRECISE_DP ++ __m128d mul = _mm_mul_pd(a, b); ++ const __m128d mulMask = ++ _mm_castsi128_pd(_mm_set_epi64x(bit5Mask, bit4Mask)); ++ __m128d tmp = _mm_and_pd(mul, mulMask); ++#else ++#if defined(__aarch64__) ++ double d0 = (imm & 0x10) ? vgetq_lane_f64(vreinterpretq_f64_m128d(a), 0) * ++ vgetq_lane_f64(vreinterpretq_f64_m128d(b), 0) ++ : 0; ++ double d1 = (imm & 0x20) ? vgetq_lane_f64(vreinterpretq_f64_m128d(a), 1) * ++ vgetq_lane_f64(vreinterpretq_f64_m128d(b), 1) ++ : 0; ++#else ++ double d0 = (imm & 0x10) ? ((double *) &a)[0] * ((double *) &b)[0] : 0; ++ double d1 = (imm & 0x20) ? ((double *) &a)[1] * ((double *) &b)[1] : 0; ++#endif ++ __m128d tmp = _mm_set_pd(d1, d0); ++#endif ++ // Sum the products ++#if defined(__aarch64__) ++ double sum = vpaddd_f64(vreinterpretq_f64_m128d(tmp)); ++#else ++ double sum = *((double *) &tmp) + *(((double *) &tmp) + 1); ++#endif ++ // Conditionally store the sum ++ const __m128d sumMask = ++ _mm_castsi128_pd(_mm_set_epi64x(bit1Mask, bit0Mask)); ++ __m128d res = _mm_and_pd(_mm_set_pd1(sum), sumMask); ++ return res; ++} ++ ++// Conditionally multiply the packed single-precision (32-bit) floating-point ++// elements in a and b using the high 4 bits in imm8, sum the four products, ++// and conditionally store the sum in dst using the low 4 bits of imm. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_dp_ps ++FORCE_INLINE __m128 _mm_dp_ps(__m128 a, __m128 b, const int imm) ++{ ++#if defined(__aarch64__) ++ /* shortcuts */ ++ if (imm == 0xFF) { ++ return _mm_set1_ps(vaddvq_f32(_mm_mul_ps(a, b))); ++ } ++ if (imm == 0x7F) { ++ float32x4_t m = _mm_mul_ps(a, b); ++ m[3] = 0; ++ return _mm_set1_ps(vaddvq_f32(m)); ++ } ++#endif ++ ++ float s = 0, c = 0; ++ float32x4_t f32a = vreinterpretq_f32_m128(a); ++ float32x4_t f32b = vreinterpretq_f32_m128(b); ++ ++ /* To improve the accuracy of floating-point summation, Kahan algorithm ++ * is used for each operation. ++ */ ++ if (imm & (1 << 4)) ++ _sse2neon_kadd_f32(&s, &c, f32a[0] * f32b[0]); ++ if (imm & (1 << 5)) ++ _sse2neon_kadd_f32(&s, &c, f32a[1] * f32b[1]); ++ if (imm & (1 << 6)) ++ _sse2neon_kadd_f32(&s, &c, f32a[2] * f32b[2]); ++ if (imm & (1 << 7)) ++ _sse2neon_kadd_f32(&s, &c, f32a[3] * f32b[3]); ++ s += c; ++ ++ float32x4_t res = { ++ (imm & 0x1) ? s : 0, ++ (imm & 0x2) ? s : 0, ++ (imm & 0x4) ? s : 0, ++ (imm & 0x8) ? s : 0, ++ }; ++ return vreinterpretq_m128_f32(res); ++} ++ ++// Extracts the selected signed or unsigned 32-bit integer from a and zero ++// extends. ++// FORCE_INLINE int _mm_extract_epi32(__m128i a, __constrange(0,4) int imm) ++#define _mm_extract_epi32(a, imm) \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm)) ++ ++// Extracts the selected signed or unsigned 64-bit integer from a and zero ++// extends. ++// FORCE_INLINE __int64 _mm_extract_epi64(__m128i a, __constrange(0,2) int imm) ++#define _mm_extract_epi64(a, imm) \ ++ vgetq_lane_s64(vreinterpretq_s64_m128i(a), (imm)) ++ ++// Extracts the selected signed or unsigned 8-bit integer from a and zero ++// extends. ++// FORCE_INLINE int _mm_extract_epi8(__m128i a, __constrange(0,16) int imm) ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_extract_epi8 ++#define _mm_extract_epi8(a, imm) vgetq_lane_u8(vreinterpretq_u8_m128i(a), (imm)) ++ ++// Extracts the selected single-precision (32-bit) floating-point from a. ++// FORCE_INLINE int _mm_extract_ps(__m128 a, __constrange(0,4) int imm) ++#define _mm_extract_ps(a, imm) vgetq_lane_s32(vreinterpretq_s32_m128(a), (imm)) ++ ++// Round the packed double-precision (64-bit) floating-point elements in a down ++// to an integer value, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_floor_pd ++FORCE_INLINE __m128d _mm_floor_pd(__m128d a) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128d_f64(vrndmq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double *f = (double *) &a; ++ return _mm_set_pd(floor(f[1]), floor(f[0])); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a down ++// to an integer value, and store the results as packed single-precision ++// floating-point elements in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_floor_ps ++FORCE_INLINE __m128 _mm_floor_ps(__m128 a) ++{ ++#if defined(__aarch64__) || defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpretq_m128_f32(vrndmq_f32(vreinterpretq_f32_m128(a))); ++#else ++ float *f = (float *) &a; ++ return _mm_set_ps(floorf(f[3]), floorf(f[2]), floorf(f[1]), floorf(f[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b down to ++// an integer value, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_floor_sd ++FORCE_INLINE __m128d _mm_floor_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_floor_pd(b)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b down to ++// an integer value, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. ++// ++// dst[31:0] := FLOOR(b[31:0]) ++// dst[127:32] := a[127:32] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_floor_ss ++FORCE_INLINE __m128 _mm_floor_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_floor_ps(b)); ++} ++ ++// Inserts the least significant 32 bits of b into the selected 32-bit integer ++// of a. ++// FORCE_INLINE __m128i _mm_insert_epi32(__m128i a, int b, ++// __constrange(0,4) int imm) ++#define _mm_insert_epi32(a, b, imm) \ ++ __extension__({ \ ++ vreinterpretq_m128i_s32( \ ++ vsetq_lane_s32((b), vreinterpretq_s32_m128i(a), (imm))); \ ++ }) ++ ++// Inserts the least significant 64 bits of b into the selected 64-bit integer ++// of a. ++// FORCE_INLINE __m128i _mm_insert_epi64(__m128i a, __int64 b, ++// __constrange(0,2) int imm) ++#define _mm_insert_epi64(a, b, imm) \ ++ __extension__({ \ ++ vreinterpretq_m128i_s64( \ ++ vsetq_lane_s64((b), vreinterpretq_s64_m128i(a), (imm))); \ ++ }) ++ ++// Inserts the least significant 8 bits of b into the selected 8-bit integer ++// of a. ++// FORCE_INLINE __m128i _mm_insert_epi8(__m128i a, int b, ++// __constrange(0,16) int imm) ++#define _mm_insert_epi8(a, b, imm) \ ++ __extension__({ \ ++ vreinterpretq_m128i_s8( \ ++ vsetq_lane_s8((b), vreinterpretq_s8_m128i(a), (imm))); \ ++ }) ++ ++// Copy a to tmp, then insert a single-precision (32-bit) floating-point ++// element from b into tmp using the control in imm8. Store tmp to dst using ++// the mask in imm8 (elements are zeroed out when the corresponding bit is set). ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=insert_ps ++#define _mm_insert_ps(a, b, imm8) \ ++ __extension__({ \ ++ float32x4_t tmp1 = \ ++ vsetq_lane_f32(vgetq_lane_f32(b, (imm8 >> 6) & 0x3), \ ++ vreinterpretq_f32_m128(a), 0); \ ++ float32x4_t tmp2 = \ ++ vsetq_lane_f32(vgetq_lane_f32(tmp1, 0), vreinterpretq_f32_m128(a), \ ++ ((imm8 >> 4) & 0x3)); \ ++ const uint32_t data[4] = {((imm8) & (1 << 0)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 1)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 2)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 3)) ? UINT32_MAX : 0}; \ ++ uint32x4_t mask = vld1q_u32(data); \ ++ float32x4_t all_zeros = vdupq_n_f32(0); \ ++ \ ++ vreinterpretq_m128_f32( \ ++ vbslq_f32(mask, all_zeros, vreinterpretq_f32_m128(tmp2))); \ ++ }) ++ ++// epi versions of min/max ++// Computes the pariwise maximums of the four signed 32-bit integer values of a ++// and b. ++// ++// A 128-bit parameter that can be defined with the following equations: ++// r0 := (a0 > b0) ? a0 : b0 ++// r1 := (a1 > b1) ? a1 : b1 ++// r2 := (a2 > b2) ? a2 : b2 ++// r3 := (a3 > b3) ? a3 : b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/bb514055(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_max_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vmaxq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_max_epi8 ++FORCE_INLINE __m128i _mm_max_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vmaxq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed unsigned 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_max_epu16 ++FORCE_INLINE __m128i _mm_max_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vmaxq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Compare packed unsigned 32-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_max_epu32 ++FORCE_INLINE __m128i _mm_max_epu32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vmaxq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b))); ++} ++ ++// Computes the pariwise minima of the four signed 32-bit integer values of a ++// and b. ++// ++// A 128-bit parameter that can be defined with the following equations: ++// r0 := (a0 < b0) ? a0 : b0 ++// r1 := (a1 < b1) ? a1 : b1 ++// r2 := (a2 < b2) ? a2 : b2 ++// r3 := (a3 < b3) ? a3 : b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/bb531476(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_min_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vminq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_min_epi8 ++FORCE_INLINE __m128i _mm_min_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vminq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed unsigned 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_min_epu16 ++FORCE_INLINE __m128i _mm_min_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vminq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Compare packed unsigned 32-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_max_epu32 ++FORCE_INLINE __m128i _mm_min_epu32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vminq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b))); ++} ++ ++// Horizontally compute the minimum amongst the packed unsigned 16-bit integers ++// in a, store the minimum and index in dst, and zero the remaining bits in dst. ++// ++// index[2:0] := 0 ++// min[15:0] := a[15:0] ++// FOR j := 0 to 7 ++// i := j*16 ++// IF a[i+15:i] < min[15:0] ++// index[2:0] := j ++// min[15:0] := a[i+15:i] ++// FI ++// ENDFOR ++// dst[15:0] := min[15:0] ++// dst[18:16] := index[2:0] ++// dst[127:19] := 0 ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_minpos_epu16 ++FORCE_INLINE __m128i _mm_minpos_epu16(__m128i a) ++{ ++ __m128i dst; ++ uint16_t min, idx = 0; ++ // Find the minimum value ++#if defined(__aarch64__) ++ min = vminvq_u16(vreinterpretq_u16_m128i(a)); ++#else ++ __m64 tmp; ++ tmp = vreinterpret_m64_u16( ++ vmin_u16(vget_low_u16(vreinterpretq_u16_m128i(a)), ++ vget_high_u16(vreinterpretq_u16_m128i(a)))); ++ tmp = vreinterpret_m64_u16( ++ vpmin_u16(vreinterpret_u16_m64(tmp), vreinterpret_u16_m64(tmp))); ++ tmp = vreinterpret_m64_u16( ++ vpmin_u16(vreinterpret_u16_m64(tmp), vreinterpret_u16_m64(tmp))); ++ min = vget_lane_u16(vreinterpret_u16_m64(tmp), 0); ++#endif ++ // Get the index of the minimum value ++ int i; ++ for (i = 0; i < 8; i++) { ++ if (min == vgetq_lane_u16(vreinterpretq_u16_m128i(a), 0)) { ++ idx = (uint16_t) i; ++ break; ++ } ++ a = _mm_srli_si128(a, 2); ++ } ++ // Generate result ++ dst = _mm_setzero_si128(); ++ dst = vreinterpretq_m128i_u16( ++ vsetq_lane_u16(min, vreinterpretq_u16_m128i(dst), 0)); ++ dst = vreinterpretq_m128i_u16( ++ vsetq_lane_u16(idx, vreinterpretq_u16_m128i(dst), 1)); ++ return dst; ++} ++ ++// Compute the sum of absolute differences (SADs) of quadruplets of unsigned ++// 8-bit integers in a compared to those in b, and store the 16-bit results in ++// dst. Eight SADs are performed using one quadruplet from b and eight ++// quadruplets from a. One quadruplet is selected from b starting at on the ++// offset specified in imm8. Eight quadruplets are formed from sequential 8-bit ++// integers selected from a starting at the offset specified in imm8. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_mpsadbw_epu8 ++FORCE_INLINE __m128i _mm_mpsadbw_epu8(__m128i a, __m128i b, const int imm) ++{ ++ uint8x16_t _a, _b; ++ ++ switch (imm & 0x4) { ++ case 0: ++ // do nothing ++ _a = vreinterpretq_u8_m128i(a); ++ break; ++ case 4: ++ _a = vreinterpretq_u8_u32(vextq_u32(vreinterpretq_u32_m128i(a), ++ vreinterpretq_u32_m128i(a), 1)); ++ break; ++ default: ++#if defined(__GNUC__) || defined(__clang__) ++ __builtin_unreachable(); ++#endif ++ break; ++ } ++ ++ switch (imm & 0x3) { ++ case 0: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 0))); ++ break; ++ case 1: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 1))); ++ break; ++ case 2: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 2))); ++ break; ++ case 3: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 3))); ++ break; ++ default: ++#if defined(__GNUC__) || defined(__clang__) ++ __builtin_unreachable(); ++#endif ++ break; ++ } ++ ++ int16x8_t c04, c15, c26, c37; ++ uint8x8_t low_b = vget_low_u8(_b); ++ c04 = vabsq_s16(vreinterpretq_s16_u16(vsubl_u8(vget_low_u8(_a), low_b))); ++ _a = vextq_u8(_a, _a, 1); ++ c15 = vabsq_s16(vreinterpretq_s16_u16(vsubl_u8(vget_low_u8(_a), low_b))); ++ _a = vextq_u8(_a, _a, 1); ++ c26 = vabsq_s16(vreinterpretq_s16_u16(vsubl_u8(vget_low_u8(_a), low_b))); ++ _a = vextq_u8(_a, _a, 1); ++ c37 = vabsq_s16(vreinterpretq_s16_u16(vsubl_u8(vget_low_u8(_a), low_b))); ++#if defined(__aarch64__) ++ // |0|4|2|6| ++ c04 = vpaddq_s16(c04, c26); ++ // |1|5|3|7| ++ c15 = vpaddq_s16(c15, c37); ++ ++ int32x4_t trn1_c = ++ vtrn1q_s32(vreinterpretq_s32_s16(c04), vreinterpretq_s32_s16(c15)); ++ int32x4_t trn2_c = ++ vtrn2q_s32(vreinterpretq_s32_s16(c04), vreinterpretq_s32_s16(c15)); ++ return vreinterpretq_m128i_s16(vpaddq_s16(vreinterpretq_s16_s32(trn1_c), ++ vreinterpretq_s16_s32(trn2_c))); ++#else ++ int16x4_t c01, c23, c45, c67; ++ c01 = vpadd_s16(vget_low_s16(c04), vget_low_s16(c15)); ++ c23 = vpadd_s16(vget_low_s16(c26), vget_low_s16(c37)); ++ c45 = vpadd_s16(vget_high_s16(c04), vget_high_s16(c15)); ++ c67 = vpadd_s16(vget_high_s16(c26), vget_high_s16(c37)); ++ ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vpadd_s16(c01, c23), vpadd_s16(c45, c67))); ++#endif ++} ++ ++// Multiply the low signed 32-bit integers from each packed 64-bit element in ++// a and b, and store the signed 64-bit results in dst. ++// ++// r0 := (int64_t)(int32_t)a0 * (int64_t)(int32_t)b0 ++// r1 := (int64_t)(int32_t)a2 * (int64_t)(int32_t)b2 ++FORCE_INLINE __m128i _mm_mul_epi32(__m128i a, __m128i b) ++{ ++ // vmull_s32 upcasts instead of masking, so we downcast. ++ int32x2_t a_lo = vmovn_s64(vreinterpretq_s64_m128i(a)); ++ int32x2_t b_lo = vmovn_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vmull_s32(a_lo, b_lo)); ++} ++ ++// Multiplies the 4 signed or unsigned 32-bit integers from a by the 4 signed or ++// unsigned 32-bit integers from b. ++// https://msdn.microsoft.com/en-us/library/vstudio/bb531409(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_mullo_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vmulq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Packs the 8 unsigned 32-bit integers from a and b into unsigned 16-bit ++// integers and saturates. ++// ++// r0 := UnsignedSaturate(a0) ++// r1 := UnsignedSaturate(a1) ++// r2 := UnsignedSaturate(a2) ++// r3 := UnsignedSaturate(a3) ++// r4 := UnsignedSaturate(b0) ++// r5 := UnsignedSaturate(b1) ++// r6 := UnsignedSaturate(b2) ++// r7 := UnsignedSaturate(b3) ++FORCE_INLINE __m128i _mm_packus_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcombine_u16(vqmovun_s32(vreinterpretq_s32_m128i(a)), ++ vqmovun_s32(vreinterpretq_s32_m128i(b)))); ++} ++ ++// Round the packed double-precision (64-bit) floating-point elements in a using ++// the rounding parameter, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_round_pd ++FORCE_INLINE __m128d _mm_round_pd(__m128d a, int rounding) ++{ ++#if defined(__aarch64__) ++ switch (rounding) { ++ case (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128d_f64(vrndnq_f64(vreinterpretq_f64_m128d(a))); ++ case (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC): ++ return _mm_floor_pd(a); ++ case (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC): ++ return _mm_ceil_pd(a); ++ case (_MM_FROUND_TO_ZERO | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128d_f64(vrndq_f64(vreinterpretq_f64_m128d(a))); ++ default: //_MM_FROUND_CUR_DIRECTION ++ return vreinterpretq_m128d_f64(vrndiq_f64(vreinterpretq_f64_m128d(a))); ++ } ++#else ++ double *v_double = (double *) &a; ++ ++ if (rounding == (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_NEAREST)) { ++ double res[2], tmp; ++ for (int i = 0; i < 2; i++) { ++ tmp = (v_double[i] < 0) ? -v_double[i] : v_double[i]; ++ double roundDown = floor(tmp); // Round down value ++ double roundUp = ceil(tmp); // Round up value ++ double diffDown = tmp - roundDown; ++ double diffUp = roundUp - tmp; ++ if (diffDown < diffUp) { ++ /* If it's closer to the round down value, then use it */ ++ res[i] = roundDown; ++ } else if (diffDown > diffUp) { ++ /* If it's closer to the round up value, then use it */ ++ res[i] = roundUp; ++ } else { ++ /* If it's equidistant between round up and round down value, ++ * pick the one which is an even number */ ++ double half = roundDown / 2; ++ if (half != floor(half)) { ++ /* If the round down value is odd, return the round up value ++ */ ++ res[i] = roundUp; ++ } else { ++ /* If the round up value is odd, return the round down value ++ */ ++ res[i] = roundDown; ++ } ++ } ++ res[i] = (v_double[i] < 0) ? -res[i] : res[i]; ++ } ++ return _mm_set_pd(res[1], res[0]); ++ } else if (rounding == (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_DOWN)) { ++ return _mm_floor_pd(a); ++ } else if (rounding == (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_UP)) { ++ return _mm_ceil_pd(a); ++ } ++ return _mm_set_pd(v_double[1] > 0 ? floor(v_double[1]) : ceil(v_double[1]), ++ v_double[0] > 0 ? floor(v_double[0]) : ceil(v_double[0])); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a using ++// the rounding parameter, and store the results as packed single-precision ++// floating-point elements in dst. ++// software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_round_ps ++FORCE_INLINE __m128 _mm_round_ps(__m128 a, int rounding) ++{ ++#if defined(__aarch64__) || defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ switch (rounding) { ++ case (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128_f32(vrndnq_f32(vreinterpretq_f32_m128(a))); ++ case (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC): ++ return _mm_floor_ps(a); ++ case (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC): ++ return _mm_ceil_ps(a); ++ case (_MM_FROUND_TO_ZERO | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128_f32(vrndq_f32(vreinterpretq_f32_m128(a))); ++ default: //_MM_FROUND_CUR_DIRECTION ++ return vreinterpretq_m128_f32(vrndiq_f32(vreinterpretq_f32_m128(a))); ++ } ++#else ++ float *v_float = (float *) &a; ++ ++ if (rounding == (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_NEAREST)) { ++ uint32x4_t signmask = vdupq_n_u32(0x80000000); ++ float32x4_t half = vbslq_f32(signmask, vreinterpretq_f32_m128(a), ++ vdupq_n_f32(0.5f)); /* +/- 0.5 */ ++ int32x4_t r_normal = vcvtq_s32_f32(vaddq_f32( ++ vreinterpretq_f32_m128(a), half)); /* round to integer: [a + 0.5]*/ ++ int32x4_t r_trunc = vcvtq_s32_f32( ++ vreinterpretq_f32_m128(a)); /* truncate to integer: [a] */ ++ int32x4_t plusone = vreinterpretq_s32_u32(vshrq_n_u32( ++ vreinterpretq_u32_s32(vnegq_s32(r_trunc)), 31)); /* 1 or 0 */ ++ int32x4_t r_even = vbicq_s32(vaddq_s32(r_trunc, plusone), ++ vdupq_n_s32(1)); /* ([a] + {0,1}) & ~1 */ ++ float32x4_t delta = vsubq_f32( ++ vreinterpretq_f32_m128(a), ++ vcvtq_f32_s32(r_trunc)); /* compute delta: delta = (a - [a]) */ ++ uint32x4_t is_delta_half = ++ vceqq_f32(delta, half); /* delta == +/- 0.5 */ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_s32(vbslq_s32(is_delta_half, r_even, r_normal))); ++ } else if (rounding == (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_DOWN)) { ++ return _mm_floor_ps(a); ++ } else if (rounding == (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_UP)) { ++ return _mm_ceil_ps(a); ++ } ++ return _mm_set_ps(v_float[3] > 0 ? floorf(v_float[3]) : ceilf(v_float[3]), ++ v_float[2] > 0 ? floorf(v_float[2]) : ceilf(v_float[2]), ++ v_float[1] > 0 ? floorf(v_float[1]) : ceilf(v_float[1]), ++ v_float[0] > 0 ? floorf(v_float[0]) : ceilf(v_float[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b using ++// the rounding parameter, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_round_sd ++FORCE_INLINE __m128d _mm_round_sd(__m128d a, __m128d b, int rounding) ++{ ++ return _mm_move_sd(a, _mm_round_pd(b, rounding)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b using ++// the rounding parameter, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. Rounding is done according to the ++// rounding[3:0] parameter, which can be one of: ++// (_MM_FROUND_TO_NEAREST_INT |_MM_FROUND_NO_EXC) // round to nearest, and ++// suppress exceptions ++// (_MM_FROUND_TO_NEG_INF |_MM_FROUND_NO_EXC) // round down, and ++// suppress exceptions ++// (_MM_FROUND_TO_POS_INF |_MM_FROUND_NO_EXC) // round up, and suppress ++// exceptions ++// (_MM_FROUND_TO_ZERO |_MM_FROUND_NO_EXC) // truncate, and suppress ++// exceptions _MM_FROUND_CUR_DIRECTION // use MXCSR.RC; see ++// _MM_SET_ROUNDING_MODE ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_round_ss ++FORCE_INLINE __m128 _mm_round_ss(__m128 a, __m128 b, int rounding) ++{ ++ return _mm_move_ss(a, _mm_round_ps(b, rounding)); ++} ++ ++// Load 128-bits of integer data from memory into dst using a non-temporal ++// memory hint. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// ++// dst[127:0] := MEM[mem_addr+127:mem_addr] ++// ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_stream_load_si128 ++FORCE_INLINE __m128i _mm_stream_load_si128(__m128i *p) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ return __builtin_nontemporal_load(p); ++#else ++ return vreinterpretq_m128i_s64(vld1q_s64((int64_t *) p)); ++#endif ++} ++ ++// Compute the bitwise NOT of a and then AND with a 128-bit vector containing ++// all 1's, and return 1 if the result is zero, otherwise return 0. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_test_all_ones ++FORCE_INLINE int _mm_test_all_ones(__m128i a) ++{ ++ return (uint64_t) (vgetq_lane_s64(a, 0) & vgetq_lane_s64(a, 1)) == ++ ~(uint64_t) 0; ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and ++// mask, and return 1 if the result is zero, otherwise return 0. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_test_all_zeros ++FORCE_INLINE int _mm_test_all_zeros(__m128i a, __m128i mask) ++{ ++ int64x2_t a_and_mask = ++ vandq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(mask)); ++ return !(vgetq_lane_s64(a_and_mask, 0) | vgetq_lane_s64(a_and_mask, 1)); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and ++// mask, and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute ++// the bitwise NOT of a and then AND with mask, and set CF to 1 if the result is ++// zero, otherwise set CF to 0. Return 1 if both the ZF and CF values are zero, ++// otherwise return 0. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=mm_test_mix_ones_zero ++FORCE_INLINE int _mm_test_mix_ones_zeros(__m128i a, __m128i mask) ++{ ++ uint64x2_t zf = ++ vandq_u64(vreinterpretq_u64_m128i(mask), vreinterpretq_u64_m128i(a)); ++ uint64x2_t cf = ++ vbicq_u64(vreinterpretq_u64_m128i(mask), vreinterpretq_u64_m128i(a)); ++ uint64x2_t result = vandq_u64(zf, cf); ++ return !(vgetq_lane_u64(result, 0) | vgetq_lane_u64(result, 1)); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return the CF value. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_testc_si128 ++FORCE_INLINE int _mm_testc_si128(__m128i a, __m128i b) ++{ ++ int64x2_t s64 = ++ vandq_s64(vreinterpretq_s64_s32(vmvnq_s32(vreinterpretq_s32_m128i(a))), ++ vreinterpretq_s64_m128i(b)); ++ return !(vgetq_lane_s64(s64, 0) | vgetq_lane_s64(s64, 1)); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return 1 if both the ZF and CF values are zero, ++// otherwise return 0. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_testnzc_si128 ++#define _mm_testnzc_si128(a, b) _mm_test_mix_ones_zeros(a, b) ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return the ZF value. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_testz_si128 ++FORCE_INLINE int _mm_testz_si128(__m128i a, __m128i b) ++{ ++ int64x2_t s64 = ++ vandq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b)); ++ return !(vgetq_lane_s64(s64, 0) | vgetq_lane_s64(s64, 1)); ++} ++ ++/* SSE4.2 */ ++ ++// Compares the 2 signed 64-bit integers in a and the 2 signed 64-bit integers ++// in b for greater than. ++FORCE_INLINE __m128i _mm_cmpgt_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128i_u64( ++ vcgtq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++#else ++ return vreinterpretq_m128i_s64(vshrq_n_s64( ++ vqsubq_s64(vreinterpretq_s64_m128i(b), vreinterpretq_s64_m128i(a)), ++ 63)); ++#endif ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 16-bit integer v. ++// https://msdn.microsoft.com/en-us/library/bb531411(v=vs.100) ++FORCE_INLINE uint32_t _mm_crc32_u16(uint32_t crc, uint16_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32ch %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif (__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32) ++ crc = __crc32ch(crc, v); ++#else ++ crc = _mm_crc32_u8(crc, v & 0xff); ++ crc = _mm_crc32_u8(crc, (v >> 8) & 0xff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 32-bit integer v. ++// https://msdn.microsoft.com/en-us/library/bb531394(v=vs.100) ++FORCE_INLINE uint32_t _mm_crc32_u32(uint32_t crc, uint32_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cw %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif (__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32) ++ crc = __crc32cw(crc, v); ++#else ++ crc = _mm_crc32_u16(crc, v & 0xffff); ++ crc = _mm_crc32_u16(crc, (v >> 16) & 0xffff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 64-bit integer v. ++// https://msdn.microsoft.com/en-us/library/bb514033(v=vs.100) ++FORCE_INLINE uint64_t _mm_crc32_u64(uint64_t crc, uint64_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cx %w[c], %w[c], %x[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#else ++ crc = _mm_crc32_u32((uint32_t) (crc), v & 0xffffffff); ++ crc = _mm_crc32_u32((uint32_t) (crc), (v >> 32) & 0xffffffff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 8-bit integer v. ++// https://msdn.microsoft.com/en-us/library/bb514036(v=vs.100) ++FORCE_INLINE uint32_t _mm_crc32_u8(uint32_t crc, uint8_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cb %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif (__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32) ++ crc = __crc32cb(crc, v); ++#else ++ crc ^= v; ++ for (int bit = 0; bit < 8; bit++) { ++ if (crc & 1) ++ crc = (crc >> 1) ^ UINT32_C(0x82f63b78); ++ else ++ crc = (crc >> 1); ++ } ++#endif ++ return crc; ++} ++ ++/* AES */ ++ ++#if !defined(__ARM_FEATURE_CRYPTO) ++/* clang-format off */ ++#define SSE2NEON_AES_DATA(w) \ ++ { \ ++ w(0x63), w(0x7c), w(0x77), w(0x7b), w(0xf2), w(0x6b), w(0x6f), \ ++ w(0xc5), w(0x30), w(0x01), w(0x67), w(0x2b), w(0xfe), w(0xd7), \ ++ w(0xab), w(0x76), w(0xca), w(0x82), w(0xc9), w(0x7d), w(0xfa), \ ++ w(0x59), w(0x47), w(0xf0), w(0xad), w(0xd4), w(0xa2), w(0xaf), \ ++ w(0x9c), w(0xa4), w(0x72), w(0xc0), w(0xb7), w(0xfd), w(0x93), \ ++ w(0x26), w(0x36), w(0x3f), w(0xf7), w(0xcc), w(0x34), w(0xa5), \ ++ w(0xe5), w(0xf1), w(0x71), w(0xd8), w(0x31), w(0x15), w(0x04), \ ++ w(0xc7), w(0x23), w(0xc3), w(0x18), w(0x96), w(0x05), w(0x9a), \ ++ w(0x07), w(0x12), w(0x80), w(0xe2), w(0xeb), w(0x27), w(0xb2), \ ++ w(0x75), w(0x09), w(0x83), w(0x2c), w(0x1a), w(0x1b), w(0x6e), \ ++ w(0x5a), w(0xa0), w(0x52), w(0x3b), w(0xd6), w(0xb3), w(0x29), \ ++ w(0xe3), w(0x2f), w(0x84), w(0x53), w(0xd1), w(0x00), w(0xed), \ ++ w(0x20), w(0xfc), w(0xb1), w(0x5b), w(0x6a), w(0xcb), w(0xbe), \ ++ w(0x39), w(0x4a), w(0x4c), w(0x58), w(0xcf), w(0xd0), w(0xef), \ ++ w(0xaa), w(0xfb), w(0x43), w(0x4d), w(0x33), w(0x85), w(0x45), \ ++ w(0xf9), w(0x02), w(0x7f), w(0x50), w(0x3c), w(0x9f), w(0xa8), \ ++ w(0x51), w(0xa3), w(0x40), w(0x8f), w(0x92), w(0x9d), w(0x38), \ ++ w(0xf5), w(0xbc), w(0xb6), w(0xda), w(0x21), w(0x10), w(0xff), \ ++ w(0xf3), w(0xd2), w(0xcd), w(0x0c), w(0x13), w(0xec), w(0x5f), \ ++ w(0x97), w(0x44), w(0x17), w(0xc4), w(0xa7), w(0x7e), w(0x3d), \ ++ w(0x64), w(0x5d), w(0x19), w(0x73), w(0x60), w(0x81), w(0x4f), \ ++ w(0xdc), w(0x22), w(0x2a), w(0x90), w(0x88), w(0x46), w(0xee), \ ++ w(0xb8), w(0x14), w(0xde), w(0x5e), w(0x0b), w(0xdb), w(0xe0), \ ++ w(0x32), w(0x3a), w(0x0a), w(0x49), w(0x06), w(0x24), w(0x5c), \ ++ w(0xc2), w(0xd3), w(0xac), w(0x62), w(0x91), w(0x95), w(0xe4), \ ++ w(0x79), w(0xe7), w(0xc8), w(0x37), w(0x6d), w(0x8d), w(0xd5), \ ++ w(0x4e), w(0xa9), w(0x6c), w(0x56), w(0xf4), w(0xea), w(0x65), \ ++ w(0x7a), w(0xae), w(0x08), w(0xba), w(0x78), w(0x25), w(0x2e), \ ++ w(0x1c), w(0xa6), w(0xb4), w(0xc6), w(0xe8), w(0xdd), w(0x74), \ ++ w(0x1f), w(0x4b), w(0xbd), w(0x8b), w(0x8a), w(0x70), w(0x3e), \ ++ w(0xb5), w(0x66), w(0x48), w(0x03), w(0xf6), w(0x0e), w(0x61), \ ++ w(0x35), w(0x57), w(0xb9), w(0x86), w(0xc1), w(0x1d), w(0x9e), \ ++ w(0xe1), w(0xf8), w(0x98), w(0x11), w(0x69), w(0xd9), w(0x8e), \ ++ w(0x94), w(0x9b), w(0x1e), w(0x87), w(0xe9), w(0xce), w(0x55), \ ++ w(0x28), w(0xdf), w(0x8c), w(0xa1), w(0x89), w(0x0d), w(0xbf), \ ++ w(0xe6), w(0x42), w(0x68), w(0x41), w(0x99), w(0x2d), w(0x0f), \ ++ w(0xb0), w(0x54), w(0xbb), w(0x16) \ ++ } ++/* clang-format on */ ++ ++/* X Macro trick. See https://en.wikipedia.org/wiki/X_Macro */ ++#define SSE2NEON_AES_H0(x) (x) ++static const uint8_t SSE2NEON_sbox[256] = SSE2NEON_AES_DATA(SSE2NEON_AES_H0); ++#undef SSE2NEON_AES_H0 ++ ++// In the absence of crypto extensions, implement aesenc using regular neon ++// intrinsics instead. See: ++// https://www.workofard.com/2017/01/accelerated-aes-for-the-arm64-linux-kernel/ ++// https://www.workofard.com/2017/07/ghash-for-low-end-cores/ and ++// https://github.com/ColinIanKing/linux-next-mirror/blob/b5f466091e130caaf0735976648f72bd5e09aa84/crypto/aegis128-neon-inner.c#L52 ++// for more information Reproduced with permission of the author. ++FORCE_INLINE __m128i _mm_aesenc_si128(__m128i EncBlock, __m128i RoundKey) ++{ ++#if defined(__aarch64__) ++ static const uint8_t shift_rows[] = {0x0, 0x5, 0xa, 0xf, 0x4, 0x9, ++ 0xe, 0x3, 0x8, 0xd, 0x2, 0x7, ++ 0xc, 0x1, 0x6, 0xb}; ++ static const uint8_t ror32by8[] = {0x1, 0x2, 0x3, 0x0, 0x5, 0x6, 0x7, 0x4, ++ 0x9, 0xa, 0xb, 0x8, 0xd, 0xe, 0xf, 0xc}; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(EncBlock); ++ ++ // shift rows ++ w = vqtbl1q_u8(w, vld1q_u8(shift_rows)); ++ ++ // sub bytes ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(SSE2NEON_sbox), w); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(SSE2NEON_sbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(SSE2NEON_sbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(SSE2NEON_sbox + 0xc0), w - 0xc0); ++ ++ // mix columns ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w ^= (uint8x16_t) vrev32q_u16((uint16x8_t) v); ++ w ^= vqtbl1q_u8(v ^ w, vld1q_u8(ror32by8)); ++ ++ // add round key ++ return vreinterpretq_m128i_u8(w) ^ RoundKey; ++ ++#else /* ARMv7-A NEON implementation */ ++#define SSE2NEON_AES_B2W(b0, b1, b2, b3) \ ++ (((uint32_t) (b3) << 24) | ((uint32_t) (b2) << 16) | \ ++ ((uint32_t) (b1) << 8) | (uint32_t) (b0)) ++#define SSE2NEON_AES_F2(x) ((x << 1) ^ (((x >> 7) & 1) * 0x011b /* WPOLY */)) ++#define SSE2NEON_AES_F3(x) (SSE2NEON_AES_F2(x) ^ x) ++#define SSE2NEON_AES_U0(p) \ ++ SSE2NEON_AES_B2W(SSE2NEON_AES_F2(p), p, p, SSE2NEON_AES_F3(p)) ++#define SSE2NEON_AES_U1(p) \ ++ SSE2NEON_AES_B2W(SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p), p, p) ++#define SSE2NEON_AES_U2(p) \ ++ SSE2NEON_AES_B2W(p, SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p), p) ++#define SSE2NEON_AES_U3(p) \ ++ SSE2NEON_AES_B2W(p, p, SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p)) ++ static const uint32_t ALIGN_STRUCT(16) aes_table[4][256] = { ++ SSE2NEON_AES_DATA(SSE2NEON_AES_U0), ++ SSE2NEON_AES_DATA(SSE2NEON_AES_U1), ++ SSE2NEON_AES_DATA(SSE2NEON_AES_U2), ++ SSE2NEON_AES_DATA(SSE2NEON_AES_U3), ++ }; ++#undef SSE2NEON_AES_B2W ++#undef SSE2NEON_AES_F2 ++#undef SSE2NEON_AES_F3 ++#undef SSE2NEON_AES_U0 ++#undef SSE2NEON_AES_U1 ++#undef SSE2NEON_AES_U2 ++#undef SSE2NEON_AES_U3 ++ ++ uint32_t x0 = _mm_cvtsi128_si32(EncBlock); ++ uint32_t x1 = _mm_cvtsi128_si32(_mm_shuffle_epi32(EncBlock, 0x55)); ++ uint32_t x2 = _mm_cvtsi128_si32(_mm_shuffle_epi32(EncBlock, 0xAA)); ++ uint32_t x3 = _mm_cvtsi128_si32(_mm_shuffle_epi32(EncBlock, 0xFF)); ++ ++ __m128i out = _mm_set_epi32( ++ (aes_table[0][x3 & 0xff] ^ aes_table[1][(x0 >> 8) & 0xff] ^ ++ aes_table[2][(x1 >> 16) & 0xff] ^ aes_table[3][x2 >> 24]), ++ (aes_table[0][x2 & 0xff] ^ aes_table[1][(x3 >> 8) & 0xff] ^ ++ aes_table[2][(x0 >> 16) & 0xff] ^ aes_table[3][x1 >> 24]), ++ (aes_table[0][x1 & 0xff] ^ aes_table[1][(x2 >> 8) & 0xff] ^ ++ aes_table[2][(x3 >> 16) & 0xff] ^ aes_table[3][x0 >> 24]), ++ (aes_table[0][x0 & 0xff] ^ aes_table[1][(x1 >> 8) & 0xff] ^ ++ aes_table[2][(x2 >> 16) & 0xff] ^ aes_table[3][x3 >> 24])); ++ ++ return _mm_xor_si128(out, RoundKey); ++#endif ++} ++ ++// Perform the last round of an AES encryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_aesenclast_si128 ++FORCE_INLINE __m128i _mm_aesenclast_si128(__m128i a, __m128i RoundKey) ++{ ++ /* FIXME: optimized for NEON */ ++ uint8_t v[4][4] = { ++ {SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 0)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 5)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 10)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 15)]}, ++ {SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 4)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 9)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 14)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 3)]}, ++ {SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 8)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 13)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 2)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 7)]}, ++ {SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 12)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 1)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 6)], ++ SSE2NEON_sbox[vreinterpretq_nth_u8_m128i(a, 11)]}, ++ }; ++ for (int i = 0; i < 16; i++) ++ vreinterpretq_nth_u8_m128i(a, i) = ++ v[i / 4][i % 4] ^ vreinterpretq_nth_u8_m128i(RoundKey, i); ++ return a; ++} ++ ++// Emits the Advanced Encryption Standard (AES) instruction aeskeygenassist. ++// This instruction generates a round key for AES encryption. See ++// https://kazakov.life/2017/11/01/cryptocurrency-mining-on-ios-devices/ ++// for details. ++// ++// https://msdn.microsoft.com/en-us/library/cc714138(v=vs.120).aspx ++FORCE_INLINE __m128i _mm_aeskeygenassist_si128(__m128i key, const int rcon) ++{ ++ uint32_t X1 = _mm_cvtsi128_si32(_mm_shuffle_epi32(key, 0x55)); ++ uint32_t X3 = _mm_cvtsi128_si32(_mm_shuffle_epi32(key, 0xFF)); ++ for (int i = 0; i < 4; ++i) { ++ ((uint8_t *) &X1)[i] = SSE2NEON_sbox[((uint8_t *) &X1)[i]]; ++ ((uint8_t *) &X3)[i] = SSE2NEON_sbox[((uint8_t *) &X3)[i]]; ++ } ++ return _mm_set_epi32(((X3 >> 8) | (X3 << 24)) ^ rcon, X3, ++ ((X1 >> 8) | (X1 << 24)) ^ rcon, X1); ++} ++#undef SSE2NEON_AES_DATA ++ ++#else /* __ARM_FEATURE_CRYPTO */ ++// Implements equivalent of 'aesenc' by combining AESE (with an empty key) and ++// AESMC and then manually applying the real key as an xor operation. This ++// unfortunately means an additional xor op; the compiler should be able to ++// optimize this away for repeated calls however. See ++// https://blog.michaelbrase.com/2018/05/08/emulating-x86-aes-intrinsics-on-armv8-a ++// for more details. ++FORCE_INLINE __m128i _mm_aesenc_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vaesmcq_u8(vaeseq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0))) ^ ++ vreinterpretq_u8_m128i(b)); ++} ++ ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_aesenclast_si128 ++FORCE_INLINE __m128i _mm_aesenclast_si128(__m128i a, __m128i RoundKey) ++{ ++ return _mm_xor_si128(vreinterpretq_m128i_u8(vaeseq_u8( ++ vreinterpretq_u8_m128i(a), vdupq_n_u8(0))), ++ RoundKey); ++} ++ ++FORCE_INLINE __m128i _mm_aeskeygenassist_si128(__m128i a, const int rcon) ++{ ++ // AESE does ShiftRows and SubBytes on A ++ uint8x16_t u8 = vaeseq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0)); ++ ++ uint8x16_t dest = { ++ // Undo ShiftRows step from AESE and extract X1 and X3 ++ u8[0x4], u8[0x1], u8[0xE], u8[0xB], // SubBytes(X1) ++ u8[0x1], u8[0xE], u8[0xB], u8[0x4], // ROT(SubBytes(X1)) ++ u8[0xC], u8[0x9], u8[0x6], u8[0x3], // SubBytes(X3) ++ u8[0x9], u8[0x6], u8[0x3], u8[0xC], // ROT(SubBytes(X3)) ++ }; ++ uint32x4_t r = {0, (unsigned) rcon, 0, (unsigned) rcon}; ++ return vreinterpretq_m128i_u8(dest) ^ vreinterpretq_m128i_u32(r); ++} ++#endif ++ ++/* Others */ ++ ++// Perform a carry-less multiplication of two 64-bit integers, selected from a ++// and b according to imm8, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_clmulepi64_si128 ++FORCE_INLINE __m128i _mm_clmulepi64_si128(__m128i _a, __m128i _b, const int imm) ++{ ++ uint64x2_t a = vreinterpretq_u64_m128i(_a); ++ uint64x2_t b = vreinterpretq_u64_m128i(_b); ++ switch (imm & 0x11) { ++ case 0x00: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_low_u64(a), vget_low_u64(b))); ++ case 0x01: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_high_u64(a), vget_low_u64(b))); ++ case 0x10: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_low_u64(a), vget_high_u64(b))); ++ case 0x11: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_high_u64(a), vget_high_u64(b))); ++ default: ++ abort(); ++ } ++} ++ ++FORCE_INLINE unsigned int _sse2neon_mm_get_denormals_zero_mode() ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("mrs %0, FPCR" : "=r"(r.value)); /* read */ ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ return r.field.bit24 ? _MM_DENORMALS_ZERO_ON : _MM_DENORMALS_ZERO_OFF; ++} ++ ++// Count the number of bits set to 1 in unsigned 32-bit integer a, and ++// return that count in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_popcnt_u32 ++FORCE_INLINE int _mm_popcnt_u32(unsigned int a) ++{ ++#if defined(__aarch64__) ++#if __has_builtin(__builtin_popcount) ++ return __builtin_popcount(a); ++#else ++ return (int) vaddlv_u8(vcnt_u8(vcreate_u8((uint64_t) a))); ++#endif ++#else ++ uint32_t count = 0; ++ uint8x8_t input_val, count8x8_val; ++ uint16x4_t count16x4_val; ++ uint32x2_t count32x2_val; ++ ++ input_val = vld1_u8((uint8_t *) &a); ++ count8x8_val = vcnt_u8(input_val); ++ count16x4_val = vpaddl_u8(count8x8_val); ++ count32x2_val = vpaddl_u16(count16x4_val); ++ ++ vst1_u32(&count, count32x2_val); ++ return count; ++#endif ++} ++ ++// Count the number of bits set to 1 in unsigned 64-bit integer a, and ++// return that count in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_popcnt_u64 ++FORCE_INLINE int64_t _mm_popcnt_u64(uint64_t a) ++{ ++#if defined(__aarch64__) ++#if __has_builtin(__builtin_popcountll) ++ return __builtin_popcountll(a); ++#else ++ return (int64_t) vaddlv_u8(vcnt_u8(vcreate_u8(a))); ++#endif ++#else ++ uint64_t count = 0; ++ uint8x8_t input_val, count8x8_val; ++ uint16x4_t count16x4_val; ++ uint32x2_t count32x2_val; ++ uint64x1_t count64x1_val; ++ ++ input_val = vld1_u8((uint8_t *) &a); ++ count8x8_val = vcnt_u8(input_val); ++ count16x4_val = vpaddl_u8(count8x8_val); ++ count32x2_val = vpaddl_u16(count16x4_val); ++ count64x1_val = vpaddl_u32(count32x2_val); ++ vst1_u64(&count, count64x1_val); ++ return count; ++#endif ++} ++ ++FORCE_INLINE void _sse2neon_mm_set_denormals_zero_mode(unsigned int flag) ++{ ++ // AArch32 Advanced SIMD arithmetic always uses the Flush-to-zero setting, ++ // regardless of the value of the FZ bit. ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("mrs %0, FPCR" : "=r"(r.value)); /* read */ ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ r.field.bit24 = (flag & _MM_DENORMALS_ZERO_MASK) == _MM_DENORMALS_ZERO_ON; ++ ++#if defined(__aarch64__) ++ __asm__ __volatile__("msr FPCR, %0" ::"r"(r)); /* write */ ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Return the current 64-bit value of the processor's time-stamp counter. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=rdtsc ++ ++FORCE_INLINE uint64_t _rdtsc(void) ++{ ++#if defined(__aarch64__) ++ uint64_t val; ++ ++ /* According to ARM DDI 0487F.c, from Armv8.0 to Armv8.5 inclusive, the ++ * system counter is at least 56 bits wide; from Armv8.6, the counter ++ * must be 64 bits wide. So the system counter could be less than 64 ++ * bits wide and it is attributed with the flag 'cap_user_time_short' ++ * is true. ++ */ ++ asm volatile("mrs %0, cntvct_el0" : "=r"(val)); ++ ++ return val; ++#else ++ uint32_t pmccntr, pmuseren, pmcntenset; ++ // Read the user mode Performance Monitoring Unit (PMU) ++ // User Enable Register (PMUSERENR) access permissions. ++ asm volatile("mrc p15, 0, %0, c9, c14, 0" : "=r"(pmuseren)); ++ if (pmuseren & 1) { // Allows reading PMUSERENR for user mode code. ++ asm volatile("mrc p15, 0, %0, c9, c12, 1" : "=r"(pmcntenset)); ++ if (pmcntenset & 0x80000000UL) { // Is it counting? ++ asm volatile("mrc p15, 0, %0, c9, c13, 0" : "=r"(pmccntr)); ++ // The counter is set up to count every 64th cycle ++ return (uint64_t) (pmccntr) << 6; ++ } ++ } ++ ++ // Fallback to syscall as we can't enable PMUSERENR in user mode. ++ struct timeval tv; ++ gettimeofday(&tv, NULL); ++ return (uint64_t) (tv.tv_sec) * 1000000 + tv.tv_usec; ++#endif ++} ++ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma pop_macro("ALIGN_STRUCT") ++#pragma pop_macro("FORCE_INLINE") ++#endif ++ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC pop_options ++#endif ++ ++#endif diff --git a/recipes/graphmap/meta.yaml b/recipes/graphmap/meta.yaml index d630a578f3403..9ea30c2ab95d3 100644 --- a/recipes/graphmap/meta.yaml +++ b/recipes/graphmap/meta.yaml @@ -1,18 +1,22 @@ {% set name = "graphmap" %} -{% set version = "0.6.3" %} +{% set version = "0.6.4" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 4 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} source: git_url: https://github.com/lbcb-sci/graphmap2 git_rev: v{{ version }} sha256: unused + patches: + - graphmap2-aarch64.patch # [aarch64] requirements: build: @@ -33,7 +37,11 @@ about: license: MIT license_file: LICENCE summary: 'A highly sensitive and accurate mapper for long, error-prone reads.' + dev_url: https://github.com/lbcb-sci/graphmap2 + doc_url: https://www.nature.com/articles/ncomms11307 extra: + additional-platforms: + - linux-aarch64 skip-lints: - uses_vcs_url diff --git a/recipes/graphtyper/arm_hwcap.patch b/recipes/graphtyper/arm_hwcap.patch new file mode 100644 index 0000000000000..0701b6a203859 --- /dev/null +++ b/recipes/graphtyper/arm_hwcap.patch @@ -0,0 +1,15 @@ +Conda-forge's build environment on ARM uses sysroot_linux-aarch64 2.17, which +is based on glibc 2.17 so does not define HWCAP_* values on ARM. +Work around this by including the kernel header to get the desired values. + +--- a/htslib/htscodecs/htscodecs/rANS_static4x16pr.c 2023-10-10 02:54:16 ++++ b/htslib/htscodecs/htscodecs/rANS_static4x16pr.c 2024-03-06 00:01:14 +@@ -1011,6 +1011,8 @@ unsigned char *(*rans_dec_func(int do_simd, int order)) + + #if defined(__linux__) || defined(__FreeBSD__) + #include ++// Ensure ARM HWCAP_* values are defined even on old glibc ++#include + #elif defined(_WIN32) + #include + #endif diff --git a/recipes/graphtyper/build.sh b/recipes/graphtyper/build.sh index 2289d6ac687ba..87a61e37604f4 100644 --- a/recipes/graphtyper/build.sh +++ b/recipes/graphtyper/build.sh @@ -1,12 +1,23 @@ #!/usr/bin/env bash +set -xe + +case $(uname -m) in + aarch64) + ARCH_OPTS="-Dpaw_BUILD_FLAGS=-DCMAKE_CXX_FLAGS_ARCH=" + ;; + *) + ARCH_OPTS= + ;; +esac + # Generate build mkdir -p build cd build -cmake -DCFLAGS="${CFLAGS}" -DLDFLAGS="${LDFLAGS}" .. +cmake -DCFLAGS="${CFLAGS}" -DLDFLAGS="${LDFLAGS}" ${ARCH_OPTS} .. # Build -VERBOSE=1 make graphtyper +VERBOSE=1 make -j ${CPU_COUNT} graphtyper # Install mkdir -p $PREFIX/bin diff --git a/recipes/graphtyper/build_failure.linux-64.yaml b/recipes/graphtyper/build_failure.linux-64.yaml deleted file mode 100644 index d1737b1a43ae5..0000000000000 --- a/recipes/graphtyper/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 9bcf12d0f66b21c75e96c579b00d8cccd0b621146c9afc850e5fc26fe0245ed9 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - [ 12%] No update step for 'project_libdeflate' - $BUILD_PREFIX/bin/cmake -E echo_append - $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/libdeflate/src/project_libdeflate-stamp/project_libdeflate-update - [ 14%] No patch step for 'project_libdeflate' - $BUILD_PREFIX/bin/cmake -E echo_append - $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/libdeflate/src/project_libdeflate-stamp/project_libdeflate-patch - [ 15%] No configure step for 'project_libdeflate' - cd $SRC_DIR/libdeflate && $BUILD_PREFIX/bin/cmake -E echo_append - cd $SRC_DIR/libdeflate && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/libdeflate/src/project_libdeflate-stamp/project_libdeflate-configure - [ 16%] Performing build step for 'project_libdeflate' - cd $SRC_DIR/libdeflate && make -C $SRC_DIR/libdeflate CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc "CFLAGS=-fPIC -O3 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/graphtyper-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix" libdeflate.a - make[4]: Entering directory '$SRC_DIR/libdeflate' - CC lib/deflate_decompress.o - CC lib/utils.o - CC lib/arm/cpu_features.o - CC lib/x86/cpu_features.o - CC lib/deflate_compress.o - CC lib/adler32.o - CC lib/zlib_decompress.o - CC lib/zlib_compress.o - CC lib/crc32.o - CC lib/gzip_decompress.o - CC lib/gzip_compress.o - AR libdeflate.a - make[4]: Leaving directory '$SRC_DIR/libdeflate' - cd $SRC_DIR/libdeflate && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/libdeflate/src/project_libdeflate-stamp/project_libdeflate-build - [ 17%] No install step for 'project_libdeflate' - cd $SRC_DIR/libdeflate && $BUILD_PREFIX/bin/cmake -E echo_append - cd $SRC_DIR/libdeflate && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/libdeflate/src/project_libdeflate-stamp/project_libdeflate-install - [ 18%] Completed 'project_libdeflate' - $BUILD_PREFIX/bin/cmake -E make_directory $SRC_DIR/build/CMakeFiles - $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/CMakeFiles/project_libdeflate-complete - $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/libdeflate/src/project_libdeflate-stamp/project_libdeflate-done - make[3]: Leaving directory '$SRC_DIR/build' - [ 18%] Built target project_libdeflate - make -f CMakeFiles/project_htslib.dir/build.make CMakeFiles/project_htslib.dir/depend - make[3]: Entering directory '$SRC_DIR/build' - cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR $SRC_DIR/build $SRC_DIR/build $SRC_DIR/build/CMakeFiles/project_htslib.dir/DependInfo.cmake --color= - make[3]: Leaving directory '$SRC_DIR/build' - make -f CMakeFiles/project_htslib.dir/build.make CMakeFiles/project_htslib.dir/build - make[3]: Entering directory '$SRC_DIR/build' - [ 20%] Creating directories for 'project_htslib' - $BUILD_PREFIX/bin/cmake -Dcfgdir= -P $SRC_DIR/htslib/tmp/project_htslib-mkdirs.cmake - $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/htslib/src/project_htslib-stamp/project_htslib-mkdir - [ 21%] No download step for 'project_htslib' - $BUILD_PREFIX/bin/cmake -E echo_append - $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/htslib/src/project_htslib-stamp/project_htslib-download - [ 22%] No update step for 'project_htslib' - $BUILD_PREFIX/bin/cmake -E echo_append - $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/htslib/src/project_htslib-stamp/project_htslib-update - [ 23%] No patch step for 'project_htslib' - $BUILD_PREFIX/bin/cmake -E echo_append - $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/htslib/src/project_htslib-stamp/project_htslib-patch - [ 24%] No configure step for 'project_htslib' - cd $SRC_DIR/htslib && $BUILD_PREFIX/bin/cmake -E echo_append - cd $SRC_DIR/htslib && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/htslib/src/project_htslib-stamp/project_htslib-configure - [ 25%] Performing build step for 'project_htslib' - cd $SRC_DIR/htslib && autoheader - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - cd $SRC_DIR/htslib && autoconf - cd $SRC_DIR/htslib && $SRC_DIR/htslib/configure --disable-libcurl --disable-gcs --with-libdeflate "CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/graphtyper-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O3 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/graphtyper-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$SRC_DIR/libdeflate" "LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/libdeflate" CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - configure: error: cannot find required auxiliary files: config.guess config.sub - make[3]: *** [CMakeFiles/project_htslib.dir/build.make:88: /opt/conda/conda-bld/graphtyper_1685351107399/work/htslib/src/project_htslib-stamp/project_htslib-build] Error 1 - make[3]: Leaving directory '$SRC_DIR/build' - make[2]: *** [CMakeFiles/Makefile2:158: CMakeFiles/project_htslib.dir/all] Error 2 - make[2]: Leaving directory '$SRC_DIR/build' - make[1]: *** [CMakeFiles/Makefile2:247: src/CMakeFiles/graphtyper.dir/rule] Error 2 - make[1]: Leaving directory '$SRC_DIR/build' - make: *** [Makefile:231: graphtyper] Error 2 - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/graphtyper_1685351107399/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/graphtyper/meta.yaml b/recipes/graphtyper/meta.yaml index 11ba606ba83bf..4c943b875e2cb 100644 --- a/recipes/graphtyper/meta.yaml +++ b/recipes/graphtyper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "graphtyper" %} -{% set version = "2.7.2" %} +{% set version = "2.7.7" %} package: name: {{ name }} @@ -9,11 +9,15 @@ source: # git_url is required for submodule retrieval git_url: https://github.com/DecodeGenetics/{{ name }}.git git_rev: v{{ version }} + patches: + - arm_hwcap.patch # [aarch64] build: - number: 2 + number: 0 #binary_relocation: false skip: true # [not linux] + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: @@ -47,6 +51,8 @@ about: summary: Population-scale genotyping using pangenome graphs extra: + additional-platforms: + - linux-aarch64 skip-lints: - uses_vcs_url - missing_hash diff --git a/recipes/grenedalf/meta.yaml b/recipes/grenedalf/meta.yaml index 63645f633c571..50a33338455c5 100644 --- a/recipes/grenedalf/meta.yaml +++ b/recipes/grenedalf/meta.yaml @@ -1,6 +1,6 @@ package: name: grenedalf - version: "0.6.0" + version: "0.6.2" build: number: 0 @@ -9,8 +9,8 @@ build: - {{ pin_subpackage('grenedalf', max_pin='x.x') }} source: - url: https://github.com/lczech/grenedalf/archive/refs/tags/v0.6.0.tar.gz - sha256: 43f7654d9b67fdce0b65096e0b1a4ac6160d838664a65151d44ea382d2489a3f + url: https://github.com/lczech/grenedalf/archive/refs/tags/v0.6.2.tar.gz + sha256: 64aea7bbbe443048144b56de990b2afa9aa3379137aa98adb815d0d4d5f7b298 requirements: build: diff --git a/recipes/gsearch/build.sh b/recipes/gsearch/build.sh index 255e702c00317..530cb231081c0 100644 --- a/recipes/gsearch/build.sh +++ b/recipes/gsearch/build.sh @@ -5,4 +5,4 @@ export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" # build statically linked binary with Rust -RUST_BACKTRACE=1 cargo install --features annembed_intel-mkl,simdeez_f --verbose --path . --root $PREFIX +RUST_BACKTRACE=1 cargo install --features simdeez_f --verbose --path . --root $PREFIX diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index 45b11240f819f..b5933506444d4 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.0" %} +{% set version = "0.2.2" %} package: name: gsearch @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/gsearch/archive/v{{ version }}.tar.gz - sha256: eb535c1757667a61fb85469910ece55a4344c18c77e1b7013a22b050535d1531 + sha256: 2f0247712a302f152b1f08d153f5555a5e7d1608b23f6f9a7eb90e6fa2990945 requirements: build: @@ -33,3 +33,5 @@ extra: maintainers: - Jean Pierre-Both - Jianshu Zhao + identifiers: + - https://doi.org/10.1093/nar/gkae609 diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml index 6955b5089cf72..3adba0cd806f8 100644 --- a/recipes/gtotree/meta.yaml +++ b/recipes/gtotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "GToTree" %} -{% set version = "1.8.6" %} +{% set version = "1.8.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/AstrobioMike/GToTree/archive/v{{ version }}.tar.gz - sha256: 1712d9e18f128bbeeb585b1528a8e207c3a36cc7f1dbb7df66416ec0278d5a9a + sha256: 2ec94fa0bbcfa98edca126ee3446ab7fa8982cd746604b371f74a125e3e44435 build: number: 0 diff --git a/recipes/guidescan/build.sh b/recipes/guidescan/build.sh index 2385814a50278..bb59e1fc4528b 100644 --- a/recipes/guidescan/build.sh +++ b/recipes/guidescan/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + mkdir -p $PREFIX/bin mkdir -p build @@ -10,6 +12,6 @@ cd build # Further, certain features (related to filesystem/path.h) are only available in macOS 10.15 cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -make +make -j ${CPU_COUNT} cp bin/guidescan $PREFIX/bin chmod +x $PREFIX/bin/guidescan diff --git a/recipes/guidescan/build_failure.osx-64.yaml b/recipes/guidescan/build_failure.osx-64.yaml deleted file mode 100644 index b8e3ec35afd30..0000000000000 --- a/recipes/guidescan/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: a17179d188e714827d6bbac62906797d0e10fa8175f281936ae9a98790ac17ae # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - - CMake Deprecation Warning at sdsl/external/googletest/googletest/CMakeLists.txt:48 (cmake_minimum_required): - Compatibility with CMake < 2.8.12 will be removed from a future version of - CMake. - - Update the VERSION argument value or use a ... suffix to tell - CMake that the project does not need compatibility with older versions. - - - -- Found PythonInterp: /opt/mambaforge/envs/bioconda/bin/python (found version "3.8.16") - -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success - -- Found Threads: TRUE - -- Looking for C include cstdio - -- Looking for C include cstdio - found - -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) - -- Found CURL: /Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libcurl.dylib (found version "7.30.0") - -- Configuring done (19.2s) - -- Generating done (1.3s) - -- Build files have been written to: $SRC_DIR/build - [ 0%] Building C object sdsl/external/libdivsufsort/lib/CMakeFiles/divsufsort.dir/divsufsort.o - [ 0%] Building C object sdsl/external/libdivsufsort/lib/CMakeFiles/divsufsort.dir/sssort.o - [ 0%] Building C object sdsl/external/libdivsufsort/lib/CMakeFiles/divsufsort.dir/trsort.o - [ 8%] Building C object sdsl/external/libdivsufsort/lib/CMakeFiles/divsufsort.dir/utils.o - [ 8%] Linking C static library libdivsufsort.a - [ 8%] Built target divsufsort - [ 8%] Building C object sdsl/external/libdivsufsort/lib/CMakeFiles/divsufsort64.dir/divsufsort.o - [ 8%] Building C object sdsl/external/libdivsufsort/lib/CMakeFiles/divsufsort64.dir/sssort.o - [ 16%] Building C object sdsl/external/libdivsufsort/lib/CMakeFiles/divsufsort64.dir/trsort.o - [ 16%] Building C object sdsl/external/libdivsufsort/lib/CMakeFiles/divsufsort64.dir/utils.o - [ 16%] Linking C static library libdivsufsort64.a - [ 16%] Built target divsufsort64 - [ 25%] Building CXX object sdsl/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/src/gtest-all.cc:39: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/gtest.h:62: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/gtest-param-test.h:193: - /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/internal/gtest-param-util-generated.h:107:8: warning: definition of implicit copy constructor for 'ValueArray2' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] - void operator=(const ValueArray2& other); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/gtest-param-test.h:354:10: note: in implicit copy constructor for 'testing::internal::ValueArray2' first required here - return internal::ValueArray2(v1, v2); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/gtest-param-test.h:1221:10: note: in instantiation of function template specialization 'testing::Values' requested here - return Values(false, true); - ^ - 1 warning generated. - [ 25%] Linking CXX static library libgtest.a - [ 25%] Built target gtest - [ 25%] Building CXX object sdsl/external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/src/gtest_main.cc:32: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/gtest.h:62: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/gtest-param-test.h:193: - /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/internal/gtest-param-util-generated.h:107:8: warning: definition of implicit copy constructor for 'ValueArray2' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] - void operator=(const ValueArray2& other); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/gtest-param-test.h:354:10: note: in implicit copy constructor for 'testing::internal::ValueArray2' first required here - return internal::ValueArray2(v1, v2); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/external/googletest/googletest/include/gtest/gtest-param-test.h:1221:10: note: in instantiation of function template specialization 'testing::Values' requested here - return Values(false, true); - ^ - 1 warning generated. - [ 25%] Linking CXX static library libgtest_main.a - [ 25%] Built target gtest_main - [ 33%] Building CXX object sdsl/lib/CMakeFiles/sdsl.dir/bits.cpp.o - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/sdsl/lib/bits.cpp:17: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/build/sdsl/lib/../include/sdsl/bits.hpp:25: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/iostream:43: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/ios:221: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/__locale:18: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/mutex:191: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/__memory/shared_ptr.h:22: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/__memory/allocation_guard.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/__memory/allocator_traits.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/__memory/construct_at.h:23: - /opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/_build_env/bin/../include/c/v1/new:355:14: error: no member named 'aligned_alloc' in the global namespace - return ::aligned_alloc(__alignment, __size > __rounded_size ? __size : __rounded_size); - ~~^ - 1 error generated. - make[2]: *** [sdsl/lib/CMakeFiles/sdsl.dir/build.make:76: sdsl/lib/CMakeFiles/sdsl.dir/bits.cpp.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:682: sdsl/lib/CMakeFiles/sdsl.dir/all] Error 2 - make: *** [Makefile:156: all] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/guidescan_1685353540554/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/guidescan/meta.yaml b/recipes/guidescan/meta.yaml index 9aea5a66ea70d..a77e8729aca56 100644 --- a/recipes/guidescan/meta.yaml +++ b/recipes/guidescan/meta.yaml @@ -1,5 +1,5 @@ {% set name="guidescan" %} -{% set version="2.2.0" %} +{% set version="2.2.1" %} package: name: {{ name }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/pritykinlab/guidescan-cli/releases/download/v{{ version }}/guidescan-v{{ version }}-src.tar.gz - sha256: b1fd82fc65bbcd883e6006ed921762e8075edd61b693f1a4d084e1fda6305f72 + sha256: 24075dc9c391e16af7ac7bf0af4cba0682b420e7ed63ca7c928f16a61adc5ff1 build: - number: 0 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -22,6 +22,11 @@ requirements: run: - libcurl +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + test: commands: - "guidescan --version" diff --git a/recipes/gw/build.sh b/recipes/gw/build.sh index 7fddb127f886d..41ea8b9fe293b 100644 --- a/recipes/gw/build.sh +++ b/recipes/gw/build.sh @@ -1,14 +1,34 @@ #!/usr/bin/bash set -e -export USE_GL=1 + +# Get pre-compiled skia from jetbrains +USE_GL=1 make prep > /dev/null 2>&1 + +if [[ "$OSTYPE" != "darwin"* ]]; then + sed -i 's/-lEGL -lGLESv2/-lEGL -lGLESv2 -lGL -lGLX/' Makefile + sed -i 's/GLFW_EGL_CONTEXT_API/GLFW_NATIVE_CONTEXT_API/' src/plot_manager.cpp +fi + +# Set flags conditionally based on the OS type if [[ "$OSTYPE" != "darwin"* ]]; then - sed -i 's/-lEGL -lGLESv2/-lGL/' Makefile + SYSROOT_FLAGS="--sysroot=${BUILD_PREFIX}/${HOST}/sysroot" + CPPFLAGS="${CPPFLAGS} -I${BUILD_PREFIX}/${HOST}/sysroot/usr/include ${SYSROOT_FLAGS}" + LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -L${BUILD_PREFIX}/${HOST}/sysroot/usr/lib -L${BUILD_PREFIX}/${HOST}/sysroot/usr/lib64 ${SYSROOT_FLAGS}" +else + # No sysroot settings for macOS + SYSROOT_FLAGS="" + CPPFLAGS="${CPPFLAGS}" + LDFLAGS="${LDFLAGS} -L${PREFIX}" fi -make prep -CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" LDFLAGS="${LDFLAGS} -L${PREFIX}" prefix="${PREFIX}" make -j ${CPU_COUNT} + +CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" \ +CPPFLAGS="${CPPFLAGS}" \ +LDFLAGS="${LDFLAGS}" \ +prefix="${PREFIX}" \ +make -j ${CPU_COUNT} + mkdir -p $PREFIX/bin cp gw $PREFIX/bin/gw cp -n .gw.ini $PREFIX/bin/.gw.ini chmod +x $PREFIX/bin/gw chmod +rw $PREFIX/bin/.gw.ini - diff --git a/recipes/gw/fix-context.patch b/recipes/gw/fix-context.patch new file mode 100644 index 0000000000000..6a5aa5d6a9e0c --- /dev/null +++ b/recipes/gw/fix-context.patch @@ -0,0 +1,9 @@ +--- a/src/plot_manager.cpp ++++ b/src/plot_manager.cpp +@@ -252,1 +252,1 @@ +- glfwWindowHint(GLFW_CONTEXT_VERSION_MINOR, (minor_v == -1) ? 1 : major_v); ++ glfwWindowHint(GLFW_CONTEXT_VERSION_MINOR, (minor_v == -1) ? 1 : minor_v); + +@@ -258,1 +258,1 @@ +- glfwWindowHint(GLFW_CONTEXT_VERSION_MINOR, (minor_v == -1) ? 1 : major_v); ++ glfwWindowHint(GLFW_CONTEXT_VERSION_MINOR, (minor_v == -1) ? 1 : minor_v); diff --git a/recipes/gw/meta.yaml b/recipes/gw/meta.yaml index d91101eaef266..decc50a9fcd20 100644 --- a/recipes/gw/meta.yaml +++ b/recipes/gw/meta.yaml @@ -1,37 +1,43 @@ - -{% set version = "1.0.1" %} -{% set sha256 = "aacd161bb7131d7874a75b2ed409ee22109be3f87dd062c5590c6d30d1503e68" %} - +{% set version = "1.1.0" %} +{% set sha256 = "dc96521b8252bde02d9cc68bb3cee156c0469889d2783ee72682338d10657892" %} package: name: gw version: {{ version }} - source: url: https://github.com/kcleal/gw/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} patches: - fix-linker-issues.patch # [linux] - + - fix-context.patch build: - number: 1 + number: 0 run_exports: - - {{ pin_subpackage('gw', max_pin="x") }} + - {{ pin_subpackage('gw', max_pin="x") }} + ignore_run_exports: + - libglx # [linux] + - libgles # [linux] + - libegl # [linux] + - xorg-libsm # [linux] + - xorg-libice # [linux] + - xorg-libx11 # [linux] + - xorg-libxau # [linux] + - xorg-libxext # [linux] + - libxcb # [linux] + - freetype # [osx] + - fontconfig # [osx] + - zlib # [osx] + - libuuid + - libdeflate requirements: build: - make + - {{ compiler('c') }} - {{ compiler('cxx') }} - - {{ cdt('xorg-x11-proto-devel') }} # [linux] - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - {{ cdt('libxfixes') }} # [linux] - - {{ cdt('libxext') }} # [linux] + host: - fontconfig - libuuid @@ -39,24 +45,30 @@ requirements: - libdeflate >=1.0 - htslib >=1.12 - glfw >=3.3 - - wget - unzip - freetype - - xorg-libxfixes # [linux] - - xorg-libx11 # [linux] - - xorg-libxcb # [linux] - - expat # [linux] + - zlib + - pthread-stubs # [linux] + - xorg-libsm # [linux] + - xorg-libice # [linux] + - xorg-libx11 # [linux] + - libxcb # [linux] + - libegl-devel # [linux] + - libgl-devel # [linux] + - libglx-devel # [linux] + - libgles-devel # [linux] + - wayland # [linux] + run: - - {{ cdt('xorg-x11-proto-devel') }} # [linux] - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - {{ cdt('libxfixes') }} # [linux] - - {{ cdt('libxext') }} # [linux] - glfw >=3.3 - - htslib >=1.12 + - htslib >=1.12 + - xorg-libxt # [linux] + - xorg-libxau # [linux] + - xorg-libxfixes # [linux] + - xorg-libxxf86vm # [linux] + - xorg-libxdamage # [linux] + - mesalib # [linux] + - wayland # [linux] test: commands: @@ -69,7 +81,9 @@ about: summary: 'View genomic sequencing data and vcf files' extra: + additional-platforms: + - osx-arm64 container: - extended-base: True + extended-base: True recipe-maintainers: - kcleal diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml index a0b0d0160416c..61af4d475731e 100644 --- a/recipes/gxf2bed/meta.yaml +++ b/recipes/gxf2bed/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gxf2bed" %} -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} package: name: gxf2bed @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: ee500e08e8c94b2663ea511482d6520300cb81c9cbbb05a288563e4a808f5377 + sha256: 1f8358a972bded0c4906bf03532ba4ee9f7fc6bf9b84063e4b25b98f37ced45f build: number: 0 diff --git a/recipes/gxformat2/meta.yaml b/recipes/gxformat2/meta.yaml index 94eda22a18411..dac668815b47c 100644 --- a/recipes/gxformat2/meta.yaml +++ b/recipes/gxformat2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gxformat2" %} -{% set version = "0.19.0" %} +{% set version = "0.20.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 19cf7d4301ef3a7545c465e5daa7127042758bf4d9eba1f1dcc122eb47b99cfc + sha256: 9697b1548c7a016e211581831c48242718f2cbe8987c7db0dc75c20e65931df8 build: number: 0 diff --git a/recipes/hackgap/meta.yaml b/recipes/hackgap/meta.yaml new file mode 100644 index 0000000000000..a419fc79b6312 --- /dev/null +++ b/recipes/hackgap/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "hackgap" %} +{% set version = "1.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 35c5705d8ca1de0d8064c9869730b65f596a0a378a9d14f8a58368e4a71aab22 + +build: + number: 0 + entry_points: + - hackgap = hackgap.hackgap.hackgap_main:main + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + +requirements: + host: + - pip + - python >=3.12 + run: + - python >=3.12 + - numpy >=2 + - numba >=0.60 + - pigz + - xz + - bzip2 + +test: + imports: + - hackgap + commands: + - hackgap --help + - hackgap count --help + +about: + home: https://gitlab.com/rahmannlab/hackgap + license: MIT + license_file: LICENSE + license_family: MIT + summary: "hackgap (hash-based counting of k-mers with gaps) provides a fast jit-compiled k-kmer counter which supports gapped k-mers." + dev_url: https://gitlab.com/rahmannlab/hackgap + +extra: + identifiers: + - doi:10.4230/LIPICS.WABI.2022.12 + recipe-maintainers: + - JZentgraf diff --git a/recipes/hairsplitter/build.sh b/recipes/hairsplitter/build.sh index 978ddf0265bd8..cb5aef39527fd 100644 --- a/recipes/hairsplitter/build.sh +++ b/recipes/hairsplitter/build.sh @@ -1,9 +1,13 @@ +#!/usr/bin/env bash + +set -xe + mkdir -p $PREFIX/bin mkdir src/build cd src/build/ cmake .. -make +make -j ${CPU_COUNT} cp ../../hairsplitter.py $PREFIX/bin chmod +x $PREFIX/bin/hairsplitter.py @@ -25,5 +29,8 @@ cp -r ../GraphUnzip/repolish.py $PREFIX/bin cp -r ../GraphUnzip/transform_gfa.py $PREFIX/bin cp -r ../GraphUnzip/input_output.py $PREFIX/bin cp -r ../GraphUnzip/determine_multiplicity.py $PREFIX/bin +cp -r ../GraphUnzip/solve_with_long_reads.py $PREFIX/bin +cp -r ../GraphUnzip/solve_with_HiC.py $PREFIX/bin +cp -r ../GraphUnzip/contig_DBG.py $PREFIX/bin chmod +x $PREFIX/bin/determine_multiplicity.py diff --git a/recipes/hairsplitter/hairsplitter-aarch64.patch b/recipes/hairsplitter/hairsplitter-aarch64.patch new file mode 100644 index 0000000000000..7a0bbee7822da --- /dev/null +++ b/recipes/hairsplitter/hairsplitter-aarch64.patch @@ -0,0 +1,42 @@ +diff --git i/src/CMakeLists.txt w/src/CMakeLists.txt +index f351aa6..edc0f62 100644 +--- i/src/CMakeLists.txt ++++ w/src/CMakeLists.txt +@@ -100,7 +100,7 @@ target_compile_options (HS_call_variants PRIVATE -lm) + target_compile_options (HS_call_variants PRIVATE -fopenmp) + target_compile_options (HS_call_variants PRIVATE -std=c++17) + target_compile_options (HS_call_variants PRIVATE -O3) +-target_compile_options (HS_call_variants PRIVATE -march=x86-64) ++#target_compile_options (HS_call_variants PRIVATE -march=x86-64) + + + file (GLOB SOURCE_SEPARATE_READS "separate_reads.cpp" "input_output.cpp" "cluster_graph.cpp" "robin_hood.h" "tools.cpp" "read.cpp" "sequence.cpp" "Partition.cpp") +@@ -111,7 +111,7 @@ target_compile_options (HS_separate_reads PRIVATE -lm) + target_compile_options (HS_separate_reads PRIVATE -fopenmp) + target_compile_options (HS_separate_reads PRIVATE -std=c++17) + target_compile_options (HS_separate_reads PRIVATE -O3) +-target_compile_options (HS_separate_reads PRIVATE -march=x86-64) ++#target_compile_options (HS_separate_reads PRIVATE -march=x86-64) + + file (GLOB SOURCE_CREATE_NEW_CONTIG "create_new_contigs.cpp" "input_output.cpp" "robin_hood.h" "tools.cpp" "read.cpp" "sequence.cpp" "Partition.cpp") + add_executable(HS_create_new_contigs ${SOURCE_CREATE_NEW_CONTIG} edlib/src/edlib.cpp) +@@ -120,7 +120,7 @@ target_compile_options (HS_create_new_contigs PRIVATE -lm) + target_compile_options (HS_create_new_contigs PRIVATE -fopenmp) + target_compile_options (HS_create_new_contigs PRIVATE -std=c++17) + target_compile_options (HS_create_new_contigs PRIVATE -O3) +-target_compile_options (HS_create_new_contigs PRIVATE -march=x86-64) ++#target_compile_options (HS_create_new_contigs PRIVATE -march=x86-64) + + find_package(OpenMP) + if(OpenMP_CXX_FOUND) +diff --git i/src/HS_GenomeTailor/CMakeLists.txt w/src/HS_GenomeTailor/CMakeLists.txt +index 80ee4dc..f117ecc 100644 +--- i/src/HS_GenomeTailor/CMakeLists.txt ++++ w/src/HS_GenomeTailor/CMakeLists.txt +@@ -25,4 +25,4 @@ target_compile_options (HS_GenomeTailor PRIVATE -g) + target_compile_options (HS_GenomeTailor PRIVATE -lm) + target_compile_options (HS_GenomeTailor PRIVATE -std=c++17) + target_compile_options (HS_GenomeTailor PRIVATE -O3) +-target_compile_options (HS_GenomeTailor PRIVATE -march=x86-64) +\ No newline at end of file ++#target_compile_options (HS_GenomeTailor PRIVATE -march=x86-64) diff --git a/recipes/hairsplitter/meta.yaml b/recipes/hairsplitter/meta.yaml index a6711415add34..ab11e4a74d624 100644 --- a/recipes/hairsplitter/meta.yaml +++ b/recipes/hairsplitter/meta.yaml @@ -1,6 +1,7 @@ {% set name = "HairSplitter" %} -{% set version = "1.9.5" %} -{% set sha256 = "b05e9e6681056c18af7e136b3d537dac18a5ed24402612ca2173a4cced115c0b" %} +{% set version = "1.9.10" %} +{% set sha256 = "ab20c7700d9b4cc04fed68933a1c4081167c4c0dd560de7b19672a7fe39b50f8" %} + package: name: {{ name|lower }} @@ -9,9 +10,11 @@ package: source: url: https://github.com/RolandFaure/HairSplitter/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + - hairsplitter-aarch64.patch build: - number : 0 + number : 1 run_exports: - {{ pin_subpackage("hairsplitter", max_pin="x.x") }} @@ -19,8 +22,11 @@ requirements: build: - cmake - make - - openmp - {{ compiler('cxx') }} + - libcxx <18 # [osx] + host: + - libgomp # [linux] + - llvm-openmp # [osx] run: - python - scipy @@ -29,7 +35,8 @@ requirements: - minigraph >=0.20 - racon - samtools >=1.16 - - openmp + - libgomp # [linux] + - llvm-openmp # [osx] - raven-assembler test: @@ -37,6 +44,8 @@ test: - hairsplitter.py --help extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - rolandfaure @@ -46,4 +55,3 @@ about: license_file: LICENSE summary: "Recovers collapsed haplotypes from a draft assembly and long reads" maintainer : RolandFaure # Optional - diff --git a/recipes/handyreadgenotyper/meta.yaml b/recipes/handyreadgenotyper/meta.yaml index 7460e9d78995f..eab10ed133b51 100644 --- a/recipes/handyreadgenotyper/meta.yaml +++ b/recipes/handyreadgenotyper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "HandyReadGenotyper" %} -{% set version = "0.1.22" %} +{% set version = "0.1.24" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/AntonS-bio/HandyReadGenotyper/archive/{{ version }}.tar.gz - sha256: e969f57238a517c6483de0eabdad57e0359168ac6a6be1ebed34c03cffb2d48d + sha256: 11970c9bff8b4b7569e7a124030ccc9a0c53a70bb55fe49fcda735857781a731 build: noarch: python diff --git a/recipes/haplotaglr/meta.yaml b/recipes/haplotaglr/meta.yaml index f7f9cae84e6d8..16e231f12c2eb 100644 --- a/recipes/haplotaglr/meta.yaml +++ b/recipes/haplotaglr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "HaplotagLR" %} -{% set version = "1.1.7" %} +{% set version = "1.1.9" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f3da6fe189e57754f2d6911d1cf497a08dcc4ab9f9a4ee25998023fcde602ed3 + sha256: e8bdcdf8628583fc3e24f2d53fc316ac8a30c1514c258c62996251523f0a9299 build: number: 0 diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 7447eeb08d075..6b04a85e4821e 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.4.2" %} -{% set sha256 = "8e8beb3e0782fb9eac2bdeba4896ecdd46a690b8472ff8699684e65c77f6043d" %} +{% set version = "1.8.2" %} +{% set sha256 = "b2459f6ed5514c406ce82b1303a242dcafc93e0c7aa7d1ac78273dee79b35654" %} package: name: harpy @@ -10,32 +10,34 @@ source: sha256: '{{ sha256 }}' build: - skip: True # [osx] number: 0 - missing_dso_whitelist: - - /lib64/libstdc++.so.6 - - /lib64/libc.so.6 + skip: True # [osx or py < 39] + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} run_exports: - - {{ pin_subpackage('harpy', max_pin="x.x") }} + - {{ pin_subpackage('harpy', max_pin="x") }} script: | mkdir -p ${PREFIX}/bin - "${CXX}" src/harpy/bin/extractReads.cpp -O3 -o ${PREFIX}/bin/extractReads - ${PYTHON} -m pip install . --no-deps -vvv - chmod +x src/harpy/bin/* - cp src/harpy/bin/* ${PREFIX}/bin/ + "${CXX}" harpy/bin/extractReads.cpp -O3 -o ${PREFIX}/bin/extractReads + ${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + chmod 0755 harpy/bin/* + cp -rf harpy/bin/* ${PREFIX}/bin/ + entry_points: + - harpy = harpy.__main__:cli requirements: build: - {{ compiler('cxx') }} host: - - python =3.12 + - python - pip + - setuptools-scm >=3.4 run: - apptainer - bcftools =1.20 - pandas - pysam - - python >3.10 + - python - rich-click - snakemake-minimal >7 - samtools =1.20 @@ -48,7 +50,7 @@ test: - "harpy --version" about: - home: "https://github.com/pdimens/harpy/" + home: "https://github.com/pdimens/harpy" license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE @@ -60,13 +62,11 @@ about: to Snakemake directly. With an emphasis on user-friendliness, parallelization, transparency, and reproducibility, Harpy aims to quickly handle data processing so that you can focus more on analyzing your data. - doc_url: https://pdimens.github.io/harpy/ - dev_url: https://github.com/pdimens/harpy + doc_url: "https://pdimens.github.io/harpy" + dev_url: "https://github.com/pdimens/harpy" extra: additional-platforms: - linux-aarch64 recipe-maintainers: - pdimens - skip-lints: - - should_be_noarch_generic diff --git a/recipes/haystac/meta.yaml b/recipes/haystac/meta.yaml index dad3655e9430e..3564d22685597 100644 --- a/recipes/haystac/meta.yaml +++ b/recipes/haystac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "haystac" %} -{% set version = "0.4.10" %} +{% set version = "0.4.11" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8cf707410549ba312001875a1b11ccf6eb40c10c2b0ca09e9b4c669f585fe022 + sha256: 77727ce69b8df4211c43b424a292cd703987946e889a370337ce4afc7b6f0edd build: number: 0 @@ -15,6 +15,8 @@ build: entry_points: - haystac = haystac.cli:Haystac script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps" + run_exports: + - {{ pin_subpackage("haystac", max_pin="x.x") }} requirements: host: @@ -24,11 +26,10 @@ requirements: - python - setuptools run: - - argparse =1.4.0 - - numpy =1.19.2 - - pandas =1.0.3 + - numpy =2.0.0 + - pandas =2.2.2 - psutil =5.7.2 - - python =3.6.7 + - python =3.9.19 - pyyaml =5.4.1 - requests =2.24.0 - snakemake-minimal =6.3.0 @@ -53,4 +54,3 @@ extra: - antonisdim skip-lints: - uses_setuptools - diff --git a/recipes/hhsuite/build.sh b/recipes/hhsuite/build.sh index 17e152530bc6a..42d2304291652 100644 --- a/recipes/hhsuite/build.sh +++ b/recipes/hhsuite/build.sh @@ -20,3 +20,6 @@ cmake -DCHECK_MPI=0 \ make -j${CPU_COUNT} ${VERBOSE_CM} make install -j${CPU_COUNT} + +# Move the `reformat.pl` script to ${PREFIX}/bin to ensure it's available in the PATH +mv ${SRC_DIR}/scripts/reformat.pl ${PREFIX}/bin diff --git a/recipes/hhsuite/meta.yaml b/recipes/hhsuite/meta.yaml index 2ab1c8ec9b788..3c13879216cec 100644 --- a/recipes/hhsuite/meta.yaml +++ b/recipes/hhsuite/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 12 + number: 13 run_exports: - {{ pin_subpackage('hhsuite', max_pin="x") }} @@ -15,6 +15,7 @@ source: sha256: {{ sha256 }} patches: - fix_cs219_include.patch + - reformat_pl.patch requirements: build: @@ -36,9 +37,11 @@ test: - hhblits -h > /dev/null - hhsearch -h > /dev/null - hhalign -h > /dev/null + - reformat.pl > /dev/null about: home: https://github.com/soedinglab/hh-suite + doc_url: https://github.com/soedinglab/hh-suite/wiki license: GPLv3 license_file: LICENSE summary: "HH-suite3 for fast remote homology detection and deep protein annotation" diff --git a/recipes/hhsuite/reformat_pl.patch b/recipes/hhsuite/reformat_pl.patch new file mode 100644 index 0000000000000..b1046f6c4a7f8 --- /dev/null +++ b/recipes/hhsuite/reformat_pl.patch @@ -0,0 +1,151 @@ +diff --git a/scripts/reformat.pl b/scripts/reformat.pl +index 0c46c66..3b04399 100755 +--- a/scripts/reformat.pl ++++ b/scripts/reformat.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + # reformat.pl + # Reformat a multiple alignment file +@@ -33,7 +33,7 @@ my $numres=100; # number of residues per line + my $desclen=1000; # maximum number of characters in nameline + my $ARGC=scalar(@ARGV); + if ($ARGC<2) { +- die(" ++ print(" + reformat.pl from HHsuite3 + Read a multiple alignment in one format and write it in another format + Usage: reformat.pl [informat] [outformat] infile outfile [options] +@@ -85,6 +85,7 @@ Examples: reformat.pl 1hjra.a3m 1hjra.a2m + reformat.pl test.a3m test.fas -num -r 90 + reformat.pl fas sto '*.fasta' .stockholm + \n"); ++exit 0; + # clu: clustal format (hmmer output) + # sel: Selex format + # phy: Phylip format +@@ -168,7 +169,7 @@ if ($options=~s/(\S+)\s*$//) { + elsif ($outformat eq "afas") {$outformat="fas";} + elsif ($outformat eq "afasta") {$outformat="fas";} + } else { +- print ("Using FASTA output format: '$options'\n"); $outformat="fas"; ++ print STDERR "Using FASTA output format: '$options'\n"; $outformat="fas"; + } + } + if ($options=~s/(\S+)\s*$//) { +@@ -180,7 +181,7 @@ if ($options=~s/(\S+)\s*$//) { + elsif ($informat eq "fa") {$informat="fas";} + elsif ($informat eq "fasta") {$informat="fas";} + } else { +- print ("Using FASTA input format: '$options'\n"); $informat="fas"; ++ print STDERR "Using FASTA input format: '$options'\n"; $informat = "fas"; + } + } + +@@ -188,7 +189,7 @@ if ($options=~s/(\S+)\s*$//) { + # Warn if unknown options found + if ($options!~/^\s*$/) { + $options=~s/^\s*(.*?)\s*$/$1/g; +- print("\nWARNING: unknown options '$options'\n"); ++ print STDERR "\nWARNING: unknown options '$options'\n"; + } + + # Check if input and output formats are valid +@@ -210,20 +211,20 @@ if ($infile=~/\*/ || $outfile=~/^\./) # if infile contains '*' or outfile is jus + $outfile=~/.*\.(\S*)$/; + my $outext=$1; + my @infiles=glob($infile); +- printf("%i files to reformat\n",scalar(@infiles)); ++ printf STDERR "%i files to reformat\n", scalar(@infiles); + foreach $infile (@infiles) + { + if ($infile!~/(\S+)\.\S+/) {$infile=~/(\S+)/} + $outfile="$1.$outext"; + if ($update && -e $outfile) {next;} +- if ($v>=3) {print("Reformatting $infile from $informat to $outformat ...\n");} ++ if ($v>=3) {print STDERR "Reformatting $infile from $informat to $outformat ...\n";} + &reformat($infile,$outfile); + } + exit 0; + } + else + { +- if ($v>=3) {print("Reformatting $infile from $informat to $outformat ...\n");} ++ if ($v>=3) {print STDERR "Reformatting $infile from $informat to $outformat ...\n";} + &reformat($infile,$outfile); + exit 0; + } +@@ -367,7 +368,7 @@ sub reformat() + } + $name=$1; + $residues=$2; +- print("WARNING: Found no space between name and residues in $infile, line $.: '$line'\n"); ++ print STDERR "WARNING: Found no space between name and residues in $infile, line $.: '$line'\n"; + } else { + if ($noss && ($line=~/^aa_/ || $line=~/^ss_/ || $line=~/^sa_/)) {next;} # do not read in >ss_ and >aa_ sequences + if ($line=~/^aa_/ || $line=~/^sa_/) {next;} # do not read in >ss_ and >aa_ sequences +@@ -388,7 +389,7 @@ sub reformat() + } else { + $seqs[$k].=$residues; + if ($names[$k] ne $name) { +- print("WARNING: name of sequence $k in block 1 ($names[$k]) is not the same as in block $block ($name) in $infile\n"); ++ print STDERR "WARNING: name of sequence $k in block 1 ($names[$k]) is not the same as in block $block ($name) in $infile\n"; + } + } + # printf("%3i %3i %-16.16s %s\n",$block,$k,$names[$k],$seqs[$k]); +@@ -439,7 +440,7 @@ sub reformat() + } else { + $seqs[$k].=$residues; + if ($names[$k] ne $name) { +- print("WARNING: name of sequence $k in block 1 ($names[$k]) is not the same as in block $block ($name) in $infile\n"); ++ print STDERR "WARNING: name of sequence $k in block 1 ($names[$k]) is not the same as in block $block ($name) in $infile\n"; + } + } + # printf("%3i %3i %-16.16s %s\n",$block,$k,$names[$k],$seqs[$k]); +@@ -480,7 +481,7 @@ sub reformat() + # Insertion of '.' only needed for a3m if: NOT -r option OR -M first OR -M option + if ($informat eq "a3m" && (!$remove_inserts || $matchmode)) + { +- print("inserting gaps...\n"); ++ print STDERR "inserting gaps...\n"; + my @len_ins; # $len_ins[$j] will count the maximum number of inserted residues after match state $i. + my $j; # counts match states + my @inserts; # $inserts[$j] contains the insert (in small case) of sequence $i after the $j'th match state +@@ -663,7 +664,7 @@ sub reformat() + my $nin=$n; + for ($k=0; $k<$n; $k++) { + if (($seqs[$k]=~tr/a-zA-Z0-9/a-zA-Z0-9/==0)) { +- if ($v>=2) {print("Sequence contains only gaps and is removed: $names[$k]\n");} ++ if ($v>=2) {print STDERR "Sequence contains only gaps and is removed: $names[$k]\n";} + splice(@seqs,$k,1); + splice(@names,$k,1); + $k--; $n--; +@@ -699,10 +700,10 @@ sub reformat() + my $len=length($seqs[0]); + for($k=1; $k<$n; $k++) { + if (length($seqs[$k])!=$len) { +- printf("\nError: Sequences in $infile do not all have same length, e.g. >%-.20s (len=%i) and >%-.20s (len=%i)\n", +- $names[0],$len,$names[$k],length($seqs[$k])); ++ printf STDERR "\nError: Sequences in $infile do not all have same length, e.g. >%-.20s (len=%i) and >%-.20s (len=%i)\n", ++ $names[0],$len,$names[$k],length($seqs[$k]); + if ($v>=3) { +- printf("%.20s %s\n%.20s %s\n\n",$names[0],$seqs[0],$names[$k],$seqs[$k]); ++ printf STDERR "\nError: Sequences in $infile do not all have same length, e.g. >%-.20s (len=%i) and >%-.20s (len=%i)\n", + } + exit 1; + } +@@ -813,10 +814,10 @@ sub reformat() + + close OUTFILE; + if ($v>=2) { +- if ($nin==1) {print("Reformatted $infile with 1 sequence from $informat to $outformat and written to file $outfile\n");} ++ if ($nin==1) {print STDERR "Reformatted $infile with 1 sequence from $informat to $outformat and written to file $outfile\n";} + else { +- if (!$nin==$n) {printf("Removed %i sequences which contained no residues\n",$nin-$n); } +- print("Reformatted $infile with $n sequences from $informat to $outformat and written to file $outfile\n"); ++ if (!$nin==$n) {printf STDERR "Removed %i sequences which contained no residues\n", $nin - $n;} ++ print STDERR "Reformatted $infile with $n sequences from $informat to $outformat and written to file $outfile\n"; + } + } + diff --git a/recipes/hictk/build_failure.linux-aarch64.yaml b/recipes/hictk/build_failure.linux-aarch64.yaml deleted file mode 100644 index 49cb43e2fe9a7..0000000000000 --- a/recipes/hictk/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 5def4a5bc1369a463033268d7ed2b6dc19d35b7407bb8c10c74902b523d2b014 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("pysam"), MatchSpec("cooler==0.10.0=pyhdfd78af_0")} - Encountered problems while solving: - - package cooler-0.10.0-pyhdfd78af_0 requires pysam, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - [32mcooler >=0.9.3 [0m is installable and it requires - [32mpysam [ |>0.8 ][0m, which requires - [32mlibdeflate >=1.18,<1.19.0a0 [0m, which can be installed; - [31mlibdeflate >=1.20,<1.21.0a0 [0m is not installable because it conflicts with any installable versions previously reported. - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("pysam"), MatchSpec("cooler==0.10.0=pyhdfd78af_0")} - Encountered problems while solving: - - package cooler-0.10.0-pyhdfd78af_0 requires pysam, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - [32mcooler >=0.9.3 [0m is installable and it requires - [32mpysam [ |>0.8 ][0m, which requires - [32mlibdeflate >=1.18,<1.19.0a0 [0m, which can be installed; - [31mlibdeflate >=1.20,<1.21.0a0 [0m is not installable because it conflicts with any installable versions previously reported. - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("pysam"), MatchSpec("cooler==0.10.0=pyhdfd78af_0")} - Encountered problems while solving: - - package cooler-0.10.0-pyhdfd78af_0 requires pysam, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - [32mcooler >=0.9.3 [0m is installable and it requires - [32mpysam [ |>0.8 ][0m, which requires - [32mlibdeflate >=1.18,<1.19.0a0 [0m, which can be installed; - [31mlibdeflate >=1.20,<1.21.0a0 [0m is not installable because it conflicts with any installable versions previously reported. -# Last 100 lines of the build log. diff --git a/recipes/hictk/build_failure.osx-64.yaml b/recipes/hictk/build_failure.osx-64.yaml deleted file mode 100644 index 9f4bd89807a52..0000000000000 --- a/recipes/hictk/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 5def4a5bc1369a463033268d7ed2b6dc19d35b7407bb8c10c74902b523d2b014 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hictk-0.0.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hictk-0.0.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - patching file conanfile.txt - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 - -- Detecting C compiler ABI info - -- Detecting C compiler ABI info - done - -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting C compile features - -- Detecting C compile features - done - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- Developer mode is OFF. For developement, use -DENABLE_DEVELOPER_MODE:BOOL=ON. Building the project for the end-user... - -- Conan: Target declared 'bshoshany-thread-pool::bshoshany-thread-pool' - -- Conan: Target declared 'phmap' - -- Conan: Component target declared 'nonstd::span-lite' - -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success - -- Found Threads: TRUE - -- HIGHFIVE 2.9.0: (Re)Detecting Highfive dependencies (HIGHFIVE_USE_INSTALL_DEPS=NO) - -- Conan: Target declared 'phmap' - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - -- Conan: Target declared 'phmap' - -- Conan: Target declared 'phmap' - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - -- Conan: Target declared 'bshoshany-thread-pool::bshoshany-thread-pool' - -- Conan: Target declared 'concurrentqueue::concurrentqueue' - -- Conan: Target declared 'phmap' - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hictk_1717508836832/work/conda_build.sh']' returned non-zero exit status 2. - -- Conan: Target declared 'readerwriterqueue::readerwriterqueue' - -- Conan: Target declared 'phmap' - -- Building cli tools. - -- Conan: Target declared 'readerwriterqueue::readerwriterqueue' - -- Looking for C include filesystem - -- Looking for C include filesystem - found - -- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED - -- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED - Success - -- Building unit tests. - -- Downloading test dataset... - -- Configuring done (71.5s) - -- Generating done (0.3s) - -- Build files have been written to: $SRC_DIR/build - [ 1%] Building CXX object src/hictk/CMakeFiles/hictk.dir/main.cpp.o - [ 2%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli.cpp.o - [ 3%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_balance.cpp.o - [ 4%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_convert.cpp.o - [ 5%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_dump.cpp.o - [ 6%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_fix_mcool.cpp.o - [ 8%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_load.cpp.o - [ 9%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_merge.cpp.o - [ 10%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_rename_chromosomes.cpp.o - [ 11%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_validate.cpp.o - [ 12%] Building CXX object src/hictk/CMakeFiles/hictk.dir/cli/cli_zoomify.cpp.o - [ 13%] Building CXX object src/hictk/CMakeFiles/hictk.dir/balance/balance.cpp.o - [ 15%] Building CXX object src/hictk/CMakeFiles/hictk.dir/convert/convert.cpp.o - [ 16%] Building CXX object src/hictk/CMakeFiles/hictk.dir/convert/cool_to_hic.cpp.o - [ 17%] Building CXX object src/hictk/CMakeFiles/hictk.dir/convert/hic_to_cool.cpp.o - [ 18%] Building CXX object src/hictk/CMakeFiles/hictk.dir/dump/dump.cpp.o - [ 19%] Building CXX object src/hictk/CMakeFiles/hictk.dir/dump/dump_common.cpp.o - [ 20%] Building CXX object src/hictk/CMakeFiles/hictk.dir/fix_mcool/fix_mcool.cpp.o - [ 22%] Building CXX object src/hictk/CMakeFiles/hictk.dir/load/load.cpp.o - [ 23%] Building CXX object src/hictk/CMakeFiles/hictk.dir/merge/merge.cpp.o - [ 24%] Building CXX object src/hictk/CMakeFiles/hictk.dir/rename_chromosomes/rename_chromosomes.cpp.o - [ 25%] Building CXX object src/hictk/CMakeFiles/hictk.dir/validate/validate.cpp.o - [ 26%] Building CXX object src/hictk/CMakeFiles/hictk.dir/zoomify/zoomify.cpp.o - [ 27%] Linking CXX executable hictk - [ 27%] Built target hictk - [ 29%] Building CXX object test/units/balancing/CMakeFiles/hictk_balancing_tests.dir/balancing_test.cpp.o - [ 30%] Linking CXX executable hictk_balancing_tests - [ 30%] Built target hictk_balancing_tests - [ 31%] Building CXX object test/units/bin_table/CMakeFiles/bin_table_tests.dir/bin_test.cpp.o - [ 32%] Building CXX object test/units/bin_table/CMakeFiles/bin_table_tests.dir/bin_table_test.cpp.o - [ 33%] Linking CXX executable bin_table_tests - [ 33%] Built target bin_table_tests - [ 34%] Building CXX object test/units/binary_buffer/CMakeFiles/hictk_binary_buffer_tests.dir/binary_buffer_test.cpp.o - [ 36%] Linking CXX executable hictk_binary_buffer_tests - [ 36%] Built target hictk_binary_buffer_tests - [ 37%] Building CXX object test/units/chromosome/CMakeFiles/hictk_chromosome_tests.dir/chromosome_test.cpp.o - [ 38%] Linking CXX executable hictk_chromosome_tests - [ 38%] Built target hictk_chromosome_tests - [ 39%] Building CXX object test/units/cooler/CMakeFiles/hictk_cooler_tests.dir/attribute_numeric_conversions_test.cpp.o - [ 40%] Building CXX object test/units/cooler/CMakeFiles/hictk_cooler_tests.dir/attribute_read_test.cpp.o -# Last 100 lines of the build log. diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index e0bfbfc37556e..42a5eb4d57b4a 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('hictk', max_pin='x') }} diff --git a/recipes/hictkpy/build_failure.osx-64.yaml b/recipes/hictkpy/build_failure.osx-64.yaml deleted file mode 100644 index 2edc9b8a419d3..0000000000000 --- a/recipes/hictkpy/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c5aa91b5b109d0c9a825beb2ef6338e94f047a845e5424de084fb12467d9ada6 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - pysocks: 1.7.1-pyha2e5f31_6 conda-forge - python: 3.12.3-h1411813_0_cpython conda-forge - python-dateutil: 2.9.0-pyhd8ed1ab_0 conda-forge - python_abi: 3.12-4_cp312 conda-forge - pyyaml: 6.0.1-py312h104f124_1 conda-forge - readline: 8.2-h9e318b2_1 conda-forge - requests: 2.32.3-pyhd8ed1ab_0 conda-forge - rhash: 1.4.4-h0dc2134_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - six: 1.16.0-pyh6c4a22f_0 conda-forge - spdlog: 1.13.0-h1a4aec9_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - tk: 8.6.13-h1abcd95_1 conda-forge - tzdata: 2024a-h0c530f3_0 conda-forge - urllib3: 1.26.18-pyhd8ed1ab_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - yaml: 0.2.5-h0d85af4_2 conda-forge - zstd: 1.5.6-h915ae27_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: v0.0.5_e9576a1a71.tar.gz - Downloading https://github.com/paulsengroup/hictkpy/archive/refs/tags/v0.0.5.tar.gz - Success - /opt/mambaforge/envs/bioconda/conda-bld/hictkpy_1717517114516/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/python: No module named pip - Extracting download - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/hictkpy_1717517114516/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hictkpy_1717517114516/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hictkpy_1717517114516/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/hictkpy_1717517114516/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hictkpy-0.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hictkpy_1717517114516/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hictkpy-0.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hictkpy-0.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hictkpy-0.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - patching file CMakeLists.txt - patching file conanfile.txt - patching file pyproject.toml - -DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin -DPython_EXECUTABLE=$PREFIX/bin/python -# Last 100 lines of the build log. diff --git a/recipes/hictkpy/meta.yaml b/recipes/hictkpy/meta.yaml index 86e219bae94e2..084412b76ff50 100644 --- a/recipes/hictkpy/meta.yaml +++ b/recipes/hictkpy/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [py < 39] run_exports: - {{ pin_subpackage('hictkpy', max_pin='x.x') }} @@ -29,6 +29,7 @@ requirements: - spdlog >=1.12 host: - python + - pip - hdf5 >=1.12 - libdeflate - scikit-build-core @@ -69,3 +70,4 @@ extra: - doi:10.5281/zenodo.8220300 additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/hifiasm_meta/build.sh b/recipes/hifiasm_meta/build.sh index 038578306214d..203ecd2114aef 100644 --- a/recipes/hifiasm_meta/build.sh +++ b/recipes/hifiasm_meta/build.sh @@ -1,6 +1,8 @@ #!/bin/bash +set -xe + mkdir -p $PREFIX/bin -make INCLUDES="-I$PREFIX/include" CXXFLAGS="-L$PREFIX/lib" CC=${CC} CXX=${CXX} +make -j ${CPU_COUNT} INCLUDES="-I$PREFIX/include" CXXFLAGS="-L$PREFIX/lib" CC=${CC} CXX=${CXX} cp hifiasm_meta $PREFIX/bin diff --git a/recipes/hifiasm_meta/hifiasm_meta-aarch64.patch b/recipes/hifiasm_meta/hifiasm_meta-aarch64.patch new file mode 100644 index 0000000000000..ef87b0fb9cb08 --- /dev/null +++ b/recipes/hifiasm_meta/hifiasm_meta-aarch64.patch @@ -0,0 +1,9358 @@ +diff --git c/Levenshtein_distance.h i/Levenshtein_distance.h +index 5e2a7bf..d17bd01 100644 +--- c/Levenshtein_distance.h ++++ i/Levenshtein_distance.h +@@ -1,10 +1,14 @@ + #ifndef __LEVENSHTEIN__ + #define __LEVENSHTEIN__ + #include ++#ifdef __ARM_NEON ++#include "sse2neon.h" ++#else + #include "emmintrin.h" + #include "nmmintrin.h" + #include "smmintrin.h" + #include ++#endif + #include + #include + #include +diff --git c/Makefile i/Makefile +index a31eb89..56ff4cd 100644 +--- c/Makefile ++++ i/Makefile +@@ -1,6 +1,6 @@ + CXX= g++ + CC= gcc +-CXXFLAGS= -g3 -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall -Wno-unused -Wno-sign-compare ++CXXFLAGS= -g3 -O3 -fomit-frame-pointer -Wall -Wno-unused -Wno-sign-compare + CFLAGS= $(CXXFLAGS) + CPPFLAGS= + INCLUDES= +diff --git c/ksw2_extz2_sse.c i/ksw2_extz2_sse.c +index 02bb4c2..5265fdb 100644 +--- c/ksw2_extz2_sse.c ++++ i/ksw2_extz2_sse.c +@@ -2,8 +2,15 @@ + #include + #include "ksw2.h" + ++#ifdef __ARM_NEON ++#include "sse2neon.h" ++#define __SSE2__ ++#endif ++ + #ifdef __SSE2__ ++#ifdef __x86_64__ + #include ++#endif + + #ifdef KSW_SSE2_ONLY + #undef __SSE4_1__ +diff --git c/sse2neon.h i/sse2neon.h +new file mode 100644 +index 0000000..2b12721 +--- /dev/null ++++ i/sse2neon.h +@@ -0,0 +1,9301 @@ ++#ifndef SSE2NEON_H ++#define SSE2NEON_H ++ ++/* ++ * sse2neon is freely redistributable under the MIT License. ++ * ++ * Copyright (c) 2015-2024 SSE2NEON Contributors. ++ * ++ * Permission is hereby granted, free of charge, to any person obtaining a copy ++ * of this software and associated documentation files (the "Software"), to deal ++ * in the Software without restriction, including without limitation the rights ++ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell ++ * copies of the Software, and to permit persons to whom the Software is ++ * furnished to do so, subject to the following conditions: ++ * ++ * The above copyright notice and this permission notice shall be included in ++ * all copies or substantial portions of the Software. ++ * ++ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR ++ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, ++ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE ++ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER ++ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, ++ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE ++ * SOFTWARE. ++ */ ++ ++// This header file provides a simple API translation layer ++// between SSE intrinsics to their corresponding Arm/Aarch64 NEON versions ++// ++// Contributors to this work are: ++// John W. Ratcliff ++// Brandon Rowlett ++// Ken Fast ++// Eric van Beurden ++// Alexander Potylitsin ++// Hasindu Gamaarachchi ++// Jim Huang ++// Mark Cheng ++// Malcolm James MacLeod ++// Devin Hussey (easyaspi314) ++// Sebastian Pop ++// Developer Ecosystem Engineering ++// Danila Kutenin ++// François Turban (JishinMaster) ++// Pei-Hsuan Hung ++// Yang-Hao Yuan ++// Syoyo Fujita ++// Brecht Van Lommel ++// Jonathan Hue ++// Cuda Chen ++// Aymen Qader ++// Anthony Roberts ++ ++/* Tunable configurations */ ++ ++/* Enable precise implementation of math operations ++ * This would slow down the computation a bit, but gives consistent result with ++ * x86 SSE. (e.g. would solve a hole or NaN pixel in the rendering result) ++ */ ++/* _mm_min|max_ps|ss|pd|sd */ ++#ifndef SSE2NEON_PRECISE_MINMAX ++#define SSE2NEON_PRECISE_MINMAX (0) ++#endif ++/* _mm_rcp_ps */ ++#ifndef SSE2NEON_PRECISE_DIV ++#define SSE2NEON_PRECISE_DIV (0) ++#endif ++/* _mm_sqrt_ps and _mm_rsqrt_ps */ ++#ifndef SSE2NEON_PRECISE_SQRT ++#define SSE2NEON_PRECISE_SQRT (0) ++#endif ++/* _mm_dp_pd */ ++#ifndef SSE2NEON_PRECISE_DP ++#define SSE2NEON_PRECISE_DP (0) ++#endif ++ ++/* Enable inclusion of windows.h on MSVC platforms ++ * This makes _mm_clflush functional on windows, as there is no builtin. ++ */ ++#ifndef SSE2NEON_INCLUDE_WINDOWS_H ++#define SSE2NEON_INCLUDE_WINDOWS_H (0) ++#endif ++ ++/* compiler specific definitions */ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma push_macro("FORCE_INLINE") ++#pragma push_macro("ALIGN_STRUCT") ++#define FORCE_INLINE static inline __attribute__((always_inline)) ++#define ALIGN_STRUCT(x) __attribute__((aligned(x))) ++#define _sse2neon_likely(x) __builtin_expect(!!(x), 1) ++#define _sse2neon_unlikely(x) __builtin_expect(!!(x), 0) ++#elif defined(_MSC_VER) ++#if _MSVC_TRADITIONAL ++#error Using the traditional MSVC preprocessor is not supported! Use /Zc:preprocessor instead. ++#endif ++#ifndef FORCE_INLINE ++#define FORCE_INLINE static inline ++#endif ++#ifndef ALIGN_STRUCT ++#define ALIGN_STRUCT(x) __declspec(align(x)) ++#endif ++#define _sse2neon_likely(x) (x) ++#define _sse2neon_unlikely(x) (x) ++#else ++#pragma message("Macro name collisions may happen with unsupported compilers.") ++#endif ++ ++ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma push_macro("FORCE_INLINE_OPTNONE") ++#define FORCE_INLINE_OPTNONE static inline __attribute__((optimize("O0"))) ++#elif defined(__clang__) ++#pragma push_macro("FORCE_INLINE_OPTNONE") ++#define FORCE_INLINE_OPTNONE static inline __attribute__((optnone)) ++#else ++#define FORCE_INLINE_OPTNONE FORCE_INLINE ++#endif ++ ++#if !defined(__clang__) && defined(__GNUC__) && __GNUC__ < 10 ++#warning "GCC versions earlier than 10 are not supported." ++#endif ++ ++/* C language does not allow initializing a variable with a function call. */ ++#ifdef __cplusplus ++#define _sse2neon_const static const ++#else ++#define _sse2neon_const const ++#endif ++ ++#include ++#include ++ ++#if defined(_WIN32) ++/* Definitions for _mm_{malloc,free} are provided by ++ * from both MinGW-w64 and MSVC. ++ */ ++#define SSE2NEON_ALLOC_DEFINED ++#endif ++ ++/* If using MSVC */ ++#ifdef _MSC_VER ++#include ++#if SSE2NEON_INCLUDE_WINDOWS_H ++#include ++#include ++#endif ++ ++#if !defined(__cplusplus) ++#error SSE2NEON only supports C++ compilation with this compiler ++#endif ++ ++#ifdef SSE2NEON_ALLOC_DEFINED ++#include ++#endif ++ ++#if (defined(_M_AMD64) || defined(__x86_64__)) || \ ++ (defined(_M_ARM64) || defined(__arm64__)) ++#define SSE2NEON_HAS_BITSCAN64 ++#endif ++#endif ++ ++#if defined(__GNUC__) || defined(__clang__) ++#define _sse2neon_define0(type, s, body) \ ++ __extension__({ \ ++ type _a = (s); \ ++ body \ ++ }) ++#define _sse2neon_define1(type, s, body) \ ++ __extension__({ \ ++ type _a = (s); \ ++ body \ ++ }) ++#define _sse2neon_define2(type, a, b, body) \ ++ __extension__({ \ ++ type _a = (a), _b = (b); \ ++ body \ ++ }) ++#define _sse2neon_return(ret) (ret) ++#else ++#define _sse2neon_define0(type, a, body) [=](type _a) { body }(a) ++#define _sse2neon_define1(type, a, body) [](type _a) { body }(a) ++#define _sse2neon_define2(type, a, b, body) \ ++ [](type _a, type _b) { body }((a), (b)) ++#define _sse2neon_return(ret) return ret ++#endif ++ ++#define _sse2neon_init(...) \ ++ { \ ++ __VA_ARGS__ \ ++ } ++ ++/* Compiler barrier */ ++#if defined(_MSC_VER) ++#define SSE2NEON_BARRIER() _ReadWriteBarrier() ++#else ++#define SSE2NEON_BARRIER() \ ++ do { \ ++ __asm__ __volatile__("" ::: "memory"); \ ++ (void) 0; \ ++ } while (0) ++#endif ++ ++/* Memory barriers ++ * __atomic_thread_fence does not include a compiler barrier; instead, ++ * the barrier is part of __atomic_load/__atomic_store's "volatile-like" ++ * semantics. ++ */ ++#if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 201112L) ++#include ++#endif ++ ++FORCE_INLINE void _sse2neon_smp_mb(void) ++{ ++ SSE2NEON_BARRIER(); ++#if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 201112L) && \ ++ !defined(__STDC_NO_ATOMICS__) ++ atomic_thread_fence(memory_order_seq_cst); ++#elif defined(__GNUC__) || defined(__clang__) ++ __atomic_thread_fence(__ATOMIC_SEQ_CST); ++#else /* MSVC */ ++ __dmb(_ARM64_BARRIER_ISH); ++#endif ++} ++ ++/* Architecture-specific build options */ ++/* FIXME: #pragma GCC push_options is only available on GCC */ ++#if defined(__GNUC__) ++#if defined(__arm__) && __ARM_ARCH == 7 ++/* According to ARM C Language Extensions Architecture specification, ++ * __ARM_NEON is defined to a value indicating the Advanced SIMD (NEON) ++ * architecture supported. ++ */ ++#if !defined(__ARM_NEON) || !defined(__ARM_NEON__) ++#error "You must enable NEON instructions (e.g. -mfpu=neon) to use SSE2NEON." ++#endif ++#if !defined(__clang__) ++#pragma GCC push_options ++#pragma GCC target("fpu=neon") ++#endif ++#elif defined(__aarch64__) || defined(_M_ARM64) ++#if !defined(__clang__) && !defined(_MSC_VER) ++#pragma GCC push_options ++#pragma GCC target("+simd") ++#endif ++#elif __ARM_ARCH == 8 ++#if !defined(__ARM_NEON) || !defined(__ARM_NEON__) ++#error \ ++ "You must enable NEON instructions (e.g. -mfpu=neon-fp-armv8) to use SSE2NEON." ++#endif ++#if !defined(__clang__) && !defined(_MSC_VER) ++#pragma GCC push_options ++#endif ++#else ++#error \ ++ "Unsupported target. Must be either ARMv7-A+NEON or ARMv8-A \ ++(you could try setting target explicitly with -march or -mcpu)" ++#endif ++#endif ++ ++#include ++#if (!defined(__aarch64__) && !defined(_M_ARM64)) && (__ARM_ARCH == 8) ++#if defined __has_include && __has_include() ++#include ++#endif ++#endif ++ ++/* Apple Silicon cache lines are double of what is commonly used by Intel, AMD ++ * and other Arm microarchitectures use. ++ * From sysctl -a on Apple M1: ++ * hw.cachelinesize: 128 ++ */ ++#if defined(__APPLE__) && (defined(__aarch64__) || defined(__arm64__)) ++#define SSE2NEON_CACHELINE_SIZE 128 ++#else ++#define SSE2NEON_CACHELINE_SIZE 64 ++#endif ++ ++/* Rounding functions require either Aarch64 instructions or libm fallback */ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++#include ++#endif ++ ++/* On ARMv7, some registers, such as PMUSERENR and PMCCNTR, are read-only ++ * or even not accessible in user mode. ++ * To write or access to these registers in user mode, ++ * we have to perform syscall instead. ++ */ ++#if (!defined(__aarch64__) && !defined(_M_ARM64)) ++#include ++#endif ++ ++/* "__has_builtin" can be used to query support for built-in functions ++ * provided by gcc/clang and other compilers that support it. ++ */ ++#ifndef __has_builtin /* GCC prior to 10 or non-clang compilers */ ++/* Compatibility with gcc <= 9 */ ++#if defined(__GNUC__) && (__GNUC__ <= 9) ++#define __has_builtin(x) HAS##x ++#define HAS__builtin_popcount 1 ++#define HAS__builtin_popcountll 1 ++ ++// __builtin_shuffle introduced in GCC 4.7.0 ++#if (__GNUC__ >= 5) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)) ++#define HAS__builtin_shuffle 1 ++#else ++#define HAS__builtin_shuffle 0 ++#endif ++ ++#define HAS__builtin_shufflevector 0 ++#define HAS__builtin_nontemporal_store 0 ++#else ++#define __has_builtin(x) 0 ++#endif ++#endif ++ ++/** ++ * MACRO for shuffle parameter for _mm_shuffle_ps(). ++ * Argument fp3 is a digit[0123] that represents the fp from argument "b" ++ * of mm_shuffle_ps that will be placed in fp3 of result. fp2 is the same ++ * for fp2 in result. fp1 is a digit[0123] that represents the fp from ++ * argument "a" of mm_shuffle_ps that will be places in fp1 of result. ++ * fp0 is the same for fp0 of result. ++ */ ++#define _MM_SHUFFLE(fp3, fp2, fp1, fp0) \ ++ (((fp3) << 6) | ((fp2) << 4) | ((fp1) << 2) | ((fp0))) ++ ++#if __has_builtin(__builtin_shufflevector) ++#define _sse2neon_shuffle(type, a, b, ...) \ ++ __builtin_shufflevector(a, b, __VA_ARGS__) ++#elif __has_builtin(__builtin_shuffle) ++#define _sse2neon_shuffle(type, a, b, ...) \ ++ __extension__({ \ ++ type tmp = {__VA_ARGS__}; \ ++ __builtin_shuffle(a, b, tmp); \ ++ }) ++#endif ++ ++#ifdef _sse2neon_shuffle ++#define vshuffle_s16(a, b, ...) _sse2neon_shuffle(int16x4_t, a, b, __VA_ARGS__) ++#define vshuffleq_s16(a, b, ...) _sse2neon_shuffle(int16x8_t, a, b, __VA_ARGS__) ++#define vshuffle_s32(a, b, ...) _sse2neon_shuffle(int32x2_t, a, b, __VA_ARGS__) ++#define vshuffleq_s32(a, b, ...) _sse2neon_shuffle(int32x4_t, a, b, __VA_ARGS__) ++#define vshuffle_s64(a, b, ...) _sse2neon_shuffle(int64x1_t, a, b, __VA_ARGS__) ++#define vshuffleq_s64(a, b, ...) _sse2neon_shuffle(int64x2_t, a, b, __VA_ARGS__) ++#endif ++ ++/* Rounding mode macros. */ ++#define _MM_FROUND_TO_NEAREST_INT 0x00 ++#define _MM_FROUND_TO_NEG_INF 0x01 ++#define _MM_FROUND_TO_POS_INF 0x02 ++#define _MM_FROUND_TO_ZERO 0x03 ++#define _MM_FROUND_CUR_DIRECTION 0x04 ++#define _MM_FROUND_NO_EXC 0x08 ++#define _MM_FROUND_RAISE_EXC 0x00 ++#define _MM_FROUND_NINT (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_FLOOR (_MM_FROUND_TO_NEG_INF | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_CEIL (_MM_FROUND_TO_POS_INF | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_TRUNC (_MM_FROUND_TO_ZERO | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_RINT (_MM_FROUND_CUR_DIRECTION | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_NEARBYINT (_MM_FROUND_CUR_DIRECTION | _MM_FROUND_NO_EXC) ++#define _MM_ROUND_NEAREST 0x0000 ++#define _MM_ROUND_DOWN 0x2000 ++#define _MM_ROUND_UP 0x4000 ++#define _MM_ROUND_TOWARD_ZERO 0x6000 ++/* Flush zero mode macros. */ ++#define _MM_FLUSH_ZERO_MASK 0x8000 ++#define _MM_FLUSH_ZERO_ON 0x8000 ++#define _MM_FLUSH_ZERO_OFF 0x0000 ++/* Denormals are zeros mode macros. */ ++#define _MM_DENORMALS_ZERO_MASK 0x0040 ++#define _MM_DENORMALS_ZERO_ON 0x0040 ++#define _MM_DENORMALS_ZERO_OFF 0x0000 ++ ++/* indicate immediate constant argument in a given range */ ++#define __constrange(a, b) const ++ ++/* A few intrinsics accept traditional data types like ints or floats, but ++ * most operate on data types that are specific to SSE. ++ * If a vector type ends in d, it contains doubles, and if it does not have ++ * a suffix, it contains floats. An integer vector type can contain any type ++ * of integer, from chars to shorts to unsigned long longs. ++ */ ++typedef int64x1_t __m64; ++typedef float32x4_t __m128; /* 128-bit vector containing 4 floats */ ++// On ARM 32-bit architecture, the float64x2_t is not supported. ++// The data type __m128d should be represented in a different way for related ++// intrinsic conversion. ++#if defined(__aarch64__) || defined(_M_ARM64) ++typedef float64x2_t __m128d; /* 128-bit vector containing 2 doubles */ ++#else ++typedef float32x4_t __m128d; ++#endif ++typedef int64x2_t __m128i; /* 128-bit vector containing integers */ ++ ++// Some intrinsics operate on unaligned data types. ++typedef int16_t ALIGN_STRUCT(1) unaligned_int16_t; ++typedef int32_t ALIGN_STRUCT(1) unaligned_int32_t; ++typedef int64_t ALIGN_STRUCT(1) unaligned_int64_t; ++ ++// __int64 is defined in the Intrinsics Guide which maps to different datatype ++// in different data model ++#if !(defined(_WIN32) || defined(_WIN64) || defined(__int64)) ++#if (defined(__x86_64__) || defined(__i386__)) ++#define __int64 long long ++#else ++#define __int64 int64_t ++#endif ++#endif ++ ++/* type-safe casting between types */ ++ ++#define vreinterpretq_m128_f16(x) vreinterpretq_f32_f16(x) ++#define vreinterpretq_m128_f32(x) (x) ++#define vreinterpretq_m128_f64(x) vreinterpretq_f32_f64(x) ++ ++#define vreinterpretq_m128_u8(x) vreinterpretq_f32_u8(x) ++#define vreinterpretq_m128_u16(x) vreinterpretq_f32_u16(x) ++#define vreinterpretq_m128_u32(x) vreinterpretq_f32_u32(x) ++#define vreinterpretq_m128_u64(x) vreinterpretq_f32_u64(x) ++ ++#define vreinterpretq_m128_s8(x) vreinterpretq_f32_s8(x) ++#define vreinterpretq_m128_s16(x) vreinterpretq_f32_s16(x) ++#define vreinterpretq_m128_s32(x) vreinterpretq_f32_s32(x) ++#define vreinterpretq_m128_s64(x) vreinterpretq_f32_s64(x) ++ ++#define vreinterpretq_f16_m128(x) vreinterpretq_f16_f32(x) ++#define vreinterpretq_f32_m128(x) (x) ++#define vreinterpretq_f64_m128(x) vreinterpretq_f64_f32(x) ++ ++#define vreinterpretq_u8_m128(x) vreinterpretq_u8_f32(x) ++#define vreinterpretq_u16_m128(x) vreinterpretq_u16_f32(x) ++#define vreinterpretq_u32_m128(x) vreinterpretq_u32_f32(x) ++#define vreinterpretq_u64_m128(x) vreinterpretq_u64_f32(x) ++ ++#define vreinterpretq_s8_m128(x) vreinterpretq_s8_f32(x) ++#define vreinterpretq_s16_m128(x) vreinterpretq_s16_f32(x) ++#define vreinterpretq_s32_m128(x) vreinterpretq_s32_f32(x) ++#define vreinterpretq_s64_m128(x) vreinterpretq_s64_f32(x) ++ ++#define vreinterpretq_m128i_s8(x) vreinterpretq_s64_s8(x) ++#define vreinterpretq_m128i_s16(x) vreinterpretq_s64_s16(x) ++#define vreinterpretq_m128i_s32(x) vreinterpretq_s64_s32(x) ++#define vreinterpretq_m128i_s64(x) (x) ++ ++#define vreinterpretq_m128i_u8(x) vreinterpretq_s64_u8(x) ++#define vreinterpretq_m128i_u16(x) vreinterpretq_s64_u16(x) ++#define vreinterpretq_m128i_u32(x) vreinterpretq_s64_u32(x) ++#define vreinterpretq_m128i_u64(x) vreinterpretq_s64_u64(x) ++ ++#define vreinterpretq_f32_m128i(x) vreinterpretq_f32_s64(x) ++#define vreinterpretq_f64_m128i(x) vreinterpretq_f64_s64(x) ++ ++#define vreinterpretq_s8_m128i(x) vreinterpretq_s8_s64(x) ++#define vreinterpretq_s16_m128i(x) vreinterpretq_s16_s64(x) ++#define vreinterpretq_s32_m128i(x) vreinterpretq_s32_s64(x) ++#define vreinterpretq_s64_m128i(x) (x) ++ ++#define vreinterpretq_u8_m128i(x) vreinterpretq_u8_s64(x) ++#define vreinterpretq_u16_m128i(x) vreinterpretq_u16_s64(x) ++#define vreinterpretq_u32_m128i(x) vreinterpretq_u32_s64(x) ++#define vreinterpretq_u64_m128i(x) vreinterpretq_u64_s64(x) ++ ++#define vreinterpret_m64_s8(x) vreinterpret_s64_s8(x) ++#define vreinterpret_m64_s16(x) vreinterpret_s64_s16(x) ++#define vreinterpret_m64_s32(x) vreinterpret_s64_s32(x) ++#define vreinterpret_m64_s64(x) (x) ++ ++#define vreinterpret_m64_u8(x) vreinterpret_s64_u8(x) ++#define vreinterpret_m64_u16(x) vreinterpret_s64_u16(x) ++#define vreinterpret_m64_u32(x) vreinterpret_s64_u32(x) ++#define vreinterpret_m64_u64(x) vreinterpret_s64_u64(x) ++ ++#define vreinterpret_m64_f16(x) vreinterpret_s64_f16(x) ++#define vreinterpret_m64_f32(x) vreinterpret_s64_f32(x) ++#define vreinterpret_m64_f64(x) vreinterpret_s64_f64(x) ++ ++#define vreinterpret_u8_m64(x) vreinterpret_u8_s64(x) ++#define vreinterpret_u16_m64(x) vreinterpret_u16_s64(x) ++#define vreinterpret_u32_m64(x) vreinterpret_u32_s64(x) ++#define vreinterpret_u64_m64(x) vreinterpret_u64_s64(x) ++ ++#define vreinterpret_s8_m64(x) vreinterpret_s8_s64(x) ++#define vreinterpret_s16_m64(x) vreinterpret_s16_s64(x) ++#define vreinterpret_s32_m64(x) vreinterpret_s32_s64(x) ++#define vreinterpret_s64_m64(x) (x) ++ ++#define vreinterpret_f32_m64(x) vreinterpret_f32_s64(x) ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#define vreinterpretq_m128d_s32(x) vreinterpretq_f64_s32(x) ++#define vreinterpretq_m128d_s64(x) vreinterpretq_f64_s64(x) ++ ++#define vreinterpretq_m128d_u64(x) vreinterpretq_f64_u64(x) ++ ++#define vreinterpretq_m128d_f32(x) vreinterpretq_f64_f32(x) ++#define vreinterpretq_m128d_f64(x) (x) ++ ++#define vreinterpretq_s64_m128d(x) vreinterpretq_s64_f64(x) ++ ++#define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f64(x) ++#define vreinterpretq_u64_m128d(x) vreinterpretq_u64_f64(x) ++ ++#define vreinterpretq_f64_m128d(x) (x) ++#define vreinterpretq_f32_m128d(x) vreinterpretq_f32_f64(x) ++#else ++#define vreinterpretq_m128d_s32(x) vreinterpretq_f32_s32(x) ++#define vreinterpretq_m128d_s64(x) vreinterpretq_f32_s64(x) ++ ++#define vreinterpretq_m128d_u32(x) vreinterpretq_f32_u32(x) ++#define vreinterpretq_m128d_u64(x) vreinterpretq_f32_u64(x) ++ ++#define vreinterpretq_m128d_f32(x) (x) ++ ++#define vreinterpretq_s64_m128d(x) vreinterpretq_s64_f32(x) ++ ++#define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f32(x) ++#define vreinterpretq_u64_m128d(x) vreinterpretq_u64_f32(x) ++ ++#define vreinterpretq_f32_m128d(x) (x) ++#endif ++ ++// A struct is defined in this header file called 'SIMDVec' which can be used ++// by applications which attempt to access the contents of an __m128 struct ++// directly. It is important to note that accessing the __m128 struct directly ++// is bad coding practice by Microsoft: @see: ++// https://learn.microsoft.com/en-us/cpp/cpp/m128 ++// ++// However, some legacy source code may try to access the contents of an __m128 ++// struct directly so the developer can use the SIMDVec as an alias for it. Any ++// casting must be done manually by the developer, as you cannot cast or ++// otherwise alias the base NEON data type for intrinsic operations. ++// ++// union intended to allow direct access to an __m128 variable using the names ++// that the MSVC compiler provides. This union should really only be used when ++// trying to access the members of the vector as integer values. GCC/clang ++// allow native access to the float members through a simple array access ++// operator (in C since 4.6, in C++ since 4.8). ++// ++// Ideally direct accesses to SIMD vectors should not be used since it can cause ++// a performance hit. If it really is needed however, the original __m128 ++// variable can be aliased with a pointer to this union and used to access ++// individual components. The use of this union should be hidden behind a macro ++// that is used throughout the codebase to access the members instead of always ++// declaring this type of variable. ++typedef union ALIGN_STRUCT(16) SIMDVec { ++ float m128_f32[4]; // as floats - DON'T USE. Added for convenience. ++ int8_t m128_i8[16]; // as signed 8-bit integers. ++ int16_t m128_i16[8]; // as signed 16-bit integers. ++ int32_t m128_i32[4]; // as signed 32-bit integers. ++ int64_t m128_i64[2]; // as signed 64-bit integers. ++ uint8_t m128_u8[16]; // as unsigned 8-bit integers. ++ uint16_t m128_u16[8]; // as unsigned 16-bit integers. ++ uint32_t m128_u32[4]; // as unsigned 32-bit integers. ++ uint64_t m128_u64[2]; // as unsigned 64-bit integers. ++} SIMDVec; ++ ++// casting using SIMDVec ++#define vreinterpretq_nth_u64_m128i(x, n) (((SIMDVec *) &x)->m128_u64[n]) ++#define vreinterpretq_nth_u32_m128i(x, n) (((SIMDVec *) &x)->m128_u32[n]) ++#define vreinterpretq_nth_u8_m128i(x, n) (((SIMDVec *) &x)->m128_u8[n]) ++ ++/* SSE macros */ ++#define _MM_GET_FLUSH_ZERO_MODE _sse2neon_mm_get_flush_zero_mode ++#define _MM_SET_FLUSH_ZERO_MODE _sse2neon_mm_set_flush_zero_mode ++#define _MM_GET_DENORMALS_ZERO_MODE _sse2neon_mm_get_denormals_zero_mode ++#define _MM_SET_DENORMALS_ZERO_MODE _sse2neon_mm_set_denormals_zero_mode ++ ++// Function declaration ++// SSE ++FORCE_INLINE unsigned int _MM_GET_ROUNDING_MODE(void); ++FORCE_INLINE __m128 _mm_move_ss(__m128, __m128); ++FORCE_INLINE __m128 _mm_or_ps(__m128, __m128); ++FORCE_INLINE __m128 _mm_set_ps1(float); ++FORCE_INLINE __m128 _mm_setzero_ps(void); ++// SSE2 ++FORCE_INLINE __m128i _mm_and_si128(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_castps_si128(__m128); ++FORCE_INLINE __m128i _mm_cmpeq_epi32(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_cvtps_epi32(__m128); ++FORCE_INLINE __m128d _mm_move_sd(__m128d, __m128d); ++FORCE_INLINE __m128i _mm_or_si128(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_set_epi32(int, int, int, int); ++FORCE_INLINE __m128i _mm_set_epi64x(int64_t, int64_t); ++FORCE_INLINE __m128d _mm_set_pd(double, double); ++FORCE_INLINE __m128i _mm_set1_epi32(int); ++FORCE_INLINE __m128i _mm_setzero_si128(void); ++// SSE4.1 ++FORCE_INLINE __m128d _mm_ceil_pd(__m128d); ++FORCE_INLINE __m128 _mm_ceil_ps(__m128); ++FORCE_INLINE __m128d _mm_floor_pd(__m128d); ++FORCE_INLINE __m128 _mm_floor_ps(__m128); ++FORCE_INLINE_OPTNONE __m128d _mm_round_pd(__m128d, int); ++FORCE_INLINE_OPTNONE __m128 _mm_round_ps(__m128, int); ++// SSE4.2 ++FORCE_INLINE uint32_t _mm_crc32_u8(uint32_t, uint8_t); ++ ++/* Backwards compatibility for compilers with lack of specific type support */ ++ ++// Older gcc does not define vld1q_u8_x4 type ++#if defined(__GNUC__) && !defined(__clang__) && \ ++ ((__GNUC__ <= 13 && defined(__arm__)) || \ ++ (__GNUC__ == 10 && __GNUC_MINOR__ < 3 && defined(__aarch64__)) || \ ++ (__GNUC__ <= 9 && defined(__aarch64__))) ++FORCE_INLINE uint8x16x4_t _sse2neon_vld1q_u8_x4(const uint8_t *p) ++{ ++ uint8x16x4_t ret; ++ ret.val[0] = vld1q_u8(p + 0); ++ ret.val[1] = vld1q_u8(p + 16); ++ ret.val[2] = vld1q_u8(p + 32); ++ ret.val[3] = vld1q_u8(p + 48); ++ return ret; ++} ++#else ++// Wraps vld1q_u8_x4 ++FORCE_INLINE uint8x16x4_t _sse2neon_vld1q_u8_x4(const uint8_t *p) ++{ ++ return vld1q_u8_x4(p); ++} ++#endif ++ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++/* emulate vaddv u8 variant */ ++FORCE_INLINE uint8_t _sse2neon_vaddv_u8(uint8x8_t v8) ++{ ++ const uint64x1_t v1 = vpaddl_u32(vpaddl_u16(vpaddl_u8(v8))); ++ return vget_lane_u8(vreinterpret_u8_u64(v1), 0); ++} ++#else ++// Wraps vaddv_u8 ++FORCE_INLINE uint8_t _sse2neon_vaddv_u8(uint8x8_t v8) ++{ ++ return vaddv_u8(v8); ++} ++#endif ++ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++/* emulate vaddvq u8 variant */ ++FORCE_INLINE uint8_t _sse2neon_vaddvq_u8(uint8x16_t a) ++{ ++ uint8x8_t tmp = vpadd_u8(vget_low_u8(a), vget_high_u8(a)); ++ uint8_t res = 0; ++ for (int i = 0; i < 8; ++i) ++ res += tmp[i]; ++ return res; ++} ++#else ++// Wraps vaddvq_u8 ++FORCE_INLINE uint8_t _sse2neon_vaddvq_u8(uint8x16_t a) ++{ ++ return vaddvq_u8(a); ++} ++#endif ++ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++/* emulate vaddvq u16 variant */ ++FORCE_INLINE uint16_t _sse2neon_vaddvq_u16(uint16x8_t a) ++{ ++ uint32x4_t m = vpaddlq_u16(a); ++ uint64x2_t n = vpaddlq_u32(m); ++ uint64x1_t o = vget_low_u64(n) + vget_high_u64(n); ++ ++ return vget_lane_u32((uint32x2_t) o, 0); ++} ++#else ++// Wraps vaddvq_u16 ++FORCE_INLINE uint16_t _sse2neon_vaddvq_u16(uint16x8_t a) ++{ ++ return vaddvq_u16(a); ++} ++#endif ++ ++/* Function Naming Conventions ++ * The naming convention of SSE intrinsics is straightforward. A generic SSE ++ * intrinsic function is given as follows: ++ * _mm__ ++ * ++ * The parts of this format are given as follows: ++ * 1. describes the operation performed by the intrinsic ++ * 2. identifies the data type of the function's primary arguments ++ * ++ * This last part, , is a little complicated. It identifies the ++ * content of the input values, and can be set to any of the following values: ++ * + ps - vectors contain floats (ps stands for packed single-precision) ++ * + pd - vectors contain doubles (pd stands for packed double-precision) ++ * + epi8/epi16/epi32/epi64 - vectors contain 8-bit/16-bit/32-bit/64-bit ++ * signed integers ++ * + epu8/epu16/epu32/epu64 - vectors contain 8-bit/16-bit/32-bit/64-bit ++ * unsigned integers ++ * + si128 - unspecified 128-bit vector or 256-bit vector ++ * + m128/m128i/m128d - identifies input vector types when they are different ++ * than the type of the returned vector ++ * ++ * For example, _mm_setzero_ps. The _mm implies that the function returns ++ * a 128-bit vector. The _ps at the end implies that the argument vectors ++ * contain floats. ++ * ++ * A complete example: Byte Shuffle - pshufb (_mm_shuffle_epi8) ++ * // Set packed 16-bit integers. 128 bits, 8 short, per 16 bits ++ * __m128i v_in = _mm_setr_epi16(1, 2, 3, 4, 5, 6, 7, 8); ++ * // Set packed 8-bit integers ++ * // 128 bits, 16 chars, per 8 bits ++ * __m128i v_perm = _mm_setr_epi8(1, 0, 2, 3, 8, 9, 10, 11, ++ * 4, 5, 12, 13, 6, 7, 14, 15); ++ * // Shuffle packed 8-bit integers ++ * __m128i v_out = _mm_shuffle_epi8(v_in, v_perm); // pshufb ++ */ ++ ++/* Constants for use with _mm_prefetch. */ ++enum _mm_hint { ++ _MM_HINT_NTA = 0, /* load data to L1 and L2 cache, mark it as NTA */ ++ _MM_HINT_T0 = 1, /* load data to L1 and L2 cache */ ++ _MM_HINT_T1 = 2, /* load data to L2 cache only */ ++ _MM_HINT_T2 = 3, /* load data to L2 cache only, mark it as NTA */ ++}; ++ ++// The bit field mapping to the FPCR(floating-point control register) ++typedef struct { ++ uint16_t res0; ++ uint8_t res1 : 6; ++ uint8_t bit22 : 1; ++ uint8_t bit23 : 1; ++ uint8_t bit24 : 1; ++ uint8_t res2 : 7; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint32_t res3; ++#endif ++} fpcr_bitfield; ++ ++// Takes the upper 64 bits of a and places it in the low end of the result ++// Takes the lower 64 bits of b and places it into the high end of the result. ++FORCE_INLINE __m128 _mm_shuffle_ps_1032(__m128 a, __m128 b) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a32, b10)); ++} ++ ++// takes the lower two 32-bit values from a and swaps them and places in high ++// end of result takes the higher two 32 bit values from b and swaps them and ++// places in low end of result. ++FORCE_INLINE __m128 _mm_shuffle_ps_2301(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b23 = vrev64_f32(vget_high_f32(vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b23)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0321(__m128 a, __m128 b) ++{ ++ float32x2_t a21 = vget_high_f32( ++ vextq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 3)); ++ float32x2_t b03 = vget_low_f32( ++ vextq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b), 3)); ++ return vreinterpretq_m128_f32(vcombine_f32(a21, b03)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2103(__m128 a, __m128 b) ++{ ++ float32x2_t a03 = vget_low_f32( ++ vextq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 3)); ++ float32x2_t b21 = vget_high_f32( ++ vextq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b), 3)); ++ return vreinterpretq_m128_f32(vcombine_f32(a03, b21)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1010(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b10)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1001(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b10)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0101(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b01)); ++} ++ ++// keeps the low 64 bits of b in the low and puts the high 64 bits of a in the ++// high ++FORCE_INLINE __m128 _mm_shuffle_ps_3210(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b32)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0011(__m128 a, __m128 b) ++{ ++ float32x2_t a11 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(a)), 1); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a11, b00)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0022(__m128 a, __m128 b) ++{ ++ float32x2_t a22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a22, b00)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2200(__m128 a, __m128 b) ++{ ++ float32x2_t a00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t b22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a00, b22)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_3202(__m128 a, __m128 b) ++{ ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ float32x2_t a22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t a02 = vset_lane_f32(a0, a22, 1); /* TODO: use vzip ?*/ ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a02, b32)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1133(__m128 a, __m128 b) ++{ ++ float32x2_t a33 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 1); ++ float32x2_t b11 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a33, b11)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2010(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32_t b2 = vgetq_lane_f32(vreinterpretq_f32_m128(b), 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b20)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2001(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32_t b2 = vgetq_lane_f32(b, 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b20)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2032(__m128 a, __m128 b) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32_t b2 = vgetq_lane_f32(b, 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a32, b20)); ++} ++ ++// For MSVC, we check only if it is ARM64, as every single ARM64 processor ++// supported by WoA has crypto extensions. If this changes in the future, ++// this can be verified via the runtime-only method of: ++// IsProcessorFeaturePresent(PF_ARM_V8_CRYPTO_INSTRUCTIONS_AVAILABLE) ++#if (defined(_M_ARM64) && !defined(__clang__)) || \ ++ (defined(__ARM_FEATURE_CRYPTO) && \ ++ (defined(__aarch64__) || __has_builtin(__builtin_arm_crypto_vmullp64))) ++// Wraps vmull_p64 ++FORCE_INLINE uint64x2_t _sse2neon_vmull_p64(uint64x1_t _a, uint64x1_t _b) ++{ ++ poly64_t a = vget_lane_p64(vreinterpret_p64_u64(_a), 0); ++ poly64_t b = vget_lane_p64(vreinterpret_p64_u64(_b), 0); ++#if defined(_MSC_VER) ++ __n64 a1 = {a}, b1 = {b}; ++ return vreinterpretq_u64_p128(vmull_p64(a1, b1)); ++#else ++ return vreinterpretq_u64_p128(vmull_p64(a, b)); ++#endif ++} ++#else // ARMv7 polyfill ++// ARMv7/some A64 lacks vmull_p64, but it has vmull_p8. ++// ++// vmull_p8 calculates 8 8-bit->16-bit polynomial multiplies, but we need a ++// 64-bit->128-bit polynomial multiply. ++// ++// It needs some work and is somewhat slow, but it is still faster than all ++// known scalar methods. ++// ++// Algorithm adapted to C from ++// https://www.workofard.com/2017/07/ghash-for-low-end-cores/, which is adapted ++// from "Fast Software Polynomial Multiplication on ARM Processors Using the ++// NEON Engine" by Danilo Camara, Conrado Gouvea, Julio Lopez and Ricardo Dahab ++// (https://hal.inria.fr/hal-01506572) ++static uint64x2_t _sse2neon_vmull_p64(uint64x1_t _a, uint64x1_t _b) ++{ ++ poly8x8_t a = vreinterpret_p8_u64(_a); ++ poly8x8_t b = vreinterpret_p8_u64(_b); ++ ++ // Masks ++ uint8x16_t k48_32 = vcombine_u8(vcreate_u8(0x0000ffffffffffff), ++ vcreate_u8(0x00000000ffffffff)); ++ uint8x16_t k16_00 = vcombine_u8(vcreate_u8(0x000000000000ffff), ++ vcreate_u8(0x0000000000000000)); ++ ++ // Do the multiplies, rotating with vext to get all combinations ++ uint8x16_t d = vreinterpretq_u8_p16(vmull_p8(a, b)); // D = A0 * B0 ++ uint8x16_t e = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 1))); // E = A0 * B1 ++ uint8x16_t f = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 1), b)); // F = A1 * B0 ++ uint8x16_t g = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 2))); // G = A0 * B2 ++ uint8x16_t h = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 2), b)); // H = A2 * B0 ++ uint8x16_t i = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 3))); // I = A0 * B3 ++ uint8x16_t j = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 3), b)); // J = A3 * B0 ++ uint8x16_t k = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 4))); // L = A0 * B4 ++ ++ // Add cross products ++ uint8x16_t l = veorq_u8(e, f); // L = E + F ++ uint8x16_t m = veorq_u8(g, h); // M = G + H ++ uint8x16_t n = veorq_u8(i, j); // N = I + J ++ ++ // Interleave. Using vzip1 and vzip2 prevents Clang from emitting TBL ++ // instructions. ++#if defined(__aarch64__) ++ uint8x16_t lm_p0 = vreinterpretq_u8_u64( ++ vzip1q_u64(vreinterpretq_u64_u8(l), vreinterpretq_u64_u8(m))); ++ uint8x16_t lm_p1 = vreinterpretq_u8_u64( ++ vzip2q_u64(vreinterpretq_u64_u8(l), vreinterpretq_u64_u8(m))); ++ uint8x16_t nk_p0 = vreinterpretq_u8_u64( ++ vzip1q_u64(vreinterpretq_u64_u8(n), vreinterpretq_u64_u8(k))); ++ uint8x16_t nk_p1 = vreinterpretq_u8_u64( ++ vzip2q_u64(vreinterpretq_u64_u8(n), vreinterpretq_u64_u8(k))); ++#else ++ uint8x16_t lm_p0 = vcombine_u8(vget_low_u8(l), vget_low_u8(m)); ++ uint8x16_t lm_p1 = vcombine_u8(vget_high_u8(l), vget_high_u8(m)); ++ uint8x16_t nk_p0 = vcombine_u8(vget_low_u8(n), vget_low_u8(k)); ++ uint8x16_t nk_p1 = vcombine_u8(vget_high_u8(n), vget_high_u8(k)); ++#endif ++ // t0 = (L) (P0 + P1) << 8 ++ // t1 = (M) (P2 + P3) << 16 ++ uint8x16_t t0t1_tmp = veorq_u8(lm_p0, lm_p1); ++ uint8x16_t t0t1_h = vandq_u8(lm_p1, k48_32); ++ uint8x16_t t0t1_l = veorq_u8(t0t1_tmp, t0t1_h); ++ ++ // t2 = (N) (P4 + P5) << 24 ++ // t3 = (K) (P6 + P7) << 32 ++ uint8x16_t t2t3_tmp = veorq_u8(nk_p0, nk_p1); ++ uint8x16_t t2t3_h = vandq_u8(nk_p1, k16_00); ++ uint8x16_t t2t3_l = veorq_u8(t2t3_tmp, t2t3_h); ++ ++ // De-interleave ++#if defined(__aarch64__) ++ uint8x16_t t0 = vreinterpretq_u8_u64( ++ vuzp1q_u64(vreinterpretq_u64_u8(t0t1_l), vreinterpretq_u64_u8(t0t1_h))); ++ uint8x16_t t1 = vreinterpretq_u8_u64( ++ vuzp2q_u64(vreinterpretq_u64_u8(t0t1_l), vreinterpretq_u64_u8(t0t1_h))); ++ uint8x16_t t2 = vreinterpretq_u8_u64( ++ vuzp1q_u64(vreinterpretq_u64_u8(t2t3_l), vreinterpretq_u64_u8(t2t3_h))); ++ uint8x16_t t3 = vreinterpretq_u8_u64( ++ vuzp2q_u64(vreinterpretq_u64_u8(t2t3_l), vreinterpretq_u64_u8(t2t3_h))); ++#else ++ uint8x16_t t1 = vcombine_u8(vget_high_u8(t0t1_l), vget_high_u8(t0t1_h)); ++ uint8x16_t t0 = vcombine_u8(vget_low_u8(t0t1_l), vget_low_u8(t0t1_h)); ++ uint8x16_t t3 = vcombine_u8(vget_high_u8(t2t3_l), vget_high_u8(t2t3_h)); ++ uint8x16_t t2 = vcombine_u8(vget_low_u8(t2t3_l), vget_low_u8(t2t3_h)); ++#endif ++ // Shift the cross products ++ uint8x16_t t0_shift = vextq_u8(t0, t0, 15); // t0 << 8 ++ uint8x16_t t1_shift = vextq_u8(t1, t1, 14); // t1 << 16 ++ uint8x16_t t2_shift = vextq_u8(t2, t2, 13); // t2 << 24 ++ uint8x16_t t3_shift = vextq_u8(t3, t3, 12); // t3 << 32 ++ ++ // Accumulate the products ++ uint8x16_t cross1 = veorq_u8(t0_shift, t1_shift); ++ uint8x16_t cross2 = veorq_u8(t2_shift, t3_shift); ++ uint8x16_t mix = veorq_u8(d, cross1); ++ uint8x16_t r = veorq_u8(mix, cross2); ++ return vreinterpretq_u64_u8(r); ++} ++#endif // ARMv7 polyfill ++ ++// C equivalent: ++// __m128i _mm_shuffle_epi32_default(__m128i a, ++// __constrange(0, 255) int imm) { ++// __m128i ret; ++// ret[0] = a[imm & 0x3]; ret[1] = a[(imm >> 2) & 0x3]; ++// ret[2] = a[(imm >> 4) & 0x03]; ret[3] = a[(imm >> 6) & 0x03]; ++// return ret; ++// } ++#define _mm_shuffle_epi32_default(a, imm) \ ++ vreinterpretq_m128i_s32(vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 6) & 0x3), \ ++ vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 4) & 0x3), \ ++ vsetq_lane_s32(vgetq_lane_s32(vreinterpretq_s32_m128i(a), \ ++ ((imm) >> 2) & 0x3), \ ++ vmovq_n_s32(vgetq_lane_s32( \ ++ vreinterpretq_s32_m128i(a), (imm) & (0x3))), \ ++ 1), \ ++ 2), \ ++ 3)) ++ ++// Takes the upper 64 bits of a and places it in the low end of the result ++// Takes the lower 64 bits of a and places it into the high end of the result. ++FORCE_INLINE __m128i _mm_shuffle_epi_1032(__m128i a) ++{ ++ int32x2_t a32 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a32, a10)); ++} ++ ++// takes the lower two 32-bit values from a and swaps them and places in low end ++// of result takes the higher two 32 bit values from a and swaps them and places ++// in high end of result. ++FORCE_INLINE __m128i _mm_shuffle_epi_2301(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ int32x2_t a23 = vrev64_s32(vget_high_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a23)); ++} ++ ++// rotates the least significant 32 bits into the most significant 32 bits, and ++// shifts the rest down ++FORCE_INLINE __m128i _mm_shuffle_epi_0321(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vextq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(a), 1)); ++} ++ ++// rotates the most significant 32 bits into the least significant 32 bits, and ++// shifts the rest up ++FORCE_INLINE __m128i _mm_shuffle_epi_2103(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vextq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(a), 3)); ++} ++ ++// gets the lower 64 bits of a, and places it in the upper 64 bits ++// gets the lower 64 bits of a and places it in the lower 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_1010(__m128i a) ++{ ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a10, a10)); ++} ++ ++// gets the lower 64 bits of a, swaps the 0 and 1 elements, and places it in the ++// lower 64 bits gets the lower 64 bits of a, and places it in the upper 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_1001(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a10)); ++} ++ ++// gets the lower 64 bits of a, swaps the 0 and 1 elements and places it in the ++// upper 64 bits gets the lower 64 bits of a, swaps the 0 and 1 elements, and ++// places it in the lower 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_0101(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a01)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_2211(__m128i a) ++{ ++ int32x2_t a11 = vdup_lane_s32(vget_low_s32(vreinterpretq_s32_m128i(a)), 1); ++ int32x2_t a22 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 0); ++ return vreinterpretq_m128i_s32(vcombine_s32(a11, a22)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_0122(__m128i a) ++{ ++ int32x2_t a22 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 0); ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a22, a01)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_3332(__m128i a) ++{ ++ int32x2_t a32 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t a33 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 1); ++ return vreinterpretq_m128i_s32(vcombine_s32(a32, a33)); ++} ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#define _mm_shuffle_epi32_splat(a, imm) \ ++ vreinterpretq_m128i_s32(vdupq_laneq_s32(vreinterpretq_s32_m128i(a), (imm))) ++#else ++#define _mm_shuffle_epi32_splat(a, imm) \ ++ vreinterpretq_m128i_s32( \ ++ vdupq_n_s32(vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm)))) ++#endif ++ ++// NEON does not support a general purpose permute intrinsic. ++// Shuffle single-precision (32-bit) floating-point elements in a using the ++// control in imm8, and store the results in dst. ++// ++// C equivalent: ++// __m128 _mm_shuffle_ps_default(__m128 a, __m128 b, ++// __constrange(0, 255) int imm) { ++// __m128 ret; ++// ret[0] = a[imm & 0x3]; ret[1] = a[(imm >> 2) & 0x3]; ++// ret[2] = b[(imm >> 4) & 0x03]; ret[3] = b[(imm >> 6) & 0x03]; ++// return ret; ++// } ++// ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_ps ++#define _mm_shuffle_ps_default(a, b, imm) \ ++ vreinterpretq_m128_f32(vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(b), ((imm) >> 6) & 0x3), \ ++ vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(b), ((imm) >> 4) & 0x3), \ ++ vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(a), ((imm) >> 2) & 0x3), \ ++ vmovq_n_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(a), (imm) & (0x3))), \ ++ 1), \ ++ 2), \ ++ 3)) ++ ++// Shuffle 16-bit integers in the low 64 bits of a using the control in imm8. ++// Store the results in the low 64 bits of dst, with the high 64 bits being ++// copied from a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shufflelo_epi16 ++#define _mm_shufflelo_epi16_function(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, int16x8_t ret = vreinterpretq_s16_m128i(_a); \ ++ int16x4_t lowBits = vget_low_s16(ret); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, (imm) & (0x3)), ret, 0); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 2) & 0x3), ret, \ ++ 1); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 4) & 0x3), ret, \ ++ 2); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 6) & 0x3), ret, \ ++ 3); \ ++ _sse2neon_return(vreinterpretq_m128i_s16(ret));) ++ ++// Shuffle 16-bit integers in the high 64 bits of a using the control in imm8. ++// Store the results in the high 64 bits of dst, with the low 64 bits being ++// copied from a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shufflehi_epi16 ++#define _mm_shufflehi_epi16_function(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, int16x8_t ret = vreinterpretq_s16_m128i(_a); \ ++ int16x4_t highBits = vget_high_s16(ret); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, (imm) & (0x3)), ret, 4); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 2) & 0x3), ret, \ ++ 5); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 4) & 0x3), ret, \ ++ 6); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 6) & 0x3), ret, \ ++ 7); \ ++ _sse2neon_return(vreinterpretq_m128i_s16(ret));) ++ ++/* MMX */ ++ ++//_mm_empty is a no-op on arm ++FORCE_INLINE void _mm_empty(void) {} ++ ++/* SSE */ ++ ++// Add packed single-precision (32-bit) floating-point elements in a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_ps ++FORCE_INLINE __m128 _mm_add_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vaddq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Add the lower single-precision (32-bit) floating-point element in a and b, ++// store the result in the lower element of dst, and copy the upper 3 packed ++// elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_ss ++FORCE_INLINE __m128 _mm_add_ss(__m128 a, __m128 b) ++{ ++ float32_t b0 = vgetq_lane_f32(vreinterpretq_f32_m128(b), 0); ++ float32x4_t value = vsetq_lane_f32(b0, vdupq_n_f32(0), 0); ++ // the upper values in the result must be the remnants of . ++ return vreinterpretq_m128_f32(vaddq_f32(a, value)); ++} ++ ++// Compute the bitwise AND of packed single-precision (32-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_and_ps ++FORCE_INLINE __m128 _mm_and_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vandq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Compute the bitwise NOT of packed single-precision (32-bit) floating-point ++// elements in a and then AND with b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_andnot_ps ++FORCE_INLINE __m128 _mm_andnot_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vbicq_s32(vreinterpretq_s32_m128(b), ++ vreinterpretq_s32_m128(a))); // *NOTE* argument swap ++} ++ ++// Average packed unsigned 16-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_avg_pu16 ++FORCE_INLINE __m64 _mm_avg_pu16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u16( ++ vrhadd_u16(vreinterpret_u16_m64(a), vreinterpret_u16_m64(b))); ++} ++ ++// Average packed unsigned 8-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_avg_pu8 ++FORCE_INLINE __m64 _mm_avg_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vrhadd_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for equality, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_ps ++FORCE_INLINE __m128 _mm_cmpeq_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for equality, store the result in the lower element of dst, and copy the ++// upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_ss ++FORCE_INLINE __m128 _mm_cmpeq_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpeq_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for greater-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpge_ps ++FORCE_INLINE __m128 _mm_cmpge_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for greater-than-or-equal, store the result in the lower element of dst, ++// and copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpge_ss ++FORCE_INLINE __m128 _mm_cmpge_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpge_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for greater-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_ps ++FORCE_INLINE __m128 _mm_cmpgt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for greater-than, store the result in the lower element of dst, and copy ++// the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_ss ++FORCE_INLINE __m128 _mm_cmpgt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpgt_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for less-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmple_ps ++FORCE_INLINE __m128 _mm_cmple_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for less-than-or-equal, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmple_ss ++FORCE_INLINE __m128 _mm_cmple_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmple_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for less-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_ps ++FORCE_INLINE __m128 _mm_cmplt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for less-than, store the result in the lower element of dst, and copy the ++// upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_ss ++FORCE_INLINE __m128 _mm_cmplt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmplt_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpneq_ps ++FORCE_INLINE __m128 _mm_cmpneq_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-equal, store the result in the lower element of dst, and copy the ++// upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpneq_ss ++FORCE_INLINE __m128 _mm_cmpneq_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpneq_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-greater-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnge_ps ++FORCE_INLINE __m128 _mm_cmpnge_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-greater-than-or-equal, store the result in the lower element of ++// dst, and copy the upper 3 packed elements from a to the upper elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnge_ss ++FORCE_INLINE __m128 _mm_cmpnge_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnge_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-greater-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpngt_ps ++FORCE_INLINE __m128 _mm_cmpngt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-greater-than, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpngt_ss ++FORCE_INLINE __m128 _mm_cmpngt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpngt_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-less-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnle_ps ++FORCE_INLINE __m128 _mm_cmpnle_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-less-than-or-equal, store the result in the lower element of dst, ++// and copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnle_ss ++FORCE_INLINE __m128 _mm_cmpnle_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnle_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-less-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnlt_ps ++FORCE_INLINE __m128 _mm_cmpnlt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-less-than, store the result in the lower element of dst, and copy ++// the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnlt_ss ++FORCE_INLINE __m128 _mm_cmpnlt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnlt_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// to see if neither is NaN, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpord_ps ++// ++// See also: ++// http://stackoverflow.com/questions/8627331/what-does-ordered-unordered-comparison-mean ++// http://stackoverflow.com/questions/29349621/neon-isnanval-intrinsics ++FORCE_INLINE __m128 _mm_cmpord_ps(__m128 a, __m128 b) ++{ ++ // Note: NEON does not have ordered compare builtin ++ // Need to compare a eq a and b eq b to check for NaN ++ // Do AND of results to get final ++ uint32x4_t ceqaa = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t ceqbb = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_u32(vandq_u32(ceqaa, ceqbb)); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b to see if neither is NaN, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpord_ss ++FORCE_INLINE __m128 _mm_cmpord_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpord_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// to see if either is NaN, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpunord_ps ++FORCE_INLINE __m128 _mm_cmpunord_ps(__m128 a, __m128 b) ++{ ++ uint32x4_t f32a = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t f32b = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_u32(vmvnq_u32(vandq_u32(f32a, f32b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b to see if either is NaN, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpunord_ss ++FORCE_INLINE __m128 _mm_cmpunord_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpunord_ps(a, b)); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for equality, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comieq_ss ++FORCE_INLINE int _mm_comieq_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_eq_b = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_eq_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for greater-than-or-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comige_ss ++FORCE_INLINE int _mm_comige_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_ge_b = ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_ge_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for greater-than, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comigt_ss ++FORCE_INLINE int _mm_comigt_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_gt_b = ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_gt_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for less-than-or-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comile_ss ++FORCE_INLINE int _mm_comile_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_le_b = ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_le_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for less-than, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comilt_ss ++FORCE_INLINE int _mm_comilt_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_lt_b = ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_lt_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for not-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comineq_ss ++FORCE_INLINE int _mm_comineq_ss(__m128 a, __m128 b) ++{ ++ return !_mm_comieq_ss(a, b); ++} ++ ++// Convert packed signed 32-bit integers in b to packed single-precision ++// (32-bit) floating-point elements, store the results in the lower 2 elements ++// of dst, and copy the upper 2 packed elements from a to the upper elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvt_pi2ps ++FORCE_INLINE __m128 _mm_cvt_pi2ps(__m128 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vcvt_f32_s32(vreinterpret_s32_m64(b)), ++ vget_high_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvt_ps2pi ++FORCE_INLINE __m64 _mm_cvt_ps2pi(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpret_m64_s32( ++ vget_low_s32(vcvtnq_s32_f32(vrndiq_f32(vreinterpretq_f32_m128(a))))); ++#else ++ return vreinterpret_m64_s32(vcvt_s32_f32(vget_low_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION))))); ++#endif ++} ++ ++// Convert the signed 32-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvt_si2ss ++FORCE_INLINE __m128 _mm_cvt_si2ss(__m128 a, int b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32((float) b, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvt_ss2si ++FORCE_INLINE int _mm_cvt_ss2si(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vgetq_lane_s32(vcvtnq_s32_f32(vrndiq_f32(vreinterpretq_f32_m128(a))), ++ 0); ++#else ++ float32_t data = vgetq_lane_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION)), 0); ++ return (int32_t) data; ++#endif ++} ++ ++// Convert packed 16-bit integers in a to packed single-precision (32-bit) ++// floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi16_ps ++FORCE_INLINE __m128 _mm_cvtpi16_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_s32(vmovl_s16(vreinterpret_s16_m64(a)))); ++} ++ ++// Convert packed 32-bit integers in b to packed single-precision (32-bit) ++// floating-point elements, store the results in the lower 2 elements of dst, ++// and copy the upper 2 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi32_ps ++FORCE_INLINE __m128 _mm_cvtpi32_ps(__m128 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vcvt_f32_s32(vreinterpret_s32_m64(b)), ++ vget_high_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert packed signed 32-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, store the results in the lower 2 elements ++// of dst, then convert the packed signed 32-bit integers in b to ++// single-precision (32-bit) floating-point element, and store the results in ++// the upper 2 elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi32x2_ps ++FORCE_INLINE __m128 _mm_cvtpi32x2_ps(__m64 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32( ++ vcombine_s32(vreinterpret_s32_m64(a), vreinterpret_s32_m64(b)))); ++} ++ ++// Convert the lower packed 8-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi8_ps ++FORCE_INLINE __m128 _mm_cvtpi8_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32( ++ vmovl_s16(vget_low_s16(vmovl_s8(vreinterpret_s8_m64(a)))))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 16-bit integers, and store the results in dst. Note: this intrinsic ++// will generate 0x7FFF, rather than 0x8000, for input values between 0x7FFF and ++// 0x7FFFFFFF. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_pi16 ++FORCE_INLINE __m64 _mm_cvtps_pi16(__m128 a) ++{ ++ return vreinterpret_m64_s16( ++ vqmovn_s32(vreinterpretq_s32_m128i(_mm_cvtps_epi32(a)))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_pi32 ++#define _mm_cvtps_pi32(a) _mm_cvt_ps2pi(a) ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 8-bit integers, and store the results in lower 4 elements of dst. ++// Note: this intrinsic will generate 0x7F, rather than 0x80, for input values ++// between 0x7F and 0x7FFFFFFF. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_pi8 ++FORCE_INLINE __m64 _mm_cvtps_pi8(__m128 a) ++{ ++ return vreinterpret_m64_s8(vqmovn_s16( ++ vcombine_s16(vreinterpret_s16_m64(_mm_cvtps_pi16(a)), vdup_n_s16(0)))); ++} ++ ++// Convert packed unsigned 16-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpu16_ps ++FORCE_INLINE __m128 _mm_cvtpu16_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_u32(vmovl_u16(vreinterpret_u16_m64(a)))); ++} ++ ++// Convert the lower packed unsigned 8-bit integers in a to packed ++// single-precision (32-bit) floating-point elements, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpu8_ps ++FORCE_INLINE __m128 _mm_cvtpu8_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_u32( ++ vmovl_u16(vget_low_u16(vmovl_u8(vreinterpret_u8_m64(a)))))); ++} ++ ++// Convert the signed 32-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi32_ss ++#define _mm_cvtsi32_ss(a, b) _mm_cvt_si2ss(a, b) ++ ++// Convert the signed 64-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64_ss ++FORCE_INLINE __m128 _mm_cvtsi64_ss(__m128 a, int64_t b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32((float) b, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Copy the lower single-precision (32-bit) floating-point element of a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtss_f32 ++FORCE_INLINE float _mm_cvtss_f32(__m128 a) ++{ ++ return vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtss_si32 ++#define _mm_cvtss_si32(a) _mm_cvt_ss2si(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtss_si64 ++FORCE_INLINE int64_t _mm_cvtss_si64(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return (int64_t) vgetq_lane_f32(vrndiq_f32(vreinterpretq_f32_m128(a)), 0); ++#else ++ float32_t data = vgetq_lane_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION)), 0); ++ return (int64_t) data; ++#endif ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtt_ps2pi ++FORCE_INLINE __m64 _mm_cvtt_ps2pi(__m128 a) ++{ ++ return vreinterpret_m64_s32( ++ vget_low_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtt_ss2si ++FORCE_INLINE int _mm_cvtt_ss2si(__m128 a) ++{ ++ return vgetq_lane_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a)), 0); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttps_pi32 ++#define _mm_cvttps_pi32(a) _mm_cvtt_ps2pi(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttss_si32 ++#define _mm_cvttss_si32(a) _mm_cvtt_ss2si(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttss_si64 ++FORCE_INLINE int64_t _mm_cvttss_si64(__m128 a) ++{ ++ return (int64_t) vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++} ++ ++// Divide packed single-precision (32-bit) floating-point elements in a by ++// packed elements in b, and store the results in dst. ++// Due to ARMv7-A NEON's lack of a precise division intrinsic, we implement ++// division by multiplying a by b's reciprocal before using the Newton-Raphson ++// method to approximate the results. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_div_ps ++FORCE_INLINE __m128 _mm_div_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vdivq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x4_t recip = vrecpeq_f32(vreinterpretq_f32_m128(b)); ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(b))); ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vmulq_f32(vreinterpretq_f32_m128(a), recip)); ++#endif ++} ++ ++// Divide the lower single-precision (32-bit) floating-point element in a by the ++// lower single-precision (32-bit) floating-point element in b, store the result ++// in the lower element of dst, and copy the upper 3 packed elements from a to ++// the upper elements of dst. ++// Warning: ARMv7-A does not produce the same result compared to Intel and not ++// IEEE-compliant. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_div_ss ++FORCE_INLINE __m128 _mm_div_ss(__m128 a, __m128 b) ++{ ++ float32_t value = ++ vgetq_lane_f32(vreinterpretq_f32_m128(_mm_div_ps(a, b)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Extract a 16-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_pi16 ++#define _mm_extract_pi16(a, imm) \ ++ (int32_t) vget_lane_u16(vreinterpret_u16_m64(a), (imm)) ++ ++// Free aligned memory that was allocated with _mm_malloc. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_free ++#if !defined(SSE2NEON_ALLOC_DEFINED) ++FORCE_INLINE void _mm_free(void *addr) ++{ ++ free(addr); ++} ++#endif ++ ++FORCE_INLINE uint64_t _sse2neon_get_fpcr(void) ++{ ++ uint64_t value; ++#if defined(_MSC_VER) ++ value = _ReadStatusReg(ARM64_FPCR); ++#else ++ __asm__ __volatile__("mrs %0, FPCR" : "=r"(value)); /* read */ ++#endif ++ return value; ++} ++ ++FORCE_INLINE void _sse2neon_set_fpcr(uint64_t value) ++{ ++#if defined(_MSC_VER) ++ _WriteStatusReg(ARM64_FPCR, value); ++#else ++ __asm__ __volatile__("msr FPCR, %0" ::"r"(value)); /* write */ ++#endif ++} ++ ++// Macro: Get the flush zero bits from the MXCSR control and status register. ++// The flush zero may contain any of the following flags: _MM_FLUSH_ZERO_ON or ++// _MM_FLUSH_ZERO_OFF ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_MM_GET_FLUSH_ZERO_MODE ++FORCE_INLINE unsigned int _sse2neon_mm_get_flush_zero_mode(void) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ return r.field.bit24 ? _MM_FLUSH_ZERO_ON : _MM_FLUSH_ZERO_OFF; ++} ++ ++// Macro: Get the rounding mode bits from the MXCSR control and status register. ++// The rounding mode may contain any of the following flags: _MM_ROUND_NEAREST, ++// _MM_ROUND_DOWN, _MM_ROUND_UP, _MM_ROUND_TOWARD_ZERO ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_MM_GET_ROUNDING_MODE ++FORCE_INLINE unsigned int _MM_GET_ROUNDING_MODE(void) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ if (r.field.bit22) { ++ return r.field.bit23 ? _MM_ROUND_TOWARD_ZERO : _MM_ROUND_UP; ++ } else { ++ return r.field.bit23 ? _MM_ROUND_DOWN : _MM_ROUND_NEAREST; ++ } ++} ++ ++// Copy a to dst, and insert the 16-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_pi16 ++#define _mm_insert_pi16(a, b, imm) \ ++ vreinterpret_m64_s16(vset_lane_s16((b), vreinterpret_s16_m64(a), (imm))) ++ ++// Load 128-bits (composed of 4 packed single-precision (32-bit) floating-point ++// elements) from memory into dst. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_ps ++FORCE_INLINE __m128 _mm_load_ps(const float *p) ++{ ++ return vreinterpretq_m128_f32(vld1q_f32(p)); ++} ++ ++// Load a single-precision (32-bit) floating-point element from memory into all ++// elements of dst. ++// ++// dst[31:0] := MEM[mem_addr+31:mem_addr] ++// dst[63:32] := MEM[mem_addr+31:mem_addr] ++// dst[95:64] := MEM[mem_addr+31:mem_addr] ++// dst[127:96] := MEM[mem_addr+31:mem_addr] ++// ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_ps1 ++#define _mm_load_ps1 _mm_load1_ps ++ ++// Load a single-precision (32-bit) floating-point element from memory into the ++// lower of dst, and zero the upper 3 elements. mem_addr does not need to be ++// aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_ss ++FORCE_INLINE __m128 _mm_load_ss(const float *p) ++{ ++ return vreinterpretq_m128_f32(vsetq_lane_f32(*p, vdupq_n_f32(0), 0)); ++} ++ ++// Load a single-precision (32-bit) floating-point element from memory into all ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load1_ps ++FORCE_INLINE __m128 _mm_load1_ps(const float *p) ++{ ++ return vreinterpretq_m128_f32(vld1q_dup_f32(p)); ++} ++ ++// Load 2 single-precision (32-bit) floating-point elements from memory into the ++// upper 2 elements of dst, and copy the lower 2 elements from a to dst. ++// mem_addr does not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadh_pi ++FORCE_INLINE __m128 _mm_loadh_pi(__m128 a, __m64 const *p) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vget_low_f32(a), vld1_f32((const float32_t *) p))); ++} ++ ++// Load 2 single-precision (32-bit) floating-point elements from memory into the ++// lower 2 elements of dst, and copy the upper 2 elements from a to dst. ++// mem_addr does not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadl_pi ++FORCE_INLINE __m128 _mm_loadl_pi(__m128 a, __m64 const *p) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vld1_f32((const float32_t *) p), vget_high_f32(a))); ++} ++ ++// Load 4 single-precision (32-bit) floating-point elements from memory into dst ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadr_ps ++FORCE_INLINE __m128 _mm_loadr_ps(const float *p) ++{ ++ float32x4_t v = vrev64q_f32(vld1q_f32(p)); ++ return vreinterpretq_m128_f32(vextq_f32(v, v, 2)); ++} ++ ++// Load 128-bits (composed of 4 packed single-precision (32-bit) floating-point ++// elements) from memory into dst. mem_addr does not need to be aligned on any ++// particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_ps ++FORCE_INLINE __m128 _mm_loadu_ps(const float *p) ++{ ++ // for neon, alignment doesn't matter, so _mm_load_ps and _mm_loadu_ps are ++ // equivalent for neon ++ return vreinterpretq_m128_f32(vld1q_f32(p)); ++} ++ ++// Load unaligned 16-bit integer from memory into the first element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_si16 ++FORCE_INLINE __m128i _mm_loadu_si16(const void *p) ++{ ++ return vreinterpretq_m128i_s16( ++ vsetq_lane_s16(*(const unaligned_int16_t *) p, vdupq_n_s16(0), 0)); ++} ++ ++// Load unaligned 64-bit integer from memory into the first element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_si64 ++FORCE_INLINE __m128i _mm_loadu_si64(const void *p) ++{ ++ return vreinterpretq_m128i_s64( ++ vsetq_lane_s64(*(const unaligned_int64_t *) p, vdupq_n_s64(0), 0)); ++} ++ ++// Allocate size bytes of memory, aligned to the alignment specified in align, ++// and return a pointer to the allocated memory. _mm_free should be used to free ++// memory that is allocated with _mm_malloc. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_malloc ++#if !defined(SSE2NEON_ALLOC_DEFINED) ++FORCE_INLINE void *_mm_malloc(size_t size, size_t align) ++{ ++ void *ptr; ++ if (align == 1) ++ return malloc(size); ++ if (align == 2 || (sizeof(void *) == 8 && align == 4)) ++ align = sizeof(void *); ++ if (!posix_memalign(&ptr, align, size)) ++ return ptr; ++ return NULL; ++} ++#endif ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_maskmove_si64 ++FORCE_INLINE void _mm_maskmove_si64(__m64 a, __m64 mask, char *mem_addr) ++{ ++ int8x8_t shr_mask = vshr_n_s8(vreinterpret_s8_m64(mask), 7); ++ __m128 b = _mm_load_ps((const float *) mem_addr); ++ int8x8_t masked = ++ vbsl_s8(vreinterpret_u8_s8(shr_mask), vreinterpret_s8_m64(a), ++ vreinterpret_s8_u64(vget_low_u64(vreinterpretq_u64_m128(b)))); ++ vst1_s8((int8_t *) mem_addr, masked); ++} ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_maskmovq ++#define _m_maskmovq(a, mask, mem_addr) _mm_maskmove_si64(a, mask, mem_addr) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_pi16 ++FORCE_INLINE __m64 _mm_max_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vmax_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b, ++// and store packed maximum values in dst. dst does not follow the IEEE Standard ++// for Floating-Point Arithmetic (IEEE 754) maximum value when inputs are NaN or ++// signed-zero values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_ps ++FORCE_INLINE __m128 _mm_max_ps(__m128 a, __m128 b) ++{ ++#if SSE2NEON_PRECISE_MINMAX ++ float32x4_t _a = vreinterpretq_f32_m128(a); ++ float32x4_t _b = vreinterpretq_f32_m128(b); ++ return vreinterpretq_m128_f32(vbslq_f32(vcgtq_f32(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128_f32( ++ vmaxq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#endif ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_pu8 ++FORCE_INLINE __m64 _mm_max_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vmax_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b, store the maximum value in the lower element of dst, and copy the upper 3 ++// packed elements from a to the upper element of dst. dst does not follow the ++// IEEE Standard for Floating-Point Arithmetic (IEEE 754) maximum value when ++// inputs are NaN or signed-zero values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_ss ++FORCE_INLINE __m128 _mm_max_ss(__m128 a, __m128 b) ++{ ++ float32_t value = vgetq_lane_f32(_mm_max_ps(a, b), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Compare packed signed 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_pi16 ++FORCE_INLINE __m64 _mm_min_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vmin_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b, ++// and store packed minimum values in dst. dst does not follow the IEEE Standard ++// for Floating-Point Arithmetic (IEEE 754) minimum value when inputs are NaN or ++// signed-zero values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_ps ++FORCE_INLINE __m128 _mm_min_ps(__m128 a, __m128 b) ++{ ++#if SSE2NEON_PRECISE_MINMAX ++ float32x4_t _a = vreinterpretq_f32_m128(a); ++ float32x4_t _b = vreinterpretq_f32_m128(b); ++ return vreinterpretq_m128_f32(vbslq_f32(vcltq_f32(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128_f32( ++ vminq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#endif ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_pu8 ++FORCE_INLINE __m64 _mm_min_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vmin_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b, store the minimum value in the lower element of dst, and copy the upper 3 ++// packed elements from a to the upper element of dst. dst does not follow the ++// IEEE Standard for Floating-Point Arithmetic (IEEE 754) minimum value when ++// inputs are NaN or signed-zero values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_ss ++FORCE_INLINE __m128 _mm_min_ss(__m128 a, __m128 b) ++{ ++ float32_t value = vgetq_lane_f32(_mm_min_ps(a, b), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Move the lower single-precision (32-bit) floating-point element from b to the ++// lower element of dst, and copy the upper 3 packed elements from a to the ++// upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_move_ss ++FORCE_INLINE __m128 _mm_move_ss(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(vgetq_lane_f32(vreinterpretq_f32_m128(b), 0), ++ vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Move the upper 2 single-precision (32-bit) floating-point elements from b to ++// the lower 2 elements of dst, and copy the upper 2 elements from a to the ++// upper 2 elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movehl_ps ++FORCE_INLINE __m128 _mm_movehl_ps(__m128 a, __m128 b) ++{ ++#if defined(aarch64__) ++ return vreinterpretq_m128_u64( ++ vzip2q_u64(vreinterpretq_u64_m128(b), vreinterpretq_u64_m128(a))); ++#else ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(b32, a32)); ++#endif ++} ++ ++// Move the lower 2 single-precision (32-bit) floating-point elements from b to ++// the upper 2 elements of dst, and copy the lower 2 elements from a to the ++// lower 2 elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movelh_ps ++FORCE_INLINE __m128 _mm_movelh_ps(__m128 __A, __m128 __B) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(__A)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(__B)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b10)); ++} ++ ++// Create mask from the most significant bit of each 8-bit element in a, and ++// store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movemask_pi8 ++FORCE_INLINE int _mm_movemask_pi8(__m64 a) ++{ ++ uint8x8_t input = vreinterpret_u8_m64(a); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ static const int8_t shift[8] = {0, 1, 2, 3, 4, 5, 6, 7}; ++ uint8x8_t tmp = vshr_n_u8(input, 7); ++ return vaddv_u8(vshl_u8(tmp, vld1_s8(shift))); ++#else ++ // Refer the implementation of `_mm_movemask_epi8` ++ uint16x4_t high_bits = vreinterpret_u16_u8(vshr_n_u8(input, 7)); ++ uint32x2_t paired16 = ++ vreinterpret_u32_u16(vsra_n_u16(high_bits, high_bits, 7)); ++ uint8x8_t paired32 = ++ vreinterpret_u8_u32(vsra_n_u32(paired16, paired16, 14)); ++ return vget_lane_u8(paired32, 0) | ((int) vget_lane_u8(paired32, 4) << 4); ++#endif ++} ++ ++// Set each bit of mask dst based on the most significant bit of the ++// corresponding packed single-precision (32-bit) floating-point element in a. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movemask_ps ++FORCE_INLINE int _mm_movemask_ps(__m128 a) ++{ ++ uint32x4_t input = vreinterpretq_u32_m128(a); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ static const int32_t shift[4] = {0, 1, 2, 3}; ++ uint32x4_t tmp = vshrq_n_u32(input, 31); ++ return vaddvq_u32(vshlq_u32(tmp, vld1q_s32(shift))); ++#else ++ // Uses the exact same method as _mm_movemask_epi8, see that for details. ++ // Shift out everything but the sign bits with a 32-bit unsigned shift ++ // right. ++ uint64x2_t high_bits = vreinterpretq_u64_u32(vshrq_n_u32(input, 31)); ++ // Merge the two pairs together with a 64-bit unsigned shift right + add. ++ uint8x16_t paired = ++ vreinterpretq_u8_u64(vsraq_n_u64(high_bits, high_bits, 31)); ++ // Extract the result. ++ return vgetq_lane_u8(paired, 0) | (vgetq_lane_u8(paired, 8) << 2); ++#endif ++} ++ ++// Multiply packed single-precision (32-bit) floating-point elements in a and b, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_ps ++FORCE_INLINE_OPTNONE __m128 _mm_mul_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vmulq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Multiply the lower single-precision (32-bit) floating-point element in a and ++// b, store the result in the lower element of dst, and copy the upper 3 packed ++// elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_ss ++FORCE_INLINE __m128 _mm_mul_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_mul_ps(a, b)); ++} ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhi_pu16 ++FORCE_INLINE __m64 _mm_mulhi_pu16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u16(vshrn_n_u32( ++ vmull_u16(vreinterpret_u16_m64(a), vreinterpret_u16_m64(b)), 16)); ++} ++ ++// Compute the bitwise OR of packed single-precision (32-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_or_ps ++FORCE_INLINE __m128 _mm_or_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vorrq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Average packed unsigned 8-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pavgb ++#define _m_pavgb(a, b) _mm_avg_pu8(a, b) ++ ++// Average packed unsigned 16-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pavgw ++#define _m_pavgw(a, b) _mm_avg_pu16(a, b) ++ ++// Extract a 16-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pextrw ++#define _m_pextrw(a, imm) _mm_extract_pi16(a, imm) ++ ++// Copy a to dst, and insert the 16-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=m_pinsrw ++#define _m_pinsrw(a, i, imm) _mm_insert_pi16(a, i, imm) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pmaxsw ++#define _m_pmaxsw(a, b) _mm_max_pi16(a, b) ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pmaxub ++#define _m_pmaxub(a, b) _mm_max_pu8(a, b) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pminsw ++#define _m_pminsw(a, b) _mm_min_pi16(a, b) ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pminub ++#define _m_pminub(a, b) _mm_min_pu8(a, b) ++ ++// Create mask from the most significant bit of each 8-bit element in a, and ++// store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pmovmskb ++#define _m_pmovmskb(a) _mm_movemask_pi8(a) ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pmulhuw ++#define _m_pmulhuw(a, b) _mm_mulhi_pu16(a, b) ++ ++// Fetch the line of data from memory that contains address p to a location in ++// the cache hierarchy specified by the locality hint i. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_prefetch ++FORCE_INLINE void _mm_prefetch(char const *p, int i) ++{ ++ (void) i; ++#if defined(_MSC_VER) ++ switch (i) { ++ case _MM_HINT_NTA: ++ __prefetch2(p, 1); ++ break; ++ case _MM_HINT_T0: ++ __prefetch2(p, 0); ++ break; ++ case _MM_HINT_T1: ++ __prefetch2(p, 2); ++ break; ++ case _MM_HINT_T2: ++ __prefetch2(p, 4); ++ break; ++ } ++#else ++ switch (i) { ++ case _MM_HINT_NTA: ++ __builtin_prefetch(p, 0, 0); ++ break; ++ case _MM_HINT_T0: ++ __builtin_prefetch(p, 0, 3); ++ break; ++ case _MM_HINT_T1: ++ __builtin_prefetch(p, 0, 2); ++ break; ++ case _MM_HINT_T2: ++ __builtin_prefetch(p, 0, 1); ++ break; ++ } ++#endif ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce four ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=m_psadbw ++#define _m_psadbw(a, b) _mm_sad_pu8(a, b) ++ ++// Shuffle 16-bit integers in a using the control in imm8, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pshufw ++#define _m_pshufw(a, imm) _mm_shuffle_pi16(a, imm) ++ ++// Compute the approximate reciprocal of packed single-precision (32-bit) ++// floating-point elements in a, and store the results in dst. The maximum ++// relative error for this approximation is less than 1.5*2^-12. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_rcp_ps ++FORCE_INLINE __m128 _mm_rcp_ps(__m128 in) ++{ ++ float32x4_t recip = vrecpeq_f32(vreinterpretq_f32_m128(in)); ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(in))); ++#if SSE2NEON_PRECISE_DIV ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(in))); ++#endif ++ return vreinterpretq_m128_f32(recip); ++} ++ ++// Compute the approximate reciprocal of the lower single-precision (32-bit) ++// floating-point element in a, store the result in the lower element of dst, ++// and copy the upper 3 packed elements from a to the upper elements of dst. The ++// maximum relative error for this approximation is less than 1.5*2^-12. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_rcp_ss ++FORCE_INLINE __m128 _mm_rcp_ss(__m128 a) ++{ ++ return _mm_move_ss(a, _mm_rcp_ps(a)); ++} ++ ++// Compute the approximate reciprocal square root of packed single-precision ++// (32-bit) floating-point elements in a, and store the results in dst. The ++// maximum relative error for this approximation is less than 1.5*2^-12. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_rsqrt_ps ++FORCE_INLINE __m128 _mm_rsqrt_ps(__m128 in) ++{ ++ float32x4_t out = vrsqrteq_f32(vreinterpretq_f32_m128(in)); ++ ++ // Generate masks for detecting whether input has any 0.0f/-0.0f ++ // (which becomes positive/negative infinity by IEEE-754 arithmetic rules). ++ const uint32x4_t pos_inf = vdupq_n_u32(0x7F800000); ++ const uint32x4_t neg_inf = vdupq_n_u32(0xFF800000); ++ const uint32x4_t has_pos_zero = ++ vceqq_u32(pos_inf, vreinterpretq_u32_f32(out)); ++ const uint32x4_t has_neg_zero = ++ vceqq_u32(neg_inf, vreinterpretq_u32_f32(out)); ++ ++ out = vmulq_f32( ++ out, vrsqrtsq_f32(vmulq_f32(vreinterpretq_f32_m128(in), out), out)); ++#if SSE2NEON_PRECISE_SQRT ++ // Additional Netwon-Raphson iteration for accuracy ++ out = vmulq_f32( ++ out, vrsqrtsq_f32(vmulq_f32(vreinterpretq_f32_m128(in), out), out)); ++#endif ++ ++ // Set output vector element to infinity/negative-infinity if ++ // the corresponding input vector element is 0.0f/-0.0f. ++ out = vbslq_f32(has_pos_zero, (float32x4_t) pos_inf, out); ++ out = vbslq_f32(has_neg_zero, (float32x4_t) neg_inf, out); ++ ++ return vreinterpretq_m128_f32(out); ++} ++ ++// Compute the approximate reciprocal square root of the lower single-precision ++// (32-bit) floating-point element in a, store the result in the lower element ++// of dst, and copy the upper 3 packed elements from a to the upper elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_rsqrt_ss ++FORCE_INLINE __m128 _mm_rsqrt_ss(__m128 in) ++{ ++ return vsetq_lane_f32(vgetq_lane_f32(_mm_rsqrt_ps(in), 0), in, 0); ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce four ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sad_pu8 ++FORCE_INLINE __m64 _mm_sad_pu8(__m64 a, __m64 b) ++{ ++ uint64x1_t t = vpaddl_u32(vpaddl_u16( ++ vpaddl_u8(vabd_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))))); ++ return vreinterpret_m64_u16( ++ vset_lane_u16((int) vget_lane_u64(t, 0), vdup_n_u16(0), 0)); ++} ++ ++// Macro: Set the flush zero bits of the MXCSR control and status register to ++// the value in unsigned 32-bit integer a. The flush zero may contain any of the ++// following flags: _MM_FLUSH_ZERO_ON or _MM_FLUSH_ZERO_OFF ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_MM_SET_FLUSH_ZERO_MODE ++FORCE_INLINE void _sse2neon_mm_set_flush_zero_mode(unsigned int flag) ++{ ++ // AArch32 Advanced SIMD arithmetic always uses the Flush-to-zero setting, ++ // regardless of the value of the FZ bit. ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ r.field.bit24 = (flag & _MM_FLUSH_ZERO_MASK) == _MM_FLUSH_ZERO_ON; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ _sse2neon_set_fpcr(r.value); ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Set packed single-precision (32-bit) floating-point elements in dst with the ++// supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_ps ++FORCE_INLINE __m128 _mm_set_ps(float w, float z, float y, float x) ++{ ++ float ALIGN_STRUCT(16) data[4] = {x, y, z, w}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Broadcast single-precision (32-bit) floating-point value a to all elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_ps1 ++FORCE_INLINE __m128 _mm_set_ps1(float _w) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(_w)); ++} ++ ++// Macro: Set the rounding mode bits of the MXCSR control and status register to ++// the value in unsigned 32-bit integer a. The rounding mode may contain any of ++// the following flags: _MM_ROUND_NEAREST, _MM_ROUND_DOWN, _MM_ROUND_UP, ++// _MM_ROUND_TOWARD_ZERO ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_MM_SET_ROUNDING_MODE ++FORCE_INLINE void _MM_SET_ROUNDING_MODE(int rounding) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ switch (rounding) { ++ case _MM_ROUND_TOWARD_ZERO: ++ r.field.bit22 = 1; ++ r.field.bit23 = 1; ++ break; ++ case _MM_ROUND_DOWN: ++ r.field.bit22 = 0; ++ r.field.bit23 = 1; ++ break; ++ case _MM_ROUND_UP: ++ r.field.bit22 = 1; ++ r.field.bit23 = 0; ++ break; ++ default: //_MM_ROUND_NEAREST ++ r.field.bit22 = 0; ++ r.field.bit23 = 0; ++ } ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ _sse2neon_set_fpcr(r.value); ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Copy single-precision (32-bit) floating-point element a to the lower element ++// of dst, and zero the upper 3 elements. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_ss ++FORCE_INLINE __m128 _mm_set_ss(float a) ++{ ++ return vreinterpretq_m128_f32(vsetq_lane_f32(a, vdupq_n_f32(0), 0)); ++} ++ ++// Broadcast single-precision (32-bit) floating-point value a to all elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_ps ++FORCE_INLINE __m128 _mm_set1_ps(float _w) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(_w)); ++} ++ ++// Set the MXCSR control and status register with the value in unsigned 32-bit ++// integer a. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setcsr ++// FIXME: _mm_setcsr() implementation supports changing the rounding mode only. ++FORCE_INLINE void _mm_setcsr(unsigned int a) ++{ ++ _MM_SET_ROUNDING_MODE(a); ++} ++ ++// Get the unsigned 32-bit value of the MXCSR control and status register. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_getcsr ++// FIXME: _mm_getcsr() implementation supports reading the rounding mode only. ++FORCE_INLINE unsigned int _mm_getcsr(void) ++{ ++ return _MM_GET_ROUNDING_MODE(); ++} ++ ++// Set packed single-precision (32-bit) floating-point elements in dst with the ++// supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_ps ++FORCE_INLINE __m128 _mm_setr_ps(float w, float z, float y, float x) ++{ ++ float ALIGN_STRUCT(16) data[4] = {w, z, y, x}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Return vector of type __m128 with all elements set to zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setzero_ps ++FORCE_INLINE __m128 _mm_setzero_ps(void) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(0)); ++} ++ ++// Shuffle 16-bit integers in a using the control in imm8, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_pi16 ++#ifdef _sse2neon_shuffle ++#define _mm_shuffle_pi16(a, imm) \ ++ vreinterpret_m64_s16(vshuffle_s16( \ ++ vreinterpret_s16_m64(a), vreinterpret_s16_m64(a), (imm & 0x3), \ ++ ((imm >> 2) & 0x3), ((imm >> 4) & 0x3), ((imm >> 6) & 0x3))) ++#else ++#define _mm_shuffle_pi16(a, imm) \ ++ _sse2neon_define1( \ ++ __m64, a, int16x4_t ret; \ ++ ret = vmov_n_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(_a), (imm) & (0x3))); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(_a), ((imm) >> 2) & 0x3), ret, \ ++ 1); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(_a), ((imm) >> 4) & 0x3), ret, \ ++ 2); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(_a), ((imm) >> 6) & 0x3), ret, \ ++ 3); \ ++ _sse2neon_return(vreinterpret_m64_s16(ret));) ++#endif ++ ++// Perform a serializing operation on all store-to-memory instructions that were ++// issued prior to this instruction. Guarantees that every store instruction ++// that precedes, in program order, is globally visible before any store ++// instruction which follows the fence in program order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sfence ++FORCE_INLINE void _mm_sfence(void) ++{ ++ _sse2neon_smp_mb(); ++} ++ ++// Perform a serializing operation on all load-from-memory and store-to-memory ++// instructions that were issued prior to this instruction. Guarantees that ++// every memory access that precedes, in program order, the memory fence ++// instruction is globally visible before any memory instruction which follows ++// the fence in program order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mfence ++FORCE_INLINE void _mm_mfence(void) ++{ ++ _sse2neon_smp_mb(); ++} ++ ++// Perform a serializing operation on all load-from-memory instructions that ++// were issued prior to this instruction. Guarantees that every load instruction ++// that precedes, in program order, is globally visible before any load ++// instruction which follows the fence in program order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_lfence ++FORCE_INLINE void _mm_lfence(void) ++{ ++ _sse2neon_smp_mb(); ++} ++ ++// FORCE_INLINE __m128 _mm_shuffle_ps(__m128 a, __m128 b, __constrange(0,255) ++// int imm) ++#ifdef _sse2neon_shuffle ++#define _mm_shuffle_ps(a, b, imm) \ ++ __extension__({ \ ++ float32x4_t _input1 = vreinterpretq_f32_m128(a); \ ++ float32x4_t _input2 = vreinterpretq_f32_m128(b); \ ++ float32x4_t _shuf = \ ++ vshuffleq_s32(_input1, _input2, (imm) & (0x3), ((imm) >> 2) & 0x3, \ ++ (((imm) >> 4) & 0x3) + 4, (((imm) >> 6) & 0x3) + 4); \ ++ vreinterpretq_m128_f32(_shuf); \ ++ }) ++#else // generic ++#define _mm_shuffle_ps(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m128, a, b, __m128 ret; switch (imm) { \ ++ case _MM_SHUFFLE(1, 0, 3, 2): \ ++ ret = _mm_shuffle_ps_1032(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 3, 0, 1): \ ++ ret = _mm_shuffle_ps_2301(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(0, 3, 2, 1): \ ++ ret = _mm_shuffle_ps_0321(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 1, 0, 3): \ ++ ret = _mm_shuffle_ps_2103(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 1, 0): \ ++ ret = _mm_movelh_ps(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 0, 1): \ ++ ret = _mm_shuffle_ps_1001(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 0, 1): \ ++ ret = _mm_shuffle_ps_0101(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 1, 0): \ ++ ret = _mm_shuffle_ps_3210(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 1, 1): \ ++ ret = _mm_shuffle_ps_0011(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 2, 2): \ ++ ret = _mm_shuffle_ps_0022(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 0, 0): \ ++ ret = _mm_shuffle_ps_2200(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 0, 2): \ ++ ret = _mm_shuffle_ps_3202(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 3, 2): \ ++ ret = _mm_movehl_ps(_b, _a); \ ++ break; \ ++ case _MM_SHUFFLE(1, 1, 3, 3): \ ++ ret = _mm_shuffle_ps_1133(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 1, 0): \ ++ ret = _mm_shuffle_ps_2010(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 0, 1): \ ++ ret = _mm_shuffle_ps_2001(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 3, 2): \ ++ ret = _mm_shuffle_ps_2032(_a, _b); \ ++ break; \ ++ default: \ ++ ret = _mm_shuffle_ps_default(_a, _b, (imm)); \ ++ break; \ ++ } _sse2neon_return(ret);) ++#endif ++ ++// Compute the square root of packed single-precision (32-bit) floating-point ++// elements in a, and store the results in dst. ++// Due to ARMv7-A NEON's lack of a precise square root intrinsic, we implement ++// square root by multiplying input in with its reciprocal square root before ++// using the Newton-Raphson method to approximate the results. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sqrt_ps ++FORCE_INLINE __m128 _mm_sqrt_ps(__m128 in) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) && !SSE2NEON_PRECISE_SQRT ++ return vreinterpretq_m128_f32(vsqrtq_f32(vreinterpretq_f32_m128(in))); ++#else ++ float32x4_t recip = vrsqrteq_f32(vreinterpretq_f32_m128(in)); ++ ++ // Test for vrsqrteq_f32(0) -> positive infinity case. ++ // Change to zero, so that s * 1/sqrt(s) result is zero too. ++ const uint32x4_t pos_inf = vdupq_n_u32(0x7F800000); ++ const uint32x4_t div_by_zero = ++ vceqq_u32(pos_inf, vreinterpretq_u32_f32(recip)); ++ recip = vreinterpretq_f32_u32( ++ vandq_u32(vmvnq_u32(div_by_zero), vreinterpretq_u32_f32(recip))); ++ ++ recip = vmulq_f32( ++ vrsqrtsq_f32(vmulq_f32(recip, recip), vreinterpretq_f32_m128(in)), ++ recip); ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32( ++ vrsqrtsq_f32(vmulq_f32(recip, recip), vreinterpretq_f32_m128(in)), ++ recip); ++ ++ // sqrt(s) = s * 1/sqrt(s) ++ return vreinterpretq_m128_f32(vmulq_f32(vreinterpretq_f32_m128(in), recip)); ++#endif ++} ++ ++// Compute the square root of the lower single-precision (32-bit) floating-point ++// element in a, store the result in the lower element of dst, and copy the ++// upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sqrt_ss ++FORCE_INLINE __m128 _mm_sqrt_ss(__m128 in) ++{ ++ float32_t value = ++ vgetq_lane_f32(vreinterpretq_f32_m128(_mm_sqrt_ps(in)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(in), 0)); ++} ++ ++// Store 128-bits (composed of 4 packed single-precision (32-bit) floating-point ++// elements) from a into memory. mem_addr must be aligned on a 16-byte boundary ++// or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_ps ++FORCE_INLINE void _mm_store_ps(float *p, __m128 a) ++{ ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++} ++ ++// Store the lower single-precision (32-bit) floating-point element from a into ++// 4 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_ps1 ++FORCE_INLINE void _mm_store_ps1(float *p, __m128 a) ++{ ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ vst1q_f32(p, vdupq_n_f32(a0)); ++} ++ ++// Store the lower single-precision (32-bit) floating-point element from a into ++// memory. mem_addr does not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_ss ++FORCE_INLINE void _mm_store_ss(float *p, __m128 a) ++{ ++ vst1q_lane_f32(p, vreinterpretq_f32_m128(a), 0); ++} ++ ++// Store the lower single-precision (32-bit) floating-point element from a into ++// 4 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store1_ps ++#define _mm_store1_ps _mm_store_ps1 ++ ++// Store the upper 2 single-precision (32-bit) floating-point elements from a ++// into memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeh_pi ++FORCE_INLINE void _mm_storeh_pi(__m64 *p, __m128 a) ++{ ++ *p = vreinterpret_m64_f32(vget_high_f32(a)); ++} ++ ++// Store the lower 2 single-precision (32-bit) floating-point elements from a ++// into memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storel_pi ++FORCE_INLINE void _mm_storel_pi(__m64 *p, __m128 a) ++{ ++ *p = vreinterpret_m64_f32(vget_low_f32(a)); ++} ++ ++// Store 4 single-precision (32-bit) floating-point elements from a into memory ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storer_ps ++FORCE_INLINE void _mm_storer_ps(float *p, __m128 a) ++{ ++ float32x4_t tmp = vrev64q_f32(vreinterpretq_f32_m128(a)); ++ float32x4_t rev = vextq_f32(tmp, tmp, 2); ++ vst1q_f32(p, rev); ++} ++ ++// Store 128-bits (composed of 4 packed single-precision (32-bit) floating-point ++// elements) from a into memory. mem_addr does not need to be aligned on any ++// particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_ps ++FORCE_INLINE void _mm_storeu_ps(float *p, __m128 a) ++{ ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++} ++ ++// Stores 16-bits of integer data a at the address p. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_si16 ++FORCE_INLINE void _mm_storeu_si16(void *p, __m128i a) ++{ ++ vst1q_lane_s16((int16_t *) p, vreinterpretq_s16_m128i(a), 0); ++} ++ ++// Stores 64-bits of integer data a at the address p. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_si64 ++FORCE_INLINE void _mm_storeu_si64(void *p, __m128i a) ++{ ++ vst1q_lane_s64((int64_t *) p, vreinterpretq_s64_m128i(a), 0); ++} ++ ++// Store 64-bits of integer data from a into memory using a non-temporal memory ++// hint. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_pi ++FORCE_INLINE void _mm_stream_pi(__m64 *p, __m64 a) ++{ ++ vst1_s64((int64_t *) p, vreinterpret_s64_m64(a)); ++} ++ ++// Store 128-bits (composed of 4 packed single-precision (32-bit) floating- ++// point elements) from a into memory using a non-temporal memory hint. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_ps ++FORCE_INLINE void _mm_stream_ps(float *p, __m128 a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, (float32x4_t *) p); ++#else ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++#endif ++} ++ ++// Subtract packed single-precision (32-bit) floating-point elements in b from ++// packed single-precision (32-bit) floating-point elements in a, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_ps ++FORCE_INLINE __m128 _mm_sub_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vsubq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Subtract the lower single-precision (32-bit) floating-point element in b from ++// the lower single-precision (32-bit) floating-point element in a, store the ++// result in the lower element of dst, and copy the upper 3 packed elements from ++// a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_ss ++FORCE_INLINE __m128 _mm_sub_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_sub_ps(a, b)); ++} ++ ++// Macro: Transpose the 4x4 matrix formed by the 4 rows of single-precision ++// (32-bit) floating-point elements in row0, row1, row2, and row3, and store the ++// transposed matrix in these vectors (row0 now contains column 0, etc.). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=MM_TRANSPOSE4_PS ++#define _MM_TRANSPOSE4_PS(row0, row1, row2, row3) \ ++ do { \ ++ float32x4x2_t ROW01 = vtrnq_f32(row0, row1); \ ++ float32x4x2_t ROW23 = vtrnq_f32(row2, row3); \ ++ row0 = vcombine_f32(vget_low_f32(ROW01.val[0]), \ ++ vget_low_f32(ROW23.val[0])); \ ++ row1 = vcombine_f32(vget_low_f32(ROW01.val[1]), \ ++ vget_low_f32(ROW23.val[1])); \ ++ row2 = vcombine_f32(vget_high_f32(ROW01.val[0]), \ ++ vget_high_f32(ROW23.val[0])); \ ++ row3 = vcombine_f32(vget_high_f32(ROW01.val[1]), \ ++ vget_high_f32(ROW23.val[1])); \ ++ } while (0) ++ ++// according to the documentation, these intrinsics behave the same as the ++// non-'u' versions. We'll just alias them here. ++#define _mm_ucomieq_ss _mm_comieq_ss ++#define _mm_ucomige_ss _mm_comige_ss ++#define _mm_ucomigt_ss _mm_comigt_ss ++#define _mm_ucomile_ss _mm_comile_ss ++#define _mm_ucomilt_ss _mm_comilt_ss ++#define _mm_ucomineq_ss _mm_comineq_ss ++ ++// Return vector of type __m128i with undefined elements. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_undefined_si128 ++FORCE_INLINE __m128i _mm_undefined_si128(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128i a; ++#if defined(_MSC_VER) ++ a = _mm_setzero_si128(); ++#endif ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Return vector of type __m128 with undefined elements. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_undefined_ps ++FORCE_INLINE __m128 _mm_undefined_ps(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128 a; ++#if defined(_MSC_VER) ++ a = _mm_setzero_ps(); ++#endif ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Unpack and interleave single-precision (32-bit) floating-point elements from ++// the high half a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_ps ++FORCE_INLINE __m128 _mm_unpackhi_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vzip2q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a1 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b1 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ float32x2x2_t result = vzip_f32(a1, b1); ++ return vreinterpretq_m128_f32(vcombine_f32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave single-precision (32-bit) floating-point elements from ++// the low half of a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_ps ++FORCE_INLINE __m128 _mm_unpacklo_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vzip1q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a1 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b1 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ float32x2x2_t result = vzip_f32(a1, b1); ++ return vreinterpretq_m128_f32(vcombine_f32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Compute the bitwise XOR of packed single-precision (32-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_xor_ps ++FORCE_INLINE __m128 _mm_xor_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ veorq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++/* SSE2 */ ++ ++// Add packed 16-bit integers in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_epi16 ++FORCE_INLINE __m128i _mm_add_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vaddq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Add packed 32-bit integers in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_epi32 ++FORCE_INLINE __m128i _mm_add_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vaddq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Add packed 64-bit integers in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_epi64 ++FORCE_INLINE __m128i _mm_add_epi64(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s64( ++ vaddq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++} ++ ++// Add packed 8-bit integers in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_epi8 ++FORCE_INLINE __m128i _mm_add_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vaddq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Add packed double-precision (64-bit) floating-point elements in a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_pd ++FORCE_INLINE __m128d _mm_add_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vaddq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] + db[0]; ++ c[1] = da[1] + db[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Add the lower double-precision (64-bit) floating-point element in a and b, ++// store the result in the lower element of dst, and copy the upper element from ++// a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_sd ++FORCE_INLINE __m128d _mm_add_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_add_pd(a, b)); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] + db[0]; ++ c[1] = da[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Add 64-bit integers a and b, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_si64 ++FORCE_INLINE __m64 _mm_add_si64(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s64( ++ vadd_s64(vreinterpret_s64_m64(a), vreinterpret_s64_m64(b))); ++} ++ ++// Add packed signed 16-bit integers in a and b using saturation, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_adds_epi16 ++FORCE_INLINE __m128i _mm_adds_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vqaddq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Add packed signed 8-bit integers in a and b using saturation, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_adds_epi8 ++FORCE_INLINE __m128i _mm_adds_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vqaddq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Add packed unsigned 16-bit integers in a and b using saturation, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_adds_epu16 ++FORCE_INLINE __m128i _mm_adds_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vqaddq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Add packed unsigned 8-bit integers in a and b using saturation, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_adds_epu8 ++FORCE_INLINE __m128i _mm_adds_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vqaddq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compute the bitwise AND of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_and_pd ++FORCE_INLINE __m128d _mm_and_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ vandq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_and_si128 ++FORCE_INLINE __m128i _mm_and_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vandq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compute the bitwise NOT of packed double-precision (64-bit) floating-point ++// elements in a and then AND with b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_andnot_pd ++FORCE_INLINE __m128d _mm_andnot_pd(__m128d a, __m128d b) ++{ ++ // *NOTE* argument swap ++ return vreinterpretq_m128d_s64( ++ vbicq_s64(vreinterpretq_s64_m128d(b), vreinterpretq_s64_m128d(a))); ++} ++ ++// Compute the bitwise NOT of 128 bits (representing integer data) in a and then ++// AND with b, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_andnot_si128 ++FORCE_INLINE __m128i _mm_andnot_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vbicq_s32(vreinterpretq_s32_m128i(b), ++ vreinterpretq_s32_m128i(a))); // *NOTE* argument swap ++} ++ ++// Average packed unsigned 16-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_avg_epu16 ++FORCE_INLINE __m128i _mm_avg_epu16(__m128i a, __m128i b) ++{ ++ return (__m128i) vrhaddq_u16(vreinterpretq_u16_m128i(a), ++ vreinterpretq_u16_m128i(b)); ++} ++ ++// Average packed unsigned 8-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_avg_epu8 ++FORCE_INLINE __m128i _mm_avg_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vrhaddq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Shift a left by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_bslli_si128 ++#define _mm_bslli_si128(a, imm) _mm_slli_si128(a, imm) ++ ++// Shift a right by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_bsrli_si128 ++#define _mm_bsrli_si128(a, imm) _mm_srli_si128(a, imm) ++ ++// Cast vector of type __m128d to type __m128. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castpd_ps ++FORCE_INLINE __m128 _mm_castpd_ps(__m128d a) ++{ ++ return vreinterpretq_m128_s64(vreinterpretq_s64_m128d(a)); ++} ++ ++// Cast vector of type __m128d to type __m128i. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castpd_si128 ++FORCE_INLINE __m128i _mm_castpd_si128(__m128d a) ++{ ++ return vreinterpretq_m128i_s64(vreinterpretq_s64_m128d(a)); ++} ++ ++// Cast vector of type __m128 to type __m128d. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castps_pd ++FORCE_INLINE __m128d _mm_castps_pd(__m128 a) ++{ ++ return vreinterpretq_m128d_s32(vreinterpretq_s32_m128(a)); ++} ++ ++// Cast vector of type __m128 to type __m128i. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castps_si128 ++FORCE_INLINE __m128i _mm_castps_si128(__m128 a) ++{ ++ return vreinterpretq_m128i_s32(vreinterpretq_s32_m128(a)); ++} ++ ++// Cast vector of type __m128i to type __m128d. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castsi128_pd ++FORCE_INLINE __m128d _mm_castsi128_pd(__m128i a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vreinterpretq_f64_m128i(a)); ++#else ++ return vreinterpretq_m128d_f32(vreinterpretq_f32_m128i(a)); ++#endif ++} ++ ++// Cast vector of type __m128i to type __m128. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castsi128_ps ++FORCE_INLINE __m128 _mm_castsi128_ps(__m128i a) ++{ ++ return vreinterpretq_m128_s32(vreinterpretq_s32_m128i(a)); ++} ++ ++// Invalidate and flush the cache line that contains p from all levels of the ++// cache hierarchy. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_clflush ++#if defined(__APPLE__) ++#include ++#endif ++FORCE_INLINE void _mm_clflush(void const *p) ++{ ++ (void) p; ++ ++ /* sys_icache_invalidate is supported since macOS 10.5. ++ * However, it does not work on non-jailbroken iOS devices, although the ++ * compilation is successful. ++ */ ++#if defined(__APPLE__) ++ sys_icache_invalidate((void *) (uintptr_t) p, SSE2NEON_CACHELINE_SIZE); ++#elif defined(__GNUC__) || defined(__clang__) ++ uintptr_t ptr = (uintptr_t) p; ++ __builtin___clear_cache((char *) ptr, ++ (char *) ptr + SSE2NEON_CACHELINE_SIZE); ++#elif (_MSC_VER) && SSE2NEON_INCLUDE_WINDOWS_H ++ FlushInstructionCache(GetCurrentProcess(), p, SSE2NEON_CACHELINE_SIZE); ++#endif ++} ++ ++// Compare packed 16-bit integers in a and b for equality, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_epi16 ++FORCE_INLINE __m128i _mm_cmpeq_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vceqq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed 32-bit integers in a and b for equality, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_epi32 ++FORCE_INLINE __m128i _mm_cmpeq_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vceqq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed 8-bit integers in a and b for equality, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_epi8 ++FORCE_INLINE __m128i _mm_cmpeq_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vceqq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for equality, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_pd ++FORCE_INLINE __m128d _mm_cmpeq_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128d_u32(vandq_u32(cmp, swapped)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for equality, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_sd ++FORCE_INLINE __m128d _mm_cmpeq_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpeq_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for greater-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpge_pd ++FORCE_INLINE __m128d _mm_cmpge_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vcgeq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) >= (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (*(double *) &a1) >= (*(double *) &b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for greater-than-or-equal, store the result in the lower element of dst, ++// and copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpge_sd ++FORCE_INLINE __m128d _mm_cmpge_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmpge_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) >= (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed signed 16-bit integers in a and b for greater-than, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_epi16 ++FORCE_INLINE __m128i _mm_cmpgt_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcgtq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed signed 32-bit integers in a and b for greater-than, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_epi32 ++FORCE_INLINE __m128i _mm_cmpgt_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vcgtq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b for greater-than, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_epi8 ++FORCE_INLINE __m128i _mm_cmpgt_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcgtq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for greater-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_pd ++FORCE_INLINE __m128d _mm_cmpgt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vcgtq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) > (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (*(double *) &a1) > (*(double *) &b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for greater-than, store the result in the lower element of dst, and copy ++// the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_sd ++FORCE_INLINE __m128d _mm_cmpgt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmpgt_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) > (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for less-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmple_pd ++FORCE_INLINE __m128d _mm_cmple_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vcleq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) <= (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (*(double *) &a1) <= (*(double *) &b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for less-than-or-equal, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmple_sd ++FORCE_INLINE __m128d _mm_cmple_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmple_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) <= (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed signed 16-bit integers in a and b for less-than, and store the ++// results in dst. Note: This intrinsic emits the pcmpgtw instruction with the ++// order of the operands switched. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_epi16 ++FORCE_INLINE __m128i _mm_cmplt_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcltq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed signed 32-bit integers in a and b for less-than, and store the ++// results in dst. Note: This intrinsic emits the pcmpgtd instruction with the ++// order of the operands switched. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_epi32 ++FORCE_INLINE __m128i _mm_cmplt_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vcltq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b for less-than, and store the ++// results in dst. Note: This intrinsic emits the pcmpgtb instruction with the ++// order of the operands switched. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_epi8 ++FORCE_INLINE __m128i _mm_cmplt_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcltq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for less-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_pd ++FORCE_INLINE __m128d _mm_cmplt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vcltq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) < (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (*(double *) &a1) < (*(double *) &b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for less-than, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_sd ++FORCE_INLINE __m128d _mm_cmplt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmplt_pd(a, b)); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) < (*(double *) &b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpneq_pd ++FORCE_INLINE __m128d _mm_cmpneq_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_s32(vmvnq_s32(vreinterpretq_s32_u64( ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))))); ++#else ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128d_u32(vmvnq_u32(vandq_u32(cmp, swapped))); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-equal, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpneq_sd ++FORCE_INLINE __m128d _mm_cmpneq_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpneq_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-greater-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnge_pd ++FORCE_INLINE __m128d _mm_cmpnge_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcgeq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ++ !((*(double *) &a0) >= (*(double *) &b0)) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = ++ !((*(double *) &a1) >= (*(double *) &b1)) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-greater-than-or-equal, store the result in the lower element of ++// dst, and copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnge_sd ++FORCE_INLINE __m128d _mm_cmpnge_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnge_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-greater-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_cmpngt_pd ++FORCE_INLINE __m128d _mm_cmpngt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcgtq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ++ !((*(double *) &a0) > (*(double *) &b0)) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = ++ !((*(double *) &a1) > (*(double *) &b1)) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-greater-than, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpngt_sd ++FORCE_INLINE __m128d _mm_cmpngt_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpngt_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-less-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnle_pd ++FORCE_INLINE __m128d _mm_cmpnle_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcleq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ++ !((*(double *) &a0) <= (*(double *) &b0)) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = ++ !((*(double *) &a1) <= (*(double *) &b1)) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-less-than-or-equal, store the result in the lower element of dst, ++// and copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnle_sd ++FORCE_INLINE __m128d _mm_cmpnle_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnle_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-less-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnlt_pd ++FORCE_INLINE __m128d _mm_cmpnlt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcltq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ++ !((*(double *) &a0) < (*(double *) &b0)) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = ++ !((*(double *) &a1) < (*(double *) &b1)) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-less-than, store the result in the lower element of dst, and copy ++// the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnlt_sd ++FORCE_INLINE __m128d _mm_cmpnlt_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnlt_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// to see if neither is NaN, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpord_pd ++FORCE_INLINE __m128d _mm_cmpord_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ // Excluding NaNs, any two floating point numbers can be compared. ++ uint64x2_t not_nan_a = ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(a)); ++ uint64x2_t not_nan_b = ++ vceqq_f64(vreinterpretq_f64_m128d(b), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_u64(vandq_u64(not_nan_a, not_nan_b)); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ((*(double *) &a0) == (*(double *) &a0) && ++ (*(double *) &b0) == (*(double *) &b0)) ++ ? ~UINT64_C(0) ++ : UINT64_C(0); ++ d[1] = ((*(double *) &a1) == (*(double *) &a1) && ++ (*(double *) &b1) == (*(double *) &b1)) ++ ? ~UINT64_C(0) ++ : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b to see if neither is NaN, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpord_sd ++FORCE_INLINE __m128d _mm_cmpord_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmpord_pd(a, b)); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t d[2]; ++ d[0] = ((*(double *) &a0) == (*(double *) &a0) && ++ (*(double *) &b0) == (*(double *) &b0)) ++ ? ~UINT64_C(0) ++ : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// to see if either is NaN, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpunord_pd ++FORCE_INLINE __m128d _mm_cmpunord_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ // Two NaNs are not equal in comparison operation. ++ uint64x2_t not_nan_a = ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(a)); ++ uint64x2_t not_nan_b = ++ vceqq_f64(vreinterpretq_f64_m128d(b), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_s32( ++ vmvnq_s32(vreinterpretq_s32_u64(vandq_u64(not_nan_a, not_nan_b)))); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = ((*(double *) &a0) == (*(double *) &a0) && ++ (*(double *) &b0) == (*(double *) &b0)) ++ ? UINT64_C(0) ++ : ~UINT64_C(0); ++ d[1] = ((*(double *) &a1) == (*(double *) &a1) && ++ (*(double *) &b1) == (*(double *) &b1)) ++ ? UINT64_C(0) ++ : ~UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b to see if either is NaN, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpunord_sd ++FORCE_INLINE __m128d _mm_cmpunord_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmpunord_pd(a, b)); ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t d[2]; ++ d[0] = ((*(double *) &a0) == (*(double *) &a0) && ++ (*(double *) &b0) == (*(double *) &b0)) ++ ? UINT64_C(0) ++ : ~UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for greater-than-or-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comige_sd ++FORCE_INLINE int _mm_comige_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vcgeq_f64(a, b), 0) & 0x1; ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ ++ return (*(double *) &a0 >= *(double *) &b0); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for greater-than, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comigt_sd ++FORCE_INLINE int _mm_comigt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vcgtq_f64(a, b), 0) & 0x1; ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ ++ return (*(double *) &a0 > *(double *) &b0); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for less-than-or-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comile_sd ++FORCE_INLINE int _mm_comile_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vcleq_f64(a, b), 0) & 0x1; ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ ++ return (*(double *) &a0 <= *(double *) &b0); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for less-than, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comilt_sd ++FORCE_INLINE int _mm_comilt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vcltq_f64(a, b), 0) & 0x1; ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ ++ return (*(double *) &a0 < *(double *) &b0); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for equality, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comieq_sd ++FORCE_INLINE int _mm_comieq_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vceqq_f64(a, b), 0) & 0x1; ++#else ++ uint32x4_t a_not_nan = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(a)); ++ uint32x4_t b_not_nan = ++ vceqq_u32(vreinterpretq_u32_m128d(b), vreinterpretq_u32_m128d(b)); ++ uint32x4_t a_and_b_not_nan = vandq_u32(a_not_nan, b_not_nan); ++ uint32x4_t a_eq_b = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint64x2_t and_results = vandq_u64(vreinterpretq_u64_u32(a_and_b_not_nan), ++ vreinterpretq_u64_u32(a_eq_b)); ++ return vgetq_lane_u64(and_results, 0) & 0x1; ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for not-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comineq_sd ++FORCE_INLINE int _mm_comineq_sd(__m128d a, __m128d b) ++{ ++ return !_mm_comieq_sd(a, b); ++} ++ ++// Convert packed signed 32-bit integers in a to packed double-precision ++// (64-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi32_pd ++FORCE_INLINE __m128d _mm_cvtepi32_pd(__m128i a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcvtq_f64_s64(vmovl_s32(vget_low_s32(vreinterpretq_s32_m128i(a))))); ++#else ++ double a0 = (double) vgetq_lane_s32(vreinterpretq_s32_m128i(a), 0); ++ double a1 = (double) vgetq_lane_s32(vreinterpretq_s32_m128i(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Convert packed signed 32-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi32_ps ++FORCE_INLINE __m128 _mm_cvtepi32_ps(__m128i a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32(vreinterpretq_s32_m128i(a))); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpd_epi32 ++FORCE_INLINE_OPTNONE __m128i _mm_cvtpd_epi32(__m128d a) ++{ ++// vrnd32xq_f64 not supported on clang ++#if defined(__ARM_FEATURE_FRINT) && !defined(__clang__) ++ float64x2_t rounded = vrnd32xq_f64(vreinterpretq_f64_m128d(a)); ++ int64x2_t integers = vcvtq_s64_f64(rounded); ++ return vreinterpretq_m128i_s32( ++ vcombine_s32(vmovn_s64(integers), vdup_n_s32(0))); ++#else ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double d0 = ((double *) &rnd)[0]; ++ double d1 = ((double *) &rnd)[1]; ++ return _mm_set_epi32(0, 0, (int32_t) d1, (int32_t) d0); ++#endif ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpd_pi32 ++FORCE_INLINE_OPTNONE __m64 _mm_cvtpd_pi32(__m128d a) ++{ ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double d0 = ((double *) &rnd)[0]; ++ double d1 = ((double *) &rnd)[1]; ++ int32_t ALIGN_STRUCT(16) data[2] = {(int32_t) d0, (int32_t) d1}; ++ return vreinterpret_m64_s32(vld1_s32(data)); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed single-precision (32-bit) floating-point elements, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpd_ps ++FORCE_INLINE __m128 _mm_cvtpd_ps(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float32x2_t tmp = vcvt_f32_f64(vreinterpretq_f64_m128d(a)); ++ return vreinterpretq_m128_f32(vcombine_f32(tmp, vdup_n_f32(0))); ++#else ++ float a0 = (float) ((double *) &a)[0]; ++ float a1 = (float) ((double *) &a)[1]; ++ return _mm_set_ps(0, 0, a1, a0); ++#endif ++} ++ ++// Convert packed signed 32-bit integers in a to packed double-precision ++// (64-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi32_pd ++FORCE_INLINE __m128d _mm_cvtpi32_pd(__m64 a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcvtq_f64_s64(vmovl_s32(vreinterpret_s32_m64(a)))); ++#else ++ double a0 = (double) vget_lane_s32(vreinterpret_s32_m64(a), 0); ++ double a1 = (double) vget_lane_s32(vreinterpret_s32_m64(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_epi32 ++// *NOTE*. The default rounding mode on SSE is 'round to even', which ARMv7-A ++// does not support! It is supported on ARMv8-A however. ++FORCE_INLINE __m128i _mm_cvtps_epi32(__m128 a) ++{ ++#if defined(__ARM_FEATURE_FRINT) ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(vrnd32xq_f32(a))); ++#elif (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ switch (_MM_GET_ROUNDING_MODE()) { ++ case _MM_ROUND_NEAREST: ++ return vreinterpretq_m128i_s32(vcvtnq_s32_f32(a)); ++ case _MM_ROUND_DOWN: ++ return vreinterpretq_m128i_s32(vcvtmq_s32_f32(a)); ++ case _MM_ROUND_UP: ++ return vreinterpretq_m128i_s32(vcvtpq_s32_f32(a)); ++ default: // _MM_ROUND_TOWARD_ZERO ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(a)); ++ } ++#else ++ float *f = (float *) &a; ++ switch (_MM_GET_ROUNDING_MODE()) { ++ case _MM_ROUND_NEAREST: { ++ uint32x4_t signmask = vdupq_n_u32(0x80000000); ++ float32x4_t half = vbslq_f32(signmask, vreinterpretq_f32_m128(a), ++ vdupq_n_f32(0.5f)); /* +/- 0.5 */ ++ int32x4_t r_normal = vcvtq_s32_f32(vaddq_f32( ++ vreinterpretq_f32_m128(a), half)); /* round to integer: [a + 0.5]*/ ++ int32x4_t r_trunc = vcvtq_s32_f32( ++ vreinterpretq_f32_m128(a)); /* truncate to integer: [a] */ ++ int32x4_t plusone = vreinterpretq_s32_u32(vshrq_n_u32( ++ vreinterpretq_u32_s32(vnegq_s32(r_trunc)), 31)); /* 1 or 0 */ ++ int32x4_t r_even = vbicq_s32(vaddq_s32(r_trunc, plusone), ++ vdupq_n_s32(1)); /* ([a] + {0,1}) & ~1 */ ++ float32x4_t delta = vsubq_f32( ++ vreinterpretq_f32_m128(a), ++ vcvtq_f32_s32(r_trunc)); /* compute delta: delta = (a - [a]) */ ++ uint32x4_t is_delta_half = ++ vceqq_f32(delta, half); /* delta == +/- 0.5 */ ++ return vreinterpretq_m128i_s32( ++ vbslq_s32(is_delta_half, r_even, r_normal)); ++ } ++ case _MM_ROUND_DOWN: ++ return _mm_set_epi32(floorf(f[3]), floorf(f[2]), floorf(f[1]), ++ floorf(f[0])); ++ case _MM_ROUND_UP: ++ return _mm_set_epi32(ceilf(f[3]), ceilf(f[2]), ceilf(f[1]), ++ ceilf(f[0])); ++ default: // _MM_ROUND_TOWARD_ZERO ++ return _mm_set_epi32((int32_t) f[3], (int32_t) f[2], (int32_t) f[1], ++ (int32_t) f[0]); ++ } ++#endif ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed double-precision (64-bit) floating-point elements, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_pd ++FORCE_INLINE __m128d _mm_cvtps_pd(__m128 a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcvt_f64_f32(vget_low_f32(vreinterpretq_f32_m128(a)))); ++#else ++ double a0 = (double) vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ double a1 = (double) vgetq_lane_f32(vreinterpretq_f32_m128(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Copy the lower double-precision (64-bit) floating-point element of a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_f64 ++FORCE_INLINE double _mm_cvtsd_f64(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return (double) vgetq_lane_f64(vreinterpretq_f64_m128d(a), 0); ++#else ++ return ((double *) &a)[0]; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_si32 ++FORCE_INLINE int32_t _mm_cvtsd_si32(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return (int32_t) vgetq_lane_f64(vrndiq_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double ret = ((double *) &rnd)[0]; ++ return (int32_t) ret; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_si64 ++FORCE_INLINE int64_t _mm_cvtsd_si64(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return (int64_t) vgetq_lane_f64(vrndiq_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double ret = ((double *) &rnd)[0]; ++ return (int64_t) ret; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_si64x ++#define _mm_cvtsd_si64x _mm_cvtsd_si64 ++ ++// Convert the lower double-precision (64-bit) floating-point element in b to a ++// single-precision (32-bit) floating-point element, store the result in the ++// lower element of dst, and copy the upper 3 packed elements from a to the ++// upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_ss ++FORCE_INLINE __m128 _mm_cvtsd_ss(__m128 a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32(vsetq_lane_f32( ++ vget_lane_f32(vcvt_f32_f64(vreinterpretq_f64_m128d(b)), 0), ++ vreinterpretq_f32_m128(a), 0)); ++#else ++ return vreinterpretq_m128_f32(vsetq_lane_f32((float) ((double *) &b)[0], ++ vreinterpretq_f32_m128(a), 0)); ++#endif ++} ++ ++// Copy the lower 32-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi128_si32 ++FORCE_INLINE int _mm_cvtsi128_si32(__m128i a) ++{ ++ return vgetq_lane_s32(vreinterpretq_s32_m128i(a), 0); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi128_si64 ++FORCE_INLINE int64_t _mm_cvtsi128_si64(__m128i a) ++{ ++ return vgetq_lane_s64(vreinterpretq_s64_m128i(a), 0); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi128_si64x ++#define _mm_cvtsi128_si64x(a) _mm_cvtsi128_si64(a) ++ ++// Convert the signed 32-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi32_sd ++FORCE_INLINE __m128d _mm_cvtsi32_sd(__m128d a, int32_t b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64((double) b, vreinterpretq_f64_m128d(a), 0)); ++#else ++ double bf = (double) b; ++ return vreinterpretq_m128d_s64( ++ vsetq_lane_s64(*(int64_t *) &bf, vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi128_si64x ++#define _mm_cvtsi128_si64x(a) _mm_cvtsi128_si64(a) ++ ++// Copy 32-bit integer a to the lower elements of dst, and zero the upper ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi32_si128 ++FORCE_INLINE __m128i _mm_cvtsi32_si128(int a) ++{ ++ return vreinterpretq_m128i_s32(vsetq_lane_s32(a, vdupq_n_s32(0), 0)); ++} ++ ++// Convert the signed 64-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64_sd ++FORCE_INLINE __m128d _mm_cvtsi64_sd(__m128d a, int64_t b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64((double) b, vreinterpretq_f64_m128d(a), 0)); ++#else ++ double bf = (double) b; ++ return vreinterpretq_m128d_s64( ++ vsetq_lane_s64(*(int64_t *) &bf, vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Copy 64-bit integer a to the lower element of dst, and zero the upper ++// element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64_si128 ++FORCE_INLINE __m128i _mm_cvtsi64_si128(int64_t a) ++{ ++ return vreinterpretq_m128i_s64(vsetq_lane_s64(a, vdupq_n_s64(0), 0)); ++} ++ ++// Copy 64-bit integer a to the lower element of dst, and zero the upper ++// element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64x_si128 ++#define _mm_cvtsi64x_si128(a) _mm_cvtsi64_si128(a) ++ ++// Convert the signed 64-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64x_sd ++#define _mm_cvtsi64x_sd(a, b) _mm_cvtsi64_sd(a, b) ++ ++// Convert the lower single-precision (32-bit) floating-point element in b to a ++// double-precision (64-bit) floating-point element, store the result in the ++// lower element of dst, and copy the upper element from a to the upper element ++// of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtss_sd ++FORCE_INLINE __m128d _mm_cvtss_sd(__m128d a, __m128 b) ++{ ++ double d = (double) vgetq_lane_f32(vreinterpretq_f32_m128(b), 0); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64(d, vreinterpretq_f64_m128d(a), 0)); ++#else ++ return vreinterpretq_m128d_s64( ++ vsetq_lane_s64(*(int64_t *) &d, vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttpd_epi32 ++FORCE_INLINE __m128i _mm_cvttpd_epi32(__m128d a) ++{ ++ double a0 = ((double *) &a)[0]; ++ double a1 = ((double *) &a)[1]; ++ return _mm_set_epi32(0, 0, (int32_t) a1, (int32_t) a0); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttpd_pi32 ++FORCE_INLINE __m64 _mm_cvttpd_pi32(__m128d a) ++{ ++ double a0 = ((double *) &a)[0]; ++ double a1 = ((double *) &a)[1]; ++ int32_t ALIGN_STRUCT(16) data[2] = {(int32_t) a0, (int32_t) a1}; ++ return vreinterpret_m64_s32(vld1_s32(data)); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttps_epi32 ++FORCE_INLINE __m128i _mm_cvttps_epi32(__m128 a) ++{ ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a))); ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttsd_si32 ++FORCE_INLINE int32_t _mm_cvttsd_si32(__m128d a) ++{ ++ double ret = *((double *) &a); ++ return (int32_t) ret; ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttsd_si64 ++FORCE_INLINE int64_t _mm_cvttsd_si64(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_s64(vcvtq_s64_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ double ret = *((double *) &a); ++ return (int64_t) ret; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttsd_si64x ++#define _mm_cvttsd_si64x(a) _mm_cvttsd_si64(a) ++ ++// Divide packed double-precision (64-bit) floating-point elements in a by ++// packed elements in b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_div_pd ++FORCE_INLINE __m128d _mm_div_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vdivq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] / db[0]; ++ c[1] = da[1] / db[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Divide the lower double-precision (64-bit) floating-point element in a by the ++// lower double-precision (64-bit) floating-point element in b, store the result ++// in the lower element of dst, and copy the upper element from a to the upper ++// element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_div_sd ++FORCE_INLINE __m128d _mm_div_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x2_t tmp = ++ vdivq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64(vgetq_lane_f64(vreinterpretq_f64_m128d(a), 1), tmp, 1)); ++#else ++ return _mm_move_sd(a, _mm_div_pd(a, b)); ++#endif ++} ++ ++// Extract a 16-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi16 ++// FORCE_INLINE int _mm_extract_epi16(__m128i a, __constrange(0,8) int imm) ++#define _mm_extract_epi16(a, imm) \ ++ vgetq_lane_u16(vreinterpretq_u16_m128i(a), (imm)) ++ ++// Copy a to dst, and insert the 16-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_epi16 ++// FORCE_INLINE __m128i _mm_insert_epi16(__m128i a, int b, ++// __constrange(0,8) int imm) ++#define _mm_insert_epi16(a, b, imm) \ ++ vreinterpretq_m128i_s16( \ ++ vsetq_lane_s16((b), vreinterpretq_s16_m128i(a), (imm))) ++ ++// Load 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from memory into dst. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_pd ++FORCE_INLINE __m128d _mm_load_pd(const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vld1q_f64(p)); ++#else ++ const float *fp = (const float *) p; ++ float ALIGN_STRUCT(16) data[4] = {fp[0], fp[1], fp[2], fp[3]}; ++ return vreinterpretq_m128d_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_pd1 ++#define _mm_load_pd1 _mm_load1_pd ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// lower of dst, and zero the upper element. mem_addr does not need to be ++// aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_sd ++FORCE_INLINE __m128d _mm_load_sd(const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vsetq_lane_f64(*p, vdupq_n_f64(0), 0)); ++#else ++ const float *fp = (const float *) p; ++ float ALIGN_STRUCT(16) data[4] = {fp[0], fp[1], 0, 0}; ++ return vreinterpretq_m128d_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Load 128-bits of integer data from memory into dst. mem_addr must be aligned ++// on a 16-byte boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_si128 ++FORCE_INLINE __m128i _mm_load_si128(const __m128i *p) ++{ ++ return vreinterpretq_m128i_s32(vld1q_s32((const int32_t *) p)); ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load1_pd ++FORCE_INLINE __m128d _mm_load1_pd(const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vld1q_dup_f64(p)); ++#else ++ return vreinterpretq_m128d_s64(vdupq_n_s64(*(const int64_t *) p)); ++#endif ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// upper element of dst, and copy the lower element from a to dst. mem_addr does ++// not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadh_pd ++FORCE_INLINE __m128d _mm_loadh_pd(__m128d a, const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcombine_f64(vget_low_f64(vreinterpretq_f64_m128d(a)), vld1_f64(p))); ++#else ++ return vreinterpretq_m128d_f32(vcombine_f32( ++ vget_low_f32(vreinterpretq_f32_m128d(a)), vld1_f32((const float *) p))); ++#endif ++} ++ ++// Load 64-bit integer from memory into the first element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadl_epi64 ++FORCE_INLINE __m128i _mm_loadl_epi64(__m128i const *p) ++{ ++ /* Load the lower 64 bits of the value pointed to by p into the ++ * lower 64 bits of the result, zeroing the upper 64 bits of the result. ++ */ ++ return vreinterpretq_m128i_s32( ++ vcombine_s32(vld1_s32((int32_t const *) p), vcreate_s32(0))); ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// lower element of dst, and copy the upper element from a to dst. mem_addr does ++// not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadl_pd ++FORCE_INLINE __m128d _mm_loadl_pd(__m128d a, const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcombine_f64(vld1_f64(p), vget_high_f64(vreinterpretq_f64_m128d(a)))); ++#else ++ return vreinterpretq_m128d_f32( ++ vcombine_f32(vld1_f32((const float *) p), ++ vget_high_f32(vreinterpretq_f32_m128d(a)))); ++#endif ++} ++ ++// Load 2 double-precision (64-bit) floating-point elements from memory into dst ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadr_pd ++FORCE_INLINE __m128d _mm_loadr_pd(const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x2_t v = vld1q_f64(p); ++ return vreinterpretq_m128d_f64(vextq_f64(v, v, 1)); ++#else ++ int64x2_t v = vld1q_s64((const int64_t *) p); ++ return vreinterpretq_m128d_s64(vextq_s64(v, v, 1)); ++#endif ++} ++ ++// Loads two double-precision from unaligned memory, floating-point values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_pd ++FORCE_INLINE __m128d _mm_loadu_pd(const double *p) ++{ ++ return _mm_load_pd(p); ++} ++ ++// Load 128-bits of integer data from memory into dst. mem_addr does not need to ++// be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_si128 ++FORCE_INLINE __m128i _mm_loadu_si128(const __m128i *p) ++{ ++ return vreinterpretq_m128i_s32(vld1q_s32((const unaligned_int32_t *) p)); ++} ++ ++// Load unaligned 32-bit integer from memory into the first element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_si32 ++FORCE_INLINE __m128i _mm_loadu_si32(const void *p) ++{ ++ return vreinterpretq_m128i_s32( ++ vsetq_lane_s32(*(const unaligned_int32_t *) p, vdupq_n_s32(0), 0)); ++} ++ ++// Multiply packed signed 16-bit integers in a and b, producing intermediate ++// signed 32-bit integers. Horizontally add adjacent pairs of intermediate ++// 32-bit integers, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_madd_epi16 ++FORCE_INLINE __m128i _mm_madd_epi16(__m128i a, __m128i b) ++{ ++ int32x4_t low = vmull_s16(vget_low_s16(vreinterpretq_s16_m128i(a)), ++ vget_low_s16(vreinterpretq_s16_m128i(b))); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int32x4_t high = ++ vmull_high_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b)); ++ ++ return vreinterpretq_m128i_s32(vpaddq_s32(low, high)); ++#else ++ int32x4_t high = vmull_s16(vget_high_s16(vreinterpretq_s16_m128i(a)), ++ vget_high_s16(vreinterpretq_s16_m128i(b))); ++ ++ int32x2_t low_sum = vpadd_s32(vget_low_s32(low), vget_high_s32(low)); ++ int32x2_t high_sum = vpadd_s32(vget_low_s32(high), vget_high_s32(high)); ++ ++ return vreinterpretq_m128i_s32(vcombine_s32(low_sum, high_sum)); ++#endif ++} ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. mem_addr does not need to be aligned ++// on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_maskmoveu_si128 ++FORCE_INLINE void _mm_maskmoveu_si128(__m128i a, __m128i mask, char *mem_addr) ++{ ++ int8x16_t shr_mask = vshrq_n_s8(vreinterpretq_s8_m128i(mask), 7); ++ __m128 b = _mm_load_ps((const float *) mem_addr); ++ int8x16_t masked = ++ vbslq_s8(vreinterpretq_u8_s8(shr_mask), vreinterpretq_s8_m128i(a), ++ vreinterpretq_s8_m128(b)); ++ vst1q_s8((int8_t *) mem_addr, masked); ++} ++ ++// Compare packed signed 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epi16 ++FORCE_INLINE __m128i _mm_max_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vmaxq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epu8 ++FORCE_INLINE __m128i _mm_max_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vmaxq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b, ++// and store packed maximum values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_pd ++FORCE_INLINE __m128d _mm_max_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#if SSE2NEON_PRECISE_MINMAX ++ float64x2_t _a = vreinterpretq_f64_m128d(a); ++ float64x2_t _b = vreinterpretq_f64_m128d(b); ++ return vreinterpretq_m128d_f64(vbslq_f64(vcgtq_f64(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128d_f64( ++ vmaxq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#endif ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) > (*(double *) &b0) ? a0 : b0; ++ d[1] = (*(double *) &a1) > (*(double *) &b1) ? a1 : b1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b, store the maximum value in the lower element of dst, and copy the upper ++// element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_sd ++FORCE_INLINE __m128d _mm_max_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_max_pd(a, b)); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2] = {da[0] > db[0] ? da[0] : db[0], da[1]}; ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) c)); ++#endif ++} ++ ++// Compare packed signed 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epi16 ++FORCE_INLINE __m128i _mm_min_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vminq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epu8 ++FORCE_INLINE __m128i _mm_min_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vminq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b, ++// and store packed minimum values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_pd ++FORCE_INLINE __m128d _mm_min_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#if SSE2NEON_PRECISE_MINMAX ++ float64x2_t _a = vreinterpretq_f64_m128d(a); ++ float64x2_t _b = vreinterpretq_f64_m128d(b); ++ return vreinterpretq_m128d_f64(vbslq_f64(vcltq_f64(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128d_f64( ++ vminq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#endif ++#else ++ uint64_t a0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t a1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(a)); ++ uint64_t b0 = (uint64_t) vget_low_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t b1 = (uint64_t) vget_high_u64(vreinterpretq_u64_m128d(b)); ++ uint64_t d[2]; ++ d[0] = (*(double *) &a0) < (*(double *) &b0) ? a0 : b0; ++ d[1] = (*(double *) &a1) < (*(double *) &b1) ? a1 : b1; ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b, store the minimum value in the lower element of dst, and copy the upper ++// element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_sd ++FORCE_INLINE __m128d _mm_min_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_min_pd(a, b)); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2] = {da[0] < db[0] ? da[0] : db[0], da[1]}; ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) c)); ++#endif ++} ++ ++// Copy the lower 64-bit integer in a to the lower element of dst, and zero the ++// upper element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_move_epi64 ++FORCE_INLINE __m128i _mm_move_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_s64( ++ vsetq_lane_s64(0, vreinterpretq_s64_m128i(a), 1)); ++} ++ ++// Move the lower double-precision (64-bit) floating-point element from b to the ++// lower element of dst, and copy the upper element from a to the upper element ++// of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_move_sd ++FORCE_INLINE __m128d _mm_move_sd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_f32( ++ vcombine_f32(vget_low_f32(vreinterpretq_f32_m128d(b)), ++ vget_high_f32(vreinterpretq_f32_m128d(a)))); ++} ++ ++// Create mask from the most significant bit of each 8-bit element in a, and ++// store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movemask_epi8 ++FORCE_INLINE int _mm_movemask_epi8(__m128i a) ++{ ++ // Use increasingly wide shifts+adds to collect the sign bits ++ // together. ++ // Since the widening shifts would be rather confusing to follow in little ++ // endian, everything will be illustrated in big endian order instead. This ++ // has a different result - the bits would actually be reversed on a big ++ // endian machine. ++ ++ // Starting input (only half the elements are shown): ++ // 89 ff 1d c0 00 10 99 33 ++ uint8x16_t input = vreinterpretq_u8_m128i(a); ++ ++ // Shift out everything but the sign bits with an unsigned shift right. ++ // ++ // Bytes of the vector:: ++ // 89 ff 1d c0 00 10 99 33 ++ // \ \ \ \ \ \ \ \ high_bits = (uint16x4_t)(input >> 7) ++ // | | | | | | | | ++ // 01 01 00 01 00 00 01 00 ++ // ++ // Bits of first important lane(s): ++ // 10001001 (89) ++ // \______ ++ // | ++ // 00000001 (01) ++ uint16x8_t high_bits = vreinterpretq_u16_u8(vshrq_n_u8(input, 7)); ++ ++ // Merge the even lanes together with a 16-bit unsigned shift right + add. ++ // 'xx' represents garbage data which will be ignored in the final result. ++ // In the important bytes, the add functions like a binary OR. ++ // ++ // 01 01 00 01 00 00 01 00 ++ // \_ | \_ | \_ | \_ | paired16 = (uint32x4_t)(input + (input >> 7)) ++ // \| \| \| \| ++ // xx 03 xx 01 xx 00 xx 02 ++ // ++ // 00000001 00000001 (01 01) ++ // \_______ | ++ // \| ++ // xxxxxxxx xxxxxx11 (xx 03) ++ uint32x4_t paired16 = ++ vreinterpretq_u32_u16(vsraq_n_u16(high_bits, high_bits, 7)); ++ ++ // Repeat with a wider 32-bit shift + add. ++ // xx 03 xx 01 xx 00 xx 02 ++ // \____ | \____ | paired32 = (uint64x1_t)(paired16 + (paired16 >> ++ // 14)) ++ // \| \| ++ // xx xx xx 0d xx xx xx 02 ++ // ++ // 00000011 00000001 (03 01) ++ // \\_____ || ++ // '----.\|| ++ // xxxxxxxx xxxx1101 (xx 0d) ++ uint64x2_t paired32 = ++ vreinterpretq_u64_u32(vsraq_n_u32(paired16, paired16, 14)); ++ ++ // Last, an even wider 64-bit shift + add to get our result in the low 8 bit ++ // lanes. xx xx xx 0d xx xx xx 02 ++ // \_________ | paired64 = (uint8x8_t)(paired32 + (paired32 >> ++ // 28)) ++ // \| ++ // xx xx xx xx xx xx xx d2 ++ // ++ // 00001101 00000010 (0d 02) ++ // \ \___ | | ++ // '---. \| | ++ // xxxxxxxx 11010010 (xx d2) ++ uint8x16_t paired64 = ++ vreinterpretq_u8_u64(vsraq_n_u64(paired32, paired32, 28)); ++ ++ // Extract the low 8 bits from each 64-bit lane with 2 8-bit extracts. ++ // xx xx xx xx xx xx xx d2 ++ // || return paired64[0] ++ // d2 ++ // Note: Little endian would return the correct value 4b (01001011) instead. ++ return vgetq_lane_u8(paired64, 0) | ((int) vgetq_lane_u8(paired64, 8) << 8); ++} ++ ++// Set each bit of mask dst based on the most significant bit of the ++// corresponding packed double-precision (64-bit) floating-point element in a. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movemask_pd ++FORCE_INLINE int _mm_movemask_pd(__m128d a) ++{ ++ uint64x2_t input = vreinterpretq_u64_m128d(a); ++ uint64x2_t high_bits = vshrq_n_u64(input, 63); ++ return (int) (vgetq_lane_u64(high_bits, 0) | ++ (vgetq_lane_u64(high_bits, 1) << 1)); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movepi64_pi64 ++FORCE_INLINE __m64 _mm_movepi64_pi64(__m128i a) ++{ ++ return vreinterpret_m64_s64(vget_low_s64(vreinterpretq_s64_m128i(a))); ++} ++ ++// Copy the 64-bit integer a to the lower element of dst, and zero the upper ++// element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movpi64_epi64 ++FORCE_INLINE __m128i _mm_movpi64_epi64(__m64 a) ++{ ++ return vreinterpretq_m128i_s64( ++ vcombine_s64(vreinterpret_s64_m64(a), vdup_n_s64(0))); ++} ++ ++// Multiply the low unsigned 32-bit integers from each packed 64-bit element in ++// a and b, and store the unsigned 64-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_epu32 ++FORCE_INLINE __m128i _mm_mul_epu32(__m128i a, __m128i b) ++{ ++ // vmull_u32 upcasts instead of masking, so we downcast. ++ uint32x2_t a_lo = vmovn_u64(vreinterpretq_u64_m128i(a)); ++ uint32x2_t b_lo = vmovn_u64(vreinterpretq_u64_m128i(b)); ++ return vreinterpretq_m128i_u64(vmull_u32(a_lo, b_lo)); ++} ++ ++// Multiply packed double-precision (64-bit) floating-point elements in a and b, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_pd ++FORCE_INLINE __m128d _mm_mul_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vmulq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] * db[0]; ++ c[1] = da[1] * db[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Multiply the lower double-precision (64-bit) floating-point element in a and ++// b, store the result in the lower element of dst, and copy the upper element ++// from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_mul_sd ++FORCE_INLINE __m128d _mm_mul_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_mul_pd(a, b)); ++} ++ ++// Multiply the low unsigned 32-bit integers from a and b, and store the ++// unsigned 64-bit result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_su32 ++FORCE_INLINE __m64 _mm_mul_su32(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u64(vget_low_u64( ++ vmull_u32(vreinterpret_u32_m64(a), vreinterpret_u32_m64(b)))); ++} ++ ++// Multiply the packed signed 16-bit integers in a and b, producing intermediate ++// 32-bit integers, and store the high 16 bits of the intermediate integers in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhi_epi16 ++FORCE_INLINE __m128i _mm_mulhi_epi16(__m128i a, __m128i b) ++{ ++ /* FIXME: issue with large values because of result saturation */ ++ // int16x8_t ret = vqdmulhq_s16(vreinterpretq_s16_m128i(a), ++ // vreinterpretq_s16_m128i(b)); /* =2*a*b */ return ++ // vreinterpretq_m128i_s16(vshrq_n_s16(ret, 1)); ++ int16x4_t a3210 = vget_low_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b3210 = vget_low_s16(vreinterpretq_s16_m128i(b)); ++ int32x4_t ab3210 = vmull_s16(a3210, b3210); /* 3333222211110000 */ ++ int16x4_t a7654 = vget_high_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b7654 = vget_high_s16(vreinterpretq_s16_m128i(b)); ++ int32x4_t ab7654 = vmull_s16(a7654, b7654); /* 7777666655554444 */ ++ uint16x8x2_t r = ++ vuzpq_u16(vreinterpretq_u16_s32(ab3210), vreinterpretq_u16_s32(ab7654)); ++ return vreinterpretq_m128i_u16(r.val[1]); ++} ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhi_epu16 ++FORCE_INLINE __m128i _mm_mulhi_epu16(__m128i a, __m128i b) ++{ ++ uint16x4_t a3210 = vget_low_u16(vreinterpretq_u16_m128i(a)); ++ uint16x4_t b3210 = vget_low_u16(vreinterpretq_u16_m128i(b)); ++ uint32x4_t ab3210 = vmull_u16(a3210, b3210); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint32x4_t ab7654 = ++ vmull_high_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b)); ++ uint16x8_t r = vuzp2q_u16(vreinterpretq_u16_u32(ab3210), ++ vreinterpretq_u16_u32(ab7654)); ++ return vreinterpretq_m128i_u16(r); ++#else ++ uint16x4_t a7654 = vget_high_u16(vreinterpretq_u16_m128i(a)); ++ uint16x4_t b7654 = vget_high_u16(vreinterpretq_u16_m128i(b)); ++ uint32x4_t ab7654 = vmull_u16(a7654, b7654); ++ uint16x8x2_t r = ++ vuzpq_u16(vreinterpretq_u16_u32(ab3210), vreinterpretq_u16_u32(ab7654)); ++ return vreinterpretq_m128i_u16(r.val[1]); ++#endif ++} ++ ++// Multiply the packed 16-bit integers in a and b, producing intermediate 32-bit ++// integers, and store the low 16 bits of the intermediate integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mullo_epi16 ++FORCE_INLINE __m128i _mm_mullo_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vmulq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compute the bitwise OR of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_or_pd ++FORCE_INLINE __m128d _mm_or_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ vorrq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Compute the bitwise OR of 128 bits (representing integer data) in a and b, ++// and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_or_si128 ++FORCE_INLINE __m128i _mm_or_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vorrq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Convert packed signed 16-bit integers from a and b to packed 8-bit integers ++// using signed saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_packs_epi16 ++FORCE_INLINE __m128i _mm_packs_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vcombine_s8(vqmovn_s16(vreinterpretq_s16_m128i(a)), ++ vqmovn_s16(vreinterpretq_s16_m128i(b)))); ++} ++ ++// Convert packed signed 32-bit integers from a and b to packed 16-bit integers ++// using signed saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_packs_epi32 ++FORCE_INLINE __m128i _mm_packs_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vqmovn_s32(vreinterpretq_s32_m128i(a)), ++ vqmovn_s32(vreinterpretq_s32_m128i(b)))); ++} ++ ++// Convert packed signed 16-bit integers from a and b to packed 8-bit integers ++// using unsigned saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_packus_epi16 ++FORCE_INLINE __m128i _mm_packus_epi16(const __m128i a, const __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcombine_u8(vqmovun_s16(vreinterpretq_s16_m128i(a)), ++ vqmovun_s16(vreinterpretq_s16_m128i(b)))); ++} ++ ++// Pause the processor. This is typically used in spin-wait loops and depending ++// on the x86 processor typical values are in the 40-100 cycle range. The ++// 'yield' instruction isn't a good fit because it's effectively a nop on most ++// Arm cores. Experience with several databases has shown has shown an 'isb' is ++// a reasonable approximation. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_pause ++FORCE_INLINE void _mm_pause(void) ++{ ++#if defined(_MSC_VER) ++ __isb(_ARM64_BARRIER_SY); ++#else ++ __asm__ __volatile__("isb\n"); ++#endif ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce two ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of 64-bit elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sad_epu8 ++FORCE_INLINE __m128i _mm_sad_epu8(__m128i a, __m128i b) ++{ ++ uint16x8_t t = vpaddlq_u8(vabdq_u8((uint8x16_t) a, (uint8x16_t) b)); ++ return vreinterpretq_m128i_u64(vpaddlq_u32(vpaddlq_u16(t))); ++} ++ ++// Set packed 16-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi16 ++FORCE_INLINE __m128i _mm_set_epi16(short i7, ++ short i6, ++ short i5, ++ short i4, ++ short i3, ++ short i2, ++ short i1, ++ short i0) ++{ ++ int16_t ALIGN_STRUCT(16) data[8] = {i0, i1, i2, i3, i4, i5, i6, i7}; ++ return vreinterpretq_m128i_s16(vld1q_s16(data)); ++} ++ ++// Set packed 32-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi32 ++FORCE_INLINE __m128i _mm_set_epi32(int i3, int i2, int i1, int i0) ++{ ++ int32_t ALIGN_STRUCT(16) data[4] = {i0, i1, i2, i3}; ++ return vreinterpretq_m128i_s32(vld1q_s32(data)); ++} ++ ++// Set packed 64-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi64 ++FORCE_INLINE __m128i _mm_set_epi64(__m64 i1, __m64 i2) ++{ ++ return _mm_set_epi64x(vget_lane_s64(i1, 0), vget_lane_s64(i2, 0)); ++} ++ ++// Set packed 64-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi64x ++FORCE_INLINE __m128i _mm_set_epi64x(int64_t i1, int64_t i2) ++{ ++ return vreinterpretq_m128i_s64( ++ vcombine_s64(vcreate_s64(i2), vcreate_s64(i1))); ++} ++ ++// Set packed 8-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi8 ++FORCE_INLINE __m128i _mm_set_epi8(signed char b15, ++ signed char b14, ++ signed char b13, ++ signed char b12, ++ signed char b11, ++ signed char b10, ++ signed char b9, ++ signed char b8, ++ signed char b7, ++ signed char b6, ++ signed char b5, ++ signed char b4, ++ signed char b3, ++ signed char b2, ++ signed char b1, ++ signed char b0) ++{ ++ int8_t ALIGN_STRUCT(16) ++ data[16] = {(int8_t) b0, (int8_t) b1, (int8_t) b2, (int8_t) b3, ++ (int8_t) b4, (int8_t) b5, (int8_t) b6, (int8_t) b7, ++ (int8_t) b8, (int8_t) b9, (int8_t) b10, (int8_t) b11, ++ (int8_t) b12, (int8_t) b13, (int8_t) b14, (int8_t) b15}; ++ return (__m128i) vld1q_s8(data); ++} ++ ++// Set packed double-precision (64-bit) floating-point elements in dst with the ++// supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_pd ++FORCE_INLINE __m128d _mm_set_pd(double e1, double e0) ++{ ++ double ALIGN_STRUCT(16) data[2] = {e0, e1}; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vld1q_f64((float64_t *) data)); ++#else ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) data)); ++#endif ++} ++ ++// Broadcast double-precision (64-bit) floating-point value a to all elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_pd1 ++#define _mm_set_pd1 _mm_set1_pd ++ ++// Copy double-precision (64-bit) floating-point element a to the lower element ++// of dst, and zero the upper element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_sd ++FORCE_INLINE __m128d _mm_set_sd(double a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vsetq_lane_f64(a, vdupq_n_f64(0), 0)); ++#else ++ return _mm_set_pd(0, a); ++#endif ++} ++ ++// Broadcast 16-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi16 ++FORCE_INLINE __m128i _mm_set1_epi16(short w) ++{ ++ return vreinterpretq_m128i_s16(vdupq_n_s16(w)); ++} ++ ++// Broadcast 32-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi32 ++FORCE_INLINE __m128i _mm_set1_epi32(int _i) ++{ ++ return vreinterpretq_m128i_s32(vdupq_n_s32(_i)); ++} ++ ++// Broadcast 64-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi64 ++FORCE_INLINE __m128i _mm_set1_epi64(__m64 _i) ++{ ++ return vreinterpretq_m128i_s64(vdupq_lane_s64(_i, 0)); ++} ++ ++// Broadcast 64-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi64x ++FORCE_INLINE __m128i _mm_set1_epi64x(int64_t _i) ++{ ++ return vreinterpretq_m128i_s64(vdupq_n_s64(_i)); ++} ++ ++// Broadcast 8-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi8 ++FORCE_INLINE __m128i _mm_set1_epi8(signed char w) ++{ ++ return vreinterpretq_m128i_s8(vdupq_n_s8(w)); ++} ++ ++// Broadcast double-precision (64-bit) floating-point value a to all elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_pd ++FORCE_INLINE __m128d _mm_set1_pd(double d) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vdupq_n_f64(d)); ++#else ++ return vreinterpretq_m128d_s64(vdupq_n_s64(*(int64_t *) &d)); ++#endif ++} ++ ++// Set packed 16-bit integers in dst with the supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_epi16 ++FORCE_INLINE __m128i _mm_setr_epi16(short w0, ++ short w1, ++ short w2, ++ short w3, ++ short w4, ++ short w5, ++ short w6, ++ short w7) ++{ ++ int16_t ALIGN_STRUCT(16) data[8] = {w0, w1, w2, w3, w4, w5, w6, w7}; ++ return vreinterpretq_m128i_s16(vld1q_s16((int16_t *) data)); ++} ++ ++// Set packed 32-bit integers in dst with the supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_epi32 ++FORCE_INLINE __m128i _mm_setr_epi32(int i3, int i2, int i1, int i0) ++{ ++ int32_t ALIGN_STRUCT(16) data[4] = {i3, i2, i1, i0}; ++ return vreinterpretq_m128i_s32(vld1q_s32(data)); ++} ++ ++// Set packed 64-bit integers in dst with the supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_epi64 ++FORCE_INLINE __m128i _mm_setr_epi64(__m64 e1, __m64 e0) ++{ ++ return vreinterpretq_m128i_s64(vcombine_s64(e1, e0)); ++} ++ ++// Set packed 8-bit integers in dst with the supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_epi8 ++FORCE_INLINE __m128i _mm_setr_epi8(signed char b0, ++ signed char b1, ++ signed char b2, ++ signed char b3, ++ signed char b4, ++ signed char b5, ++ signed char b6, ++ signed char b7, ++ signed char b8, ++ signed char b9, ++ signed char b10, ++ signed char b11, ++ signed char b12, ++ signed char b13, ++ signed char b14, ++ signed char b15) ++{ ++ int8_t ALIGN_STRUCT(16) ++ data[16] = {(int8_t) b0, (int8_t) b1, (int8_t) b2, (int8_t) b3, ++ (int8_t) b4, (int8_t) b5, (int8_t) b6, (int8_t) b7, ++ (int8_t) b8, (int8_t) b9, (int8_t) b10, (int8_t) b11, ++ (int8_t) b12, (int8_t) b13, (int8_t) b14, (int8_t) b15}; ++ return (__m128i) vld1q_s8(data); ++} ++ ++// Set packed double-precision (64-bit) floating-point elements in dst with the ++// supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_pd ++FORCE_INLINE __m128d _mm_setr_pd(double e1, double e0) ++{ ++ return _mm_set_pd(e0, e1); ++} ++ ++// Return vector of type __m128d with all elements set to zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setzero_pd ++FORCE_INLINE __m128d _mm_setzero_pd(void) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vdupq_n_f64(0)); ++#else ++ return vreinterpretq_m128d_f32(vdupq_n_f32(0)); ++#endif ++} ++ ++// Return vector of type __m128i with all elements set to zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setzero_si128 ++FORCE_INLINE __m128i _mm_setzero_si128(void) ++{ ++ return vreinterpretq_m128i_s32(vdupq_n_s32(0)); ++} ++ ++// Shuffle 32-bit integers in a using the control in imm8, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_epi32 ++// FORCE_INLINE __m128i _mm_shuffle_epi32(__m128i a, ++// __constrange(0,255) int imm) ++#if defined(_sse2neon_shuffle) ++#define _mm_shuffle_epi32(a, imm) \ ++ __extension__({ \ ++ int32x4_t _input = vreinterpretq_s32_m128i(a); \ ++ int32x4_t _shuf = \ ++ vshuffleq_s32(_input, _input, (imm) & (0x3), ((imm) >> 2) & 0x3, \ ++ ((imm) >> 4) & 0x3, ((imm) >> 6) & 0x3); \ ++ vreinterpretq_m128i_s32(_shuf); \ ++ }) ++#else // generic ++#define _mm_shuffle_epi32(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, __m128i ret; switch (imm) { \ ++ case _MM_SHUFFLE(1, 0, 3, 2): \ ++ ret = _mm_shuffle_epi_1032(_a); \ ++ break; \ ++ case _MM_SHUFFLE(2, 3, 0, 1): \ ++ ret = _mm_shuffle_epi_2301(_a); \ ++ break; \ ++ case _MM_SHUFFLE(0, 3, 2, 1): \ ++ ret = _mm_shuffle_epi_0321(_a); \ ++ break; \ ++ case _MM_SHUFFLE(2, 1, 0, 3): \ ++ ret = _mm_shuffle_epi_2103(_a); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 1, 0): \ ++ ret = _mm_shuffle_epi_1010(_a); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 0, 1): \ ++ ret = _mm_shuffle_epi_1001(_a); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 0, 1): \ ++ ret = _mm_shuffle_epi_0101(_a); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 1, 1): \ ++ ret = _mm_shuffle_epi_2211(_a); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 2, 2): \ ++ ret = _mm_shuffle_epi_0122(_a); \ ++ break; \ ++ case _MM_SHUFFLE(3, 3, 3, 2): \ ++ ret = _mm_shuffle_epi_3332(_a); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 0, 0): \ ++ ret = _mm_shuffle_epi32_splat(_a, 0); \ ++ break; \ ++ case _MM_SHUFFLE(1, 1, 1, 1): \ ++ ret = _mm_shuffle_epi32_splat(_a, 1); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 2, 2): \ ++ ret = _mm_shuffle_epi32_splat(_a, 2); \ ++ break; \ ++ case _MM_SHUFFLE(3, 3, 3, 3): \ ++ ret = _mm_shuffle_epi32_splat(_a, 3); \ ++ break; \ ++ default: \ ++ ret = _mm_shuffle_epi32_default(_a, (imm)); \ ++ break; \ ++ } _sse2neon_return(ret);) ++#endif ++ ++// Shuffle double-precision (64-bit) floating-point elements using the control ++// in imm8, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_pd ++#ifdef _sse2neon_shuffle ++#define _mm_shuffle_pd(a, b, imm8) \ ++ vreinterpretq_m128d_s64( \ ++ vshuffleq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b), \ ++ imm8 & 0x1, ((imm8 & 0x2) >> 1) + 2)) ++#else ++#define _mm_shuffle_pd(a, b, imm8) \ ++ _mm_castsi128_pd(_mm_set_epi64x( \ ++ vgetq_lane_s64(vreinterpretq_s64_m128d(b), (imm8 & 0x2) >> 1), \ ++ vgetq_lane_s64(vreinterpretq_s64_m128d(a), imm8 & 0x1))) ++#endif ++ ++// FORCE_INLINE __m128i _mm_shufflehi_epi16(__m128i a, ++// __constrange(0,255) int imm) ++#if defined(_sse2neon_shuffle) ++#define _mm_shufflehi_epi16(a, imm) \ ++ __extension__({ \ ++ int16x8_t _input = vreinterpretq_s16_m128i(a); \ ++ int16x8_t _shuf = \ ++ vshuffleq_s16(_input, _input, 0, 1, 2, 3, ((imm) & (0x3)) + 4, \ ++ (((imm) >> 2) & 0x3) + 4, (((imm) >> 4) & 0x3) + 4, \ ++ (((imm) >> 6) & 0x3) + 4); \ ++ vreinterpretq_m128i_s16(_shuf); \ ++ }) ++#else // generic ++#define _mm_shufflehi_epi16(a, imm) _mm_shufflehi_epi16_function((a), (imm)) ++#endif ++ ++// FORCE_INLINE __m128i _mm_shufflelo_epi16(__m128i a, ++// __constrange(0,255) int imm) ++#if defined(_sse2neon_shuffle) ++#define _mm_shufflelo_epi16(a, imm) \ ++ __extension__({ \ ++ int16x8_t _input = vreinterpretq_s16_m128i(a); \ ++ int16x8_t _shuf = vshuffleq_s16( \ ++ _input, _input, ((imm) & (0x3)), (((imm) >> 2) & 0x3), \ ++ (((imm) >> 4) & 0x3), (((imm) >> 6) & 0x3), 4, 5, 6, 7); \ ++ vreinterpretq_m128i_s16(_shuf); \ ++ }) ++#else // generic ++#define _mm_shufflelo_epi16(a, imm) _mm_shufflelo_epi16_function((a), (imm)) ++#endif ++ ++// Shift packed 16-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sll_epi16 ++FORCE_INLINE __m128i _mm_sll_epi16(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_setzero_si128(); ++ ++ int16x8_t vc = vdupq_n_s16((int16_t) c); ++ return vreinterpretq_m128i_s16(vshlq_s16(vreinterpretq_s16_m128i(a), vc)); ++} ++ ++// Shift packed 32-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sll_epi32 ++FORCE_INLINE __m128i _mm_sll_epi32(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_setzero_si128(); ++ ++ int32x4_t vc = vdupq_n_s32((int32_t) c); ++ return vreinterpretq_m128i_s32(vshlq_s32(vreinterpretq_s32_m128i(a), vc)); ++} ++ ++// Shift packed 64-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sll_epi64 ++FORCE_INLINE __m128i _mm_sll_epi64(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~63)) ++ return _mm_setzero_si128(); ++ ++ int64x2_t vc = vdupq_n_s64((int64_t) c); ++ return vreinterpretq_m128i_s64(vshlq_s64(vreinterpretq_s64_m128i(a), vc)); ++} ++ ++// Shift packed 16-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_slli_epi16 ++FORCE_INLINE __m128i _mm_slli_epi16(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~15)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s16( ++ vshlq_s16(vreinterpretq_s16_m128i(a), vdupq_n_s16(imm))); ++} ++ ++// Shift packed 32-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_slli_epi32 ++FORCE_INLINE __m128i _mm_slli_epi32(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~31)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s32( ++ vshlq_s32(vreinterpretq_s32_m128i(a), vdupq_n_s32(imm))); ++} ++ ++// Shift packed 64-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_slli_epi64 ++FORCE_INLINE __m128i _mm_slli_epi64(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~63)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s64( ++ vshlq_s64(vreinterpretq_s64_m128i(a), vdupq_n_s64(imm))); ++} ++ ++// Shift a left by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_slli_si128 ++#define _mm_slli_si128(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, int8x16_t ret; \ ++ if (_sse2neon_unlikely(imm == 0)) ret = vreinterpretq_s8_m128i(_a); \ ++ else if (_sse2neon_unlikely((imm) & ~15)) ret = vdupq_n_s8(0); \ ++ else ret = vextq_s8(vdupq_n_s8(0), vreinterpretq_s8_m128i(_a), \ ++ ((imm <= 0 || imm > 15) ? 0 : (16 - imm))); \ ++ _sse2neon_return(vreinterpretq_m128i_s8(ret));) ++ ++// Compute the square root of packed double-precision (64-bit) floating-point ++// elements in a, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sqrt_pd ++FORCE_INLINE __m128d _mm_sqrt_pd(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vsqrtq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double a0 = sqrt(((double *) &a)[0]); ++ double a1 = sqrt(((double *) &a)[1]); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Compute the square root of the lower double-precision (64-bit) floating-point ++// element in b, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sqrt_sd ++FORCE_INLINE __m128d _mm_sqrt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_sqrt_pd(b)); ++#else ++ return _mm_set_pd(((double *) &a)[1], sqrt(((double *) &b)[0])); ++#endif ++} ++ ++// Shift packed 16-bit integers in a right by count while shifting in sign bits, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sra_epi16 ++FORCE_INLINE __m128i _mm_sra_epi16(__m128i a, __m128i count) ++{ ++ int64_t c = vgetq_lane_s64(count, 0); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_cmplt_epi16(a, _mm_setzero_si128()); ++ return vreinterpretq_m128i_s16( ++ vshlq_s16((int16x8_t) a, vdupq_n_s16((int) -c))); ++} ++ ++// Shift packed 32-bit integers in a right by count while shifting in sign bits, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sra_epi32 ++FORCE_INLINE __m128i _mm_sra_epi32(__m128i a, __m128i count) ++{ ++ int64_t c = vgetq_lane_s64(count, 0); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_cmplt_epi32(a, _mm_setzero_si128()); ++ return vreinterpretq_m128i_s32( ++ vshlq_s32((int32x4_t) a, vdupq_n_s32((int) -c))); ++} ++ ++// Shift packed 16-bit integers in a right by imm8 while shifting in sign ++// bits, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srai_epi16 ++FORCE_INLINE __m128i _mm_srai_epi16(__m128i a, int imm) ++{ ++ const int count = (imm & ~15) ? 15 : imm; ++ return (__m128i) vshlq_s16((int16x8_t) a, vdupq_n_s16(-count)); ++} ++ ++// Shift packed 32-bit integers in a right by imm8 while shifting in sign bits, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srai_epi32 ++// FORCE_INLINE __m128i _mm_srai_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_srai_epi32(a, imm) \ ++ _sse2neon_define0( \ ++ __m128i, a, __m128i ret; if (_sse2neon_unlikely((imm) == 0)) { \ ++ ret = _a; \ ++ } else if (_sse2neon_likely(0 < (imm) && (imm) < 32)) { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshlq_s32(vreinterpretq_s32_m128i(_a), vdupq_n_s32(-(imm)))); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshrq_n_s32(vreinterpretq_s32_m128i(_a), 31)); \ ++ } _sse2neon_return(ret);) ++ ++// Shift packed 16-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srl_epi16 ++FORCE_INLINE __m128i _mm_srl_epi16(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_setzero_si128(); ++ ++ int16x8_t vc = vdupq_n_s16(-(int16_t) c); ++ return vreinterpretq_m128i_u16(vshlq_u16(vreinterpretq_u16_m128i(a), vc)); ++} ++ ++// Shift packed 32-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srl_epi32 ++FORCE_INLINE __m128i _mm_srl_epi32(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_setzero_si128(); ++ ++ int32x4_t vc = vdupq_n_s32(-(int32_t) c); ++ return vreinterpretq_m128i_u32(vshlq_u32(vreinterpretq_u32_m128i(a), vc)); ++} ++ ++// Shift packed 64-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srl_epi64 ++FORCE_INLINE __m128i _mm_srl_epi64(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~63)) ++ return _mm_setzero_si128(); ++ ++ int64x2_t vc = vdupq_n_s64(-(int64_t) c); ++ return vreinterpretq_m128i_u64(vshlq_u64(vreinterpretq_u64_m128i(a), vc)); ++} ++ ++// Shift packed 16-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srli_epi16 ++#define _mm_srli_epi16(a, imm) \ ++ _sse2neon_define0( \ ++ __m128i, a, __m128i ret; if (_sse2neon_unlikely((imm) & ~15)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u16( \ ++ vshlq_u16(vreinterpretq_u16_m128i(_a), vdupq_n_s16(-(imm)))); \ ++ } _sse2neon_return(ret);) ++ ++// Shift packed 32-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srli_epi32 ++// FORCE_INLINE __m128i _mm_srli_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_srli_epi32(a, imm) \ ++ _sse2neon_define0( \ ++ __m128i, a, __m128i ret; if (_sse2neon_unlikely((imm) & ~31)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u32( \ ++ vshlq_u32(vreinterpretq_u32_m128i(_a), vdupq_n_s32(-(imm)))); \ ++ } _sse2neon_return(ret);) ++ ++// Shift packed 64-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srli_epi64 ++#define _mm_srli_epi64(a, imm) \ ++ _sse2neon_define0( \ ++ __m128i, a, __m128i ret; if (_sse2neon_unlikely((imm) & ~63)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u64( \ ++ vshlq_u64(vreinterpretq_u64_m128i(_a), vdupq_n_s64(-(imm)))); \ ++ } _sse2neon_return(ret);) ++ ++// Shift a right by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srli_si128 ++#define _mm_srli_si128(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, int8x16_t ret; \ ++ if (_sse2neon_unlikely((imm) & ~15)) ret = vdupq_n_s8(0); \ ++ else ret = vextq_s8(vreinterpretq_s8_m128i(_a), vdupq_n_s8(0), \ ++ (imm > 15 ? 0 : imm)); \ ++ _sse2neon_return(vreinterpretq_m128i_s8(ret));) ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory. mem_addr must be aligned on a 16-byte boundary ++// or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_pd ++FORCE_INLINE void _mm_store_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ vst1q_f64((float64_t *) mem_addr, vreinterpretq_f64_m128d(a)); ++#else ++ vst1q_f32((float32_t *) mem_addr, vreinterpretq_f32_m128d(a)); ++#endif ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// 2 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_pd1 ++FORCE_INLINE void _mm_store_pd1(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x1_t a_low = vget_low_f64(vreinterpretq_f64_m128d(a)); ++ vst1q_f64((float64_t *) mem_addr, ++ vreinterpretq_f64_m128d(vcombine_f64(a_low, a_low))); ++#else ++ float32x2_t a_low = vget_low_f32(vreinterpretq_f32_m128d(a)); ++ vst1q_f32((float32_t *) mem_addr, ++ vreinterpretq_f32_m128d(vcombine_f32(a_low, a_low))); ++#endif ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// memory. mem_addr does not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_store_sd ++FORCE_INLINE void _mm_store_sd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ vst1_f64((float64_t *) mem_addr, vget_low_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_u64((uint64_t *) mem_addr, vget_low_u64(vreinterpretq_u64_m128d(a))); ++#endif ++} ++ ++// Store 128-bits of integer data from a into memory. mem_addr must be aligned ++// on a 16-byte boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_si128 ++FORCE_INLINE void _mm_store_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, vreinterpretq_s32_m128i(a)); ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// 2 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#expand=9,526,5601&text=_mm_store1_pd ++#define _mm_store1_pd _mm_store_pd1 ++ ++// Store the upper double-precision (64-bit) floating-point element from a into ++// memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeh_pd ++FORCE_INLINE void _mm_storeh_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ vst1_f64((float64_t *) mem_addr, vget_high_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_f32((float32_t *) mem_addr, vget_high_f32(vreinterpretq_f32_m128d(a))); ++#endif ++} ++ ++// Store 64-bit integer from the first element of a into memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storel_epi64 ++FORCE_INLINE void _mm_storel_epi64(__m128i *a, __m128i b) ++{ ++ vst1_u64((uint64_t *) a, vget_low_u64(vreinterpretq_u64_m128i(b))); ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storel_pd ++FORCE_INLINE void _mm_storel_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ vst1_f64((float64_t *) mem_addr, vget_low_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_f32((float32_t *) mem_addr, vget_low_f32(vreinterpretq_f32_m128d(a))); ++#endif ++} ++ ++// Store 2 double-precision (64-bit) floating-point elements from a into memory ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storer_pd ++FORCE_INLINE void _mm_storer_pd(double *mem_addr, __m128d a) ++{ ++ float32x4_t f = vreinterpretq_f32_m128d(a); ++ _mm_store_pd(mem_addr, vreinterpretq_m128d_f32(vextq_f32(f, f, 2))); ++} ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory. mem_addr does not need to be aligned on any ++// particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_pd ++FORCE_INLINE void _mm_storeu_pd(double *mem_addr, __m128d a) ++{ ++ _mm_store_pd(mem_addr, a); ++} ++ ++// Store 128-bits of integer data from a into memory. mem_addr does not need to ++// be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_si128 ++FORCE_INLINE void _mm_storeu_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, vreinterpretq_s32_m128i(a)); ++} ++ ++// Store 32-bit integer from the first element of a into memory. mem_addr does ++// not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_si32 ++FORCE_INLINE void _mm_storeu_si32(void *p, __m128i a) ++{ ++ vst1q_lane_s32((int32_t *) p, vreinterpretq_s32_m128i(a), 0); ++} ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory using a non-temporal memory hint. mem_addr must ++// be aligned on a 16-byte boundary or a general-protection exception may be ++// generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_pd ++FORCE_INLINE void _mm_stream_pd(double *p, __m128d a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, (__m128d *) p); ++#elif defined(__aarch64__) || defined(_M_ARM64) ++ vst1q_f64(p, vreinterpretq_f64_m128d(a)); ++#else ++ vst1q_s64((int64_t *) p, vreinterpretq_s64_m128d(a)); ++#endif ++} ++ ++// Store 128-bits of integer data from a into memory using a non-temporal memory ++// hint. mem_addr must be aligned on a 16-byte boundary or a general-protection ++// exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_si128 ++FORCE_INLINE void _mm_stream_si128(__m128i *p, __m128i a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, p); ++#else ++ vst1q_s64((int64_t *) p, vreinterpretq_s64_m128i(a)); ++#endif ++} ++ ++// Store 32-bit integer a into memory using a non-temporal hint to minimize ++// cache pollution. If the cache line containing address mem_addr is already in ++// the cache, the cache will be updated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_si32 ++FORCE_INLINE void _mm_stream_si32(int *p, int a) ++{ ++ vst1q_lane_s32((int32_t *) p, vdupq_n_s32(a), 0); ++} ++ ++// Store 64-bit integer a into memory using a non-temporal hint to minimize ++// cache pollution. If the cache line containing address mem_addr is already in ++// the cache, the cache will be updated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_si64 ++FORCE_INLINE void _mm_stream_si64(__int64 *p, __int64 a) ++{ ++ vst1_s64((int64_t *) p, vdup_n_s64((int64_t) a)); ++} ++ ++// Subtract packed 16-bit integers in b from packed 16-bit integers in a, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_epi16 ++FORCE_INLINE __m128i _mm_sub_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vsubq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Subtract packed 32-bit integers in b from packed 32-bit integers in a, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_epi32 ++FORCE_INLINE __m128i _mm_sub_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vsubq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Subtract packed 64-bit integers in b from packed 64-bit integers in a, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_epi64 ++FORCE_INLINE __m128i _mm_sub_epi64(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s64( ++ vsubq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++} ++ ++// Subtract packed 8-bit integers in b from packed 8-bit integers in a, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_epi8 ++FORCE_INLINE __m128i _mm_sub_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vsubq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Subtract packed double-precision (64-bit) floating-point elements in b from ++// packed double-precision (64-bit) floating-point elements in a, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_sub_pd ++FORCE_INLINE __m128d _mm_sub_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vsubq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[2]; ++ c[0] = da[0] - db[0]; ++ c[1] = da[1] - db[1]; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Subtract the lower double-precision (64-bit) floating-point element in b from ++// the lower double-precision (64-bit) floating-point element in a, store the ++// result in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_sd ++FORCE_INLINE __m128d _mm_sub_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_sub_pd(a, b)); ++} ++ ++// Subtract 64-bit integer b from 64-bit integer a, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_si64 ++FORCE_INLINE __m64 _mm_sub_si64(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s64( ++ vsub_s64(vreinterpret_s64_m64(a), vreinterpret_s64_m64(b))); ++} ++ ++// Subtract packed signed 16-bit integers in b from packed 16-bit integers in a ++// using saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_subs_epi16 ++FORCE_INLINE __m128i _mm_subs_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vqsubq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Subtract packed signed 8-bit integers in b from packed 8-bit integers in a ++// using saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_subs_epi8 ++FORCE_INLINE __m128i _mm_subs_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vqsubq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Subtract packed unsigned 16-bit integers in b from packed unsigned 16-bit ++// integers in a using saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_subs_epu16 ++FORCE_INLINE __m128i _mm_subs_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vqsubq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Subtract packed unsigned 8-bit integers in b from packed unsigned 8-bit ++// integers in a using saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_subs_epu8 ++FORCE_INLINE __m128i _mm_subs_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vqsubq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++#define _mm_ucomieq_sd _mm_comieq_sd ++#define _mm_ucomige_sd _mm_comige_sd ++#define _mm_ucomigt_sd _mm_comigt_sd ++#define _mm_ucomile_sd _mm_comile_sd ++#define _mm_ucomilt_sd _mm_comilt_sd ++#define _mm_ucomineq_sd _mm_comineq_sd ++ ++// Return vector of type __m128d with undefined elements. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_undefined_pd ++FORCE_INLINE __m128d _mm_undefined_pd(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128d a; ++#if defined(_MSC_VER) ++ a = _mm_setzero_pd(); ++#endif ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Unpack and interleave 16-bit integers from the high half of a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_epi16 ++FORCE_INLINE __m128i _mm_unpackhi_epi16(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16( ++ vzip2q_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++#else ++ int16x4_t a1 = vget_high_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b1 = vget_high_s16(vreinterpretq_s16_m128i(b)); ++ int16x4x2_t result = vzip_s16(a1, b1); ++ return vreinterpretq_m128i_s16(vcombine_s16(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave 32-bit integers from the high half of a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_epi32 ++FORCE_INLINE __m128i _mm_unpackhi_epi32(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s32( ++ vzip2q_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++#else ++ int32x2_t a1 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t b1 = vget_high_s32(vreinterpretq_s32_m128i(b)); ++ int32x2x2_t result = vzip_s32(a1, b1); ++ return vreinterpretq_m128i_s32(vcombine_s32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave 64-bit integers from the high half of a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_epi64 ++FORCE_INLINE __m128i _mm_unpackhi_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s64( ++ vzip2q_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++#else ++ int64x1_t a_h = vget_high_s64(vreinterpretq_s64_m128i(a)); ++ int64x1_t b_h = vget_high_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vcombine_s64(a_h, b_h)); ++#endif ++} ++ ++// Unpack and interleave 8-bit integers from the high half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_epi8 ++FORCE_INLINE __m128i _mm_unpackhi_epi8(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s8( ++ vzip2q_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++#else ++ int8x8_t a1 = ++ vreinterpret_s8_s16(vget_high_s16(vreinterpretq_s16_m128i(a))); ++ int8x8_t b1 = ++ vreinterpret_s8_s16(vget_high_s16(vreinterpretq_s16_m128i(b))); ++ int8x8x2_t result = vzip_s8(a1, b1); ++ return vreinterpretq_m128i_s8(vcombine_s8(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave double-precision (64-bit) floating-point elements from ++// the high half of a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_pd ++FORCE_INLINE __m128d _mm_unpackhi_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vzip2q_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ return vreinterpretq_m128d_s64( ++ vcombine_s64(vget_high_s64(vreinterpretq_s64_m128d(a)), ++ vget_high_s64(vreinterpretq_s64_m128d(b)))); ++#endif ++} ++ ++// Unpack and interleave 16-bit integers from the low half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_epi16 ++FORCE_INLINE __m128i _mm_unpacklo_epi16(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16( ++ vzip1q_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++#else ++ int16x4_t a1 = vget_low_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b1 = vget_low_s16(vreinterpretq_s16_m128i(b)); ++ int16x4x2_t result = vzip_s16(a1, b1); ++ return vreinterpretq_m128i_s16(vcombine_s16(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave 32-bit integers from the low half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_epi32 ++FORCE_INLINE __m128i _mm_unpacklo_epi32(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s32( ++ vzip1q_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++#else ++ int32x2_t a1 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t b1 = vget_low_s32(vreinterpretq_s32_m128i(b)); ++ int32x2x2_t result = vzip_s32(a1, b1); ++ return vreinterpretq_m128i_s32(vcombine_s32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave 64-bit integers from the low half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_epi64 ++FORCE_INLINE __m128i _mm_unpacklo_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s64( ++ vzip1q_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++#else ++ int64x1_t a_l = vget_low_s64(vreinterpretq_s64_m128i(a)); ++ int64x1_t b_l = vget_low_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vcombine_s64(a_l, b_l)); ++#endif ++} ++ ++// Unpack and interleave 8-bit integers from the low half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_epi8 ++FORCE_INLINE __m128i _mm_unpacklo_epi8(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s8( ++ vzip1q_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++#else ++ int8x8_t a1 = vreinterpret_s8_s16(vget_low_s16(vreinterpretq_s16_m128i(a))); ++ int8x8_t b1 = vreinterpret_s8_s16(vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int8x8x2_t result = vzip_s8(a1, b1); ++ return vreinterpretq_m128i_s8(vcombine_s8(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave double-precision (64-bit) floating-point elements from ++// the low half of a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_pd ++FORCE_INLINE __m128d _mm_unpacklo_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vzip1q_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ return vreinterpretq_m128d_s64( ++ vcombine_s64(vget_low_s64(vreinterpretq_s64_m128d(a)), ++ vget_low_s64(vreinterpretq_s64_m128d(b)))); ++#endif ++} ++ ++// Compute the bitwise XOR of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_xor_pd ++FORCE_INLINE __m128d _mm_xor_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ veorq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Compute the bitwise XOR of 128 bits (representing integer data) in a and b, ++// and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_xor_si128 ++FORCE_INLINE __m128i _mm_xor_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ veorq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++/* SSE3 */ ++ ++// Alternatively add and subtract packed double-precision (64-bit) ++// floating-point elements in a to/from packed elements in b, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_addsub_pd ++FORCE_INLINE __m128d _mm_addsub_pd(__m128d a, __m128d b) ++{ ++ _sse2neon_const __m128d mask = _mm_set_pd(1.0f, -1.0f); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vfmaq_f64(vreinterpretq_f64_m128d(a), ++ vreinterpretq_f64_m128d(b), ++ vreinterpretq_f64_m128d(mask))); ++#else ++ return _mm_add_pd(_mm_mul_pd(b, mask), a); ++#endif ++} ++ ++// Alternatively add and subtract packed single-precision (32-bit) ++// floating-point elements in a to/from packed elements in b, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=addsub_ps ++FORCE_INLINE __m128 _mm_addsub_ps(__m128 a, __m128 b) ++{ ++ _sse2neon_const __m128 mask = _mm_setr_ps(-1.0f, 1.0f, -1.0f, 1.0f); ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_FMA) /* VFPv4+ */ ++ return vreinterpretq_m128_f32(vfmaq_f32(vreinterpretq_f32_m128(a), ++ vreinterpretq_f32_m128(mask), ++ vreinterpretq_f32_m128(b))); ++#else ++ return _mm_add_ps(_mm_mul_ps(b, mask), a); ++#endif ++} ++ ++// Horizontally add adjacent pairs of double-precision (64-bit) floating-point ++// elements in a and b, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_pd ++FORCE_INLINE __m128d _mm_hadd_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vpaddq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double *da = (double *) &a; ++ double *db = (double *) &b; ++ double c[] = {da[0] + da[1], db[0] + db[1]}; ++ return vreinterpretq_m128d_u64(vld1q_u64((uint64_t *) c)); ++#endif ++} ++ ++// Horizontally add adjacent pairs of single-precision (32-bit) floating-point ++// elements in a and b, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_ps ++FORCE_INLINE __m128 _mm_hadd_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vpaddq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vpadd_f32(a10, a32), vpadd_f32(b10, b32))); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of double-precision (64-bit) ++// floating-point elements in a and b, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_pd ++FORCE_INLINE __m128d _mm_hsub_pd(__m128d _a, __m128d _b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x2_t a = vreinterpretq_f64_m128d(_a); ++ float64x2_t b = vreinterpretq_f64_m128d(_b); ++ return vreinterpretq_m128d_f64( ++ vsubq_f64(vuzp1q_f64(a, b), vuzp2q_f64(a, b))); ++#else ++ double *da = (double *) &_a; ++ double *db = (double *) &_b; ++ double c[] = {da[0] - da[1], db[0] - db[1]}; ++ return vreinterpretq_m128d_u64(vld1q_u64((uint64_t *) c)); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of single-precision (32-bit) ++// floating-point elements in a and b, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_ps ++FORCE_INLINE __m128 _mm_hsub_ps(__m128 _a, __m128 _b) ++{ ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vsubq_f32(vuzp1q_f32(a, b), vuzp2q_f32(a, b))); ++#else ++ float32x4x2_t c = vuzpq_f32(a, b); ++ return vreinterpretq_m128_f32(vsubq_f32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Load 128-bits of integer data from unaligned memory into dst. This intrinsic ++// may perform better than _mm_loadu_si128 when the data crosses a cache line ++// boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_lddqu_si128 ++#define _mm_lddqu_si128 _mm_loadu_si128 ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loaddup_pd ++#define _mm_loaddup_pd _mm_load1_pd ++ ++// Duplicate the low double-precision (64-bit) floating-point element from a, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movedup_pd ++FORCE_INLINE __m128d _mm_movedup_pd(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vdupq_laneq_f64(vreinterpretq_f64_m128d(a), 0)); ++#else ++ return vreinterpretq_m128d_u64( ++ vdupq_n_u64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0))); ++#endif ++} ++ ++// Duplicate odd-indexed single-precision (32-bit) floating-point elements ++// from a, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movehdup_ps ++FORCE_INLINE __m128 _mm_movehdup_ps(__m128 a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vtrn2q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a))); ++#elif defined(_sse2neon_shuffle) ++ return vreinterpretq_m128_f32(vshuffleq_s32( ++ vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 1, 1, 3, 3)); ++#else ++ float32_t a1 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 1); ++ float32_t a3 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 3); ++ float ALIGN_STRUCT(16) data[4] = {a1, a1, a3, a3}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Duplicate even-indexed single-precision (32-bit) floating-point elements ++// from a, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_moveldup_ps ++FORCE_INLINE __m128 _mm_moveldup_ps(__m128 a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vtrn1q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a))); ++#elif defined(_sse2neon_shuffle) ++ return vreinterpretq_m128_f32(vshuffleq_s32( ++ vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 0, 0, 2, 2)); ++#else ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ float32_t a2 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 2); ++ float ALIGN_STRUCT(16) data[4] = {a0, a0, a2, a2}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++#endif ++} ++ ++/* SSSE3 */ ++ ++// Compute the absolute value of packed signed 16-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_epi16 ++FORCE_INLINE __m128i _mm_abs_epi16(__m128i a) ++{ ++ return vreinterpretq_m128i_s16(vabsq_s16(vreinterpretq_s16_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 32-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_epi32 ++FORCE_INLINE __m128i _mm_abs_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_s32(vabsq_s32(vreinterpretq_s32_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 8-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_epi8 ++FORCE_INLINE __m128i _mm_abs_epi8(__m128i a) ++{ ++ return vreinterpretq_m128i_s8(vabsq_s8(vreinterpretq_s8_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 16-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_pi16 ++FORCE_INLINE __m64 _mm_abs_pi16(__m64 a) ++{ ++ return vreinterpret_m64_s16(vabs_s16(vreinterpret_s16_m64(a))); ++} ++ ++// Compute the absolute value of packed signed 32-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_pi32 ++FORCE_INLINE __m64 _mm_abs_pi32(__m64 a) ++{ ++ return vreinterpret_m64_s32(vabs_s32(vreinterpret_s32_m64(a))); ++} ++ ++// Compute the absolute value of packed signed 8-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_pi8 ++FORCE_INLINE __m64 _mm_abs_pi8(__m64 a) ++{ ++ return vreinterpret_m64_s8(vabs_s8(vreinterpret_s8_m64(a))); ++} ++ ++// Concatenate 16-byte blocks in a and b into a 32-byte temporary result, shift ++// the result right by imm8 bytes, and store the low 16 bytes in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_alignr_epi8 ++#if defined(__GNUC__) && !defined(__clang__) ++#define _mm_alignr_epi8(a, b, imm) \ ++ __extension__({ \ ++ uint8x16_t _a = vreinterpretq_u8_m128i(a); \ ++ uint8x16_t _b = vreinterpretq_u8_m128i(b); \ ++ __m128i ret; \ ++ if (_sse2neon_unlikely((imm) & ~31)) \ ++ ret = vreinterpretq_m128i_u8(vdupq_n_u8(0)); \ ++ else if (imm >= 16) \ ++ ret = _mm_srli_si128(a, imm >= 16 ? imm - 16 : 0); \ ++ else \ ++ ret = \ ++ vreinterpretq_m128i_u8(vextq_u8(_b, _a, imm < 16 ? imm : 0)); \ ++ ret; \ ++ }) ++ ++#else ++#define _mm_alignr_epi8(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m128i, a, b, uint8x16_t __a = vreinterpretq_u8_m128i(_a); \ ++ uint8x16_t __b = vreinterpretq_u8_m128i(_b); __m128i ret; \ ++ if (_sse2neon_unlikely((imm) & ~31)) ret = \ ++ vreinterpretq_m128i_u8(vdupq_n_u8(0)); \ ++ else if (imm >= 16) ret = \ ++ _mm_srli_si128(_a, imm >= 16 ? imm - 16 : 0); \ ++ else ret = \ ++ vreinterpretq_m128i_u8(vextq_u8(__b, __a, imm < 16 ? imm : 0)); \ ++ _sse2neon_return(ret);) ++ ++#endif ++ ++// Concatenate 8-byte blocks in a and b into a 16-byte temporary result, shift ++// the result right by imm8 bytes, and store the low 8 bytes in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_alignr_pi8 ++#define _mm_alignr_pi8(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m64, a, b, __m64 ret; if (_sse2neon_unlikely((imm) >= 16)) { \ ++ ret = vreinterpret_m64_s8(vdup_n_s8(0)); \ ++ } else { \ ++ uint8x8_t tmp_low; \ ++ uint8x8_t tmp_high; \ ++ if ((imm) >= 8) { \ ++ const int idx = (imm) -8; \ ++ tmp_low = vreinterpret_u8_m64(_a); \ ++ tmp_high = vdup_n_u8(0); \ ++ ret = vreinterpret_m64_u8(vext_u8(tmp_low, tmp_high, idx)); \ ++ } else { \ ++ const int idx = (imm); \ ++ tmp_low = vreinterpret_u8_m64(_b); \ ++ tmp_high = vreinterpret_u8_m64(_a); \ ++ ret = vreinterpret_m64_u8(vext_u8(tmp_low, tmp_high, idx)); \ ++ } \ ++ } _sse2neon_return(ret);) ++ ++// Horizontally add adjacent pairs of 16-bit integers in a and b, and pack the ++// signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_epi16 ++FORCE_INLINE __m128i _mm_hadd_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16(vpaddq_s16(a, b)); ++#else ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vpadd_s16(vget_low_s16(a), vget_high_s16(a)), ++ vpadd_s16(vget_low_s16(b), vget_high_s16(b)))); ++#endif ++} ++ ++// Horizontally add adjacent pairs of 32-bit integers in a and b, and pack the ++// signed 32-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_epi32 ++FORCE_INLINE __m128i _mm_hadd_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s32(vpaddq_s32(a, b)); ++#else ++ return vreinterpretq_m128i_s32( ++ vcombine_s32(vpadd_s32(vget_low_s32(a), vget_high_s32(a)), ++ vpadd_s32(vget_low_s32(b), vget_high_s32(b)))); ++#endif ++} ++ ++// Horizontally add adjacent pairs of 16-bit integers in a and b, and pack the ++// signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_pi16 ++FORCE_INLINE __m64 _mm_hadd_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vpadd_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Horizontally add adjacent pairs of 32-bit integers in a and b, and pack the ++// signed 32-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_pi32 ++FORCE_INLINE __m64 _mm_hadd_pi32(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s32( ++ vpadd_s32(vreinterpret_s32_m64(a), vreinterpret_s32_m64(b))); ++} ++ ++// Horizontally add adjacent pairs of signed 16-bit integers in a and b using ++// saturation, and pack the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadds_epi16 ++FORCE_INLINE __m128i _mm_hadds_epi16(__m128i _a, __m128i _b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ return vreinterpretq_s64_s16( ++ vqaddq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++ // Interleave using vshrn/vmovn ++ // [a0|a2|a4|a6|b0|b2|b4|b6] ++ // [a1|a3|a5|a7|b1|b3|b5|b7] ++ int16x8_t ab0246 = vcombine_s16(vmovn_s32(a), vmovn_s32(b)); ++ int16x8_t ab1357 = vcombine_s16(vshrn_n_s32(a, 16), vshrn_n_s32(b, 16)); ++ // Saturated add ++ return vreinterpretq_m128i_s16(vqaddq_s16(ab0246, ab1357)); ++#endif ++} ++ ++// Horizontally add adjacent pairs of signed 16-bit integers in a and b using ++// saturation, and pack the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadds_pi16 ++FORCE_INLINE __m64 _mm_hadds_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpret_s64_s16(vqadd_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t res = vuzp_s16(a, b); ++ return vreinterpret_s64_s16(vqadd_s16(res.val[0], res.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 16-bit integers in a and b, and pack ++// the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_epi16 ++FORCE_INLINE __m128i _mm_hsub_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16( ++ vsubq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int16x8x2_t c = vuzpq_s16(a, b); ++ return vreinterpretq_m128i_s16(vsubq_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 32-bit integers in a and b, and pack ++// the signed 32-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_epi32 ++FORCE_INLINE __m128i _mm_hsub_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s32( ++ vsubq_s32(vuzp1q_s32(a, b), vuzp2q_s32(a, b))); ++#else ++ int32x4x2_t c = vuzpq_s32(a, b); ++ return vreinterpretq_m128i_s32(vsubq_s32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 16-bit integers in a and b, and pack ++// the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_pi16 ++FORCE_INLINE __m64 _mm_hsub_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpret_m64_s16(vsub_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t c = vuzp_s16(a, b); ++ return vreinterpret_m64_s16(vsub_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 32-bit integers in a and b, and pack ++// the signed 32-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_hsub_pi32 ++FORCE_INLINE __m64 _mm_hsub_pi32(__m64 _a, __m64 _b) ++{ ++ int32x2_t a = vreinterpret_s32_m64(_a); ++ int32x2_t b = vreinterpret_s32_m64(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpret_m64_s32(vsub_s32(vuzp1_s32(a, b), vuzp2_s32(a, b))); ++#else ++ int32x2x2_t c = vuzp_s32(a, b); ++ return vreinterpret_m64_s32(vsub_s32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of signed 16-bit integers in a and b ++// using saturation, and pack the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsubs_epi16 ++FORCE_INLINE __m128i _mm_hsubs_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16( ++ vqsubq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int16x8x2_t c = vuzpq_s16(a, b); ++ return vreinterpretq_m128i_s16(vqsubq_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of signed 16-bit integers in a and b ++// using saturation, and pack the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsubs_pi16 ++FORCE_INLINE __m64 _mm_hsubs_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpret_m64_s16(vqsub_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t c = vuzp_s16(a, b); ++ return vreinterpret_m64_s16(vqsub_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Vertically multiply each unsigned 8-bit integer from a with the corresponding ++// signed 8-bit integer from b, producing intermediate signed 16-bit integers. ++// Horizontally add adjacent pairs of intermediate signed 16-bit integers, ++// and pack the saturated results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_maddubs_epi16 ++FORCE_INLINE __m128i _mm_maddubs_epi16(__m128i _a, __m128i _b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint8x16_t a = vreinterpretq_u8_m128i(_a); ++ int8x16_t b = vreinterpretq_s8_m128i(_b); ++ int16x8_t tl = vmulq_s16(vreinterpretq_s16_u16(vmovl_u8(vget_low_u8(a))), ++ vmovl_s8(vget_low_s8(b))); ++ int16x8_t th = vmulq_s16(vreinterpretq_s16_u16(vmovl_u8(vget_high_u8(a))), ++ vmovl_s8(vget_high_s8(b))); ++ return vreinterpretq_m128i_s16( ++ vqaddq_s16(vuzp1q_s16(tl, th), vuzp2q_s16(tl, th))); ++#else ++ // This would be much simpler if x86 would choose to zero extend OR sign ++ // extend, not both. This could probably be optimized better. ++ uint16x8_t a = vreinterpretq_u16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ ++ // Zero extend a ++ int16x8_t a_odd = vreinterpretq_s16_u16(vshrq_n_u16(a, 8)); ++ int16x8_t a_even = vreinterpretq_s16_u16(vbicq_u16(a, vdupq_n_u16(0xff00))); ++ ++ // Sign extend by shifting left then shifting right. ++ int16x8_t b_even = vshrq_n_s16(vshlq_n_s16(b, 8), 8); ++ int16x8_t b_odd = vshrq_n_s16(b, 8); ++ ++ // multiply ++ int16x8_t prod1 = vmulq_s16(a_even, b_even); ++ int16x8_t prod2 = vmulq_s16(a_odd, b_odd); ++ ++ // saturated add ++ return vreinterpretq_m128i_s16(vqaddq_s16(prod1, prod2)); ++#endif ++} ++ ++// Vertically multiply each unsigned 8-bit integer from a with the corresponding ++// signed 8-bit integer from b, producing intermediate signed 16-bit integers. ++// Horizontally add adjacent pairs of intermediate signed 16-bit integers, and ++// pack the saturated results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_maddubs_pi16 ++FORCE_INLINE __m64 _mm_maddubs_pi16(__m64 _a, __m64 _b) ++{ ++ uint16x4_t a = vreinterpret_u16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++ ++ // Zero extend a ++ int16x4_t a_odd = vreinterpret_s16_u16(vshr_n_u16(a, 8)); ++ int16x4_t a_even = vreinterpret_s16_u16(vand_u16(a, vdup_n_u16(0xff))); ++ ++ // Sign extend by shifting left then shifting right. ++ int16x4_t b_even = vshr_n_s16(vshl_n_s16(b, 8), 8); ++ int16x4_t b_odd = vshr_n_s16(b, 8); ++ ++ // multiply ++ int16x4_t prod1 = vmul_s16(a_even, b_even); ++ int16x4_t prod2 = vmul_s16(a_odd, b_odd); ++ ++ // saturated add ++ return vreinterpret_m64_s16(vqadd_s16(prod1, prod2)); ++} ++ ++// Multiply packed signed 16-bit integers in a and b, producing intermediate ++// signed 32-bit integers. Shift right by 15 bits while rounding up, and store ++// the packed 16-bit integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhrs_epi16 ++FORCE_INLINE __m128i _mm_mulhrs_epi16(__m128i a, __m128i b) ++{ ++ // Has issues due to saturation ++ // return vreinterpretq_m128i_s16(vqrdmulhq_s16(a, b)); ++ ++ // Multiply ++ int32x4_t mul_lo = vmull_s16(vget_low_s16(vreinterpretq_s16_m128i(a)), ++ vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int32x4_t mul_hi = vmull_s16(vget_high_s16(vreinterpretq_s16_m128i(a)), ++ vget_high_s16(vreinterpretq_s16_m128i(b))); ++ ++ // Rounding narrowing shift right ++ // narrow = (int16_t)((mul + 16384) >> 15); ++ int16x4_t narrow_lo = vrshrn_n_s32(mul_lo, 15); ++ int16x4_t narrow_hi = vrshrn_n_s32(mul_hi, 15); ++ ++ // Join together ++ return vreinterpretq_m128i_s16(vcombine_s16(narrow_lo, narrow_hi)); ++} ++ ++// Multiply packed signed 16-bit integers in a and b, producing intermediate ++// signed 32-bit integers. Truncate each intermediate integer to the 18 most ++// significant bits, round by adding 1, and store bits [16:1] to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhrs_pi16 ++FORCE_INLINE __m64 _mm_mulhrs_pi16(__m64 a, __m64 b) ++{ ++ int32x4_t mul_extend = ++ vmull_s16((vreinterpret_s16_m64(a)), (vreinterpret_s16_m64(b))); ++ ++ // Rounding narrowing shift right ++ return vreinterpret_m64_s16(vrshrn_n_s32(mul_extend, 15)); ++} ++ ++// Shuffle packed 8-bit integers in a according to shuffle control mask in the ++// corresponding 8-bit element of b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_epi8 ++FORCE_INLINE __m128i _mm_shuffle_epi8(__m128i a, __m128i b) ++{ ++ int8x16_t tbl = vreinterpretq_s8_m128i(a); // input a ++ uint8x16_t idx = vreinterpretq_u8_m128i(b); // input b ++ uint8x16_t idx_masked = ++ vandq_u8(idx, vdupq_n_u8(0x8F)); // avoid using meaningless bits ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s8(vqtbl1q_s8(tbl, idx_masked)); ++#elif defined(__GNUC__) ++ int8x16_t ret; ++ // %e and %f represent the even and odd D registers ++ // respectively. ++ __asm__ __volatile__( ++ "vtbl.8 %e[ret], {%e[tbl], %f[tbl]}, %e[idx]\n" ++ "vtbl.8 %f[ret], {%e[tbl], %f[tbl]}, %f[idx]\n" ++ : [ret] "=&w"(ret) ++ : [tbl] "w"(tbl), [idx] "w"(idx_masked)); ++ return vreinterpretq_m128i_s8(ret); ++#else ++ // use this line if testing on aarch64 ++ int8x8x2_t a_split = {vget_low_s8(tbl), vget_high_s8(tbl)}; ++ return vreinterpretq_m128i_s8( ++ vcombine_s8(vtbl2_s8(a_split, vget_low_u8(idx_masked)), ++ vtbl2_s8(a_split, vget_high_u8(idx_masked)))); ++#endif ++} ++ ++// Shuffle packed 8-bit integers in a according to shuffle control mask in the ++// corresponding 8-bit element of b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_pi8 ++FORCE_INLINE __m64 _mm_shuffle_pi8(__m64 a, __m64 b) ++{ ++ const int8x8_t controlMask = ++ vand_s8(vreinterpret_s8_m64(b), vdup_n_s8((int8_t) (0x1 << 7 | 0x07))); ++ int8x8_t res = vtbl1_s8(vreinterpret_s8_m64(a), controlMask); ++ return vreinterpret_m64_s8(res); ++} ++ ++// Negate packed 16-bit integers in a when the corresponding signed ++// 16-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_epi16 ++FORCE_INLINE __m128i _mm_sign_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFF : 0 ++ uint16x8_t ltMask = vreinterpretq_u16_s16(vshrq_n_s16(b, 15)); ++ // (b == 0) ? 0xFFFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int16x8_t zeroMask = vreinterpretq_s16_u16(vceqzq_s16(b)); ++#else ++ int16x8_t zeroMask = vreinterpretq_s16_u16(vceqq_s16(b, vdupq_n_s16(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s16(a) equals to negative ++ // 'a') based on ltMask ++ int16x8_t masked = vbslq_s16(ltMask, vnegq_s16(a), a); ++ // res = masked & (~zeroMask) ++ int16x8_t res = vbicq_s16(masked, zeroMask); ++ return vreinterpretq_m128i_s16(res); ++} ++ ++// Negate packed 32-bit integers in a when the corresponding signed ++// 32-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_epi32 ++FORCE_INLINE __m128i _mm_sign_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFFFFFF : 0 ++ uint32x4_t ltMask = vreinterpretq_u32_s32(vshrq_n_s32(b, 31)); ++ ++ // (b == 0) ? 0xFFFFFFFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int32x4_t zeroMask = vreinterpretq_s32_u32(vceqzq_s32(b)); ++#else ++ int32x4_t zeroMask = vreinterpretq_s32_u32(vceqq_s32(b, vdupq_n_s32(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s32(a) equals to negative ++ // 'a') based on ltMask ++ int32x4_t masked = vbslq_s32(ltMask, vnegq_s32(a), a); ++ // res = masked & (~zeroMask) ++ int32x4_t res = vbicq_s32(masked, zeroMask); ++ return vreinterpretq_m128i_s32(res); ++} ++ ++// Negate packed 8-bit integers in a when the corresponding signed ++// 8-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_epi8 ++FORCE_INLINE __m128i _mm_sign_epi8(__m128i _a, __m128i _b) ++{ ++ int8x16_t a = vreinterpretq_s8_m128i(_a); ++ int8x16_t b = vreinterpretq_s8_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFF : 0 ++ uint8x16_t ltMask = vreinterpretq_u8_s8(vshrq_n_s8(b, 7)); ++ ++ // (b == 0) ? 0xFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int8x16_t zeroMask = vreinterpretq_s8_u8(vceqzq_s8(b)); ++#else ++ int8x16_t zeroMask = vreinterpretq_s8_u8(vceqq_s8(b, vdupq_n_s8(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s8(a) return negative 'a') ++ // based on ltMask ++ int8x16_t masked = vbslq_s8(ltMask, vnegq_s8(a), a); ++ // res = masked & (~zeroMask) ++ int8x16_t res = vbicq_s8(masked, zeroMask); ++ ++ return vreinterpretq_m128i_s8(res); ++} ++ ++// Negate packed 16-bit integers in a when the corresponding signed 16-bit ++// integer in b is negative, and store the results in dst. Element in dst are ++// zeroed out when the corresponding element in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_pi16 ++FORCE_INLINE __m64 _mm_sign_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFF : 0 ++ uint16x4_t ltMask = vreinterpret_u16_s16(vshr_n_s16(b, 15)); ++ ++ // (b == 0) ? 0xFFFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int16x4_t zeroMask = vreinterpret_s16_u16(vceqz_s16(b)); ++#else ++ int16x4_t zeroMask = vreinterpret_s16_u16(vceq_s16(b, vdup_n_s16(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s16(a) return negative 'a') ++ // based on ltMask ++ int16x4_t masked = vbsl_s16(ltMask, vneg_s16(a), a); ++ // res = masked & (~zeroMask) ++ int16x4_t res = vbic_s16(masked, zeroMask); ++ ++ return vreinterpret_m64_s16(res); ++} ++ ++// Negate packed 32-bit integers in a when the corresponding signed 32-bit ++// integer in b is negative, and store the results in dst. Element in dst are ++// zeroed out when the corresponding element in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_pi32 ++FORCE_INLINE __m64 _mm_sign_pi32(__m64 _a, __m64 _b) ++{ ++ int32x2_t a = vreinterpret_s32_m64(_a); ++ int32x2_t b = vreinterpret_s32_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFFFFFF : 0 ++ uint32x2_t ltMask = vreinterpret_u32_s32(vshr_n_s32(b, 31)); ++ ++ // (b == 0) ? 0xFFFFFFFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int32x2_t zeroMask = vreinterpret_s32_u32(vceqz_s32(b)); ++#else ++ int32x2_t zeroMask = vreinterpret_s32_u32(vceq_s32(b, vdup_n_s32(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s32(a) return negative 'a') ++ // based on ltMask ++ int32x2_t masked = vbsl_s32(ltMask, vneg_s32(a), a); ++ // res = masked & (~zeroMask) ++ int32x2_t res = vbic_s32(masked, zeroMask); ++ ++ return vreinterpret_m64_s32(res); ++} ++ ++// Negate packed 8-bit integers in a when the corresponding signed 8-bit integer ++// in b is negative, and store the results in dst. Element in dst are zeroed out ++// when the corresponding element in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_pi8 ++FORCE_INLINE __m64 _mm_sign_pi8(__m64 _a, __m64 _b) ++{ ++ int8x8_t a = vreinterpret_s8_m64(_a); ++ int8x8_t b = vreinterpret_s8_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFF : 0 ++ uint8x8_t ltMask = vreinterpret_u8_s8(vshr_n_s8(b, 7)); ++ ++ // (b == 0) ? 0xFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int8x8_t zeroMask = vreinterpret_s8_u8(vceqz_s8(b)); ++#else ++ int8x8_t zeroMask = vreinterpret_s8_u8(vceq_s8(b, vdup_n_s8(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s8(a) return negative 'a') ++ // based on ltMask ++ int8x8_t masked = vbsl_s8(ltMask, vneg_s8(a), a); ++ // res = masked & (~zeroMask) ++ int8x8_t res = vbic_s8(masked, zeroMask); ++ ++ return vreinterpret_m64_s8(res); ++} ++ ++/* SSE4.1 */ ++ ++// Blend packed 16-bit integers from a and b using control mask imm8, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blend_epi16 ++// FORCE_INLINE __m128i _mm_blend_epi16(__m128i a, __m128i b, ++// __constrange(0,255) int imm) ++#define _mm_blend_epi16(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m128i, a, b, \ ++ const uint16_t _mask[8] = \ ++ _sse2neon_init(((imm) & (1 << 0)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 1)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 2)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 3)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 4)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 5)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 6)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 7)) ? (uint16_t) -1 : 0x0); \ ++ uint16x8_t _mask_vec = vld1q_u16(_mask); \ ++ uint16x8_t __a = vreinterpretq_u16_m128i(_a); \ ++ uint16x8_t __b = vreinterpretq_u16_m128i(_b); _sse2neon_return( \ ++ vreinterpretq_m128i_u16(vbslq_u16(_mask_vec, __b, __a)));) ++ ++// Blend packed double-precision (64-bit) floating-point elements from a and b ++// using control mask imm8, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blend_pd ++#define _mm_blend_pd(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m128d, a, b, \ ++ const uint64_t _mask[2] = \ ++ _sse2neon_init(((imm) & (1 << 0)) ? ~UINT64_C(0) : UINT64_C(0), \ ++ ((imm) & (1 << 1)) ? ~UINT64_C(0) : UINT64_C(0)); \ ++ uint64x2_t _mask_vec = vld1q_u64(_mask); \ ++ uint64x2_t __a = vreinterpretq_u64_m128d(_a); \ ++ uint64x2_t __b = vreinterpretq_u64_m128d(_b); _sse2neon_return( \ ++ vreinterpretq_m128d_u64(vbslq_u64(_mask_vec, __b, __a)));) ++ ++// Blend packed single-precision (32-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blend_ps ++FORCE_INLINE __m128 _mm_blend_ps(__m128 _a, __m128 _b, const char imm8) ++{ ++ const uint32_t ALIGN_STRUCT(16) ++ data[4] = {((imm8) & (1 << 0)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 1)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 2)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 3)) ? UINT32_MAX : 0}; ++ uint32x4_t mask = vld1q_u32(data); ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++ return vreinterpretq_m128_f32(vbslq_f32(mask, b, a)); ++} ++ ++// Blend packed 8-bit integers from a and b using mask, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blendv_epi8 ++FORCE_INLINE __m128i _mm_blendv_epi8(__m128i _a, __m128i _b, __m128i _mask) ++{ ++ // Use a signed shift right to create a mask with the sign bit ++ uint8x16_t mask = ++ vreinterpretq_u8_s8(vshrq_n_s8(vreinterpretq_s8_m128i(_mask), 7)); ++ uint8x16_t a = vreinterpretq_u8_m128i(_a); ++ uint8x16_t b = vreinterpretq_u8_m128i(_b); ++ return vreinterpretq_m128i_u8(vbslq_u8(mask, b, a)); ++} ++ ++// Blend packed double-precision (64-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blendv_pd ++FORCE_INLINE __m128d _mm_blendv_pd(__m128d _a, __m128d _b, __m128d _mask) ++{ ++ uint64x2_t mask = ++ vreinterpretq_u64_s64(vshrq_n_s64(vreinterpretq_s64_m128d(_mask), 63)); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x2_t a = vreinterpretq_f64_m128d(_a); ++ float64x2_t b = vreinterpretq_f64_m128d(_b); ++ return vreinterpretq_m128d_f64(vbslq_f64(mask, b, a)); ++#else ++ uint64x2_t a = vreinterpretq_u64_m128d(_a); ++ uint64x2_t b = vreinterpretq_u64_m128d(_b); ++ return vreinterpretq_m128d_u64(vbslq_u64(mask, b, a)); ++#endif ++} ++ ++// Blend packed single-precision (32-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blendv_ps ++FORCE_INLINE __m128 _mm_blendv_ps(__m128 _a, __m128 _b, __m128 _mask) ++{ ++ // Use a signed shift right to create a mask with the sign bit ++ uint32x4_t mask = ++ vreinterpretq_u32_s32(vshrq_n_s32(vreinterpretq_s32_m128(_mask), 31)); ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++ return vreinterpretq_m128_f32(vbslq_f32(mask, b, a)); ++} ++ ++// Round the packed double-precision (64-bit) floating-point elements in a up ++// to an integer value, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_ceil_pd ++FORCE_INLINE __m128d _mm_ceil_pd(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vrndpq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double *f = (double *) &a; ++ return _mm_set_pd(ceil(f[1]), ceil(f[0])); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a up to ++// an integer value, and store the results as packed single-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_ceil_ps ++FORCE_INLINE __m128 _mm_ceil_ps(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpretq_m128_f32(vrndpq_f32(vreinterpretq_f32_m128(a))); ++#else ++ float *f = (float *) &a; ++ return _mm_set_ps(ceilf(f[3]), ceilf(f[2]), ceilf(f[1]), ceilf(f[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b up to ++// an integer value, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_ceil_sd ++FORCE_INLINE __m128d _mm_ceil_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_ceil_pd(b)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b up to ++// an integer value, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_ceil_ss ++FORCE_INLINE __m128 _mm_ceil_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_ceil_ps(b)); ++} ++ ++// Compare packed 64-bit integers in a and b for equality, and store the results ++// in dst ++FORCE_INLINE __m128i _mm_cmpeq_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_u64( ++ vceqq_u64(vreinterpretq_u64_m128i(a), vreinterpretq_u64_m128i(b))); ++#else ++ // ARMv7 lacks vceqq_u64 ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128i_u32(vandq_u32(cmp, swapped)); ++#endif ++} ++ ++// Sign extend packed 16-bit integers in a to packed 32-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi16_epi32 ++FORCE_INLINE __m128i _mm_cvtepi16_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vmovl_s16(vget_low_s16(vreinterpretq_s16_m128i(a)))); ++} ++ ++// Sign extend packed 16-bit integers in a to packed 64-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi16_epi64 ++FORCE_INLINE __m128i _mm_cvtepi16_epi64(__m128i a) ++{ ++ int16x8_t s16x8 = vreinterpretq_s16_m128i(a); /* xxxx xxxx xxxx 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000x 000x 000B 000A */ ++ int64x2_t s64x2 = vmovl_s32(vget_low_s32(s32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_s64(s64x2); ++} ++ ++// Sign extend packed 32-bit integers in a to packed 64-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi32_epi64 ++FORCE_INLINE __m128i _mm_cvtepi32_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_s64( ++ vmovl_s32(vget_low_s32(vreinterpretq_s32_m128i(a)))); ++} ++ ++// Sign extend packed 8-bit integers in a to packed 16-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi8_epi16 ++FORCE_INLINE __m128i _mm_cvtepi8_epi16(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ return vreinterpretq_m128i_s16(s16x8); ++} ++ ++// Sign extend packed 8-bit integers in a to packed 32-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi8_epi32 ++FORCE_INLINE __m128i _mm_cvtepi8_epi32(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000D 000C 000B 000A */ ++ return vreinterpretq_m128i_s32(s32x4); ++} ++ ++// Sign extend packed 8-bit integers in the low 8 bytes of a to packed 64-bit ++// integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi8_epi64 ++FORCE_INLINE __m128i _mm_cvtepi8_epi64(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx xxBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0x0x 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000x 000x 000B 000A */ ++ int64x2_t s64x2 = vmovl_s32(vget_low_s32(s32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_s64(s64x2); ++} ++ ++// Zero extend packed unsigned 16-bit integers in a to packed 32-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu16_epi32 ++FORCE_INLINE __m128i _mm_cvtepu16_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_u32( ++ vmovl_u16(vget_low_u16(vreinterpretq_u16_m128i(a)))); ++} ++ ++// Zero extend packed unsigned 16-bit integers in a to packed 64-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu16_epi64 ++FORCE_INLINE __m128i _mm_cvtepu16_epi64(__m128i a) ++{ ++ uint16x8_t u16x8 = vreinterpretq_u16_m128i(a); /* xxxx xxxx xxxx 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000x 000x 000B 000A */ ++ uint64x2_t u64x2 = vmovl_u32(vget_low_u32(u32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_u64(u64x2); ++} ++ ++// Zero extend packed unsigned 32-bit integers in a to packed 64-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu32_epi64 ++FORCE_INLINE __m128i _mm_cvtepu32_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_u64( ++ vmovl_u32(vget_low_u32(vreinterpretq_u32_m128i(a)))); ++} ++ ++// Zero extend packed unsigned 8-bit integers in a to packed 16-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu8_epi16 ++FORCE_INLINE __m128i _mm_cvtepu8_epi16(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx HGFE DCBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0H0G 0F0E 0D0C 0B0A */ ++ return vreinterpretq_m128i_u16(u16x8); ++} ++ ++// Zero extend packed unsigned 8-bit integers in a to packed 32-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu8_epi32 ++FORCE_INLINE __m128i _mm_cvtepu8_epi32(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000D 000C 000B 000A */ ++ return vreinterpretq_m128i_u32(u32x4); ++} ++ ++// Zero extend packed unsigned 8-bit integers in the low 8 bytes of a to packed ++// 64-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu8_epi64 ++FORCE_INLINE __m128i _mm_cvtepu8_epi64(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx xxxx xxBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0x0x 0x0x 0x0x 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000x 000x 000B 000A */ ++ uint64x2_t u64x2 = vmovl_u32(vget_low_u32(u32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_u64(u64x2); ++} ++ ++// Conditionally multiply the packed double-precision (64-bit) floating-point ++// elements in a and b using the high 4 bits in imm8, sum the four products, and ++// conditionally store the sum in dst using the low 4 bits of imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_dp_pd ++FORCE_INLINE __m128d _mm_dp_pd(__m128d a, __m128d b, const int imm) ++{ ++ // Generate mask value from constant immediate bit value ++ const int64_t bit0Mask = imm & 0x01 ? UINT64_MAX : 0; ++ const int64_t bit1Mask = imm & 0x02 ? UINT64_MAX : 0; ++#if !SSE2NEON_PRECISE_DP ++ const int64_t bit4Mask = imm & 0x10 ? UINT64_MAX : 0; ++ const int64_t bit5Mask = imm & 0x20 ? UINT64_MAX : 0; ++#endif ++ // Conditional multiplication ++#if !SSE2NEON_PRECISE_DP ++ __m128d mul = _mm_mul_pd(a, b); ++ const __m128d mulMask = ++ _mm_castsi128_pd(_mm_set_epi64x(bit5Mask, bit4Mask)); ++ __m128d tmp = _mm_and_pd(mul, mulMask); ++#else ++#if defined(__aarch64__) || defined(_M_ARM64) ++ double d0 = (imm & 0x10) ? vgetq_lane_f64(vreinterpretq_f64_m128d(a), 0) * ++ vgetq_lane_f64(vreinterpretq_f64_m128d(b), 0) ++ : 0; ++ double d1 = (imm & 0x20) ? vgetq_lane_f64(vreinterpretq_f64_m128d(a), 1) * ++ vgetq_lane_f64(vreinterpretq_f64_m128d(b), 1) ++ : 0; ++#else ++ double d0 = (imm & 0x10) ? ((double *) &a)[0] * ((double *) &b)[0] : 0; ++ double d1 = (imm & 0x20) ? ((double *) &a)[1] * ((double *) &b)[1] : 0; ++#endif ++ __m128d tmp = _mm_set_pd(d1, d0); ++#endif ++ // Sum the products ++#if defined(__aarch64__) || defined(_M_ARM64) ++ double sum = vpaddd_f64(vreinterpretq_f64_m128d(tmp)); ++#else ++ double sum = *((double *) &tmp) + *(((double *) &tmp) + 1); ++#endif ++ // Conditionally store the sum ++ const __m128d sumMask = ++ _mm_castsi128_pd(_mm_set_epi64x(bit1Mask, bit0Mask)); ++ __m128d res = _mm_and_pd(_mm_set_pd1(sum), sumMask); ++ return res; ++} ++ ++// Conditionally multiply the packed single-precision (32-bit) floating-point ++// elements in a and b using the high 4 bits in imm8, sum the four products, ++// and conditionally store the sum in dst using the low 4 bits of imm. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_dp_ps ++FORCE_INLINE __m128 _mm_dp_ps(__m128 a, __m128 b, const int imm) ++{ ++ float32x4_t elementwise_prod = _mm_mul_ps(a, b); ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ /* shortcuts */ ++ if (imm == 0xFF) { ++ return _mm_set1_ps(vaddvq_f32(elementwise_prod)); ++ } ++ ++ if ((imm & 0x0F) == 0x0F) { ++ if (!(imm & (1 << 4))) ++ elementwise_prod = vsetq_lane_f32(0.0f, elementwise_prod, 0); ++ if (!(imm & (1 << 5))) ++ elementwise_prod = vsetq_lane_f32(0.0f, elementwise_prod, 1); ++ if (!(imm & (1 << 6))) ++ elementwise_prod = vsetq_lane_f32(0.0f, elementwise_prod, 2); ++ if (!(imm & (1 << 7))) ++ elementwise_prod = vsetq_lane_f32(0.0f, elementwise_prod, 3); ++ ++ return _mm_set1_ps(vaddvq_f32(elementwise_prod)); ++ } ++#endif ++ ++ float s = 0.0f; ++ ++ if (imm & (1 << 4)) ++ s += vgetq_lane_f32(elementwise_prod, 0); ++ if (imm & (1 << 5)) ++ s += vgetq_lane_f32(elementwise_prod, 1); ++ if (imm & (1 << 6)) ++ s += vgetq_lane_f32(elementwise_prod, 2); ++ if (imm & (1 << 7)) ++ s += vgetq_lane_f32(elementwise_prod, 3); ++ ++ const float32_t res[4] = { ++ (imm & 0x1) ? s : 0.0f, ++ (imm & 0x2) ? s : 0.0f, ++ (imm & 0x4) ? s : 0.0f, ++ (imm & 0x8) ? s : 0.0f, ++ }; ++ return vreinterpretq_m128_f32(vld1q_f32(res)); ++} ++ ++// Extract a 32-bit integer from a, selected with imm8, and store the result in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi32 ++// FORCE_INLINE int _mm_extract_epi32(__m128i a, __constrange(0,4) int imm) ++#define _mm_extract_epi32(a, imm) \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm)) ++ ++// Extract a 64-bit integer from a, selected with imm8, and store the result in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi64 ++// FORCE_INLINE __int64 _mm_extract_epi64(__m128i a, __constrange(0,2) int imm) ++#define _mm_extract_epi64(a, imm) \ ++ vgetq_lane_s64(vreinterpretq_s64_m128i(a), (imm)) ++ ++// Extract an 8-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. FORCE_INLINE int _mm_extract_epi8(__m128i a, ++// __constrange(0,16) int imm) ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi8 ++#define _mm_extract_epi8(a, imm) vgetq_lane_u8(vreinterpretq_u8_m128i(a), (imm)) ++ ++// Extracts the selected single-precision (32-bit) floating-point from a. ++// FORCE_INLINE int _mm_extract_ps(__m128 a, __constrange(0,4) int imm) ++#define _mm_extract_ps(a, imm) vgetq_lane_s32(vreinterpretq_s32_m128(a), (imm)) ++ ++// Round the packed double-precision (64-bit) floating-point elements in a down ++// to an integer value, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_floor_pd ++FORCE_INLINE __m128d _mm_floor_pd(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vrndmq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double *f = (double *) &a; ++ return _mm_set_pd(floor(f[1]), floor(f[0])); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a down ++// to an integer value, and store the results as packed single-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_floor_ps ++FORCE_INLINE __m128 _mm_floor_ps(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpretq_m128_f32(vrndmq_f32(vreinterpretq_f32_m128(a))); ++#else ++ float *f = (float *) &a; ++ return _mm_set_ps(floorf(f[3]), floorf(f[2]), floorf(f[1]), floorf(f[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b down to ++// an integer value, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_floor_sd ++FORCE_INLINE __m128d _mm_floor_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_floor_pd(b)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b down to ++// an integer value, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_floor_ss ++FORCE_INLINE __m128 _mm_floor_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_floor_ps(b)); ++} ++ ++// Copy a to dst, and insert the 32-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_epi32 ++// FORCE_INLINE __m128i _mm_insert_epi32(__m128i a, int b, ++// __constrange(0,4) int imm) ++#define _mm_insert_epi32(a, b, imm) \ ++ vreinterpretq_m128i_s32( \ ++ vsetq_lane_s32((b), vreinterpretq_s32_m128i(a), (imm))) ++ ++// Copy a to dst, and insert the 64-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_epi64 ++// FORCE_INLINE __m128i _mm_insert_epi64(__m128i a, __int64 b, ++// __constrange(0,2) int imm) ++#define _mm_insert_epi64(a, b, imm) \ ++ vreinterpretq_m128i_s64( \ ++ vsetq_lane_s64((b), vreinterpretq_s64_m128i(a), (imm))) ++ ++// Copy a to dst, and insert the lower 8-bit integer from i into dst at the ++// location specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_epi8 ++// FORCE_INLINE __m128i _mm_insert_epi8(__m128i a, int b, ++// __constrange(0,16) int imm) ++#define _mm_insert_epi8(a, b, imm) \ ++ vreinterpretq_m128i_s8(vsetq_lane_s8((b), vreinterpretq_s8_m128i(a), (imm))) ++ ++// Copy a to tmp, then insert a single-precision (32-bit) floating-point ++// element from b into tmp using the control in imm8. Store tmp to dst using ++// the mask in imm8 (elements are zeroed out when the corresponding bit is set). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=insert_ps ++#define _mm_insert_ps(a, b, imm8) \ ++ _sse2neon_define2( \ ++ __m128, a, b, \ ++ float32x4_t tmp1 = \ ++ vsetq_lane_f32(vgetq_lane_f32(_b, (imm8 >> 6) & 0x3), \ ++ vreinterpretq_f32_m128(_a), 0); \ ++ float32x4_t tmp2 = \ ++ vsetq_lane_f32(vgetq_lane_f32(tmp1, 0), \ ++ vreinterpretq_f32_m128(_a), ((imm8 >> 4) & 0x3)); \ ++ const uint32_t data[4] = \ ++ _sse2neon_init(((imm8) & (1 << 0)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 1)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 2)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 3)) ? UINT32_MAX : 0); \ ++ uint32x4_t mask = vld1q_u32(data); \ ++ float32x4_t all_zeros = vdupq_n_f32(0); \ ++ \ ++ _sse2neon_return(vreinterpretq_m128_f32( \ ++ vbslq_f32(mask, all_zeros, vreinterpretq_f32_m128(tmp2))));) ++ ++// Compare packed signed 32-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epi32 ++FORCE_INLINE __m128i _mm_max_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vmaxq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epi8 ++FORCE_INLINE __m128i _mm_max_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vmaxq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed unsigned 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epu16 ++FORCE_INLINE __m128i _mm_max_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vmaxq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Compare packed unsigned 32-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epu32 ++FORCE_INLINE __m128i _mm_max_epu32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vmaxq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b))); ++} ++ ++// Compare packed signed 32-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epi32 ++FORCE_INLINE __m128i _mm_min_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vminq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epi8 ++FORCE_INLINE __m128i _mm_min_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vminq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed unsigned 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epu16 ++FORCE_INLINE __m128i _mm_min_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vminq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Compare packed unsigned 32-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epu32 ++FORCE_INLINE __m128i _mm_min_epu32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vminq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b))); ++} ++ ++// Horizontally compute the minimum amongst the packed unsigned 16-bit integers ++// in a, store the minimum and index in dst, and zero the remaining bits in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_minpos_epu16 ++FORCE_INLINE __m128i _mm_minpos_epu16(__m128i a) ++{ ++ __m128i dst; ++ uint16_t min, idx = 0; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ // Find the minimum value ++ min = vminvq_u16(vreinterpretq_u16_m128i(a)); ++ ++ // Get the index of the minimum value ++ static const uint16_t idxv[] = {0, 1, 2, 3, 4, 5, 6, 7}; ++ uint16x8_t minv = vdupq_n_u16(min); ++ uint16x8_t cmeq = vceqq_u16(minv, vreinterpretq_u16_m128i(a)); ++ idx = vminvq_u16(vornq_u16(vld1q_u16(idxv), cmeq)); ++#else ++ // Find the minimum value ++ __m64 tmp; ++ tmp = vreinterpret_m64_u16( ++ vmin_u16(vget_low_u16(vreinterpretq_u16_m128i(a)), ++ vget_high_u16(vreinterpretq_u16_m128i(a)))); ++ tmp = vreinterpret_m64_u16( ++ vpmin_u16(vreinterpret_u16_m64(tmp), vreinterpret_u16_m64(tmp))); ++ tmp = vreinterpret_m64_u16( ++ vpmin_u16(vreinterpret_u16_m64(tmp), vreinterpret_u16_m64(tmp))); ++ min = vget_lane_u16(vreinterpret_u16_m64(tmp), 0); ++ // Get the index of the minimum value ++ int i; ++ for (i = 0; i < 8; i++) { ++ if (min == vgetq_lane_u16(vreinterpretq_u16_m128i(a), 0)) { ++ idx = (uint16_t) i; ++ break; ++ } ++ a = _mm_srli_si128(a, 2); ++ } ++#endif ++ // Generate result ++ dst = _mm_setzero_si128(); ++ dst = vreinterpretq_m128i_u16( ++ vsetq_lane_u16(min, vreinterpretq_u16_m128i(dst), 0)); ++ dst = vreinterpretq_m128i_u16( ++ vsetq_lane_u16(idx, vreinterpretq_u16_m128i(dst), 1)); ++ return dst; ++} ++ ++// Compute the sum of absolute differences (SADs) of quadruplets of unsigned ++// 8-bit integers in a compared to those in b, and store the 16-bit results in ++// dst. Eight SADs are performed using one quadruplet from b and eight ++// quadruplets from a. One quadruplet is selected from b starting at on the ++// offset specified in imm8. Eight quadruplets are formed from sequential 8-bit ++// integers selected from a starting at the offset specified in imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mpsadbw_epu8 ++FORCE_INLINE __m128i _mm_mpsadbw_epu8(__m128i a, __m128i b, const int imm) ++{ ++ uint8x16_t _a, _b; ++ ++ switch (imm & 0x4) { ++ case 0: ++ // do nothing ++ _a = vreinterpretq_u8_m128i(a); ++ break; ++ case 4: ++ _a = vreinterpretq_u8_u32(vextq_u32(vreinterpretq_u32_m128i(a), ++ vreinterpretq_u32_m128i(a), 1)); ++ break; ++ default: ++#if defined(__GNUC__) || defined(__clang__) ++ __builtin_unreachable(); ++#elif defined(_MSC_VER) ++ __assume(0); ++#endif ++ break; ++ } ++ ++ switch (imm & 0x3) { ++ case 0: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 0))); ++ break; ++ case 1: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 1))); ++ break; ++ case 2: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 2))); ++ break; ++ case 3: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 3))); ++ break; ++ default: ++#if defined(__GNUC__) || defined(__clang__) ++ __builtin_unreachable(); ++#elif defined(_MSC_VER) ++ __assume(0); ++#endif ++ break; ++ } ++ ++ int16x8_t c04, c15, c26, c37; ++ uint8x8_t low_b = vget_low_u8(_b); ++ c04 = vreinterpretq_s16_u16(vabdl_u8(vget_low_u8(_a), low_b)); ++ uint8x16_t _a_1 = vextq_u8(_a, _a, 1); ++ c15 = vreinterpretq_s16_u16(vabdl_u8(vget_low_u8(_a_1), low_b)); ++ uint8x16_t _a_2 = vextq_u8(_a, _a, 2); ++ c26 = vreinterpretq_s16_u16(vabdl_u8(vget_low_u8(_a_2), low_b)); ++ uint8x16_t _a_3 = vextq_u8(_a, _a, 3); ++ c37 = vreinterpretq_s16_u16(vabdl_u8(vget_low_u8(_a_3), low_b)); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ // |0|4|2|6| ++ c04 = vpaddq_s16(c04, c26); ++ // |1|5|3|7| ++ c15 = vpaddq_s16(c15, c37); ++ ++ int32x4_t trn1_c = ++ vtrn1q_s32(vreinterpretq_s32_s16(c04), vreinterpretq_s32_s16(c15)); ++ int32x4_t trn2_c = ++ vtrn2q_s32(vreinterpretq_s32_s16(c04), vreinterpretq_s32_s16(c15)); ++ return vreinterpretq_m128i_s16(vpaddq_s16(vreinterpretq_s16_s32(trn1_c), ++ vreinterpretq_s16_s32(trn2_c))); ++#else ++ int16x4_t c01, c23, c45, c67; ++ c01 = vpadd_s16(vget_low_s16(c04), vget_low_s16(c15)); ++ c23 = vpadd_s16(vget_low_s16(c26), vget_low_s16(c37)); ++ c45 = vpadd_s16(vget_high_s16(c04), vget_high_s16(c15)); ++ c67 = vpadd_s16(vget_high_s16(c26), vget_high_s16(c37)); ++ ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vpadd_s16(c01, c23), vpadd_s16(c45, c67))); ++#endif ++} ++ ++// Multiply the low signed 32-bit integers from each packed 64-bit element in ++// a and b, and store the signed 64-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_epi32 ++FORCE_INLINE __m128i _mm_mul_epi32(__m128i a, __m128i b) ++{ ++ // vmull_s32 upcasts instead of masking, so we downcast. ++ int32x2_t a_lo = vmovn_s64(vreinterpretq_s64_m128i(a)); ++ int32x2_t b_lo = vmovn_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vmull_s32(a_lo, b_lo)); ++} ++ ++// Multiply the packed 32-bit integers in a and b, producing intermediate 64-bit ++// integers, and store the low 32 bits of the intermediate integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mullo_epi32 ++FORCE_INLINE __m128i _mm_mullo_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vmulq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Convert packed signed 32-bit integers from a and b to packed 16-bit integers ++// using unsigned saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_packus_epi32 ++FORCE_INLINE __m128i _mm_packus_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcombine_u16(vqmovun_s32(vreinterpretq_s32_m128i(a)), ++ vqmovun_s32(vreinterpretq_s32_m128i(b)))); ++} ++ ++// Round the packed double-precision (64-bit) floating-point elements in a using ++// the rounding parameter, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_round_pd ++FORCE_INLINE_OPTNONE __m128d _mm_round_pd(__m128d a, int rounding) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ switch (rounding) { ++ case (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128d_f64(vrndnq_f64(vreinterpretq_f64_m128d(a))); ++ case (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC): ++ return _mm_floor_pd(a); ++ case (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC): ++ return _mm_ceil_pd(a); ++ case (_MM_FROUND_TO_ZERO | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128d_f64(vrndq_f64(vreinterpretq_f64_m128d(a))); ++ default: //_MM_FROUND_CUR_DIRECTION ++ return vreinterpretq_m128d_f64(vrndiq_f64(vreinterpretq_f64_m128d(a))); ++ } ++#else ++ double *v_double = (double *) &a; ++ ++ if (rounding == (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_NEAREST)) { ++ double res[2], tmp; ++ for (int i = 0; i < 2; i++) { ++ tmp = (v_double[i] < 0) ? -v_double[i] : v_double[i]; ++ double roundDown = floor(tmp); // Round down value ++ double roundUp = ceil(tmp); // Round up value ++ double diffDown = tmp - roundDown; ++ double diffUp = roundUp - tmp; ++ if (diffDown < diffUp) { ++ /* If it's closer to the round down value, then use it */ ++ res[i] = roundDown; ++ } else if (diffDown > diffUp) { ++ /* If it's closer to the round up value, then use it */ ++ res[i] = roundUp; ++ } else { ++ /* If it's equidistant between round up and round down value, ++ * pick the one which is an even number */ ++ double half = roundDown / 2; ++ if (half != floor(half)) { ++ /* If the round down value is odd, return the round up value ++ */ ++ res[i] = roundUp; ++ } else { ++ /* If the round up value is odd, return the round down value ++ */ ++ res[i] = roundDown; ++ } ++ } ++ res[i] = (v_double[i] < 0) ? -res[i] : res[i]; ++ } ++ return _mm_set_pd(res[1], res[0]); ++ } else if (rounding == (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_DOWN)) { ++ return _mm_floor_pd(a); ++ } else if (rounding == (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_UP)) { ++ return _mm_ceil_pd(a); ++ } ++ return _mm_set_pd(v_double[1] > 0 ? floor(v_double[1]) : ceil(v_double[1]), ++ v_double[0] > 0 ? floor(v_double[0]) : ceil(v_double[0])); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a using ++// the rounding parameter, and store the results as packed single-precision ++// floating-point elements in dst. ++// software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_round_ps ++FORCE_INLINE_OPTNONE __m128 _mm_round_ps(__m128 a, int rounding) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ switch (rounding) { ++ case (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128_f32(vrndnq_f32(vreinterpretq_f32_m128(a))); ++ case (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC): ++ return _mm_floor_ps(a); ++ case (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC): ++ return _mm_ceil_ps(a); ++ case (_MM_FROUND_TO_ZERO | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128_f32(vrndq_f32(vreinterpretq_f32_m128(a))); ++ default: //_MM_FROUND_CUR_DIRECTION ++ return vreinterpretq_m128_f32(vrndiq_f32(vreinterpretq_f32_m128(a))); ++ } ++#else ++ float *v_float = (float *) &a; ++ ++ if (rounding == (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_NEAREST)) { ++ uint32x4_t signmask = vdupq_n_u32(0x80000000); ++ float32x4_t half = vbslq_f32(signmask, vreinterpretq_f32_m128(a), ++ vdupq_n_f32(0.5f)); /* +/- 0.5 */ ++ int32x4_t r_normal = vcvtq_s32_f32(vaddq_f32( ++ vreinterpretq_f32_m128(a), half)); /* round to integer: [a + 0.5]*/ ++ int32x4_t r_trunc = vcvtq_s32_f32( ++ vreinterpretq_f32_m128(a)); /* truncate to integer: [a] */ ++ int32x4_t plusone = vreinterpretq_s32_u32(vshrq_n_u32( ++ vreinterpretq_u32_s32(vnegq_s32(r_trunc)), 31)); /* 1 or 0 */ ++ int32x4_t r_even = vbicq_s32(vaddq_s32(r_trunc, plusone), ++ vdupq_n_s32(1)); /* ([a] + {0,1}) & ~1 */ ++ float32x4_t delta = vsubq_f32( ++ vreinterpretq_f32_m128(a), ++ vcvtq_f32_s32(r_trunc)); /* compute delta: delta = (a - [a]) */ ++ uint32x4_t is_delta_half = ++ vceqq_f32(delta, half); /* delta == +/- 0.5 */ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_s32(vbslq_s32(is_delta_half, r_even, r_normal))); ++ } else if (rounding == (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_DOWN)) { ++ return _mm_floor_ps(a); ++ } else if (rounding == (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_UP)) { ++ return _mm_ceil_ps(a); ++ } ++ return _mm_set_ps(v_float[3] > 0 ? floorf(v_float[3]) : ceilf(v_float[3]), ++ v_float[2] > 0 ? floorf(v_float[2]) : ceilf(v_float[2]), ++ v_float[1] > 0 ? floorf(v_float[1]) : ceilf(v_float[1]), ++ v_float[0] > 0 ? floorf(v_float[0]) : ceilf(v_float[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b using ++// the rounding parameter, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_round_sd ++FORCE_INLINE __m128d _mm_round_sd(__m128d a, __m128d b, int rounding) ++{ ++ return _mm_move_sd(a, _mm_round_pd(b, rounding)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b using ++// the rounding parameter, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. Rounding is done according to the ++// rounding[3:0] parameter, which can be one of: ++// (_MM_FROUND_TO_NEAREST_INT |_MM_FROUND_NO_EXC) // round to nearest, and ++// suppress exceptions ++// (_MM_FROUND_TO_NEG_INF |_MM_FROUND_NO_EXC) // round down, and ++// suppress exceptions ++// (_MM_FROUND_TO_POS_INF |_MM_FROUND_NO_EXC) // round up, and suppress ++// exceptions ++// (_MM_FROUND_TO_ZERO |_MM_FROUND_NO_EXC) // truncate, and suppress ++// exceptions _MM_FROUND_CUR_DIRECTION // use MXCSR.RC; see ++// _MM_SET_ROUNDING_MODE ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_round_ss ++FORCE_INLINE __m128 _mm_round_ss(__m128 a, __m128 b, int rounding) ++{ ++ return _mm_move_ss(a, _mm_round_ps(b, rounding)); ++} ++ ++// Load 128-bits of integer data from memory into dst using a non-temporal ++// memory hint. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_load_si128 ++FORCE_INLINE __m128i _mm_stream_load_si128(__m128i *p) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ return __builtin_nontemporal_load(p); ++#else ++ return vreinterpretq_m128i_s64(vld1q_s64((int64_t *) p)); ++#endif ++} ++ ++// Compute the bitwise NOT of a and then AND with a 128-bit vector containing ++// all 1's, and return 1 if the result is zero, otherwise return 0. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_test_all_ones ++FORCE_INLINE int _mm_test_all_ones(__m128i a) ++{ ++ return (uint64_t) (vgetq_lane_s64(a, 0) & vgetq_lane_s64(a, 1)) == ++ ~(uint64_t) 0; ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and ++// mask, and return 1 if the result is zero, otherwise return 0. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_test_all_zeros ++FORCE_INLINE int _mm_test_all_zeros(__m128i a, __m128i mask) ++{ ++ int64x2_t a_and_mask = ++ vandq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(mask)); ++ return !(vgetq_lane_s64(a_and_mask, 0) | vgetq_lane_s64(a_and_mask, 1)); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and ++// mask, and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute ++// the bitwise NOT of a and then AND with mask, and set CF to 1 if the result is ++// zero, otherwise set CF to 0. Return 1 if both the ZF and CF values are zero, ++// otherwise return 0. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_test_mix_ones_zero ++// Note: Argument names may be wrong in the Intel intrinsics guide. ++FORCE_INLINE int _mm_test_mix_ones_zeros(__m128i a, __m128i mask) ++{ ++ uint64x2_t v = vreinterpretq_u64_m128i(a); ++ uint64x2_t m = vreinterpretq_u64_m128i(mask); ++ ++ // find ones (set-bits) and zeros (clear-bits) under clip mask ++ uint64x2_t ones = vandq_u64(m, v); ++ uint64x2_t zeros = vbicq_u64(m, v); ++ ++ // If both 128-bit variables are populated (non-zero) then return 1. ++ // For comparison purposes, first compact each var down to 32-bits. ++ uint32x2_t reduced = vpmax_u32(vqmovn_u64(ones), vqmovn_u64(zeros)); ++ ++ // if folding minimum is non-zero then both vars must be non-zero ++ return (vget_lane_u32(vpmin_u32(reduced, reduced), 0) != 0); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return the CF value. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_testc_si128 ++FORCE_INLINE int _mm_testc_si128(__m128i a, __m128i b) ++{ ++ int64x2_t s64 = ++ vbicq_s64(vreinterpretq_s64_m128i(b), vreinterpretq_s64_m128i(a)); ++ return !(vgetq_lane_s64(s64, 0) | vgetq_lane_s64(s64, 1)); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return 1 if both the ZF and CF values are zero, ++// otherwise return 0. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_testnzc_si128 ++#define _mm_testnzc_si128(a, b) _mm_test_mix_ones_zeros(a, b) ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return the ZF value. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_testz_si128 ++FORCE_INLINE int _mm_testz_si128(__m128i a, __m128i b) ++{ ++ int64x2_t s64 = ++ vandq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b)); ++ return !(vgetq_lane_s64(s64, 0) | vgetq_lane_s64(s64, 1)); ++} ++ ++/* SSE4.2 */ ++ ++static const uint16_t ALIGN_STRUCT(16) _sse2neon_cmpestr_mask16b[8] = { ++ 0x01, 0x02, 0x04, 0x08, 0x10, 0x20, 0x40, 0x80, ++}; ++static const uint8_t ALIGN_STRUCT(16) _sse2neon_cmpestr_mask8b[16] = { ++ 0x01, 0x02, 0x04, 0x08, 0x10, 0x20, 0x40, 0x80, ++ 0x01, 0x02, 0x04, 0x08, 0x10, 0x20, 0x40, 0x80, ++}; ++ ++/* specify the source data format */ ++#define _SIDD_UBYTE_OPS 0x00 /* unsigned 8-bit characters */ ++#define _SIDD_UWORD_OPS 0x01 /* unsigned 16-bit characters */ ++#define _SIDD_SBYTE_OPS 0x02 /* signed 8-bit characters */ ++#define _SIDD_SWORD_OPS 0x03 /* signed 16-bit characters */ ++ ++/* specify the comparison operation */ ++#define _SIDD_CMP_EQUAL_ANY 0x00 /* compare equal any: strchr */ ++#define _SIDD_CMP_RANGES 0x04 /* compare ranges */ ++#define _SIDD_CMP_EQUAL_EACH 0x08 /* compare equal each: strcmp */ ++#define _SIDD_CMP_EQUAL_ORDERED 0x0C /* compare equal ordered */ ++ ++/* specify the polarity */ ++#define _SIDD_POSITIVE_POLARITY 0x00 ++#define _SIDD_MASKED_POSITIVE_POLARITY 0x20 ++#define _SIDD_NEGATIVE_POLARITY 0x10 /* negate results */ ++#define _SIDD_MASKED_NEGATIVE_POLARITY \ ++ 0x30 /* negate results only before end of string */ ++ ++/* specify the output selection in _mm_cmpXstri */ ++#define _SIDD_LEAST_SIGNIFICANT 0x00 ++#define _SIDD_MOST_SIGNIFICANT 0x40 ++ ++/* specify the output selection in _mm_cmpXstrm */ ++#define _SIDD_BIT_MASK 0x00 ++#define _SIDD_UNIT_MASK 0x40 ++ ++/* Pattern Matching for C macros. ++ * https://github.com/pfultz2/Cloak/wiki/C-Preprocessor-tricks,-tips,-and-idioms ++ */ ++ ++/* catenate */ ++#define SSE2NEON_PRIMITIVE_CAT(a, ...) a##__VA_ARGS__ ++#define SSE2NEON_CAT(a, b) SSE2NEON_PRIMITIVE_CAT(a, b) ++ ++#define SSE2NEON_IIF(c) SSE2NEON_PRIMITIVE_CAT(SSE2NEON_IIF_, c) ++/* run the 2nd parameter */ ++#define SSE2NEON_IIF_0(t, ...) __VA_ARGS__ ++/* run the 1st parameter */ ++#define SSE2NEON_IIF_1(t, ...) t ++ ++#define SSE2NEON_COMPL(b) SSE2NEON_PRIMITIVE_CAT(SSE2NEON_COMPL_, b) ++#define SSE2NEON_COMPL_0 1 ++#define SSE2NEON_COMPL_1 0 ++ ++#define SSE2NEON_DEC(x) SSE2NEON_PRIMITIVE_CAT(SSE2NEON_DEC_, x) ++#define SSE2NEON_DEC_1 0 ++#define SSE2NEON_DEC_2 1 ++#define SSE2NEON_DEC_3 2 ++#define SSE2NEON_DEC_4 3 ++#define SSE2NEON_DEC_5 4 ++#define SSE2NEON_DEC_6 5 ++#define SSE2NEON_DEC_7 6 ++#define SSE2NEON_DEC_8 7 ++#define SSE2NEON_DEC_9 8 ++#define SSE2NEON_DEC_10 9 ++#define SSE2NEON_DEC_11 10 ++#define SSE2NEON_DEC_12 11 ++#define SSE2NEON_DEC_13 12 ++#define SSE2NEON_DEC_14 13 ++#define SSE2NEON_DEC_15 14 ++#define SSE2NEON_DEC_16 15 ++ ++/* detection */ ++#define SSE2NEON_CHECK_N(x, n, ...) n ++#define SSE2NEON_CHECK(...) SSE2NEON_CHECK_N(__VA_ARGS__, 0, ) ++#define SSE2NEON_PROBE(x) x, 1, ++ ++#define SSE2NEON_NOT(x) SSE2NEON_CHECK(SSE2NEON_PRIMITIVE_CAT(SSE2NEON_NOT_, x)) ++#define SSE2NEON_NOT_0 SSE2NEON_PROBE(~) ++ ++#define SSE2NEON_BOOL(x) SSE2NEON_COMPL(SSE2NEON_NOT(x)) ++#define SSE2NEON_IF(c) SSE2NEON_IIF(SSE2NEON_BOOL(c)) ++ ++#define SSE2NEON_EAT(...) ++#define SSE2NEON_EXPAND(...) __VA_ARGS__ ++#define SSE2NEON_WHEN(c) SSE2NEON_IF(c)(SSE2NEON_EXPAND, SSE2NEON_EAT) ++ ++/* recursion */ ++/* deferred expression */ ++#define SSE2NEON_EMPTY() ++#define SSE2NEON_DEFER(id) id SSE2NEON_EMPTY() ++#define SSE2NEON_OBSTRUCT(...) __VA_ARGS__ SSE2NEON_DEFER(SSE2NEON_EMPTY)() ++#define SSE2NEON_EXPAND(...) __VA_ARGS__ ++ ++#define SSE2NEON_EVAL(...) \ ++ SSE2NEON_EVAL1(SSE2NEON_EVAL1(SSE2NEON_EVAL1(__VA_ARGS__))) ++#define SSE2NEON_EVAL1(...) \ ++ SSE2NEON_EVAL2(SSE2NEON_EVAL2(SSE2NEON_EVAL2(__VA_ARGS__))) ++#define SSE2NEON_EVAL2(...) \ ++ SSE2NEON_EVAL3(SSE2NEON_EVAL3(SSE2NEON_EVAL3(__VA_ARGS__))) ++#define SSE2NEON_EVAL3(...) __VA_ARGS__ ++ ++#define SSE2NEON_REPEAT(count, macro, ...) \ ++ SSE2NEON_WHEN(count) \ ++ (SSE2NEON_OBSTRUCT(SSE2NEON_REPEAT_INDIRECT)()( \ ++ SSE2NEON_DEC(count), macro, \ ++ __VA_ARGS__) SSE2NEON_OBSTRUCT(macro)(SSE2NEON_DEC(count), \ ++ __VA_ARGS__)) ++#define SSE2NEON_REPEAT_INDIRECT() SSE2NEON_REPEAT ++ ++#define SSE2NEON_SIZE_OF_byte 8 ++#define SSE2NEON_NUMBER_OF_LANES_byte 16 ++#define SSE2NEON_SIZE_OF_word 16 ++#define SSE2NEON_NUMBER_OF_LANES_word 8 ++ ++#define SSE2NEON_COMPARE_EQUAL_THEN_FILL_LANE(i, type) \ ++ mtx[i] = vreinterpretq_m128i_##type(vceqq_##type( \ ++ vdupq_n_##type(vgetq_lane_##type(vreinterpretq_##type##_m128i(b), i)), \ ++ vreinterpretq_##type##_m128i(a))); ++ ++#define SSE2NEON_FILL_LANE(i, type) \ ++ vec_b[i] = \ ++ vdupq_n_##type(vgetq_lane_##type(vreinterpretq_##type##_m128i(b), i)); ++ ++#define PCMPSTR_RANGES(a, b, mtx, data_type_prefix, type_prefix, size, \ ++ number_of_lanes, byte_or_word) \ ++ do { \ ++ SSE2NEON_CAT( \ ++ data_type_prefix, \ ++ SSE2NEON_CAT(size, \ ++ SSE2NEON_CAT(x, SSE2NEON_CAT(number_of_lanes, _t)))) \ ++ vec_b[number_of_lanes]; \ ++ __m128i mask = SSE2NEON_IIF(byte_or_word)( \ ++ vreinterpretq_m128i_u16(vdupq_n_u16(0xff)), \ ++ vreinterpretq_m128i_u32(vdupq_n_u32(0xffff))); \ ++ SSE2NEON_EVAL(SSE2NEON_REPEAT(number_of_lanes, SSE2NEON_FILL_LANE, \ ++ SSE2NEON_CAT(type_prefix, size))) \ ++ for (int i = 0; i < number_of_lanes; i++) { \ ++ mtx[i] = SSE2NEON_CAT(vreinterpretq_m128i_u, \ ++ size)(SSE2NEON_CAT(vbslq_u, size)( \ ++ SSE2NEON_CAT(vreinterpretq_u, \ ++ SSE2NEON_CAT(size, _m128i))(mask), \ ++ SSE2NEON_CAT(vcgeq_, SSE2NEON_CAT(type_prefix, size))( \ ++ vec_b[i], \ ++ SSE2NEON_CAT( \ ++ vreinterpretq_, \ ++ SSE2NEON_CAT(type_prefix, \ ++ SSE2NEON_CAT(size, _m128i(a))))), \ ++ SSE2NEON_CAT(vcleq_, SSE2NEON_CAT(type_prefix, size))( \ ++ vec_b[i], \ ++ SSE2NEON_CAT( \ ++ vreinterpretq_, \ ++ SSE2NEON_CAT(type_prefix, \ ++ SSE2NEON_CAT(size, _m128i(a))))))); \ ++ } \ ++ } while (0) ++ ++#define PCMPSTR_EQ(a, b, mtx, size, number_of_lanes) \ ++ do { \ ++ SSE2NEON_EVAL(SSE2NEON_REPEAT(number_of_lanes, \ ++ SSE2NEON_COMPARE_EQUAL_THEN_FILL_LANE, \ ++ SSE2NEON_CAT(u, size))) \ ++ } while (0) ++ ++#define SSE2NEON_CMP_EQUAL_ANY_IMPL(type) \ ++ static int _sse2neon_cmp_##type##_equal_any(__m128i a, int la, __m128i b, \ ++ int lb) \ ++ { \ ++ __m128i mtx[16]; \ ++ PCMPSTR_EQ(a, b, mtx, SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type)); \ ++ return SSE2NEON_CAT( \ ++ _sse2neon_aggregate_equal_any_, \ ++ SSE2NEON_CAT( \ ++ SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(x, SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, \ ++ type))))(la, lb, mtx); \ ++ } ++ ++#define SSE2NEON_CMP_RANGES_IMPL(type, data_type, us, byte_or_word) \ ++ static int _sse2neon_cmp_##us##type##_ranges(__m128i a, int la, __m128i b, \ ++ int lb) \ ++ { \ ++ __m128i mtx[16]; \ ++ PCMPSTR_RANGES( \ ++ a, b, mtx, data_type, us, SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type), byte_or_word); \ ++ return SSE2NEON_CAT( \ ++ _sse2neon_aggregate_ranges_, \ ++ SSE2NEON_CAT( \ ++ SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(x, SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, \ ++ type))))(la, lb, mtx); \ ++ } ++ ++#define SSE2NEON_CMP_EQUAL_ORDERED_IMPL(type) \ ++ static int _sse2neon_cmp_##type##_equal_ordered(__m128i a, int la, \ ++ __m128i b, int lb) \ ++ { \ ++ __m128i mtx[16]; \ ++ PCMPSTR_EQ(a, b, mtx, SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type)); \ ++ return SSE2NEON_CAT( \ ++ _sse2neon_aggregate_equal_ordered_, \ ++ SSE2NEON_CAT( \ ++ SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(x, \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type))))( \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type), la, lb, mtx); \ ++ } ++ ++static int _sse2neon_aggregate_equal_any_8x16(int la, int lb, __m128i mtx[16]) ++{ ++ int res = 0; ++ int m = (1 << la) - 1; ++ uint8x8_t vec_mask = vld1_u8(_sse2neon_cmpestr_mask8b); ++ uint8x8_t t_lo = vtst_u8(vdup_n_u8(m & 0xff), vec_mask); ++ uint8x8_t t_hi = vtst_u8(vdup_n_u8(m >> 8), vec_mask); ++ uint8x16_t vec = vcombine_u8(t_lo, t_hi); ++ for (int j = 0; j < lb; j++) { ++ mtx[j] = vreinterpretq_m128i_u8( ++ vandq_u8(vec, vreinterpretq_u8_m128i(mtx[j]))); ++ mtx[j] = vreinterpretq_m128i_u8( ++ vshrq_n_u8(vreinterpretq_u8_m128i(mtx[j]), 7)); ++ int tmp = _sse2neon_vaddvq_u8(vreinterpretq_u8_m128i(mtx[j])) ? 1 : 0; ++ res |= (tmp << j); ++ } ++ return res; ++} ++ ++static int _sse2neon_aggregate_equal_any_16x8(int la, int lb, __m128i mtx[16]) ++{ ++ int res = 0; ++ int m = (1 << la) - 1; ++ uint16x8_t vec = ++ vtstq_u16(vdupq_n_u16(m), vld1q_u16(_sse2neon_cmpestr_mask16b)); ++ for (int j = 0; j < lb; j++) { ++ mtx[j] = vreinterpretq_m128i_u16( ++ vandq_u16(vec, vreinterpretq_u16_m128i(mtx[j]))); ++ mtx[j] = vreinterpretq_m128i_u16( ++ vshrq_n_u16(vreinterpretq_u16_m128i(mtx[j]), 15)); ++ int tmp = _sse2neon_vaddvq_u16(vreinterpretq_u16_m128i(mtx[j])) ? 1 : 0; ++ res |= (tmp << j); ++ } ++ return res; ++} ++ ++/* clang-format off */ ++#define SSE2NEON_GENERATE_CMP_EQUAL_ANY(prefix) \ ++ prefix##IMPL(byte) \ ++ prefix##IMPL(word) ++/* clang-format on */ ++ ++SSE2NEON_GENERATE_CMP_EQUAL_ANY(SSE2NEON_CMP_EQUAL_ANY_) ++ ++static int _sse2neon_aggregate_ranges_16x8(int la, int lb, __m128i mtx[16]) ++{ ++ int res = 0; ++ int m = (1 << la) - 1; ++ uint16x8_t vec = ++ vtstq_u16(vdupq_n_u16(m), vld1q_u16(_sse2neon_cmpestr_mask16b)); ++ for (int j = 0; j < lb; j++) { ++ mtx[j] = vreinterpretq_m128i_u16( ++ vandq_u16(vec, vreinterpretq_u16_m128i(mtx[j]))); ++ mtx[j] = vreinterpretq_m128i_u16( ++ vshrq_n_u16(vreinterpretq_u16_m128i(mtx[j]), 15)); ++ __m128i tmp = vreinterpretq_m128i_u32( ++ vshrq_n_u32(vreinterpretq_u32_m128i(mtx[j]), 16)); ++ uint32x4_t vec_res = vandq_u32(vreinterpretq_u32_m128i(mtx[j]), ++ vreinterpretq_u32_m128i(tmp)); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int t = vaddvq_u32(vec_res) ? 1 : 0; ++#else ++ uint64x2_t sumh = vpaddlq_u32(vec_res); ++ int t = vgetq_lane_u64(sumh, 0) + vgetq_lane_u64(sumh, 1); ++#endif ++ res |= (t << j); ++ } ++ return res; ++} ++ ++static int _sse2neon_aggregate_ranges_8x16(int la, int lb, __m128i mtx[16]) ++{ ++ int res = 0; ++ int m = (1 << la) - 1; ++ uint8x8_t vec_mask = vld1_u8(_sse2neon_cmpestr_mask8b); ++ uint8x8_t t_lo = vtst_u8(vdup_n_u8(m & 0xff), vec_mask); ++ uint8x8_t t_hi = vtst_u8(vdup_n_u8(m >> 8), vec_mask); ++ uint8x16_t vec = vcombine_u8(t_lo, t_hi); ++ for (int j = 0; j < lb; j++) { ++ mtx[j] = vreinterpretq_m128i_u8( ++ vandq_u8(vec, vreinterpretq_u8_m128i(mtx[j]))); ++ mtx[j] = vreinterpretq_m128i_u8( ++ vshrq_n_u8(vreinterpretq_u8_m128i(mtx[j]), 7)); ++ __m128i tmp = vreinterpretq_m128i_u16( ++ vshrq_n_u16(vreinterpretq_u16_m128i(mtx[j]), 8)); ++ uint16x8_t vec_res = vandq_u16(vreinterpretq_u16_m128i(mtx[j]), ++ vreinterpretq_u16_m128i(tmp)); ++ int t = _sse2neon_vaddvq_u16(vec_res) ? 1 : 0; ++ res |= (t << j); ++ } ++ return res; ++} ++ ++#define SSE2NEON_CMP_RANGES_IS_BYTE 1 ++#define SSE2NEON_CMP_RANGES_IS_WORD 0 ++ ++/* clang-format off */ ++#define SSE2NEON_GENERATE_CMP_RANGES(prefix) \ ++ prefix##IMPL(byte, uint, u, prefix##IS_BYTE) \ ++ prefix##IMPL(byte, int, s, prefix##IS_BYTE) \ ++ prefix##IMPL(word, uint, u, prefix##IS_WORD) \ ++ prefix##IMPL(word, int, s, prefix##IS_WORD) ++/* clang-format on */ ++ ++SSE2NEON_GENERATE_CMP_RANGES(SSE2NEON_CMP_RANGES_) ++ ++#undef SSE2NEON_CMP_RANGES_IS_BYTE ++#undef SSE2NEON_CMP_RANGES_IS_WORD ++ ++static int _sse2neon_cmp_byte_equal_each(__m128i a, int la, __m128i b, int lb) ++{ ++ uint8x16_t mtx = ++ vceqq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b)); ++ int m0 = (la < lb) ? 0 : ((1 << la) - (1 << lb)); ++ int m1 = 0x10000 - (1 << la); ++ int tb = 0x10000 - (1 << lb); ++ uint8x8_t vec_mask, vec0_lo, vec0_hi, vec1_lo, vec1_hi; ++ uint8x8_t tmp_lo, tmp_hi, res_lo, res_hi; ++ vec_mask = vld1_u8(_sse2neon_cmpestr_mask8b); ++ vec0_lo = vtst_u8(vdup_n_u8(m0), vec_mask); ++ vec0_hi = vtst_u8(vdup_n_u8(m0 >> 8), vec_mask); ++ vec1_lo = vtst_u8(vdup_n_u8(m1), vec_mask); ++ vec1_hi = vtst_u8(vdup_n_u8(m1 >> 8), vec_mask); ++ tmp_lo = vtst_u8(vdup_n_u8(tb), vec_mask); ++ tmp_hi = vtst_u8(vdup_n_u8(tb >> 8), vec_mask); ++ ++ res_lo = vbsl_u8(vec0_lo, vdup_n_u8(0), vget_low_u8(mtx)); ++ res_hi = vbsl_u8(vec0_hi, vdup_n_u8(0), vget_high_u8(mtx)); ++ res_lo = vbsl_u8(vec1_lo, tmp_lo, res_lo); ++ res_hi = vbsl_u8(vec1_hi, tmp_hi, res_hi); ++ res_lo = vand_u8(res_lo, vec_mask); ++ res_hi = vand_u8(res_hi, vec_mask); ++ ++ int res = _sse2neon_vaddv_u8(res_lo) + (_sse2neon_vaddv_u8(res_hi) << 8); ++ return res; ++} ++ ++static int _sse2neon_cmp_word_equal_each(__m128i a, int la, __m128i b, int lb) ++{ ++ uint16x8_t mtx = ++ vceqq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b)); ++ int m0 = (la < lb) ? 0 : ((1 << la) - (1 << lb)); ++ int m1 = 0x100 - (1 << la); ++ int tb = 0x100 - (1 << lb); ++ uint16x8_t vec_mask = vld1q_u16(_sse2neon_cmpestr_mask16b); ++ uint16x8_t vec0 = vtstq_u16(vdupq_n_u16(m0), vec_mask); ++ uint16x8_t vec1 = vtstq_u16(vdupq_n_u16(m1), vec_mask); ++ uint16x8_t tmp = vtstq_u16(vdupq_n_u16(tb), vec_mask); ++ mtx = vbslq_u16(vec0, vdupq_n_u16(0), mtx); ++ mtx = vbslq_u16(vec1, tmp, mtx); ++ mtx = vandq_u16(mtx, vec_mask); ++ return _sse2neon_vaddvq_u16(mtx); ++} ++ ++#define SSE2NEON_AGGREGATE_EQUAL_ORDER_IS_UBYTE 1 ++#define SSE2NEON_AGGREGATE_EQUAL_ORDER_IS_UWORD 0 ++ ++#define SSE2NEON_AGGREGATE_EQUAL_ORDER_IMPL(size, number_of_lanes, data_type) \ ++ static int _sse2neon_aggregate_equal_ordered_##size##x##number_of_lanes( \ ++ int bound, int la, int lb, __m128i mtx[16]) \ ++ { \ ++ int res = 0; \ ++ int m1 = SSE2NEON_IIF(data_type)(0x10000, 0x100) - (1 << la); \ ++ uint##size##x8_t vec_mask = SSE2NEON_IIF(data_type)( \ ++ vld1_u##size(_sse2neon_cmpestr_mask##size##b), \ ++ vld1q_u##size(_sse2neon_cmpestr_mask##size##b)); \ ++ uint##size##x##number_of_lanes##_t vec1 = SSE2NEON_IIF(data_type)( \ ++ vcombine_u##size(vtst_u##size(vdup_n_u##size(m1), vec_mask), \ ++ vtst_u##size(vdup_n_u##size(m1 >> 8), vec_mask)), \ ++ vtstq_u##size(vdupq_n_u##size(m1), vec_mask)); \ ++ uint##size##x##number_of_lanes##_t vec_minusone = vdupq_n_u##size(-1); \ ++ uint##size##x##number_of_lanes##_t vec_zero = vdupq_n_u##size(0); \ ++ for (int j = 0; j < lb; j++) { \ ++ mtx[j] = vreinterpretq_m128i_u##size(vbslq_u##size( \ ++ vec1, vec_minusone, vreinterpretq_u##size##_m128i(mtx[j]))); \ ++ } \ ++ for (int j = lb; j < bound; j++) { \ ++ mtx[j] = vreinterpretq_m128i_u##size( \ ++ vbslq_u##size(vec1, vec_minusone, vec_zero)); \ ++ } \ ++ unsigned SSE2NEON_IIF(data_type)(char, short) *ptr = \ ++ (unsigned SSE2NEON_IIF(data_type)(char, short) *) mtx; \ ++ for (int i = 0; i < bound; i++) { \ ++ int val = 1; \ ++ for (int j = 0, k = i; j < bound - i && k < bound; j++, k++) \ ++ val &= ptr[k * bound + j]; \ ++ res += val << i; \ ++ } \ ++ return res; \ ++ } ++ ++/* clang-format off */ ++#define SSE2NEON_GENERATE_AGGREGATE_EQUAL_ORDER(prefix) \ ++ prefix##IMPL(8, 16, prefix##IS_UBYTE) \ ++ prefix##IMPL(16, 8, prefix##IS_UWORD) ++/* clang-format on */ ++ ++SSE2NEON_GENERATE_AGGREGATE_EQUAL_ORDER(SSE2NEON_AGGREGATE_EQUAL_ORDER_) ++ ++#undef SSE2NEON_AGGREGATE_EQUAL_ORDER_IS_UBYTE ++#undef SSE2NEON_AGGREGATE_EQUAL_ORDER_IS_UWORD ++ ++/* clang-format off */ ++#define SSE2NEON_GENERATE_CMP_EQUAL_ORDERED(prefix) \ ++ prefix##IMPL(byte) \ ++ prefix##IMPL(word) ++/* clang-format on */ ++ ++SSE2NEON_GENERATE_CMP_EQUAL_ORDERED(SSE2NEON_CMP_EQUAL_ORDERED_) ++ ++#define SSE2NEON_CMPESTR_LIST \ ++ _(CMP_UBYTE_EQUAL_ANY, cmp_byte_equal_any) \ ++ _(CMP_UWORD_EQUAL_ANY, cmp_word_equal_any) \ ++ _(CMP_SBYTE_EQUAL_ANY, cmp_byte_equal_any) \ ++ _(CMP_SWORD_EQUAL_ANY, cmp_word_equal_any) \ ++ _(CMP_UBYTE_RANGES, cmp_ubyte_ranges) \ ++ _(CMP_UWORD_RANGES, cmp_uword_ranges) \ ++ _(CMP_SBYTE_RANGES, cmp_sbyte_ranges) \ ++ _(CMP_SWORD_RANGES, cmp_sword_ranges) \ ++ _(CMP_UBYTE_EQUAL_EACH, cmp_byte_equal_each) \ ++ _(CMP_UWORD_EQUAL_EACH, cmp_word_equal_each) \ ++ _(CMP_SBYTE_EQUAL_EACH, cmp_byte_equal_each) \ ++ _(CMP_SWORD_EQUAL_EACH, cmp_word_equal_each) \ ++ _(CMP_UBYTE_EQUAL_ORDERED, cmp_byte_equal_ordered) \ ++ _(CMP_UWORD_EQUAL_ORDERED, cmp_word_equal_ordered) \ ++ _(CMP_SBYTE_EQUAL_ORDERED, cmp_byte_equal_ordered) \ ++ _(CMP_SWORD_EQUAL_ORDERED, cmp_word_equal_ordered) ++ ++enum { ++#define _(name, func_suffix) name, ++ SSE2NEON_CMPESTR_LIST ++#undef _ ++}; ++typedef int (*cmpestr_func_t)(__m128i a, int la, __m128i b, int lb); ++static cmpestr_func_t _sse2neon_cmpfunc_table[] = { ++#define _(name, func_suffix) _sse2neon_##func_suffix, ++ SSE2NEON_CMPESTR_LIST ++#undef _ ++}; ++ ++FORCE_INLINE int _sse2neon_sido_negative(int res, int lb, int imm8, int bound) ++{ ++ switch (imm8 & 0x30) { ++ case _SIDD_NEGATIVE_POLARITY: ++ res ^= 0xffffffff; ++ break; ++ case _SIDD_MASKED_NEGATIVE_POLARITY: ++ res ^= (1 << lb) - 1; ++ break; ++ default: ++ break; ++ } ++ ++ return res & ((bound == 8) ? 0xFF : 0xFFFF); ++} ++ ++FORCE_INLINE int _sse2neon_clz(unsigned int x) ++{ ++#ifdef _MSC_VER ++ unsigned long cnt = 0; ++ if (_BitScanReverse(&cnt, x)) ++ return 31 - cnt; ++ return 32; ++#else ++ return x != 0 ? __builtin_clz(x) : 32; ++#endif ++} ++ ++FORCE_INLINE int _sse2neon_ctz(unsigned int x) ++{ ++#ifdef _MSC_VER ++ unsigned long cnt = 0; ++ if (_BitScanForward(&cnt, x)) ++ return cnt; ++ return 32; ++#else ++ return x != 0 ? __builtin_ctz(x) : 32; ++#endif ++} ++ ++FORCE_INLINE int _sse2neon_ctzll(unsigned long long x) ++{ ++#ifdef _MSC_VER ++ unsigned long cnt; ++#if defined(SSE2NEON_HAS_BITSCAN64) ++ if (_BitScanForward64(&cnt, x)) ++ return (int) (cnt); ++#else ++ if (_BitScanForward(&cnt, (unsigned long) (x))) ++ return (int) cnt; ++ if (_BitScanForward(&cnt, (unsigned long) (x >> 32))) ++ return (int) (cnt + 32); ++#endif /* SSE2NEON_HAS_BITSCAN64 */ ++ return 64; ++#else /* assume GNU compatible compilers */ ++ return x != 0 ? __builtin_ctzll(x) : 64; ++#endif ++} ++ ++#define SSE2NEON_MIN(x, y) (x) < (y) ? (x) : (y) ++ ++#define SSE2NEON_CMPSTR_SET_UPPER(var, imm) \ ++ const int var = (imm & 0x01) ? 8 : 16 ++ ++#define SSE2NEON_CMPESTRX_LEN_PAIR(a, b, la, lb) \ ++ int tmp1 = la ^ (la >> 31); \ ++ la = tmp1 - (la >> 31); \ ++ int tmp2 = lb ^ (lb >> 31); \ ++ lb = tmp2 - (lb >> 31); \ ++ la = SSE2NEON_MIN(la, bound); \ ++ lb = SSE2NEON_MIN(lb, bound) ++ ++// Compare all pairs of character in string a and b, ++// then aggregate the result. ++// As the only difference of PCMPESTR* and PCMPISTR* is the way to calculate the ++// length of string, we use SSE2NEON_CMP{I,E}STRX_GET_LEN to get the length of ++// string a and b. ++#define SSE2NEON_COMP_AGG(a, b, la, lb, imm8, IE) \ ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); \ ++ SSE2NEON_##IE##_LEN_PAIR(a, b, la, lb); \ ++ int r2 = (_sse2neon_cmpfunc_table[imm8 & 0x0f])(a, la, b, lb); \ ++ r2 = _sse2neon_sido_negative(r2, lb, imm8, bound) ++ ++#define SSE2NEON_CMPSTR_GENERATE_INDEX(r2, bound, imm8) \ ++ return (r2 == 0) ? bound \ ++ : ((imm8 & 0x40) ? (31 - _sse2neon_clz(r2)) \ ++ : _sse2neon_ctz(r2)) ++ ++#define SSE2NEON_CMPSTR_GENERATE_MASK(dst) \ ++ __m128i dst = vreinterpretq_m128i_u8(vdupq_n_u8(0)); \ ++ if (imm8 & 0x40) { \ ++ if (bound == 8) { \ ++ uint16x8_t tmp = vtstq_u16(vdupq_n_u16(r2), \ ++ vld1q_u16(_sse2neon_cmpestr_mask16b)); \ ++ dst = vreinterpretq_m128i_u16(vbslq_u16( \ ++ tmp, vdupq_n_u16(-1), vreinterpretq_u16_m128i(dst))); \ ++ } else { \ ++ uint8x16_t vec_r2 = \ ++ vcombine_u8(vdup_n_u8(r2), vdup_n_u8(r2 >> 8)); \ ++ uint8x16_t tmp = \ ++ vtstq_u8(vec_r2, vld1q_u8(_sse2neon_cmpestr_mask8b)); \ ++ dst = vreinterpretq_m128i_u8( \ ++ vbslq_u8(tmp, vdupq_n_u8(-1), vreinterpretq_u8_m128i(dst))); \ ++ } \ ++ } else { \ ++ if (bound == 16) { \ ++ dst = vreinterpretq_m128i_u16( \ ++ vsetq_lane_u16(r2 & 0xffff, vreinterpretq_u16_m128i(dst), 0)); \ ++ } else { \ ++ dst = vreinterpretq_m128i_u8( \ ++ vsetq_lane_u8(r2 & 0xff, vreinterpretq_u8_m128i(dst), 0)); \ ++ } \ ++ } \ ++ return dst ++ ++// Compare packed strings in a and b with lengths la and lb using the control ++// in imm8, and returns 1 if b did not contain a null character and the ++// resulting mask was zero, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestra ++FORCE_INLINE int _mm_cmpestra(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ int lb_cpy = lb; ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ return !r2 & (lb_cpy > bound); ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control in ++// imm8, and returns 1 if the resulting mask was non-zero, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestrc ++FORCE_INLINE int _mm_cmpestrc(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ return r2 != 0; ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control ++// in imm8, and store the generated index in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestri ++FORCE_INLINE int _mm_cmpestri(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ SSE2NEON_CMPSTR_GENERATE_INDEX(r2, bound, imm8); ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control ++// in imm8, and store the generated mask in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestrm ++FORCE_INLINE __m128i ++_mm_cmpestrm(__m128i a, int la, __m128i b, int lb, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ SSE2NEON_CMPSTR_GENERATE_MASK(dst); ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control in ++// imm8, and returns bit 0 of the resulting bit mask. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestro ++FORCE_INLINE int _mm_cmpestro(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ return r2 & 1; ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control in ++// imm8, and returns 1 if any character in a was null, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestrs ++FORCE_INLINE int _mm_cmpestrs(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ (void) a; ++ (void) b; ++ (void) lb; ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); ++ return la <= (bound - 1); ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control in ++// imm8, and returns 1 if any character in b was null, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestrz ++FORCE_INLINE int _mm_cmpestrz(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ (void) a; ++ (void) b; ++ (void) la; ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); ++ return lb <= (bound - 1); ++} ++ ++#define SSE2NEON_CMPISTRX_LENGTH(str, len, imm8) \ ++ do { \ ++ if (imm8 & 0x01) { \ ++ uint16x8_t equal_mask_##str = \ ++ vceqq_u16(vreinterpretq_u16_m128i(str), vdupq_n_u16(0)); \ ++ uint8x8_t res_##str = vshrn_n_u16(equal_mask_##str, 4); \ ++ uint64_t matches_##str = \ ++ vget_lane_u64(vreinterpret_u64_u8(res_##str), 0); \ ++ len = _sse2neon_ctzll(matches_##str) >> 3; \ ++ } else { \ ++ uint16x8_t equal_mask_##str = vreinterpretq_u16_u8( \ ++ vceqq_u8(vreinterpretq_u8_m128i(str), vdupq_n_u8(0))); \ ++ uint8x8_t res_##str = vshrn_n_u16(equal_mask_##str, 4); \ ++ uint64_t matches_##str = \ ++ vget_lane_u64(vreinterpret_u64_u8(res_##str), 0); \ ++ len = _sse2neon_ctzll(matches_##str) >> 2; \ ++ } \ ++ } while (0) ++ ++#define SSE2NEON_CMPISTRX_LEN_PAIR(a, b, la, lb) \ ++ int la, lb; \ ++ do { \ ++ SSE2NEON_CMPISTRX_LENGTH(a, la, imm8); \ ++ SSE2NEON_CMPISTRX_LENGTH(b, lb, imm8); \ ++ } while (0) ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns 1 if b did not contain a null character and the resulting ++// mask was zero, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistra ++FORCE_INLINE int _mm_cmpistra(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ return !r2 & (lb >= bound); ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns 1 if the resulting mask was non-zero, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistrc ++FORCE_INLINE int _mm_cmpistrc(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ return r2 != 0; ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and store the generated index in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistri ++FORCE_INLINE int _mm_cmpistri(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ SSE2NEON_CMPSTR_GENERATE_INDEX(r2, bound, imm8); ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and store the generated mask in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistrm ++FORCE_INLINE __m128i _mm_cmpistrm(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ SSE2NEON_CMPSTR_GENERATE_MASK(dst); ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns bit 0 of the resulting bit mask. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistro ++FORCE_INLINE int _mm_cmpistro(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ return r2 & 1; ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns 1 if any character in a was null, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistrs ++FORCE_INLINE int _mm_cmpistrs(__m128i a, __m128i b, const int imm8) ++{ ++ (void) b; ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); ++ int la; ++ SSE2NEON_CMPISTRX_LENGTH(a, la, imm8); ++ return la <= (bound - 1); ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns 1 if any character in b was null, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistrz ++FORCE_INLINE int _mm_cmpistrz(__m128i a, __m128i b, const int imm8) ++{ ++ (void) a; ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); ++ int lb; ++ SSE2NEON_CMPISTRX_LENGTH(b, lb, imm8); ++ return lb <= (bound - 1); ++} ++ ++// Compares the 2 signed 64-bit integers in a and the 2 signed 64-bit integers ++// in b for greater than. ++FORCE_INLINE __m128i _mm_cmpgt_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_u64( ++ vcgtq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++#else ++ return vreinterpretq_m128i_s64(vshrq_n_s64( ++ vqsubq_s64(vreinterpretq_s64_m128i(b), vreinterpretq_s64_m128i(a)), ++ 63)); ++#endif ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 16-bit integer v, and stores the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_crc32_u16 ++FORCE_INLINE uint32_t _mm_crc32_u16(uint32_t crc, uint16_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32ch %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif ((__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32)) || \ ++ (defined(_M_ARM64) && !defined(__clang__)) ++ crc = __crc32ch(crc, v); ++#else ++ crc = _mm_crc32_u8(crc, v & 0xff); ++ crc = _mm_crc32_u8(crc, (v >> 8) & 0xff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 32-bit integer v, and stores the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_crc32_u32 ++FORCE_INLINE uint32_t _mm_crc32_u32(uint32_t crc, uint32_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cw %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif ((__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32)) || \ ++ (defined(_M_ARM64) && !defined(__clang__)) ++ crc = __crc32cw(crc, v); ++#else ++ crc = _mm_crc32_u16(crc, v & 0xffff); ++ crc = _mm_crc32_u16(crc, (v >> 16) & 0xffff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 64-bit integer v, and stores the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_crc32_u64 ++FORCE_INLINE uint64_t _mm_crc32_u64(uint64_t crc, uint64_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cx %w[c], %w[c], %x[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif (defined(_M_ARM64) && !defined(__clang__)) ++ crc = __crc32cd((uint32_t) crc, v); ++#else ++ crc = _mm_crc32_u32((uint32_t) (crc), v & 0xffffffff); ++ crc = _mm_crc32_u32((uint32_t) (crc), (v >> 32) & 0xffffffff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 8-bit integer v, and stores the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_crc32_u8 ++FORCE_INLINE uint32_t _mm_crc32_u8(uint32_t crc, uint8_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cb %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif ((__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32)) || \ ++ (defined(_M_ARM64) && !defined(__clang__)) ++ crc = __crc32cb(crc, v); ++#else ++ crc ^= v; ++#if defined(__ARM_FEATURE_CRYPTO) ++ // Adapted from: https://mary.rs/lab/crc32/ ++ // Barrent reduction ++ uint64x2_t orig = ++ vcombine_u64(vcreate_u64((uint64_t) (crc) << 24), vcreate_u64(0x0)); ++ uint64x2_t tmp = orig; ++ ++ // Polynomial P(x) of CRC32C ++ uint64_t p = 0x105EC76F1; ++ // Barrett Reduction (in bit-reflected form) constant mu_{64} = \lfloor ++ // 2^{64} / P(x) \rfloor = 0x11f91caf6 ++ uint64_t mu = 0x1dea713f1; ++ ++ // Multiply by mu_{64} ++ tmp = _sse2neon_vmull_p64(vget_low_u64(tmp), vcreate_u64(mu)); ++ // Divide by 2^{64} (mask away the unnecessary bits) ++ tmp = ++ vandq_u64(tmp, vcombine_u64(vcreate_u64(0xFFFFFFFF), vcreate_u64(0x0))); ++ // Multiply by P(x) (shifted left by 1 for alignment reasons) ++ tmp = _sse2neon_vmull_p64(vget_low_u64(tmp), vcreate_u64(p)); ++ // Subtract original from result ++ tmp = veorq_u64(tmp, orig); ++ ++ // Extract the 'lower' (in bit-reflected sense) 32 bits ++ crc = vgetq_lane_u32(vreinterpretq_u32_u64(tmp), 1); ++#else // Fall back to the generic table lookup approach ++ // Adapted from: https://create.stephan-brumme.com/crc32/ ++ // Apply half-byte comparison algorithm for the best ratio between ++ // performance and lookup table. ++ ++ // The lookup table just needs to store every 16th entry ++ // of the standard look-up table. ++ static const uint32_t crc32_half_byte_tbl[] = { ++ 0x00000000, 0x105ec76f, 0x20bd8ede, 0x30e349b1, 0x417b1dbc, 0x5125dad3, ++ 0x61c69362, 0x7198540d, 0x82f63b78, 0x92a8fc17, 0xa24bb5a6, 0xb21572c9, ++ 0xc38d26c4, 0xd3d3e1ab, 0xe330a81a, 0xf36e6f75, ++ }; ++ ++ crc = (crc >> 4) ^ crc32_half_byte_tbl[crc & 0x0F]; ++ crc = (crc >> 4) ^ crc32_half_byte_tbl[crc & 0x0F]; ++#endif ++#endif ++ return crc; ++} ++ ++/* AES */ ++ ++#if !defined(__ARM_FEATURE_CRYPTO) && (!defined(_M_ARM64) || defined(__clang__)) ++/* clang-format off */ ++#define SSE2NEON_AES_SBOX(w) \ ++ { \ ++ w(0x63), w(0x7c), w(0x77), w(0x7b), w(0xf2), w(0x6b), w(0x6f), \ ++ w(0xc5), w(0x30), w(0x01), w(0x67), w(0x2b), w(0xfe), w(0xd7), \ ++ w(0xab), w(0x76), w(0xca), w(0x82), w(0xc9), w(0x7d), w(0xfa), \ ++ w(0x59), w(0x47), w(0xf0), w(0xad), w(0xd4), w(0xa2), w(0xaf), \ ++ w(0x9c), w(0xa4), w(0x72), w(0xc0), w(0xb7), w(0xfd), w(0x93), \ ++ w(0x26), w(0x36), w(0x3f), w(0xf7), w(0xcc), w(0x34), w(0xa5), \ ++ w(0xe5), w(0xf1), w(0x71), w(0xd8), w(0x31), w(0x15), w(0x04), \ ++ w(0xc7), w(0x23), w(0xc3), w(0x18), w(0x96), w(0x05), w(0x9a), \ ++ w(0x07), w(0x12), w(0x80), w(0xe2), w(0xeb), w(0x27), w(0xb2), \ ++ w(0x75), w(0x09), w(0x83), w(0x2c), w(0x1a), w(0x1b), w(0x6e), \ ++ w(0x5a), w(0xa0), w(0x52), w(0x3b), w(0xd6), w(0xb3), w(0x29), \ ++ w(0xe3), w(0x2f), w(0x84), w(0x53), w(0xd1), w(0x00), w(0xed), \ ++ w(0x20), w(0xfc), w(0xb1), w(0x5b), w(0x6a), w(0xcb), w(0xbe), \ ++ w(0x39), w(0x4a), w(0x4c), w(0x58), w(0xcf), w(0xd0), w(0xef), \ ++ w(0xaa), w(0xfb), w(0x43), w(0x4d), w(0x33), w(0x85), w(0x45), \ ++ w(0xf9), w(0x02), w(0x7f), w(0x50), w(0x3c), w(0x9f), w(0xa8), \ ++ w(0x51), w(0xa3), w(0x40), w(0x8f), w(0x92), w(0x9d), w(0x38), \ ++ w(0xf5), w(0xbc), w(0xb6), w(0xda), w(0x21), w(0x10), w(0xff), \ ++ w(0xf3), w(0xd2), w(0xcd), w(0x0c), w(0x13), w(0xec), w(0x5f), \ ++ w(0x97), w(0x44), w(0x17), w(0xc4), w(0xa7), w(0x7e), w(0x3d), \ ++ w(0x64), w(0x5d), w(0x19), w(0x73), w(0x60), w(0x81), w(0x4f), \ ++ w(0xdc), w(0x22), w(0x2a), w(0x90), w(0x88), w(0x46), w(0xee), \ ++ w(0xb8), w(0x14), w(0xde), w(0x5e), w(0x0b), w(0xdb), w(0xe0), \ ++ w(0x32), w(0x3a), w(0x0a), w(0x49), w(0x06), w(0x24), w(0x5c), \ ++ w(0xc2), w(0xd3), w(0xac), w(0x62), w(0x91), w(0x95), w(0xe4), \ ++ w(0x79), w(0xe7), w(0xc8), w(0x37), w(0x6d), w(0x8d), w(0xd5), \ ++ w(0x4e), w(0xa9), w(0x6c), w(0x56), w(0xf4), w(0xea), w(0x65), \ ++ w(0x7a), w(0xae), w(0x08), w(0xba), w(0x78), w(0x25), w(0x2e), \ ++ w(0x1c), w(0xa6), w(0xb4), w(0xc6), w(0xe8), w(0xdd), w(0x74), \ ++ w(0x1f), w(0x4b), w(0xbd), w(0x8b), w(0x8a), w(0x70), w(0x3e), \ ++ w(0xb5), w(0x66), w(0x48), w(0x03), w(0xf6), w(0x0e), w(0x61), \ ++ w(0x35), w(0x57), w(0xb9), w(0x86), w(0xc1), w(0x1d), w(0x9e), \ ++ w(0xe1), w(0xf8), w(0x98), w(0x11), w(0x69), w(0xd9), w(0x8e), \ ++ w(0x94), w(0x9b), w(0x1e), w(0x87), w(0xe9), w(0xce), w(0x55), \ ++ w(0x28), w(0xdf), w(0x8c), w(0xa1), w(0x89), w(0x0d), w(0xbf), \ ++ w(0xe6), w(0x42), w(0x68), w(0x41), w(0x99), w(0x2d), w(0x0f), \ ++ w(0xb0), w(0x54), w(0xbb), w(0x16) \ ++ } ++#define SSE2NEON_AES_RSBOX(w) \ ++ { \ ++ w(0x52), w(0x09), w(0x6a), w(0xd5), w(0x30), w(0x36), w(0xa5), \ ++ w(0x38), w(0xbf), w(0x40), w(0xa3), w(0x9e), w(0x81), w(0xf3), \ ++ w(0xd7), w(0xfb), w(0x7c), w(0xe3), w(0x39), w(0x82), w(0x9b), \ ++ w(0x2f), w(0xff), w(0x87), w(0x34), w(0x8e), w(0x43), w(0x44), \ ++ w(0xc4), w(0xde), w(0xe9), w(0xcb), w(0x54), w(0x7b), w(0x94), \ ++ w(0x32), w(0xa6), w(0xc2), w(0x23), w(0x3d), w(0xee), w(0x4c), \ ++ w(0x95), w(0x0b), w(0x42), w(0xfa), w(0xc3), w(0x4e), w(0x08), \ ++ w(0x2e), w(0xa1), w(0x66), w(0x28), w(0xd9), w(0x24), w(0xb2), \ ++ w(0x76), w(0x5b), w(0xa2), w(0x49), w(0x6d), w(0x8b), w(0xd1), \ ++ w(0x25), w(0x72), w(0xf8), w(0xf6), w(0x64), w(0x86), w(0x68), \ ++ w(0x98), w(0x16), w(0xd4), w(0xa4), w(0x5c), w(0xcc), w(0x5d), \ ++ w(0x65), w(0xb6), w(0x92), w(0x6c), w(0x70), w(0x48), w(0x50), \ ++ w(0xfd), w(0xed), w(0xb9), w(0xda), w(0x5e), w(0x15), w(0x46), \ ++ w(0x57), w(0xa7), w(0x8d), w(0x9d), w(0x84), w(0x90), w(0xd8), \ ++ w(0xab), w(0x00), w(0x8c), w(0xbc), w(0xd3), w(0x0a), w(0xf7), \ ++ w(0xe4), w(0x58), w(0x05), w(0xb8), w(0xb3), w(0x45), w(0x06), \ ++ w(0xd0), w(0x2c), w(0x1e), w(0x8f), w(0xca), w(0x3f), w(0x0f), \ ++ w(0x02), w(0xc1), w(0xaf), w(0xbd), w(0x03), w(0x01), w(0x13), \ ++ w(0x8a), w(0x6b), w(0x3a), w(0x91), w(0x11), w(0x41), w(0x4f), \ ++ w(0x67), w(0xdc), w(0xea), w(0x97), w(0xf2), w(0xcf), w(0xce), \ ++ w(0xf0), w(0xb4), w(0xe6), w(0x73), w(0x96), w(0xac), w(0x74), \ ++ w(0x22), w(0xe7), w(0xad), w(0x35), w(0x85), w(0xe2), w(0xf9), \ ++ w(0x37), w(0xe8), w(0x1c), w(0x75), w(0xdf), w(0x6e), w(0x47), \ ++ w(0xf1), w(0x1a), w(0x71), w(0x1d), w(0x29), w(0xc5), w(0x89), \ ++ w(0x6f), w(0xb7), w(0x62), w(0x0e), w(0xaa), w(0x18), w(0xbe), \ ++ w(0x1b), w(0xfc), w(0x56), w(0x3e), w(0x4b), w(0xc6), w(0xd2), \ ++ w(0x79), w(0x20), w(0x9a), w(0xdb), w(0xc0), w(0xfe), w(0x78), \ ++ w(0xcd), w(0x5a), w(0xf4), w(0x1f), w(0xdd), w(0xa8), w(0x33), \ ++ w(0x88), w(0x07), w(0xc7), w(0x31), w(0xb1), w(0x12), w(0x10), \ ++ w(0x59), w(0x27), w(0x80), w(0xec), w(0x5f), w(0x60), w(0x51), \ ++ w(0x7f), w(0xa9), w(0x19), w(0xb5), w(0x4a), w(0x0d), w(0x2d), \ ++ w(0xe5), w(0x7a), w(0x9f), w(0x93), w(0xc9), w(0x9c), w(0xef), \ ++ w(0xa0), w(0xe0), w(0x3b), w(0x4d), w(0xae), w(0x2a), w(0xf5), \ ++ w(0xb0), w(0xc8), w(0xeb), w(0xbb), w(0x3c), w(0x83), w(0x53), \ ++ w(0x99), w(0x61), w(0x17), w(0x2b), w(0x04), w(0x7e), w(0xba), \ ++ w(0x77), w(0xd6), w(0x26), w(0xe1), w(0x69), w(0x14), w(0x63), \ ++ w(0x55), w(0x21), w(0x0c), w(0x7d) \ ++ } ++/* clang-format on */ ++ ++/* X Macro trick. See https://en.wikipedia.org/wiki/X_Macro */ ++#define SSE2NEON_AES_H0(x) (x) ++static const uint8_t _sse2neon_sbox[256] = SSE2NEON_AES_SBOX(SSE2NEON_AES_H0); ++static const uint8_t _sse2neon_rsbox[256] = SSE2NEON_AES_RSBOX(SSE2NEON_AES_H0); ++#undef SSE2NEON_AES_H0 ++ ++/* x_time function and matrix multiply function */ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++#define SSE2NEON_XT(x) (((x) << 1) ^ ((((x) >> 7) & 1) * 0x1b)) ++#define SSE2NEON_MULTIPLY(x, y) \ ++ (((y & 1) * x) ^ ((y >> 1 & 1) * SSE2NEON_XT(x)) ^ \ ++ ((y >> 2 & 1) * SSE2NEON_XT(SSE2NEON_XT(x))) ^ \ ++ ((y >> 3 & 1) * SSE2NEON_XT(SSE2NEON_XT(SSE2NEON_XT(x)))) ^ \ ++ ((y >> 4 & 1) * SSE2NEON_XT(SSE2NEON_XT(SSE2NEON_XT(SSE2NEON_XT(x)))))) ++#endif ++ ++// In the absence of crypto extensions, implement aesenc using regular NEON ++// intrinsics instead. See: ++// https://www.workofard.com/2017/01/accelerated-aes-for-the-arm64-linux-kernel/ ++// https://www.workofard.com/2017/07/ghash-for-low-end-cores/ and ++// for more information. ++FORCE_INLINE __m128i _mm_aesenc_si128(__m128i a, __m128i RoundKey) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ static const uint8_t shift_rows[] = { ++ 0x0, 0x5, 0xa, 0xf, 0x4, 0x9, 0xe, 0x3, ++ 0x8, 0xd, 0x2, 0x7, 0xc, 0x1, 0x6, 0xb, ++ }; ++ static const uint8_t ror32by8[] = { ++ 0x1, 0x2, 0x3, 0x0, 0x5, 0x6, 0x7, 0x4, ++ 0x9, 0xa, 0xb, 0x8, 0xd, 0xe, 0xf, 0xc, ++ }; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(a); ++ ++ /* shift rows */ ++ w = vqtbl1q_u8(w, vld1q_u8(shift_rows)); ++ ++ /* sub bytes */ ++ // Here, we separate the whole 256-bytes table into 4 64-bytes tables, and ++ // look up each of the table. After each lookup, we load the next table ++ // which locates at the next 64-bytes. In the meantime, the index in the ++ // table would be smaller than it was, so the index parameters of ++ // `vqtbx4q_u8()` need to be added the same constant as the loaded tables. ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_sbox), w); ++ // 'w-0x40' equals to 'vsubq_u8(w, vdupq_n_u8(0x40))' ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0xc0), w - 0xc0); ++ ++ /* mix columns */ ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w ^= (uint8x16_t) vrev32q_u16((uint16x8_t) v); ++ w ^= vqtbl1q_u8(v ^ w, vld1q_u8(ror32by8)); ++ ++ /* add round key */ ++ return vreinterpretq_m128i_u8(w) ^ RoundKey; ++ ++#else /* ARMv7-A implementation for a table-based AES */ ++#define SSE2NEON_AES_B2W(b0, b1, b2, b3) \ ++ (((uint32_t) (b3) << 24) | ((uint32_t) (b2) << 16) | \ ++ ((uint32_t) (b1) << 8) | (uint32_t) (b0)) ++// multiplying 'x' by 2 in GF(2^8) ++#define SSE2NEON_AES_F2(x) ((x << 1) ^ (((x >> 7) & 1) * 0x011b /* WPOLY */)) ++// multiplying 'x' by 3 in GF(2^8) ++#define SSE2NEON_AES_F3(x) (SSE2NEON_AES_F2(x) ^ x) ++#define SSE2NEON_AES_U0(p) \ ++ SSE2NEON_AES_B2W(SSE2NEON_AES_F2(p), p, p, SSE2NEON_AES_F3(p)) ++#define SSE2NEON_AES_U1(p) \ ++ SSE2NEON_AES_B2W(SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p), p, p) ++#define SSE2NEON_AES_U2(p) \ ++ SSE2NEON_AES_B2W(p, SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p), p) ++#define SSE2NEON_AES_U3(p) \ ++ SSE2NEON_AES_B2W(p, p, SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p)) ++ ++ // this generates a table containing every possible permutation of ++ // shift_rows() and sub_bytes() with mix_columns(). ++ static const uint32_t ALIGN_STRUCT(16) aes_table[4][256] = { ++ SSE2NEON_AES_SBOX(SSE2NEON_AES_U0), ++ SSE2NEON_AES_SBOX(SSE2NEON_AES_U1), ++ SSE2NEON_AES_SBOX(SSE2NEON_AES_U2), ++ SSE2NEON_AES_SBOX(SSE2NEON_AES_U3), ++ }; ++#undef SSE2NEON_AES_B2W ++#undef SSE2NEON_AES_F2 ++#undef SSE2NEON_AES_F3 ++#undef SSE2NEON_AES_U0 ++#undef SSE2NEON_AES_U1 ++#undef SSE2NEON_AES_U2 ++#undef SSE2NEON_AES_U3 ++ ++ uint32_t x0 = _mm_cvtsi128_si32(a); // get a[31:0] ++ uint32_t x1 = ++ _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0x55)); // get a[63:32] ++ uint32_t x2 = ++ _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0xAA)); // get a[95:64] ++ uint32_t x3 = ++ _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0xFF)); // get a[127:96] ++ ++ // finish the modulo addition step in mix_columns() ++ __m128i out = _mm_set_epi32( ++ (aes_table[0][x3 & 0xff] ^ aes_table[1][(x0 >> 8) & 0xff] ^ ++ aes_table[2][(x1 >> 16) & 0xff] ^ aes_table[3][x2 >> 24]), ++ (aes_table[0][x2 & 0xff] ^ aes_table[1][(x3 >> 8) & 0xff] ^ ++ aes_table[2][(x0 >> 16) & 0xff] ^ aes_table[3][x1 >> 24]), ++ (aes_table[0][x1 & 0xff] ^ aes_table[1][(x2 >> 8) & 0xff] ^ ++ aes_table[2][(x3 >> 16) & 0xff] ^ aes_table[3][x0 >> 24]), ++ (aes_table[0][x0 & 0xff] ^ aes_table[1][(x1 >> 8) & 0xff] ^ ++ aes_table[2][(x2 >> 16) & 0xff] ^ aes_table[3][x3 >> 24])); ++ ++ return _mm_xor_si128(out, RoundKey); ++#endif ++} ++ ++// Perform one round of an AES decryption flow on data (state) in a using the ++// round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesdec_si128 ++FORCE_INLINE __m128i _mm_aesdec_si128(__m128i a, __m128i RoundKey) ++{ ++#if defined(__aarch64__) ++ static const uint8_t inv_shift_rows[] = { ++ 0x0, 0xd, 0xa, 0x7, 0x4, 0x1, 0xe, 0xb, ++ 0x8, 0x5, 0x2, 0xf, 0xc, 0x9, 0x6, 0x3, ++ }; ++ static const uint8_t ror32by8[] = { ++ 0x1, 0x2, 0x3, 0x0, 0x5, 0x6, 0x7, 0x4, ++ 0x9, 0xa, 0xb, 0x8, 0xd, 0xe, 0xf, 0xc, ++ }; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(a); ++ ++ // inverse shift rows ++ w = vqtbl1q_u8(w, vld1q_u8(inv_shift_rows)); ++ ++ // inverse sub bytes ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_rsbox), w); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0xc0), w - 0xc0); ++ ++ // inverse mix columns ++ // multiplying 'v' by 4 in GF(2^8) ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w = (w << 1) ^ (uint8x16_t) (((int8x16_t) w >> 7) & 0x1b); ++ v ^= w; ++ v ^= (uint8x16_t) vrev32q_u16((uint16x8_t) w); ++ ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & ++ 0x1b); // multiplying 'v' by 2 in GF(2^8) ++ w ^= (uint8x16_t) vrev32q_u16((uint16x8_t) v); ++ w ^= vqtbl1q_u8(v ^ w, vld1q_u8(ror32by8)); ++ ++ // add round key ++ return vreinterpretq_m128i_u8(w) ^ RoundKey; ++ ++#else /* ARMv7-A NEON implementation */ ++ /* FIXME: optimized for NEON */ ++ uint8_t i, e, f, g, h, v[4][4]; ++ uint8_t *_a = (uint8_t *) &a; ++ for (i = 0; i < 16; ++i) { ++ v[((i / 4) + (i % 4)) % 4][i % 4] = _sse2neon_rsbox[_a[i]]; ++ } ++ ++ // inverse mix columns ++ for (i = 0; i < 4; ++i) { ++ e = v[i][0]; ++ f = v[i][1]; ++ g = v[i][2]; ++ h = v[i][3]; ++ ++ v[i][0] = SSE2NEON_MULTIPLY(e, 0x0e) ^ SSE2NEON_MULTIPLY(f, 0x0b) ^ ++ SSE2NEON_MULTIPLY(g, 0x0d) ^ SSE2NEON_MULTIPLY(h, 0x09); ++ v[i][1] = SSE2NEON_MULTIPLY(e, 0x09) ^ SSE2NEON_MULTIPLY(f, 0x0e) ^ ++ SSE2NEON_MULTIPLY(g, 0x0b) ^ SSE2NEON_MULTIPLY(h, 0x0d); ++ v[i][2] = SSE2NEON_MULTIPLY(e, 0x0d) ^ SSE2NEON_MULTIPLY(f, 0x09) ^ ++ SSE2NEON_MULTIPLY(g, 0x0e) ^ SSE2NEON_MULTIPLY(h, 0x0b); ++ v[i][3] = SSE2NEON_MULTIPLY(e, 0x0b) ^ SSE2NEON_MULTIPLY(f, 0x0d) ^ ++ SSE2NEON_MULTIPLY(g, 0x09) ^ SSE2NEON_MULTIPLY(h, 0x0e); ++ } ++ ++ return vreinterpretq_m128i_u8(vld1q_u8((uint8_t *) v)) ^ RoundKey; ++#endif ++} ++ ++// Perform the last round of an AES encryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesenclast_si128 ++FORCE_INLINE __m128i _mm_aesenclast_si128(__m128i a, __m128i RoundKey) ++{ ++#if defined(__aarch64__) ++ static const uint8_t shift_rows[] = { ++ 0x0, 0x5, 0xa, 0xf, 0x4, 0x9, 0xe, 0x3, ++ 0x8, 0xd, 0x2, 0x7, 0xc, 0x1, 0x6, 0xb, ++ }; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(a); ++ ++ // shift rows ++ w = vqtbl1q_u8(w, vld1q_u8(shift_rows)); ++ ++ // sub bytes ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_sbox), w); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0xc0), w - 0xc0); ++ ++ // add round key ++ return vreinterpretq_m128i_u8(v) ^ RoundKey; ++ ++#else /* ARMv7-A implementation */ ++ uint8_t v[16] = { ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 0)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 5)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 10)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 15)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 4)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 9)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 14)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 3)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 8)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 13)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 2)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 7)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 12)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 1)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 6)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 11)], ++ }; ++ ++ return vreinterpretq_m128i_u8(vld1q_u8(v)) ^ RoundKey; ++#endif ++} ++ ++// Perform the last round of an AES decryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesdeclast_si128 ++FORCE_INLINE __m128i _mm_aesdeclast_si128(__m128i a, __m128i RoundKey) ++{ ++#if defined(__aarch64__) ++ static const uint8_t inv_shift_rows[] = { ++ 0x0, 0xd, 0xa, 0x7, 0x4, 0x1, 0xe, 0xb, ++ 0x8, 0x5, 0x2, 0xf, 0xc, 0x9, 0x6, 0x3, ++ }; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(a); ++ ++ // inverse shift rows ++ w = vqtbl1q_u8(w, vld1q_u8(inv_shift_rows)); ++ ++ // inverse sub bytes ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_rsbox), w); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0xc0), w - 0xc0); ++ ++ // add round key ++ return vreinterpretq_m128i_u8(v) ^ RoundKey; ++ ++#else /* ARMv7-A NEON implementation */ ++ /* FIXME: optimized for NEON */ ++ uint8_t v[4][4]; ++ uint8_t *_a = (uint8_t *) &a; ++ for (int i = 0; i < 16; ++i) { ++ v[((i / 4) + (i % 4)) % 4][i % 4] = _sse2neon_rsbox[_a[i]]; ++ } ++ ++ return vreinterpretq_m128i_u8(vld1q_u8((uint8_t *) v)) ^ RoundKey; ++#endif ++} ++ ++// Perform the InvMixColumns transformation on a and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesimc_si128 ++FORCE_INLINE __m128i _mm_aesimc_si128(__m128i a) ++{ ++#if defined(__aarch64__) ++ static const uint8_t ror32by8[] = { ++ 0x1, 0x2, 0x3, 0x0, 0x5, 0x6, 0x7, 0x4, ++ 0x9, 0xa, 0xb, 0x8, 0xd, 0xe, 0xf, 0xc, ++ }; ++ uint8x16_t v = vreinterpretq_u8_m128i(a); ++ uint8x16_t w; ++ ++ // multiplying 'v' by 4 in GF(2^8) ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w = (w << 1) ^ (uint8x16_t) (((int8x16_t) w >> 7) & 0x1b); ++ v ^= w; ++ v ^= (uint8x16_t) vrev32q_u16((uint16x8_t) w); ++ ++ // multiplying 'v' by 2 in GF(2^8) ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w ^= (uint8x16_t) vrev32q_u16((uint16x8_t) v); ++ w ^= vqtbl1q_u8(v ^ w, vld1q_u8(ror32by8)); ++ return vreinterpretq_m128i_u8(w); ++ ++#else /* ARMv7-A NEON implementation */ ++ uint8_t i, e, f, g, h, v[4][4]; ++ vst1q_u8((uint8_t *) v, vreinterpretq_u8_m128i(a)); ++ for (i = 0; i < 4; ++i) { ++ e = v[i][0]; ++ f = v[i][1]; ++ g = v[i][2]; ++ h = v[i][3]; ++ ++ v[i][0] = SSE2NEON_MULTIPLY(e, 0x0e) ^ SSE2NEON_MULTIPLY(f, 0x0b) ^ ++ SSE2NEON_MULTIPLY(g, 0x0d) ^ SSE2NEON_MULTIPLY(h, 0x09); ++ v[i][1] = SSE2NEON_MULTIPLY(e, 0x09) ^ SSE2NEON_MULTIPLY(f, 0x0e) ^ ++ SSE2NEON_MULTIPLY(g, 0x0b) ^ SSE2NEON_MULTIPLY(h, 0x0d); ++ v[i][2] = SSE2NEON_MULTIPLY(e, 0x0d) ^ SSE2NEON_MULTIPLY(f, 0x09) ^ ++ SSE2NEON_MULTIPLY(g, 0x0e) ^ SSE2NEON_MULTIPLY(h, 0x0b); ++ v[i][3] = SSE2NEON_MULTIPLY(e, 0x0b) ^ SSE2NEON_MULTIPLY(f, 0x0d) ^ ++ SSE2NEON_MULTIPLY(g, 0x09) ^ SSE2NEON_MULTIPLY(h, 0x0e); ++ } ++ ++ return vreinterpretq_m128i_u8(vld1q_u8((uint8_t *) v)); ++#endif ++} ++ ++// Assist in expanding the AES cipher key by computing steps towards generating ++// a round key for encryption cipher using data from a and an 8-bit round ++// constant specified in imm8, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aeskeygenassist_si128 ++// ++// Emits the Advanced Encryption Standard (AES) instruction aeskeygenassist. ++// This instruction generates a round key for AES encryption. See ++// https://kazakov.life/2017/11/01/cryptocurrency-mining-on-ios-devices/ ++// for details. ++FORCE_INLINE __m128i _mm_aeskeygenassist_si128(__m128i a, const int rcon) ++{ ++#if defined(__aarch64__) ++ uint8x16_t _a = vreinterpretq_u8_m128i(a); ++ uint8x16_t v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_sbox), _a); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x40), _a - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x80), _a - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0xc0), _a - 0xc0); ++ ++ uint32x4_t v_u32 = vreinterpretq_u32_u8(v); ++ uint32x4_t ror_v = vorrq_u32(vshrq_n_u32(v_u32, 8), vshlq_n_u32(v_u32, 24)); ++ uint32x4_t ror_xor_v = veorq_u32(ror_v, vdupq_n_u32(rcon)); ++ ++ return vreinterpretq_m128i_u32(vtrn2q_u32(v_u32, ror_xor_v)); ++ ++#else /* ARMv7-A NEON implementation */ ++ uint32_t X1 = _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0x55)); ++ uint32_t X3 = _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0xFF)); ++ for (int i = 0; i < 4; ++i) { ++ ((uint8_t *) &X1)[i] = _sse2neon_sbox[((uint8_t *) &X1)[i]]; ++ ((uint8_t *) &X3)[i] = _sse2neon_sbox[((uint8_t *) &X3)[i]]; ++ } ++ return _mm_set_epi32(((X3 >> 8) | (X3 << 24)) ^ rcon, X3, ++ ((X1 >> 8) | (X1 << 24)) ^ rcon, X1); ++#endif ++} ++#undef SSE2NEON_AES_SBOX ++#undef SSE2NEON_AES_RSBOX ++ ++#if defined(__aarch64__) ++#undef SSE2NEON_XT ++#undef SSE2NEON_MULTIPLY ++#endif ++ ++#else /* __ARM_FEATURE_CRYPTO */ ++// Implements equivalent of 'aesenc' by combining AESE (with an empty key) and ++// AESMC and then manually applying the real key as an xor operation. This ++// unfortunately means an additional xor op; the compiler should be able to ++// optimize this away for repeated calls however. See ++// https://blog.michaelbrase.com/2018/05/08/emulating-x86-aes-intrinsics-on-armv8-a ++// for more details. ++FORCE_INLINE __m128i _mm_aesenc_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8(veorq_u8( ++ vaesmcq_u8(vaeseq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0))), ++ vreinterpretq_u8_m128i(b))); ++} ++ ++// Perform one round of an AES decryption flow on data (state) in a using the ++// round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesdec_si128 ++FORCE_INLINE __m128i _mm_aesdec_si128(__m128i a, __m128i RoundKey) ++{ ++ return vreinterpretq_m128i_u8(veorq_u8( ++ vaesimcq_u8(vaesdq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0))), ++ vreinterpretq_u8_m128i(RoundKey))); ++} ++ ++// Perform the last round of an AES encryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesenclast_si128 ++FORCE_INLINE __m128i _mm_aesenclast_si128(__m128i a, __m128i RoundKey) ++{ ++ return _mm_xor_si128(vreinterpretq_m128i_u8(vaeseq_u8( ++ vreinterpretq_u8_m128i(a), vdupq_n_u8(0))), ++ RoundKey); ++} ++ ++// Perform the last round of an AES decryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesdeclast_si128 ++FORCE_INLINE __m128i _mm_aesdeclast_si128(__m128i a, __m128i RoundKey) ++{ ++ return vreinterpretq_m128i_u8( ++ veorq_u8(vaesdq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0)), ++ vreinterpretq_u8_m128i(RoundKey))); ++} ++ ++// Perform the InvMixColumns transformation on a and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesimc_si128 ++FORCE_INLINE __m128i _mm_aesimc_si128(__m128i a) ++{ ++ return vreinterpretq_m128i_u8(vaesimcq_u8(vreinterpretq_u8_m128i(a))); ++} ++ ++// Assist in expanding the AES cipher key by computing steps towards generating ++// a round key for encryption cipher using data from a and an 8-bit round ++// constant specified in imm8, and store the result in dst." ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aeskeygenassist_si128 ++FORCE_INLINE __m128i _mm_aeskeygenassist_si128(__m128i a, const int rcon) ++{ ++ // AESE does ShiftRows and SubBytes on A ++ uint8x16_t u8 = vaeseq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0)); ++ ++#ifndef _MSC_VER ++ uint8x16_t dest = { ++ // Undo ShiftRows step from AESE and extract X1 and X3 ++ u8[0x4], u8[0x1], u8[0xE], u8[0xB], // SubBytes(X1) ++ u8[0x1], u8[0xE], u8[0xB], u8[0x4], // ROT(SubBytes(X1)) ++ u8[0xC], u8[0x9], u8[0x6], u8[0x3], // SubBytes(X3) ++ u8[0x9], u8[0x6], u8[0x3], u8[0xC], // ROT(SubBytes(X3)) ++ }; ++ uint32x4_t r = {0, (unsigned) rcon, 0, (unsigned) rcon}; ++ return vreinterpretq_m128i_u8(dest) ^ vreinterpretq_m128i_u32(r); ++#else ++ // We have to do this hack because MSVC is strictly adhering to the CPP ++ // standard, in particular C++03 8.5.1 sub-section 15, which states that ++ // unions must be initialized by their first member type. ++ ++ // As per the Windows ARM64 ABI, it is always little endian, so this works ++ __n128 dest{ ++ ((uint64_t) u8.n128_u8[0x4] << 0) | ((uint64_t) u8.n128_u8[0x1] << 8) | ++ ((uint64_t) u8.n128_u8[0xE] << 16) | ++ ((uint64_t) u8.n128_u8[0xB] << 24) | ++ ((uint64_t) u8.n128_u8[0x1] << 32) | ++ ((uint64_t) u8.n128_u8[0xE] << 40) | ++ ((uint64_t) u8.n128_u8[0xB] << 48) | ++ ((uint64_t) u8.n128_u8[0x4] << 56), ++ ((uint64_t) u8.n128_u8[0xC] << 0) | ((uint64_t) u8.n128_u8[0x9] << 8) | ++ ((uint64_t) u8.n128_u8[0x6] << 16) | ++ ((uint64_t) u8.n128_u8[0x3] << 24) | ++ ((uint64_t) u8.n128_u8[0x9] << 32) | ++ ((uint64_t) u8.n128_u8[0x6] << 40) | ++ ((uint64_t) u8.n128_u8[0x3] << 48) | ++ ((uint64_t) u8.n128_u8[0xC] << 56)}; ++ ++ dest.n128_u32[1] = dest.n128_u32[1] ^ rcon; ++ dest.n128_u32[3] = dest.n128_u32[3] ^ rcon; ++ ++ return dest; ++#endif ++} ++#endif ++ ++/* Others */ ++ ++// Perform a carry-less multiplication of two 64-bit integers, selected from a ++// and b according to imm8, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_clmulepi64_si128 ++FORCE_INLINE __m128i _mm_clmulepi64_si128(__m128i _a, __m128i _b, const int imm) ++{ ++ uint64x2_t a = vreinterpretq_u64_m128i(_a); ++ uint64x2_t b = vreinterpretq_u64_m128i(_b); ++ switch (imm & 0x11) { ++ case 0x00: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_low_u64(a), vget_low_u64(b))); ++ case 0x01: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_high_u64(a), vget_low_u64(b))); ++ case 0x10: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_low_u64(a), vget_high_u64(b))); ++ case 0x11: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_high_u64(a), vget_high_u64(b))); ++ default: ++ abort(); ++ } ++} ++ ++FORCE_INLINE unsigned int _sse2neon_mm_get_denormals_zero_mode(void) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ return r.field.bit24 ? _MM_DENORMALS_ZERO_ON : _MM_DENORMALS_ZERO_OFF; ++} ++ ++// Count the number of bits set to 1 in unsigned 32-bit integer a, and ++// return that count in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_popcnt_u32 ++FORCE_INLINE int _mm_popcnt_u32(unsigned int a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#if __has_builtin(__builtin_popcount) ++ return __builtin_popcount(a); ++#elif defined(_MSC_VER) ++ return _CountOneBits(a); ++#else ++ return (int) vaddlv_u8(vcnt_u8(vcreate_u8((uint64_t) a))); ++#endif ++#else ++ uint32_t count = 0; ++ uint8x8_t input_val, count8x8_val; ++ uint16x4_t count16x4_val; ++ uint32x2_t count32x2_val; ++ ++ input_val = vld1_u8((uint8_t *) &a); ++ count8x8_val = vcnt_u8(input_val); ++ count16x4_val = vpaddl_u8(count8x8_val); ++ count32x2_val = vpaddl_u16(count16x4_val); ++ ++ vst1_u32(&count, count32x2_val); ++ return count; ++#endif ++} ++ ++// Count the number of bits set to 1 in unsigned 64-bit integer a, and ++// return that count in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_popcnt_u64 ++FORCE_INLINE int64_t _mm_popcnt_u64(uint64_t a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#if __has_builtin(__builtin_popcountll) ++ return __builtin_popcountll(a); ++#elif defined(_MSC_VER) ++ return _CountOneBits64(a); ++#else ++ return (int64_t) vaddlv_u8(vcnt_u8(vcreate_u8(a))); ++#endif ++#else ++ uint64_t count = 0; ++ uint8x8_t input_val, count8x8_val; ++ uint16x4_t count16x4_val; ++ uint32x2_t count32x2_val; ++ uint64x1_t count64x1_val; ++ ++ input_val = vld1_u8((uint8_t *) &a); ++ count8x8_val = vcnt_u8(input_val); ++ count16x4_val = vpaddl_u8(count8x8_val); ++ count32x2_val = vpaddl_u16(count16x4_val); ++ count64x1_val = vpaddl_u32(count32x2_val); ++ vst1_u64(&count, count64x1_val); ++ return count; ++#endif ++} ++ ++FORCE_INLINE void _sse2neon_mm_set_denormals_zero_mode(unsigned int flag) ++{ ++ // AArch32 Advanced SIMD arithmetic always uses the Flush-to-zero setting, ++ // regardless of the value of the FZ bit. ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ r.field.bit24 = (flag & _MM_DENORMALS_ZERO_MASK) == _MM_DENORMALS_ZERO_ON; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ _sse2neon_set_fpcr(r.value); ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Return the current 64-bit value of the processor's time-stamp counter. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=rdtsc ++FORCE_INLINE uint64_t _rdtsc(void) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t val; ++ ++ /* According to ARM DDI 0487F.c, from Armv8.0 to Armv8.5 inclusive, the ++ * system counter is at least 56 bits wide; from Armv8.6, the counter ++ * must be 64 bits wide. So the system counter could be less than 64 ++ * bits wide and it is attributed with the flag 'cap_user_time_short' ++ * is true. ++ */ ++#if defined(_MSC_VER) ++ val = _ReadStatusReg(ARM64_SYSREG(3, 3, 14, 0, 2)); ++#else ++ __asm__ __volatile__("mrs %0, cntvct_el0" : "=r"(val)); ++#endif ++ ++ return val; ++#else ++ uint32_t pmccntr, pmuseren, pmcntenset; ++ // Read the user mode Performance Monitoring Unit (PMU) ++ // User Enable Register (PMUSERENR) access permissions. ++ __asm__ __volatile__("mrc p15, 0, %0, c9, c14, 0" : "=r"(pmuseren)); ++ if (pmuseren & 1) { // Allows reading PMUSERENR for user mode code. ++ __asm__ __volatile__("mrc p15, 0, %0, c9, c12, 1" : "=r"(pmcntenset)); ++ if (pmcntenset & 0x80000000UL) { // Is it counting? ++ __asm__ __volatile__("mrc p15, 0, %0, c9, c13, 0" : "=r"(pmccntr)); ++ // The counter is set up to count every 64th cycle ++ return (uint64_t) (pmccntr) << 6; ++ } ++ } ++ ++ // Fallback to syscall as we can't enable PMUSERENR in user mode. ++ struct timeval tv; ++ gettimeofday(&tv, NULL); ++ return (uint64_t) (tv.tv_sec) * 1000000 + tv.tv_usec; ++#endif ++} ++ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma pop_macro("ALIGN_STRUCT") ++#pragma pop_macro("FORCE_INLINE") ++#pragma pop_macro("FORCE_INLINE_OPTNONE") ++#endif ++ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC pop_options ++#endif ++ ++#endif diff --git a/recipes/hifiasm_meta/meta.yaml b/recipes/hifiasm_meta/meta.yaml index d60ba6ffffe8d..9fa17cc01bedc 100644 --- a/recipes/hifiasm_meta/meta.yaml +++ b/recipes/hifiasm_meta/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "hamtv0.3.1" %} +{% set version = "hamtv0.3.2" %} package: name: hifiasm_meta @@ -6,10 +6,14 @@ package: source: url: https://github.com/xfengnefx/hifiasm-meta/archive/refs/tags/{{ version }}.tar.gz - sha256: 2da34f01b7ce555ad9038961331ff38786c4e9f10f5aafb3daccc24b3c6f5d4a + sha256: f295998b2dee6ab99ac86ee797bf41f927b12371608ef42da2b3db20e05d2e93 + patches: + - hifiasm_meta-aarch64.patch # [arm64 or aarch64] build: - number: 2 + number: 1 + run_exports: + - {{ pin_subpackage('hifiasm_meta', max_pin="x") }} requirements: build: @@ -30,3 +34,7 @@ about: license: MIT summary: 'Metagenome assembler for Hifi reads, based on hifiasm.' +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 20a752dc5fa27..6bc4d755dcf4b 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.4.2" %} -{% set hiphase_sha256 = "8e57dda28458286a8991be1e9466371c37d28557985fb3af160e3dd16388e925" %} +{% set version = "1.4.5" %} +{% set hiphase_sha256 = "144ed18b56873856073d27bb7daea757ab5cfe857685c033a64e331075107a04" %} package: name: {{ name }} diff --git a/recipes/hlafreq/meta.yaml b/recipes/hlafreq/meta.yaml index f9b65c5f5093b..3dfbdc5e02169 100644 --- a/recipes/hlafreq/meta.yaml +++ b/recipes/hlafreq/meta.yaml @@ -1,13 +1,13 @@ {% set name = "HLAfreq" %} -{% set version = "0.0.3" %} +{% set version = "0.0.4" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 93941536c4912180f12544251792d21098e47116a871c6c49565054987e1438f + url: "https://pypi.io/packages/source/{{ name[0]|lower }}/{{ name|lower }}/{{ name|lower }}-{{ version }}.tar.gz" + sha256: 58aa7aaa1d554a3264531f6aaa3bd0a5a29c13b58441dc6564537adf4d096051 build: number: 0 @@ -18,18 +18,18 @@ build: requirements: host: - - python >=3.8 + - python >=3.10 - pip run: - bs4 - - matplotlib-base - - numpy + - matplotlib-base >=3.6.0 + - numpy >=1.24.0 - pandas - pymc >=3 - arviz - - python >=3.8 + - python >=3.10 - requests - - scipy + - scipy >=1.10.0 test: imports: diff --git a/recipes/hmmer/build.sh b/recipes/hmmer/build.sh index 9bedf04f9819a..00abe00649fa1 100755 --- a/recipes/hmmer/build.sh +++ b/recipes/hmmer/build.sh @@ -2,6 +2,9 @@ set -e -u -x +# use newer config.guess and config.sub that support osx-arm64 +cp ${RECIPE_DIR}/config.* . + ./configure --prefix=$PREFIX make -j4 make install @@ -11,4 +14,3 @@ make install mkdir -p $PREFIX/share rm -rf ${SRC_DIR}/easel/miniapps cp -r ${SRC_DIR}/easel $PREFIX/share/ - diff --git a/recipes/hmmer/config.guess b/recipes/hmmer/config.guess new file mode 100644 index 0000000000000..1972fda8eb05d --- /dev/null +++ b/recipes/hmmer/config.guess @@ -0,0 +1,1700 @@ +#! /bin/sh +# Attempt to guess a canonical system name. +# Copyright 1992-2021 Free Software Foundation, Inc. + +timestamp='2021-01-25' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see . +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). +# +# Originally written by Per Bothner; maintained since 2000 by Ben Elliston. +# +# You can get the latest version of this script from: +# https://git.savannah.gnu.org/cgit/config.git/plain/config.guess +# +# Please send patches to . + + +me=$(echo "$0" | sed -e 's,.*/,,') + +usage="\ +Usage: $0 [OPTION] + +Output the configuration name of the system \`$me' is run on. + +Options: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.guess ($timestamp) + +Originally written by Per Bothner. +Copyright 1992-2021 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + * ) + break ;; + esac +done + +if test $# != 0; then + echo "$me: too many arguments$help" >&2 + exit 1 +fi + +# CC_FOR_BUILD -- compiler used by this script. Note that the use of a +# compiler to aid in system detection is discouraged as it requires +# temporary files to be created and, as you can see below, it is a +# headache to deal with in a portable fashion. + +# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still +# use `HOST_CC' if defined, but it is deprecated. + +# Portable tmp directory creation inspired by the Autoconf team. + +tmp= +# shellcheck disable=SC2172 +trap 'test -z "$tmp" || rm -fr "$tmp"' 0 1 2 13 15 + +set_cc_for_build() { + # prevent multiple calls if $tmp is already set + test "$tmp" && return 0 + : "${TMPDIR=/tmp}" + # shellcheck disable=SC2039 + { tmp=$( (umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null) && test -n "$tmp" && test -d "$tmp" ; } || + { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir "$tmp" 2>/dev/null) ; } || + { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir "$tmp" 2>/dev/null) && echo "Warning: creating insecure temp directory" >&2 ; } || + { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } + dummy=$tmp/dummy + case ${CC_FOR_BUILD-},${HOST_CC-},${CC-} in + ,,) echo "int x;" > "$dummy.c" + for driver in cc gcc c89 c99 ; do + if ($driver -c -o "$dummy.o" "$dummy.c") >/dev/null 2>&1 ; then + CC_FOR_BUILD="$driver" + break + fi + done + if test x"$CC_FOR_BUILD" = x ; then + CC_FOR_BUILD=no_compiler_found + fi + ;; + ,,*) CC_FOR_BUILD=$CC ;; + ,*,*) CC_FOR_BUILD=$HOST_CC ;; + esac +} + +# This is needed to find uname on a Pyramid OSx when run in the BSD universe. +# (ghazi@noc.rutgers.edu 1994-08-24) +if test -f /.attbin/uname ; then + PATH=$PATH:/.attbin ; export PATH +fi + +UNAME_MACHINE=$( (uname -m) 2>/dev/null) || UNAME_MACHINE=unknown +UNAME_RELEASE=$( (uname -r) 2>/dev/null) || UNAME_RELEASE=unknown +UNAME_SYSTEM=$( (uname -s) 2>/dev/null) || UNAME_SYSTEM=unknown +UNAME_VERSION=$( (uname -v) 2>/dev/null) || UNAME_VERSION=unknown + +case "$UNAME_SYSTEM" in +Linux|GNU|GNU/*) + LIBC=unknown + + set_cc_for_build + cat <<-EOF > "$dummy.c" + #include + #if defined(__UCLIBC__) + LIBC=uclibc + #elif defined(__dietlibc__) + LIBC=dietlibc + #elif defined(__GLIBC__) + LIBC=gnu + #else + #include + /* First heuristic to detect musl libc. */ + #ifdef __DEFINED_va_list + LIBC=musl + #endif + #endif + EOF + eval "$($CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g')" + + # Second heuristic to detect musl libc. + if [ "$LIBC" = unknown ] && + command -v ldd >/dev/null && + ldd --version 2>&1 | grep -q ^musl; then + LIBC=musl + fi + + # If the system lacks a compiler, then just pick glibc. + # We could probably try harder. + if [ "$LIBC" = unknown ]; then + LIBC=gnu + fi + ;; +esac + +# Note: order is significant - the case branches are not exclusive. + +case "$UNAME_MACHINE:$UNAME_SYSTEM:$UNAME_RELEASE:$UNAME_VERSION" in + *:NetBSD:*:*) + # NetBSD (nbsd) targets should (where applicable) match one or + # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*, + # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently + # switched to ELF, *-*-netbsd* would select the old + # object file format. This provides both forward + # compatibility and a consistent mechanism for selecting the + # object file format. + # + # Note: NetBSD doesn't particularly care about the vendor + # portion of the name. We always set it to "unknown". + UNAME_MACHINE_ARCH=$( (uname -p 2>/dev/null || \ + /sbin/sysctl -n hw.machine_arch 2>/dev/null || \ + /usr/sbin/sysctl -n hw.machine_arch 2>/dev/null || \ + echo unknown)) + case "$UNAME_MACHINE_ARCH" in + aarch64eb) machine=aarch64_be-unknown ;; + armeb) machine=armeb-unknown ;; + arm*) machine=arm-unknown ;; + sh3el) machine=shl-unknown ;; + sh3eb) machine=sh-unknown ;; + sh5el) machine=sh5le-unknown ;; + earmv*) + arch=$(echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,') + endian=$(echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p') + machine="${arch}${endian}"-unknown + ;; + *) machine="$UNAME_MACHINE_ARCH"-unknown ;; + esac + # The Operating System including object format, if it has switched + # to ELF recently (or will in the future) and ABI. + case "$UNAME_MACHINE_ARCH" in + earm*) + os=netbsdelf + ;; + arm*|i386|m68k|ns32k|sh3*|sparc|vax) + set_cc_for_build + if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ELF__ + then + # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). + # Return netbsd for either. FIX? + os=netbsd + else + os=netbsdelf + fi + ;; + *) + os=netbsd + ;; + esac + # Determine ABI tags. + case "$UNAME_MACHINE_ARCH" in + earm*) + expr='s/^earmv[0-9]/-eabi/;s/eb$//' + abi=$(echo "$UNAME_MACHINE_ARCH" | sed -e "$expr") + ;; + esac + # The OS release + # Debian GNU/NetBSD machines have a different userland, and + # thus, need a distinct triplet. However, they do not need + # kernel version information, so it can be replaced with a + # suitable tag, in the style of linux-gnu. + case "$UNAME_VERSION" in + Debian*) + release='-gnu' + ;; + *) + release=$(echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2) + ;; + esac + # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: + # contains redundant information, the shorter form: + # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. + echo "$machine-${os}${release}${abi-}" + exit ;; + *:Bitrig:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/Bitrig.//') + echo "$UNAME_MACHINE_ARCH"-unknown-bitrig"$UNAME_RELEASE" + exit ;; + *:OpenBSD:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/OpenBSD.//') + echo "$UNAME_MACHINE_ARCH"-unknown-openbsd"$UNAME_RELEASE" + exit ;; + *:LibertyBSD:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/^.*BSD\.//') + echo "$UNAME_MACHINE_ARCH"-unknown-libertybsd"$UNAME_RELEASE" + exit ;; + *:MidnightBSD:*:*) + echo "$UNAME_MACHINE"-unknown-midnightbsd"$UNAME_RELEASE" + exit ;; + *:ekkoBSD:*:*) + echo "$UNAME_MACHINE"-unknown-ekkobsd"$UNAME_RELEASE" + exit ;; + *:SolidBSD:*:*) + echo "$UNAME_MACHINE"-unknown-solidbsd"$UNAME_RELEASE" + exit ;; + *:OS108:*:*) + echo "$UNAME_MACHINE"-unknown-os108_"$UNAME_RELEASE" + exit ;; + macppc:MirBSD:*:*) + echo powerpc-unknown-mirbsd"$UNAME_RELEASE" + exit ;; + *:MirBSD:*:*) + echo "$UNAME_MACHINE"-unknown-mirbsd"$UNAME_RELEASE" + exit ;; + *:Sortix:*:*) + echo "$UNAME_MACHINE"-unknown-sortix + exit ;; + *:Twizzler:*:*) + echo "$UNAME_MACHINE"-unknown-twizzler + exit ;; + *:Redox:*:*) + echo "$UNAME_MACHINE"-unknown-redox + exit ;; + mips:OSF1:*.*) + echo mips-dec-osf1 + exit ;; + alpha:OSF1:*:*) + case $UNAME_RELEASE in + *4.0) + UNAME_RELEASE=$(/usr/sbin/sizer -v | awk '{print $3}') + ;; + *5.*) + UNAME_RELEASE=$(/usr/sbin/sizer -v | awk '{print $4}') + ;; + esac + # According to Compaq, /usr/sbin/psrinfo has been available on + # OSF/1 and Tru64 systems produced since 1995. I hope that + # covers most systems running today. This code pipes the CPU + # types through head -n 1, so we only detect the type of CPU 0. + ALPHA_CPU_TYPE=$(/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1) + case "$ALPHA_CPU_TYPE" in + "EV4 (21064)") + UNAME_MACHINE=alpha ;; + "EV4.5 (21064)") + UNAME_MACHINE=alpha ;; + "LCA4 (21066/21068)") + UNAME_MACHINE=alpha ;; + "EV5 (21164)") + UNAME_MACHINE=alphaev5 ;; + "EV5.6 (21164A)") + UNAME_MACHINE=alphaev56 ;; + "EV5.6 (21164PC)") + UNAME_MACHINE=alphapca56 ;; + "EV5.7 (21164PC)") + UNAME_MACHINE=alphapca57 ;; + "EV6 (21264)") + UNAME_MACHINE=alphaev6 ;; + "EV6.7 (21264A)") + UNAME_MACHINE=alphaev67 ;; + "EV6.8CB (21264C)") + UNAME_MACHINE=alphaev68 ;; + "EV6.8AL (21264B)") + UNAME_MACHINE=alphaev68 ;; + "EV6.8CX (21264D)") + UNAME_MACHINE=alphaev68 ;; + "EV6.9A (21264/EV69A)") + UNAME_MACHINE=alphaev69 ;; + "EV7 (21364)") + UNAME_MACHINE=alphaev7 ;; + "EV7.9 (21364A)") + UNAME_MACHINE=alphaev79 ;; + esac + # A Pn.n version is a patched version. + # A Vn.n version is a released version. + # A Tn.n version is a released field test version. + # A Xn.n version is an unreleased experimental baselevel. + # 1.2 uses "1.2" for uname -r. + echo "$UNAME_MACHINE"-dec-osf"$(echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz)" + # Reset EXIT trap before exiting to avoid spurious non-zero exit code. + exitcode=$? + trap '' 0 + exit $exitcode ;; + Amiga*:UNIX_System_V:4.0:*) + echo m68k-unknown-sysv4 + exit ;; + *:[Aa]miga[Oo][Ss]:*:*) + echo "$UNAME_MACHINE"-unknown-amigaos + exit ;; + *:[Mm]orph[Oo][Ss]:*:*) + echo "$UNAME_MACHINE"-unknown-morphos + exit ;; + *:OS/390:*:*) + echo i370-ibm-openedition + exit ;; + *:z/VM:*:*) + echo s390-ibm-zvmoe + exit ;; + *:OS400:*:*) + echo powerpc-ibm-os400 + exit ;; + arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) + echo arm-acorn-riscix"$UNAME_RELEASE" + exit ;; + arm*:riscos:*:*|arm*:RISCOS:*:*) + echo arm-unknown-riscos + exit ;; + SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) + echo hppa1.1-hitachi-hiuxmpp + exit ;; + Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) + # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. + if test "$( (/bin/universe) 2>/dev/null)" = att ; then + echo pyramid-pyramid-sysv3 + else + echo pyramid-pyramid-bsd + fi + exit ;; + NILE*:*:*:dcosx) + echo pyramid-pyramid-svr4 + exit ;; + DRS?6000:unix:4.0:6*) + echo sparc-icl-nx6 + exit ;; + DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) + case $(/usr/bin/uname -p) in + sparc) echo sparc-icl-nx7; exit ;; + esac ;; + s390x:SunOS:*:*) + echo "$UNAME_MACHINE"-ibm-solaris2"$(echo "$UNAME_RELEASE" | sed -e 's/[^.]*//')" + exit ;; + sun4H:SunOS:5.*:*) + echo sparc-hal-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) + echo sparc-sun-solaris2"$(echo "$UNAME_RELEASE" | sed -e 's/[^.]*//')" + exit ;; + i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) + echo i386-pc-auroraux"$UNAME_RELEASE" + exit ;; + i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) + set_cc_for_build + SUN_ARCH=i386 + # If there is a compiler, see if it is configured for 64-bit objects. + # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. + # This test works for both compilers. + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + SUN_ARCH=x86_64 + fi + fi + echo "$SUN_ARCH"-pc-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:6*:*) + # According to config.sub, this is the proper way to canonicalize + # SunOS6. Hard to guess exactly what SunOS6 will be like, but + # it's likely to be more like Solaris than SunOS4. + echo sparc-sun-solaris3"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:*:*) + case "$(/usr/bin/arch -k)" in + Series*|S4*) + UNAME_RELEASE=$(uname -v) + ;; + esac + # Japanese Language versions have a version number like `4.1.3-JL'. + echo sparc-sun-sunos"$(echo "$UNAME_RELEASE"|sed -e 's/-/_/')" + exit ;; + sun3*:SunOS:*:*) + echo m68k-sun-sunos"$UNAME_RELEASE" + exit ;; + sun*:*:4.2BSD:*) + UNAME_RELEASE=$( (sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null) + test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3 + case "$(/bin/arch)" in + sun3) + echo m68k-sun-sunos"$UNAME_RELEASE" + ;; + sun4) + echo sparc-sun-sunos"$UNAME_RELEASE" + ;; + esac + exit ;; + aushp:SunOS:*:*) + echo sparc-auspex-sunos"$UNAME_RELEASE" + exit ;; + # The situation for MiNT is a little confusing. The machine name + # can be virtually everything (everything which is not + # "atarist" or "atariste" at least should have a processor + # > m68000). The system name ranges from "MiNT" over "FreeMiNT" + # to the lowercase version "mint" (or "freemint"). Finally + # the system name "TOS" denotes a system which is actually not + # MiNT. But MiNT is downward compatible to TOS, so this should + # be no problem. + atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) + echo m68k-milan-mint"$UNAME_RELEASE" + exit ;; + hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) + echo m68k-hades-mint"$UNAME_RELEASE" + exit ;; + *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) + echo m68k-unknown-mint"$UNAME_RELEASE" + exit ;; + m68k:machten:*:*) + echo m68k-apple-machten"$UNAME_RELEASE" + exit ;; + powerpc:machten:*:*) + echo powerpc-apple-machten"$UNAME_RELEASE" + exit ;; + RISC*:Mach:*:*) + echo mips-dec-mach_bsd4.3 + exit ;; + RISC*:ULTRIX:*:*) + echo mips-dec-ultrix"$UNAME_RELEASE" + exit ;; + VAX*:ULTRIX*:*:*) + echo vax-dec-ultrix"$UNAME_RELEASE" + exit ;; + 2020:CLIX:*:* | 2430:CLIX:*:*) + echo clipper-intergraph-clix"$UNAME_RELEASE" + exit ;; + mips:*:*:UMIPS | mips:*:*:RISCos) + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" +#ifdef __cplusplus +#include /* for printf() prototype */ + int main (int argc, char *argv[]) { +#else + int main (argc, argv) int argc; char *argv[]; { +#endif + #if defined (host_mips) && defined (MIPSEB) + #if defined (SYSTYPE_SYSV) + printf ("mips-mips-riscos%ssysv\\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_SVR4) + printf ("mips-mips-riscos%ssvr4\\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) + printf ("mips-mips-riscos%sbsd\\n", argv[1]); exit (0); + #endif + #endif + exit (-1); + } +EOF + $CC_FOR_BUILD -o "$dummy" "$dummy.c" && + dummyarg=$(echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p') && + SYSTEM_NAME=$("$dummy" "$dummyarg") && + { echo "$SYSTEM_NAME"; exit; } + echo mips-mips-riscos"$UNAME_RELEASE" + exit ;; + Motorola:PowerMAX_OS:*:*) + echo powerpc-motorola-powermax + exit ;; + Motorola:*:4.3:PL8-*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:Power_UNIX:*:*) + echo powerpc-harris-powerunix + exit ;; + m88k:CX/UX:7*:*) + echo m88k-harris-cxux7 + exit ;; + m88k:*:4*:R4*) + echo m88k-motorola-sysv4 + exit ;; + m88k:*:3*:R3*) + echo m88k-motorola-sysv3 + exit ;; + AViiON:dgux:*:*) + # DG/UX returns AViiON for all architectures + UNAME_PROCESSOR=$(/usr/bin/uname -p) + if test "$UNAME_PROCESSOR" = mc88100 || test "$UNAME_PROCESSOR" = mc88110 + then + if test "$TARGET_BINARY_INTERFACE"x = m88kdguxelfx || \ + test "$TARGET_BINARY_INTERFACE"x = x + then + echo m88k-dg-dgux"$UNAME_RELEASE" + else + echo m88k-dg-dguxbcs"$UNAME_RELEASE" + fi + else + echo i586-dg-dgux"$UNAME_RELEASE" + fi + exit ;; + M88*:DolphinOS:*:*) # DolphinOS (SVR3) + echo m88k-dolphin-sysv3 + exit ;; + M88*:*:R3*:*) + # Delta 88k system running SVR3 + echo m88k-motorola-sysv3 + exit ;; + XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) + echo m88k-tektronix-sysv3 + exit ;; + Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) + echo m68k-tektronix-bsd + exit ;; + *:IRIX*:*:*) + echo mips-sgi-irix"$(echo "$UNAME_RELEASE"|sed -e 's/-/_/g')" + exit ;; + ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. + echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id + exit ;; # Note that: echo "'$(uname -s)'" gives 'AIX ' + i*86:AIX:*:*) + echo i386-ibm-aix + exit ;; + ia64:AIX:*:*) + if test -x /usr/bin/oslevel ; then + IBM_REV=$(/usr/bin/oslevel) + else + IBM_REV="$UNAME_VERSION.$UNAME_RELEASE" + fi + echo "$UNAME_MACHINE"-ibm-aix"$IBM_REV" + exit ;; + *:AIX:2:3) + if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + #include + + main() + { + if (!__power_pc()) + exit(1); + puts("powerpc-ibm-aix3.2.5"); + exit(0); + } +EOF + if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=$("$dummy") + then + echo "$SYSTEM_NAME" + else + echo rs6000-ibm-aix3.2.5 + fi + elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then + echo rs6000-ibm-aix3.2.4 + else + echo rs6000-ibm-aix3.2 + fi + exit ;; + *:AIX:*:[4567]) + IBM_CPU_ID=$(/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }') + if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then + IBM_ARCH=rs6000 + else + IBM_ARCH=powerpc + fi + if test -x /usr/bin/lslpp ; then + IBM_REV=$(/usr/bin/lslpp -Lqc bos.rte.libc | + awk -F: '{ print $3 }' | sed s/[0-9]*$/0/) + else + IBM_REV="$UNAME_VERSION.$UNAME_RELEASE" + fi + echo "$IBM_ARCH"-ibm-aix"$IBM_REV" + exit ;; + *:AIX:*:*) + echo rs6000-ibm-aix + exit ;; + ibmrt:4.4BSD:*|romp-ibm:4.4BSD:*) + echo romp-ibm-bsd4.4 + exit ;; + ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and + echo romp-ibm-bsd"$UNAME_RELEASE" # 4.3 with uname added to + exit ;; # report: romp-ibm BSD 4.3 + *:BOSX:*:*) + echo rs6000-bull-bosx + exit ;; + DPX/2?00:B.O.S.:*:*) + echo m68k-bull-sysv3 + exit ;; + 9000/[34]??:4.3bsd:1.*:*) + echo m68k-hp-bsd + exit ;; + hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) + echo m68k-hp-bsd4.4 + exit ;; + 9000/[34678]??:HP-UX:*:*) + HPUX_REV=$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//') + case "$UNAME_MACHINE" in + 9000/31?) HP_ARCH=m68000 ;; + 9000/[34]??) HP_ARCH=m68k ;; + 9000/[678][0-9][0-9]) + if test -x /usr/bin/getconf; then + sc_cpu_version=$(/usr/bin/getconf SC_CPU_VERSION 2>/dev/null) + sc_kernel_bits=$(/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null) + case "$sc_cpu_version" in + 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0 + 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1 + 532) # CPU_PA_RISC2_0 + case "$sc_kernel_bits" in + 32) HP_ARCH=hppa2.0n ;; + 64) HP_ARCH=hppa2.0w ;; + '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20 + esac ;; + esac + fi + if test "$HP_ARCH" = ""; then + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + + #define _HPUX_SOURCE + #include + #include + + int main () + { + #if defined(_SC_KERNEL_BITS) + long bits = sysconf(_SC_KERNEL_BITS); + #endif + long cpu = sysconf (_SC_CPU_VERSION); + + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1"); break; + case CPU_PA_RISC2_0: + #if defined(_SC_KERNEL_BITS) + switch (bits) + { + case 64: puts ("hppa2.0w"); break; + case 32: puts ("hppa2.0n"); break; + default: puts ("hppa2.0"); break; + } break; + #else /* !defined(_SC_KERNEL_BITS) */ + puts ("hppa2.0"); break; + #endif + default: puts ("hppa1.0"); break; + } + exit (0); + } +EOF + (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=$("$dummy") + test -z "$HP_ARCH" && HP_ARCH=hppa + fi ;; + esac + if test "$HP_ARCH" = hppa2.0w + then + set_cc_for_build + + # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating + # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler + # generating 64-bit code. GNU and HP use different nomenclature: + # + # $ CC_FOR_BUILD=cc ./config.guess + # => hppa2.0w-hp-hpux11.23 + # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess + # => hppa64-hp-hpux11.23 + + if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | + grep -q __LP64__ + then + HP_ARCH=hppa2.0w + else + HP_ARCH=hppa64 + fi + fi + echo "$HP_ARCH"-hp-hpux"$HPUX_REV" + exit ;; + ia64:HP-UX:*:*) + HPUX_REV=$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//') + echo ia64-hp-hpux"$HPUX_REV" + exit ;; + 3050*:HI-UX:*:*) + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + #include + int + main () + { + long cpu = sysconf (_SC_CPU_VERSION); + /* The order matters, because CPU_IS_HP_MC68K erroneously returns + true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct + results, however. */ + if (CPU_IS_PA_RISC (cpu)) + { + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; + case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; + default: puts ("hppa-hitachi-hiuxwe2"); break; + } + } + else if (CPU_IS_HP_MC68K (cpu)) + puts ("m68k-hitachi-hiuxwe2"); + else puts ("unknown-hitachi-hiuxwe2"); + exit (0); + } +EOF + $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=$("$dummy") && + { echo "$SYSTEM_NAME"; exit; } + echo unknown-hitachi-hiuxwe2 + exit ;; + 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*) + echo hppa1.1-hp-bsd + exit ;; + 9000/8??:4.3bsd:*:*) + echo hppa1.0-hp-bsd + exit ;; + *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) + echo hppa1.0-hp-mpeix + exit ;; + hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*) + echo hppa1.1-hp-osf + exit ;; + hp8??:OSF1:*:*) + echo hppa1.0-hp-osf + exit ;; + i*86:OSF1:*:*) + if test -x /usr/sbin/sysversion ; then + echo "$UNAME_MACHINE"-unknown-osf1mk + else + echo "$UNAME_MACHINE"-unknown-osf1 + fi + exit ;; + parisc*:Lites*:*:*) + echo hppa1.1-hp-lites + exit ;; + C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) + echo c1-convex-bsd + exit ;; + C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit ;; + C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) + echo c34-convex-bsd + exit ;; + C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) + echo c38-convex-bsd + exit ;; + C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) + echo c4-convex-bsd + exit ;; + CRAY*Y-MP:*:*:*) + echo ymp-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*[A-Z]90:*:*:*) + echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \ + | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ + -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ + -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*TS:*:*:*) + echo t90-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*T3E:*:*:*) + echo alphaev5-cray-unicosmk"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*SV1:*:*:*) + echo sv1-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + *:UNICOS/mp:*:*) + echo craynv-cray-unicosmp"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) + FUJITSU_PROC=$(uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz) + FUJITSU_SYS=$(uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///') + FUJITSU_REL=$(echo "$UNAME_RELEASE" | sed -e 's/ /_/') + echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + 5000:UNIX_System_V:4.*:*) + FUJITSU_SYS=$(uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///') + FUJITSU_REL=$(echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/') + echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) + echo "$UNAME_MACHINE"-pc-bsdi"$UNAME_RELEASE" + exit ;; + sparc*:BSD/OS:*:*) + echo sparc-unknown-bsdi"$UNAME_RELEASE" + exit ;; + *:BSD/OS:*:*) + echo "$UNAME_MACHINE"-unknown-bsdi"$UNAME_RELEASE" + exit ;; + arm:FreeBSD:*:*) + UNAME_PROCESSOR=$(uname -p) + set_cc_for_build + if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_PCS_VFP + then + echo "${UNAME_PROCESSOR}"-unknown-freebsd"$(echo ${UNAME_RELEASE}|sed -e 's/[-(].*//')"-gnueabi + else + echo "${UNAME_PROCESSOR}"-unknown-freebsd"$(echo ${UNAME_RELEASE}|sed -e 's/[-(].*//')"-gnueabihf + fi + exit ;; + *:FreeBSD:*:*) + UNAME_PROCESSOR=$(/usr/bin/uname -p) + case "$UNAME_PROCESSOR" in + amd64) + UNAME_PROCESSOR=x86_64 ;; + i386) + UNAME_PROCESSOR=i586 ;; + esac + echo "$UNAME_PROCESSOR"-unknown-freebsd"$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')" + exit ;; + i*:CYGWIN*:*) + echo "$UNAME_MACHINE"-pc-cygwin + exit ;; + *:MINGW64*:*) + echo "$UNAME_MACHINE"-pc-mingw64 + exit ;; + *:MINGW*:*) + echo "$UNAME_MACHINE"-pc-mingw32 + exit ;; + *:MSYS*:*) + echo "$UNAME_MACHINE"-pc-msys + exit ;; + i*:PW*:*) + echo "$UNAME_MACHINE"-pc-pw32 + exit ;; + *:Interix*:*) + case "$UNAME_MACHINE" in + x86) + echo i586-pc-interix"$UNAME_RELEASE" + exit ;; + authenticamd | genuineintel | EM64T) + echo x86_64-unknown-interix"$UNAME_RELEASE" + exit ;; + IA64) + echo ia64-unknown-interix"$UNAME_RELEASE" + exit ;; + esac ;; + i*:UWIN*:*) + echo "$UNAME_MACHINE"-pc-uwin + exit ;; + amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) + echo x86_64-pc-cygwin + exit ;; + prep*:SunOS:5.*:*) + echo powerpcle-unknown-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + *:GNU:*:*) + # the GNU system + echo "$(echo "$UNAME_MACHINE"|sed -e 's,[-/].*$,,')-unknown-$LIBC$(echo "$UNAME_RELEASE"|sed -e 's,/.*$,,')" + exit ;; + *:GNU/*:*:*) + # other systems with GNU libc and userland + echo "$UNAME_MACHINE-unknown-$(echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]")$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')-$LIBC" + exit ;; + *:Minix:*:*) + echo "$UNAME_MACHINE"-unknown-minix + exit ;; + aarch64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + aarch64_be:Linux:*:*) + UNAME_MACHINE=aarch64_be + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + alpha:Linux:*:*) + case $(sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' /proc/cpuinfo 2>/dev/null) in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep -q ld.so.1 + if test "$?" = 0 ; then LIBC=gnulibc1 ; fi + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + arc:Linux:*:* | arceb:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + arm*:Linux:*:*) + set_cc_for_build + if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_EABI__ + then + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + else + if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_PCS_VFP + then + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabi + else + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabihf + fi + fi + exit ;; + avr32*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + cris:Linux:*:*) + echo "$UNAME_MACHINE"-axis-linux-"$LIBC" + exit ;; + crisv32:Linux:*:*) + echo "$UNAME_MACHINE"-axis-linux-"$LIBC" + exit ;; + e2k:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + frv:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + hexagon:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + i*86:Linux:*:*) + echo "$UNAME_MACHINE"-pc-linux-"$LIBC" + exit ;; + ia64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + k1om:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + loongarch32:Linux:*:* | loongarch64:Linux:*:* | loongarchx32:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + m32r*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + m68*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + mips:Linux:*:* | mips64:Linux:*:*) + set_cc_for_build + IS_GLIBC=0 + test x"${LIBC}" = xgnu && IS_GLIBC=1 + sed 's/^ //' << EOF > "$dummy.c" + #undef CPU + #undef mips + #undef mipsel + #undef mips64 + #undef mips64el + #if ${IS_GLIBC} && defined(_ABI64) + LIBCABI=gnuabi64 + #else + #if ${IS_GLIBC} && defined(_ABIN32) + LIBCABI=gnuabin32 + #else + LIBCABI=${LIBC} + #endif + #endif + + #if ${IS_GLIBC} && defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 + CPU=mipsisa64r6 + #else + #if ${IS_GLIBC} && !defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 + CPU=mipsisa32r6 + #else + #if defined(__mips64) + CPU=mips64 + #else + CPU=mips + #endif + #endif + #endif + + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + MIPS_ENDIAN=el + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + MIPS_ENDIAN= + #else + MIPS_ENDIAN= + #endif + #endif +EOF + eval "$($CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU\|^MIPS_ENDIAN\|^LIBCABI')" + test "x$CPU" != x && { echo "$CPU${MIPS_ENDIAN}-unknown-linux-$LIBCABI"; exit; } + ;; + mips64el:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + openrisc*:Linux:*:*) + echo or1k-unknown-linux-"$LIBC" + exit ;; + or32:Linux:*:* | or1k*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + padre:Linux:*:*) + echo sparc-unknown-linux-"$LIBC" + exit ;; + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-"$LIBC" + exit ;; + parisc:Linux:*:* | hppa:Linux:*:*) + # Look for CPU level + case $(grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2) in + PA7*) echo hppa1.1-unknown-linux-"$LIBC" ;; + PA8*) echo hppa2.0-unknown-linux-"$LIBC" ;; + *) echo hppa-unknown-linux-"$LIBC" ;; + esac + exit ;; + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-"$LIBC" + exit ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-"$LIBC" + exit ;; + ppc64le:Linux:*:*) + echo powerpc64le-unknown-linux-"$LIBC" + exit ;; + ppcle:Linux:*:*) + echo powerpcle-unknown-linux-"$LIBC" + exit ;; + riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo "$UNAME_MACHINE"-ibm-linux-"$LIBC" + exit ;; + sh64*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + sh*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + sparc:Linux:*:* | sparc64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + tile*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + vax:Linux:*:*) + echo "$UNAME_MACHINE"-dec-linux-"$LIBC" + exit ;; + x86_64:Linux:*:*) + set_cc_for_build + LIBCABI=$LIBC + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __ILP32__'; echo IS_X32; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_X32 >/dev/null + then + LIBCABI="$LIBC"x32 + fi + fi + echo "$UNAME_MACHINE"-pc-linux-"$LIBCABI" + exit ;; + xtensa*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + i*86:DYNIX/ptx:4*:*) + # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. + # earlier versions are messed up and put the nodename in both + # sysname and nodename. + echo i386-sequent-sysv4 + exit ;; + i*86:UNIX_SV:4.2MP:2.*) + # Unixware is an offshoot of SVR4, but it has its own version + # number series starting with 2... + # I am not positive that other SVR4 systems won't match this, + # I just have to hope. -- rms. + # Use sysv4.2uw... so that sysv4* matches it. + echo "$UNAME_MACHINE"-pc-sysv4.2uw"$UNAME_VERSION" + exit ;; + i*86:OS/2:*:*) + # If we were able to find `uname', then EMX Unix compatibility + # is probably installed. + echo "$UNAME_MACHINE"-pc-os2-emx + exit ;; + i*86:XTS-300:*:STOP) + echo "$UNAME_MACHINE"-unknown-stop + exit ;; + i*86:atheos:*:*) + echo "$UNAME_MACHINE"-unknown-atheos + exit ;; + i*86:syllable:*:*) + echo "$UNAME_MACHINE"-pc-syllable + exit ;; + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) + echo i386-unknown-lynxos"$UNAME_RELEASE" + exit ;; + i*86:*DOS:*:*) + echo "$UNAME_MACHINE"-pc-msdosdjgpp + exit ;; + i*86:*:4.*:*) + UNAME_REL=$(echo "$UNAME_RELEASE" | sed 's/\/MP$//') + if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then + echo "$UNAME_MACHINE"-univel-sysv"$UNAME_REL" + else + echo "$UNAME_MACHINE"-pc-sysv"$UNAME_REL" + fi + exit ;; + i*86:*:5:[678]*) + # UnixWare 7.x, OpenUNIX and OpenServer 6. + case $(/bin/uname -X | grep "^Machine") in + *486*) UNAME_MACHINE=i486 ;; + *Pentium) UNAME_MACHINE=i586 ;; + *Pent*|*Celeron) UNAME_MACHINE=i686 ;; + esac + echo "$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}" + exit ;; + i*86:*:3.2:*) + if test -f /usr/options/cb.name; then + UNAME_REL=$(sed -n 's/.*Version //p' /dev/null >/dev/null ; then + UNAME_REL=$( (/bin/uname -X|grep Release|sed -e 's/.*= //')) + (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 + (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ + && UNAME_MACHINE=i586 + (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ + && UNAME_MACHINE=i686 + (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ + && UNAME_MACHINE=i686 + echo "$UNAME_MACHINE"-pc-sco"$UNAME_REL" + else + echo "$UNAME_MACHINE"-pc-sysv32 + fi + exit ;; + pc:*:*:*) + # Left here for compatibility: + # uname -m prints for DJGPP always 'pc', but it prints nothing about + # the processor, so we play safe by assuming i586. + # Note: whatever this is, it MUST be the same as what config.sub + # prints for the "djgpp" host, or else GDB configure will decide that + # this is a cross-build. + echo i586-pc-msdosdjgpp + exit ;; + Intel:Mach:3*:*) + echo i386-pc-mach3 + exit ;; + paragon:*:*:*) + echo i860-intel-osf1 + exit ;; + i860:*:4.*:*) # i860-SVR4 + if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then + echo i860-stardent-sysv"$UNAME_RELEASE" # Stardent Vistra i860-SVR4 + else # Add other i860-SVR4 vendors below as they are discovered. + echo i860-unknown-sysv"$UNAME_RELEASE" # Unknown i860-SVR4 + fi + exit ;; + mini*:CTIX:SYS*5:*) + # "miniframe" + echo m68010-convergent-sysv + exit ;; + mc68k:UNIX:SYSTEM5:3.51m) + echo m68k-convergent-sysv + exit ;; + M680?0:D-NIX:5.3:*) + echo m68k-diab-dnix + exit ;; + M68*:*:R3V[5678]*:*) + test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; + 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) + OS_REL='' + test -r /etc/.relid \ + && OS_REL=.$(sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; + 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4; exit; } ;; + NCR*:*:4.2:* | MPRAS*:*:4.2:*) + OS_REL='.3' + test -r /etc/.relid \ + && OS_REL=.$(sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; + m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) + echo m68k-unknown-lynxos"$UNAME_RELEASE" + exit ;; + mc68030:UNIX_System_V:4.*:*) + echo m68k-atari-sysv4 + exit ;; + TSUNAMI:LynxOS:2.*:*) + echo sparc-unknown-lynxos"$UNAME_RELEASE" + exit ;; + rs6000:LynxOS:2.*:*) + echo rs6000-unknown-lynxos"$UNAME_RELEASE" + exit ;; + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) + echo powerpc-unknown-lynxos"$UNAME_RELEASE" + exit ;; + SM[BE]S:UNIX_SV:*:*) + echo mips-dde-sysv"$UNAME_RELEASE" + exit ;; + RM*:ReliantUNIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + RM*:SINIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + *:SINIX-*:*:*) + if uname -p 2>/dev/null >/dev/null ; then + UNAME_MACHINE=$( (uname -p) 2>/dev/null) + echo "$UNAME_MACHINE"-sni-sysv4 + else + echo ns32k-sni-sysv + fi + exit ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says + echo i586-unisys-sysv4 + exit ;; + *:UNIX_System_V:4*:FTX*) + # From Gerald Hewes . + # How about differentiating between stratus architectures? -djm + echo hppa1.1-stratus-sysv4 + exit ;; + *:*:*:FTX*) + # From seanf@swdc.stratus.com. + echo i860-stratus-sysv4 + exit ;; + i*86:VOS:*:*) + # From Paul.Green@stratus.com. + echo "$UNAME_MACHINE"-stratus-vos + exit ;; + *:VOS:*:*) + # From Paul.Green@stratus.com. + echo hppa1.1-stratus-vos + exit ;; + mc68*:A/UX:*:*) + echo m68k-apple-aux"$UNAME_RELEASE" + exit ;; + news*:NEWS-OS:6*:*) + echo mips-sony-newsos6 + exit ;; + R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) + if test -d /usr/nec; then + echo mips-nec-sysv"$UNAME_RELEASE" + else + echo mips-unknown-sysv"$UNAME_RELEASE" + fi + exit ;; + BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. + echo powerpc-be-beos + exit ;; + BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. + echo powerpc-apple-beos + exit ;; + BePC:BeOS:*:*) # BeOS running on Intel PC compatible. + echo i586-pc-beos + exit ;; + BePC:Haiku:*:*) # Haiku running on Intel PC compatible. + echo i586-pc-haiku + exit ;; + x86_64:Haiku:*:*) + echo x86_64-unknown-haiku + exit ;; + SX-4:SUPER-UX:*:*) + echo sx4-nec-superux"$UNAME_RELEASE" + exit ;; + SX-5:SUPER-UX:*:*) + echo sx5-nec-superux"$UNAME_RELEASE" + exit ;; + SX-6:SUPER-UX:*:*) + echo sx6-nec-superux"$UNAME_RELEASE" + exit ;; + SX-7:SUPER-UX:*:*) + echo sx7-nec-superux"$UNAME_RELEASE" + exit ;; + SX-8:SUPER-UX:*:*) + echo sx8-nec-superux"$UNAME_RELEASE" + exit ;; + SX-8R:SUPER-UX:*:*) + echo sx8r-nec-superux"$UNAME_RELEASE" + exit ;; + SX-ACE:SUPER-UX:*:*) + echo sxace-nec-superux"$UNAME_RELEASE" + exit ;; + Power*:Rhapsody:*:*) + echo powerpc-apple-rhapsody"$UNAME_RELEASE" + exit ;; + *:Rhapsody:*:*) + echo "$UNAME_MACHINE"-apple-rhapsody"$UNAME_RELEASE" + exit ;; + arm64:Darwin:*:*) + echo aarch64-apple-darwin"$UNAME_RELEASE" + exit ;; + *:Darwin:*:*) + UNAME_PROCESSOR=$(uname -p) + case $UNAME_PROCESSOR in + unknown) UNAME_PROCESSOR=powerpc ;; + esac + if command -v xcode-select > /dev/null 2> /dev/null && \ + ! xcode-select --print-path > /dev/null 2> /dev/null ; then + # Avoid executing cc if there is no toolchain installed as + # cc will be a stub that puts up a graphical alert + # prompting the user to install developer tools. + CC_FOR_BUILD=no_compiler_found + else + set_cc_for_build + fi + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + case $UNAME_PROCESSOR in + i386) UNAME_PROCESSOR=x86_64 ;; + powerpc) UNAME_PROCESSOR=powerpc64 ;; + esac + fi + # On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc + if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_PPC >/dev/null + then + UNAME_PROCESSOR=powerpc + fi + elif test "$UNAME_PROCESSOR" = i386 ; then + # uname -m returns i386 or x86_64 + UNAME_PROCESSOR=$UNAME_MACHINE + fi + echo "$UNAME_PROCESSOR"-apple-darwin"$UNAME_RELEASE" + exit ;; + *:procnto*:*:* | *:QNX:[0123456789]*:*) + UNAME_PROCESSOR=$(uname -p) + if test "$UNAME_PROCESSOR" = x86; then + UNAME_PROCESSOR=i386 + UNAME_MACHINE=pc + fi + echo "$UNAME_PROCESSOR"-"$UNAME_MACHINE"-nto-qnx"$UNAME_RELEASE" + exit ;; + *:QNX:*:4*) + echo i386-pc-qnx + exit ;; + NEO-*:NONSTOP_KERNEL:*:*) + echo neo-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSE-*:NONSTOP_KERNEL:*:*) + echo nse-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSR-*:NONSTOP_KERNEL:*:*) + echo nsr-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSV-*:NONSTOP_KERNEL:*:*) + echo nsv-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSX-*:NONSTOP_KERNEL:*:*) + echo nsx-tandem-nsk"$UNAME_RELEASE" + exit ;; + *:NonStop-UX:*:*) + echo mips-compaq-nonstopux + exit ;; + BS2000:POSIX*:*:*) + echo bs2000-siemens-sysv + exit ;; + DS/*:UNIX_System_V:*:*) + echo "$UNAME_MACHINE"-"$UNAME_SYSTEM"-"$UNAME_RELEASE" + exit ;; + *:Plan9:*:*) + # "uname -m" is not consistent, so use $cputype instead. 386 + # is converted to i386 for consistency with other x86 + # operating systems. + # shellcheck disable=SC2154 + if test "$cputype" = 386; then + UNAME_MACHINE=i386 + else + UNAME_MACHINE="$cputype" + fi + echo "$UNAME_MACHINE"-unknown-plan9 + exit ;; + *:TOPS-10:*:*) + echo pdp10-unknown-tops10 + exit ;; + *:TENEX:*:*) + echo pdp10-unknown-tenex + exit ;; + KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) + echo pdp10-dec-tops20 + exit ;; + XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) + echo pdp10-xkl-tops20 + exit ;; + *:TOPS-20:*:*) + echo pdp10-unknown-tops20 + exit ;; + *:ITS:*:*) + echo pdp10-unknown-its + exit ;; + SEI:*:*:SEIUX) + echo mips-sei-seiux"$UNAME_RELEASE" + exit ;; + *:DragonFly:*:*) + echo "$UNAME_MACHINE"-unknown-dragonfly"$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')" + exit ;; + *:*VMS:*:*) + UNAME_MACHINE=$( (uname -p) 2>/dev/null) + case "$UNAME_MACHINE" in + A*) echo alpha-dec-vms ; exit ;; + I*) echo ia64-dec-vms ; exit ;; + V*) echo vax-dec-vms ; exit ;; + esac ;; + *:XENIX:*:SysV) + echo i386-pc-xenix + exit ;; + i*86:skyos:*:*) + echo "$UNAME_MACHINE"-pc-skyos"$(echo "$UNAME_RELEASE" | sed -e 's/ .*$//')" + exit ;; + i*86:rdos:*:*) + echo "$UNAME_MACHINE"-pc-rdos + exit ;; + *:AROS:*:*) + echo "$UNAME_MACHINE"-unknown-aros + exit ;; + x86_64:VMkernel:*:*) + echo "$UNAME_MACHINE"-unknown-esx + exit ;; + amd64:Isilon\ OneFS:*:*) + echo x86_64-unknown-onefs + exit ;; + *:Unleashed:*:*) + echo "$UNAME_MACHINE"-unknown-unleashed"$UNAME_RELEASE" + exit ;; +esac + +# No uname command or uname output not recognized. +set_cc_for_build +cat > "$dummy.c" < +#include +#endif +#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) +#if defined (vax) || defined (__vax) || defined (__vax__) || defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) +#include +#if defined(_SIZE_T_) || defined(SIGLOST) +#include +#endif +#endif +#endif +main () +{ +#if defined (sony) +#if defined (MIPSEB) + /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, + I don't know.... */ + printf ("mips-sony-bsd\n"); exit (0); +#else +#include + printf ("m68k-sony-newsos%s\n", +#ifdef NEWSOS4 + "4" +#else + "" +#endif + ); exit (0); +#endif +#endif + +#if defined (NeXT) +#if !defined (__ARCHITECTURE__) +#define __ARCHITECTURE__ "m68k" +#endif + int version; + version=$( (hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null); + if (version < 4) + printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); + else + printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); + exit (0); +#endif + +#if defined (MULTIMAX) || defined (n16) +#if defined (UMAXV) + printf ("ns32k-encore-sysv\n"); exit (0); +#else +#if defined (CMU) + printf ("ns32k-encore-mach\n"); exit (0); +#else + printf ("ns32k-encore-bsd\n"); exit (0); +#endif +#endif +#endif + +#if defined (__386BSD__) + printf ("i386-pc-bsd\n"); exit (0); +#endif + +#if defined (sequent) +#if defined (i386) + printf ("i386-sequent-dynix\n"); exit (0); +#endif +#if defined (ns32000) + printf ("ns32k-sequent-dynix\n"); exit (0); +#endif +#endif + +#if defined (_SEQUENT_) + struct utsname un; + + uname(&un); + if (strncmp(un.version, "V2", 2) == 0) { + printf ("i386-sequent-ptx2\n"); exit (0); + } + if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ + printf ("i386-sequent-ptx1\n"); exit (0); + } + printf ("i386-sequent-ptx\n"); exit (0); +#endif + +#if defined (vax) +#if !defined (ultrix) +#include +#if defined (BSD) +#if BSD == 43 + printf ("vax-dec-bsd4.3\n"); exit (0); +#else +#if BSD == 199006 + printf ("vax-dec-bsd4.3reno\n"); exit (0); +#else + printf ("vax-dec-bsd\n"); exit (0); +#endif +#endif +#else + printf ("vax-dec-bsd\n"); exit (0); +#endif +#else +#if defined(_SIZE_T_) || defined(SIGLOST) + struct utsname un; + uname (&un); + printf ("vax-dec-ultrix%s\n", un.release); exit (0); +#else + printf ("vax-dec-ultrix\n"); exit (0); +#endif +#endif +#endif +#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) +#if defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) +#if defined(_SIZE_T_) || defined(SIGLOST) + struct utsname *un; + uname (&un); + printf ("mips-dec-ultrix%s\n", un.release); exit (0); +#else + printf ("mips-dec-ultrix\n"); exit (0); +#endif +#endif +#endif + +#if defined (alliant) && defined (i860) + printf ("i860-alliant-bsd\n"); exit (0); +#endif + + exit (1); +} +EOF + +$CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null && SYSTEM_NAME=$($dummy) && + { echo "$SYSTEM_NAME"; exit; } + +# Apollos put the system type in the environment. +test -d /usr/apollo && { echo "$ISP-apollo-$SYSTYPE"; exit; } + +echo "$0: unable to guess system type" >&2 + +case "$UNAME_MACHINE:$UNAME_SYSTEM" in + mips:Linux | mips64:Linux) + # If we got here on MIPS GNU/Linux, output extra information. + cat >&2 <&2 <&2 </dev/null || echo unknown) +uname -r = $( (uname -r) 2>/dev/null || echo unknown) +uname -s = $( (uname -s) 2>/dev/null || echo unknown) +uname -v = $( (uname -v) 2>/dev/null || echo unknown) + +/usr/bin/uname -p = $( (/usr/bin/uname -p) 2>/dev/null) +/bin/uname -X = $( (/bin/uname -X) 2>/dev/null) + +hostinfo = $( (hostinfo) 2>/dev/null) +/bin/universe = $( (/bin/universe) 2>/dev/null) +/usr/bin/arch -k = $( (/usr/bin/arch -k) 2>/dev/null) +/bin/arch = $( (/bin/arch) 2>/dev/null) +/usr/bin/oslevel = $( (/usr/bin/oslevel) 2>/dev/null) +/usr/convex/getsysinfo = $( (/usr/convex/getsysinfo) 2>/dev/null) + +UNAME_MACHINE = "$UNAME_MACHINE" +UNAME_RELEASE = "$UNAME_RELEASE" +UNAME_SYSTEM = "$UNAME_SYSTEM" +UNAME_VERSION = "$UNAME_VERSION" +EOF +fi + +exit 1 + +# Local variables: +# eval: (add-hook 'before-save-hook 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/recipes/hmmer/config.sub b/recipes/hmmer/config.sub new file mode 100644 index 0000000000000..38f3d037a785f --- /dev/null +++ b/recipes/hmmer/config.sub @@ -0,0 +1,1885 @@ +#! /bin/sh +# Configuration validation subroutine script. +# Copyright 1992-2021 Free Software Foundation, Inc. + +# shellcheck disable=SC2006,SC2268 # see below for rationale + +timestamp='2021-10-27' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see . +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). + + +# Please send patches to . +# +# Configuration subroutine to validate and canonicalize a configuration type. +# Supply the specified configuration type as an argument. +# If it is invalid, we print an error message on stderr and exit with code 1. +# Otherwise, we print the canonical config type on stdout and succeed. + +# You can get the latest version of this script from: +# https://git.savannah.gnu.org/cgit/config.git/plain/config.sub + +# This file is supposed to be the same for all GNU packages +# and recognize all the CPU types, system types and aliases +# that are meaningful with *any* GNU software. +# Each package is responsible for reporting which valid configurations +# it does not support. The user should be able to distinguish +# a failure to support a valid configuration from a meaningless +# configuration. + +# The goal of this file is to map all the various variations of a given +# machine specification into a single specification in the form: +# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM +# or in some cases, the newer four-part form: +# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM +# It is wrong to echo any other type of specification. + +# The "shellcheck disable" line above the timestamp inhibits complaints +# about features and limitations of the classic Bourne shell that were +# superseded or lifted in POSIX. However, this script identifies a wide +# variety of pre-POSIX systems that do not have POSIX shells at all, and +# even some reasonably current systems (Solaris 10 as case-in-point) still +# have a pre-POSIX /bin/sh. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS + +Canonicalize a configuration name. + +Options: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.sub ($timestamp) + +Copyright 1992-2021 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + + *local*) + # First pass through any local machine types. + echo "$1" + exit ;; + + * ) + break ;; + esac +done + +case $# in + 0) echo "$me: missing argument$help" >&2 + exit 1;; + 1) ;; + *) echo "$me: too many arguments$help" >&2 + exit 1;; +esac + +# Split fields of configuration type +# shellcheck disable=SC2162 +saved_IFS=$IFS +IFS="-" read field1 field2 field3 field4 <&2 + exit 1 + ;; + *-*-*-*) + basic_machine=$field1-$field2 + basic_os=$field3-$field4 + ;; + *-*-*) + # Ambiguous whether COMPANY is present, or skipped and KERNEL-OS is two + # parts + maybe_os=$field2-$field3 + case $maybe_os in + nto-qnx* | linux-* | uclinux-uclibc* \ + | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* \ + | netbsd*-eabi* | kopensolaris*-gnu* | cloudabi*-eabi* \ + | storm-chaos* | os2-emx* | rtmk-nova*) + basic_machine=$field1 + basic_os=$maybe_os + ;; + android-linux) + basic_machine=$field1-unknown + basic_os=linux-android + ;; + *) + basic_machine=$field1-$field2 + basic_os=$field3 + ;; + esac + ;; + *-*) + # A lone config we happen to match not fitting any pattern + case $field1-$field2 in + decstation-3100) + basic_machine=mips-dec + basic_os= + ;; + *-*) + # Second component is usually, but not always the OS + case $field2 in + # Prevent following clause from handling this valid os + sun*os*) + basic_machine=$field1 + basic_os=$field2 + ;; + zephyr*) + basic_machine=$field1-unknown + basic_os=$field2 + ;; + # Manufacturers + dec* | mips* | sequent* | encore* | pc533* | sgi* | sony* \ + | att* | 7300* | 3300* | delta* | motorola* | sun[234]* \ + | unicom* | ibm* | next | hp | isi* | apollo | altos* \ + | convergent* | ncr* | news | 32* | 3600* | 3100* \ + | hitachi* | c[123]* | convex* | sun | crds | omron* | dg \ + | ultra | tti* | harris | dolphin | highlevel | gould \ + | cbm | ns | masscomp | apple | axis | knuth | cray \ + | microblaze* | sim | cisco \ + | oki | wec | wrs | winbond) + basic_machine=$field1-$field2 + basic_os= + ;; + *) + basic_machine=$field1 + basic_os=$field2 + ;; + esac + ;; + esac + ;; + *) + # Convert single-component short-hands not valid as part of + # multi-component configurations. + case $field1 in + 386bsd) + basic_machine=i386-pc + basic_os=bsd + ;; + a29khif) + basic_machine=a29k-amd + basic_os=udi + ;; + adobe68k) + basic_machine=m68010-adobe + basic_os=scout + ;; + alliant) + basic_machine=fx80-alliant + basic_os= + ;; + altos | altos3068) + basic_machine=m68k-altos + basic_os= + ;; + am29k) + basic_machine=a29k-none + basic_os=bsd + ;; + amdahl) + basic_machine=580-amdahl + basic_os=sysv + ;; + amiga) + basic_machine=m68k-unknown + basic_os= + ;; + amigaos | amigados) + basic_machine=m68k-unknown + basic_os=amigaos + ;; + amigaunix | amix) + basic_machine=m68k-unknown + basic_os=sysv4 + ;; + apollo68) + basic_machine=m68k-apollo + basic_os=sysv + ;; + apollo68bsd) + basic_machine=m68k-apollo + basic_os=bsd + ;; + aros) + basic_machine=i386-pc + basic_os=aros + ;; + aux) + basic_machine=m68k-apple + basic_os=aux + ;; + balance) + basic_machine=ns32k-sequent + basic_os=dynix + ;; + blackfin) + basic_machine=bfin-unknown + basic_os=linux + ;; + cegcc) + basic_machine=arm-unknown + basic_os=cegcc + ;; + convex-c1) + basic_machine=c1-convex + basic_os=bsd + ;; + convex-c2) + basic_machine=c2-convex + basic_os=bsd + ;; + convex-c32) + basic_machine=c32-convex + basic_os=bsd + ;; + convex-c34) + basic_machine=c34-convex + basic_os=bsd + ;; + convex-c38) + basic_machine=c38-convex + basic_os=bsd + ;; + cray) + basic_machine=j90-cray + basic_os=unicos + ;; + crds | unos) + basic_machine=m68k-crds + basic_os= + ;; + da30) + basic_machine=m68k-da30 + basic_os= + ;; + decstation | pmax | pmin | dec3100 | decstatn) + basic_machine=mips-dec + basic_os= + ;; + delta88) + basic_machine=m88k-motorola + basic_os=sysv3 + ;; + dicos) + basic_machine=i686-pc + basic_os=dicos + ;; + djgpp) + basic_machine=i586-pc + basic_os=msdosdjgpp + ;; + ebmon29k) + basic_machine=a29k-amd + basic_os=ebmon + ;; + es1800 | OSE68k | ose68k | ose | OSE) + basic_machine=m68k-ericsson + basic_os=ose + ;; + gmicro) + basic_machine=tron-gmicro + basic_os=sysv + ;; + go32) + basic_machine=i386-pc + basic_os=go32 + ;; + h8300hms) + basic_machine=h8300-hitachi + basic_os=hms + ;; + h8300xray) + basic_machine=h8300-hitachi + basic_os=xray + ;; + h8500hms) + basic_machine=h8500-hitachi + basic_os=hms + ;; + harris) + basic_machine=m88k-harris + basic_os=sysv3 + ;; + hp300 | hp300hpux) + basic_machine=m68k-hp + basic_os=hpux + ;; + hp300bsd) + basic_machine=m68k-hp + basic_os=bsd + ;; + hppaosf) + basic_machine=hppa1.1-hp + basic_os=osf + ;; + hppro) + basic_machine=hppa1.1-hp + basic_os=proelf + ;; + i386mach) + basic_machine=i386-mach + basic_os=mach + ;; + isi68 | isi) + basic_machine=m68k-isi + basic_os=sysv + ;; + m68knommu) + basic_machine=m68k-unknown + basic_os=linux + ;; + magnum | m3230) + basic_machine=mips-mips + basic_os=sysv + ;; + merlin) + basic_machine=ns32k-utek + basic_os=sysv + ;; + mingw64) + basic_machine=x86_64-pc + basic_os=mingw64 + ;; + mingw32) + basic_machine=i686-pc + basic_os=mingw32 + ;; + mingw32ce) + basic_machine=arm-unknown + basic_os=mingw32ce + ;; + monitor) + basic_machine=m68k-rom68k + basic_os=coff + ;; + morphos) + basic_machine=powerpc-unknown + basic_os=morphos + ;; + moxiebox) + basic_machine=moxie-unknown + basic_os=moxiebox + ;; + msdos) + basic_machine=i386-pc + basic_os=msdos + ;; + msys) + basic_machine=i686-pc + basic_os=msys + ;; + mvs) + basic_machine=i370-ibm + basic_os=mvs + ;; + nacl) + basic_machine=le32-unknown + basic_os=nacl + ;; + ncr3000) + basic_machine=i486-ncr + basic_os=sysv4 + ;; + netbsd386) + basic_machine=i386-pc + basic_os=netbsd + ;; + netwinder) + basic_machine=armv4l-rebel + basic_os=linux + ;; + news | news700 | news800 | news900) + basic_machine=m68k-sony + basic_os=newsos + ;; + news1000) + basic_machine=m68030-sony + basic_os=newsos + ;; + necv70) + basic_machine=v70-nec + basic_os=sysv + ;; + nh3000) + basic_machine=m68k-harris + basic_os=cxux + ;; + nh[45]000) + basic_machine=m88k-harris + basic_os=cxux + ;; + nindy960) + basic_machine=i960-intel + basic_os=nindy + ;; + mon960) + basic_machine=i960-intel + basic_os=mon960 + ;; + nonstopux) + basic_machine=mips-compaq + basic_os=nonstopux + ;; + os400) + basic_machine=powerpc-ibm + basic_os=os400 + ;; + OSE68000 | ose68000) + basic_machine=m68000-ericsson + basic_os=ose + ;; + os68k) + basic_machine=m68k-none + basic_os=os68k + ;; + paragon) + basic_machine=i860-intel + basic_os=osf + ;; + parisc) + basic_machine=hppa-unknown + basic_os=linux + ;; + psp) + basic_machine=mipsallegrexel-sony + basic_os=psp + ;; + pw32) + basic_machine=i586-unknown + basic_os=pw32 + ;; + rdos | rdos64) + basic_machine=x86_64-pc + basic_os=rdos + ;; + rdos32) + basic_machine=i386-pc + basic_os=rdos + ;; + rom68k) + basic_machine=m68k-rom68k + basic_os=coff + ;; + sa29200) + basic_machine=a29k-amd + basic_os=udi + ;; + sei) + basic_machine=mips-sei + basic_os=seiux + ;; + sequent) + basic_machine=i386-sequent + basic_os= + ;; + sps7) + basic_machine=m68k-bull + basic_os=sysv2 + ;; + st2000) + basic_machine=m68k-tandem + basic_os= + ;; + stratus) + basic_machine=i860-stratus + basic_os=sysv4 + ;; + sun2) + basic_machine=m68000-sun + basic_os= + ;; + sun2os3) + basic_machine=m68000-sun + basic_os=sunos3 + ;; + sun2os4) + basic_machine=m68000-sun + basic_os=sunos4 + ;; + sun3) + basic_machine=m68k-sun + basic_os= + ;; + sun3os3) + basic_machine=m68k-sun + basic_os=sunos3 + ;; + sun3os4) + basic_machine=m68k-sun + basic_os=sunos4 + ;; + sun4) + basic_machine=sparc-sun + basic_os= + ;; + sun4os3) + basic_machine=sparc-sun + basic_os=sunos3 + ;; + sun4os4) + basic_machine=sparc-sun + basic_os=sunos4 + ;; + sun4sol2) + basic_machine=sparc-sun + basic_os=solaris2 + ;; + sun386 | sun386i | roadrunner) + basic_machine=i386-sun + basic_os= + ;; + sv1) + basic_machine=sv1-cray + basic_os=unicos + ;; + symmetry) + basic_machine=i386-sequent + basic_os=dynix + ;; + t3e) + basic_machine=alphaev5-cray + basic_os=unicos + ;; + t90) + basic_machine=t90-cray + basic_os=unicos + ;; + toad1) + basic_machine=pdp10-xkl + basic_os=tops20 + ;; + tpf) + basic_machine=s390x-ibm + basic_os=tpf + ;; + udi29k) + basic_machine=a29k-amd + basic_os=udi + ;; + ultra3) + basic_machine=a29k-nyu + basic_os=sym1 + ;; + v810 | necv810) + basic_machine=v810-nec + basic_os=none + ;; + vaxv) + basic_machine=vax-dec + basic_os=sysv + ;; + vms) + basic_machine=vax-dec + basic_os=vms + ;; + vsta) + basic_machine=i386-pc + basic_os=vsta + ;; + vxworks960) + basic_machine=i960-wrs + basic_os=vxworks + ;; + vxworks68) + basic_machine=m68k-wrs + basic_os=vxworks + ;; + vxworks29k) + basic_machine=a29k-wrs + basic_os=vxworks + ;; + xbox) + basic_machine=i686-pc + basic_os=mingw32 + ;; + ymp) + basic_machine=ymp-cray + basic_os=unicos + ;; + *) + basic_machine=$1 + basic_os= + ;; + esac + ;; +esac + +# Decode 1-component or ad-hoc basic machines +case $basic_machine in + # Here we handle the default manufacturer of certain CPU types. It is in + # some cases the only manufacturer, in others, it is the most popular. + w89k) + cpu=hppa1.1 + vendor=winbond + ;; + op50n) + cpu=hppa1.1 + vendor=oki + ;; + op60c) + cpu=hppa1.1 + vendor=oki + ;; + ibm*) + cpu=i370 + vendor=ibm + ;; + orion105) + cpu=clipper + vendor=highlevel + ;; + mac | mpw | mac-mpw) + cpu=m68k + vendor=apple + ;; + pmac | pmac-mpw) + cpu=powerpc + vendor=apple + ;; + + # Recognize the various machine names and aliases which stand + # for a CPU type and a company and sometimes even an OS. + 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) + cpu=m68000 + vendor=att + ;; + 3b*) + cpu=we32k + vendor=att + ;; + bluegene*) + cpu=powerpc + vendor=ibm + basic_os=cnk + ;; + decsystem10* | dec10*) + cpu=pdp10 + vendor=dec + basic_os=tops10 + ;; + decsystem20* | dec20*) + cpu=pdp10 + vendor=dec + basic_os=tops20 + ;; + delta | 3300 | motorola-3300 | motorola-delta \ + | 3300-motorola | delta-motorola) + cpu=m68k + vendor=motorola + ;; + dpx2*) + cpu=m68k + vendor=bull + basic_os=sysv3 + ;; + encore | umax | mmax) + cpu=ns32k + vendor=encore + ;; + elxsi) + cpu=elxsi + vendor=elxsi + basic_os=${basic_os:-bsd} + ;; + fx2800) + cpu=i860 + vendor=alliant + ;; + genix) + cpu=ns32k + vendor=ns + ;; + h3050r* | hiux*) + cpu=hppa1.1 + vendor=hitachi + basic_os=hiuxwe2 + ;; + hp3k9[0-9][0-9] | hp9[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + hp9k2[0-9][0-9] | hp9k31[0-9]) + cpu=m68000 + vendor=hp + ;; + hp9k3[2-9][0-9]) + cpu=m68k + vendor=hp + ;; + hp9k6[0-9][0-9] | hp6[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + hp9k7[0-79][0-9] | hp7[0-79][0-9]) + cpu=hppa1.1 + vendor=hp + ;; + hp9k78[0-9] | hp78[0-9]) + # FIXME: really hppa2.0-hp + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) + # FIXME: really hppa2.0-hp + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[0-9][13679] | hp8[0-9][13679]) + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[0-9][0-9] | hp8[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + i*86v32) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv32 + ;; + i*86v4*) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv4 + ;; + i*86v) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv + ;; + i*86sol2) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=solaris2 + ;; + j90 | j90-cray) + cpu=j90 + vendor=cray + basic_os=${basic_os:-unicos} + ;; + iris | iris4d) + cpu=mips + vendor=sgi + case $basic_os in + irix*) + ;; + *) + basic_os=irix4 + ;; + esac + ;; + miniframe) + cpu=m68000 + vendor=convergent + ;; + *mint | mint[0-9]* | *MiNT | *MiNT[0-9]*) + cpu=m68k + vendor=atari + basic_os=mint + ;; + news-3600 | risc-news) + cpu=mips + vendor=sony + basic_os=newsos + ;; + next | m*-next) + cpu=m68k + vendor=next + case $basic_os in + openstep*) + ;; + nextstep*) + ;; + ns2*) + basic_os=nextstep2 + ;; + *) + basic_os=nextstep3 + ;; + esac + ;; + np1) + cpu=np1 + vendor=gould + ;; + op50n-* | op60c-*) + cpu=hppa1.1 + vendor=oki + basic_os=proelf + ;; + pa-hitachi) + cpu=hppa1.1 + vendor=hitachi + basic_os=hiuxwe2 + ;; + pbd) + cpu=sparc + vendor=tti + ;; + pbb) + cpu=m68k + vendor=tti + ;; + pc532) + cpu=ns32k + vendor=pc532 + ;; + pn) + cpu=pn + vendor=gould + ;; + power) + cpu=power + vendor=ibm + ;; + ps2) + cpu=i386 + vendor=ibm + ;; + rm[46]00) + cpu=mips + vendor=siemens + ;; + rtpc | rtpc-*) + cpu=romp + vendor=ibm + ;; + sde) + cpu=mipsisa32 + vendor=sde + basic_os=${basic_os:-elf} + ;; + simso-wrs) + cpu=sparclite + vendor=wrs + basic_os=vxworks + ;; + tower | tower-32) + cpu=m68k + vendor=ncr + ;; + vpp*|vx|vx-*) + cpu=f301 + vendor=fujitsu + ;; + w65) + cpu=w65 + vendor=wdc + ;; + w89k-*) + cpu=hppa1.1 + vendor=winbond + basic_os=proelf + ;; + none) + cpu=none + vendor=none + ;; + leon|leon[3-9]) + cpu=sparc + vendor=$basic_machine + ;; + leon-*|leon[3-9]-*) + cpu=sparc + vendor=`echo "$basic_machine" | sed 's/-.*//'` + ;; + + *-*) + # shellcheck disable=SC2162 + saved_IFS=$IFS + IFS="-" read cpu vendor <&2 + exit 1 + ;; + esac + ;; +esac + +# Here we canonicalize certain aliases for manufacturers. +case $vendor in + digital*) + vendor=dec + ;; + commodore*) + vendor=cbm + ;; + *) + ;; +esac + +# Decode manufacturer-specific aliases for certain operating systems. + +if test x$basic_os != x +then + +# First recognize some ad-hoc cases, or perhaps split kernel-os, or else just +# set os. +case $basic_os in + gnu/linux*) + kernel=linux + os=`echo "$basic_os" | sed -e 's|gnu/linux|gnu|'` + ;; + os2-emx) + kernel=os2 + os=`echo "$basic_os" | sed -e 's|os2-emx|emx|'` + ;; + nto-qnx*) + kernel=nto + os=`echo "$basic_os" | sed -e 's|nto-qnx|qnx|'` + ;; + *-*) + # shellcheck disable=SC2162 + saved_IFS=$IFS + IFS="-" read kernel os <&2 + exit 1 + ;; +esac + +# As a final step for OS-related things, validate the OS-kernel combination +# (given a valid OS), if there is a kernel. +case $kernel-$os in + linux-gnu* | linux-dietlibc* | linux-android* | linux-newlib* \ + | linux-musl* | linux-relibc* | linux-uclibc* ) + ;; + uclinux-uclibc* ) + ;; + -dietlibc* | -newlib* | -musl* | -relibc* | -uclibc* ) + # These are just libc implementations, not actual OSes, and thus + # require a kernel. + echo "Invalid configuration \`$1': libc \`$os' needs explicit kernel." 1>&2 + exit 1 + ;; + kfreebsd*-gnu* | kopensolaris*-gnu*) + ;; + vxworks-simlinux | vxworks-simwindows | vxworks-spe) + ;; + nto-qnx*) + ;; + os2-emx) + ;; + *-eabi* | *-gnueabi*) + ;; + -*) + # Blank kernel with real OS is always fine. + ;; + *-*) + echo "Invalid configuration \`$1': Kernel \`$kernel' not known to work with OS \`$os'." 1>&2 + exit 1 + ;; +esac + +# Here we handle the case where we know the os, and the CPU type, but not the +# manufacturer. We pick the logical manufacturer. +case $vendor in + unknown) + case $cpu-$os in + *-riscix*) + vendor=acorn + ;; + *-sunos*) + vendor=sun + ;; + *-cnk* | *-aix*) + vendor=ibm + ;; + *-beos*) + vendor=be + ;; + *-hpux*) + vendor=hp + ;; + *-mpeix*) + vendor=hp + ;; + *-hiux*) + vendor=hitachi + ;; + *-unos*) + vendor=crds + ;; + *-dgux*) + vendor=dg + ;; + *-luna*) + vendor=omron + ;; + *-genix*) + vendor=ns + ;; + *-clix*) + vendor=intergraph + ;; + *-mvs* | *-opened*) + vendor=ibm + ;; + *-os400*) + vendor=ibm + ;; + s390-* | s390x-*) + vendor=ibm + ;; + *-ptx*) + vendor=sequent + ;; + *-tpf*) + vendor=ibm + ;; + *-vxsim* | *-vxworks* | *-windiss*) + vendor=wrs + ;; + *-aux*) + vendor=apple + ;; + *-hms*) + vendor=hitachi + ;; + *-mpw* | *-macos*) + vendor=apple + ;; + *-*mint | *-mint[0-9]* | *-*MiNT | *-MiNT[0-9]*) + vendor=atari + ;; + *-vos*) + vendor=stratus + ;; + esac + ;; +esac + +echo "$cpu-$vendor-${kernel:+$kernel-}$os" +exit + +# Local variables: +# eval: (add-hook 'before-save-hook 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/recipes/hmmer/meta.yaml b/recipes/hmmer/meta.yaml index a5b3120a4bd0d..fdd92c051b30e 100644 --- a/recipes/hmmer/meta.yaml +++ b/recipes/hmmer/meta.yaml @@ -7,7 +7,7 @@ source: sha256: ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 build: - number: 1 + number: 2 run_exports: # commands/options have been removed or replaced between minor versions - {{ pin_subpackage('hmmer', max_pin="x.x") }} @@ -47,3 +47,4 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/hopla/meta.yaml b/recipes/hopla/meta.yaml index c628b8c8f198e..4dd3e825901cd 100644 --- a/recipes/hopla/meta.yaml +++ b/recipes/hopla/meta.yaml @@ -10,8 +10,10 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage("hopla", max_pin="x") }} requirements: run: @@ -26,7 +28,7 @@ requirements: - bioconductor-genomicranges >=1.42.0 - bioconductor-dnacopy >=1.64.0 - merlin 1.1.2.* # [not osx] - - pandoc >=2.* + - pandoc >=3.1.5 test: commands: diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml new file mode 100644 index 0000000000000..a17618e11af73 --- /dev/null +++ b/recipes/hsdecipher/meta.yaml @@ -0,0 +1,34 @@ +{% set name = "HSDecipher" %} +{% set version = "1.1.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz + sha256: de199452e123255f2a2dd574900593c9ca6d9c91722c6f150b70f633d6a31af5 + +build: + number: 0 + noarch: python + script: bash conda_build_package.sh + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + run: + - python >=3.7 + - pandas + - seaborn + - matplotlib-base +test: + commands: + - hsdecipher -h +about: + home: https://github.com/zx0223winner/HSDecipher + summary: Pipeline for the downstream analysis of highly similar duplicate genes + description: "Many tools have been developed to measure the degree of similarity between gene duplicates within and between species.Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene set, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species." + license: GPL-3.0-or-later + license_file: license + diff --git a/recipes/hsdfinder/meta.yaml b/recipes/hsdfinder/meta.yaml new file mode 100644 index 0000000000000..78c91f35e2d72 --- /dev/null +++ b/recipes/hsdfinder/meta.yaml @@ -0,0 +1,32 @@ +{% set name = "HSDFinder" %} +{% set version = "1.1.1" %} +{% set sha256 = "2e578bc3161290ff64dfd3e24c91199b562d117d2d3f2aa45dde47142899478c" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/zx0223winner/hsdfinder_conda/archive/refs/tags/{{ name|lower }}.tar.gz + sha256: {{ sha256 }} + +build: + noarch: python + number: 0 + script: bash conda_build_package.sh + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + run: + - python >=3.7 + - pandas +test: + commands: + - hsdfinder -h + - hsd_to_kegg -h +about: + home: https://github.com/zx0223winner/HSDFinder + summary: a tool to predict highly similar duplicates (HSDs) in eukaryotes + license: MIT + license_file: LICENSE.md diff --git a/recipes/htsbox/build.sh b/recipes/htsbox/build.sh index 9e8848d2dc477..e54829852c86a 100644 --- a/recipes/htsbox/build.sh +++ b/recipes/htsbox/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + #strictly use anaconda build environment export CFLAGS="${CFLAGS} -L${PREFIX}/lib" export C_INCLUDE_PATH=${PREFIX}/include @@ -7,6 +9,6 @@ export LIBRARY_PATH=${PREFIX}/lib mkdir -p $PREFIX/bin -make CC=${CC} CFLAGS="${CFLAGS}" +make -j ${CPU_COUNT} CC=${CC} CFLAGS="${CFLAGS}" mv htsbox $PREFIX/bin diff --git a/recipes/htsbox/meta.yaml b/recipes/htsbox/meta.yaml index dc6e9d426c58d..7b1af21cb9476 100644 --- a/recipes/htsbox/meta.yaml +++ b/recipes/htsbox/meta.yaml @@ -7,7 +7,9 @@ package: version: {{ version }} build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage(name, max_pin=None) }} source: url: https://github.com/lh3/htsbox/archive/6964440d791a60a22ca5ff25dc413a362bdc0abe.tar.gz @@ -30,3 +32,8 @@ about: home: https://github.com/lh3/htsbox license: Unknown summary: HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files. + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/htslib/arm_hwcap.patch b/recipes/htslib/arm_hwcap.patch index 40733dcc33b1d..1cd80981b78cf 100644 --- a/recipes/htslib/arm_hwcap.patch +++ b/recipes/htslib/arm_hwcap.patch @@ -2,6 +2,17 @@ Conda-forge's build environment on ARM uses sysroot_linux-aarch64 2.17, which is based on glibc 2.17 so does not define HWCAP_* values on ARM. Work around this by including the kernel header to get the desired values. +--- a/simd.c 2024-09-13 07:59:23.644080046 +1200 ++++ b/simd.c 2024-09-13 07:59:47.788059051 +1200 +@@ -44,6 +44,8 @@ + + #if defined __linux__ || defined __FreeBSD__ + #include ++// Ensure ARM HWCAP_* values are defined even on old glibc ++#include + #elif defined __APPLE__ + #include + #include --- a/htscodecs/htscodecs/rANS_static4x16pr.c 2023-10-10 02:54:16 +++ b/htscodecs/htscodecs/rANS_static4x16pr.c 2024-03-06 00:01:14 @@ -1030,6 +1030,8 @@ diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index a55e02f67f3a3..cde0c1dcfbca3 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.20" %} +{% set version = "1.21" %} package: name: htslib version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('htslib', max_pin='x.x') }} source: url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - sha256: e52d95b14da68e0cfd7d27faf56fef2f88c2eaf32a2be51c72e146e3aa928544 + sha256: 84b510e735f4963641f26fd88c8abdee81ff4cb62168310ae716636aac0f1823 patches: - arm_hwcap.patch diff --git a/recipes/hybkit/meta.yaml b/recipes/hybkit/meta.yaml index e350da1a32f29..ccf29b84b5449 100644 --- a/recipes/hybkit/meta.yaml +++ b/recipes/hybkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybkit" %} -{% set version = "0.3.4" %} +{% set version = "0.3.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/RenneLab/hybkit/archive/v{{ version }}.tar.gz - sha256: 6f42b1e116dd668b5fd2847691bc6b78cf641f9c1aae91ca752e6df6d18022cd + sha256: 8b977039da3c6f915215111f9f9c591734f8a18aa447a23c7c3b442caacface8 build: noarch: python diff --git a/recipes/hybpiper/meta.yaml b/recipes/hybpiper/meta.yaml index 6305cc6c34bf0..069d3780b89be 100644 --- a/recipes/hybpiper/meta.yaml +++ b/recipes/hybpiper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybpiper" %} -{% set version = "2.2.0" %} +{% set version = "2.3.0" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: "https://github.com/mossmatters/HybPiper/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 8337b1d17de9fa11f9d2b3f59ccc4597c5e3359d70e26d88346e871ccc6b1ac3 + sha256: 7b9d0af243dbdd24cb299cf8e05e65dafa873afc2c7605e3fae74b455457b491 build: - number: 1 + number: 0 noarch: python script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir entry_points: diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 15305a69002fc..2df2be7c1872a 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.7.3" %} +{% set version = "0.9.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 01ee53bb84c37ba2a4c37431dd34ada4383cf29aab4127acb3131ab1be58adac + sha256: 5b0d928520d1ead9d3007b48903f6a895a44243324f6b71276de08c896b16ae0 build: number: 0 diff --git a/recipes/hylight/build.sh b/recipes/hylight/build.sh new file mode 100644 index 0000000000000..72be420c9a094 --- /dev/null +++ b/recipes/hylight/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +if [[ "$(uname)" == "Darwin" ]]; then + ${PYTHON} -m pip install . --no-build-isolation --no-cache-dir --no-deps -vvv +else + ${PYTHON} -m pip install . --no-build-isolation --no-cache-dir --no-deps -vvv + hylight_conda_dir="${PREFIX}/lib/python3.6/site-packages/HyLight" + chmod +x $hylight_conda_dir/script/*py + cd ${SRC_DIR}/HyLight/tools/miniasm + make clean + make CC="${CC}" CPPFLAGS="${CPPFLAGS}" LIBS="${LDFLAGS} -lm -lz -lpthread -L${PREFIX}/lib" -j"${CPU_COUNT}" + cp -rf ${SRC_DIR}/HyLight/tools/miniasm/miniasm $hylight_conda_dir/tools/miniasm + cd ${SRC_DIR}/HyLight/tools/HaploConduct + make clean + make CC="${CXX}" CPPFLAGS="-Wall -fopenmp -std=c++14 -g -O3 -L${PREFIX}/lib -I${PREFIX}/include" -j"${CPU_COUNT}" + cp -rf bin quick-cliques/bin $hylight_conda_dir/tools/HaploConduct -r +fi diff --git a/recipes/hylight/meta.yaml b/recipes/hylight/meta.yaml new file mode 100644 index 0000000000000..afdf463050468 --- /dev/null +++ b/recipes/hylight/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "hylight" %} +{% set version = "1.0.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/LuoGroup2023/HyLight/releases/download/v{{ version }}/hylight.tar.gz + sha256: db01d912fef092c68d7a0dbad9c74e6330388f6524fe072f161a2a2c64f84573 + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - python ==3.6.15 + - pip + - zlib + - boost-cpp ==1.82 + run: + - python ==3.6.15 + - scipy ==1.5.3 + - numpy ==1.19.5 + - pandas ==1.1.5 + - minimap2 ==2.26 + - bfc ==r181 + - fmlrc2 ==0.1.7 + - ropebwt2 ==r187 + - racon ==1.5.0 + - boost-cpp ==1.82 + +test: + commands: + - hylight -h + +about: + home: "https://github.com/LuoGroup2023/HyLight" + license: MIT + license_family: MIT + summary: "Strain aware assembly of low coverage metagenomes." + dev_url: "https://github.com/LuoGroup2023/HyLight" + +extra: + skip-lints: + - should_be_noarch_python diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index 1a0520fed05d0..b531a053fb8a8 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("hyphy", max_pin="x.x") }} requirements: @@ -23,11 +23,7 @@ requirements: host: - libcurl - openmpi - - openssl - run: - - libcurl - - openmpi - - openssl + - zlib test: commands: @@ -47,5 +43,8 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 container: extended-base: true + identifiers: + - doi:10.1093/molbev/msz197 diff --git a/recipes/icfree-ml/meta.yaml b/recipes/icfree-ml/meta.yaml index 8ebec52264de7..d0e9659d2aa05 100644 --- a/recipes/icfree-ml/meta.yaml +++ b/recipes/icfree-ml/meta.yaml @@ -1,13 +1,13 @@ {% set name = "icfree-ml" %} -{% set version = "2.4.0" %} +{% set version = "2.5.0" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/brsynth/icfree-ml/archive/refs/tags/2.4.0.tar.gz - sha256: 7ea76c71098b86f562fd676c31b440da86d2f1c83c70b601eea58d4e28cce408 + url: https://github.com/brsynth/icfree-ml/archive/refs/tags/2.5.0.tar.gz + sha256: 9720880aba7613b582cd519749c5908195679e228a196cbc6ae941814410aef3 build: number: 0 @@ -27,6 +27,7 @@ requirements: - blast - pandas - pydoe2 + - openpyxl test: source_files: diff --git a/recipes/idemuxcpp/build.sh b/recipes/idemuxcpp/build.sh index 7e69267c6d7cc..dae53d55b2803 100644 --- a/recipes/idemuxcpp/build.sh +++ b/recipes/idemuxcpp/build.sh @@ -1,8 +1,10 @@ #!/bin/sh +set -xe + export CXXFLAGS="-I${PREFIX}/include/bamtools ${CXXFLAGS}" export LDFLAGS="-L${PREFIX}/lib/ -lbamtools ${LDFLAGS}" ./configure --enable-tests --prefix="${PREFIX}" -make +make -j ${CPU_COUNT} make install make check diff --git a/recipes/idemuxcpp/meta.yaml b/recipes/idemuxcpp/meta.yaml index 9c260e6708b31..683204c9c9c9f 100644 --- a/recipes/idemuxcpp/meta.yaml +++ b/recipes/idemuxcpp/meta.yaml @@ -1,6 +1,6 @@ {% set name = "idemuxcpp" %} -{% set version = "0.2.0" %} -{% set sha256 = "0e44ed269b57b9577141c70361e6c5871ef3d76b302f9c8a4c0ff2d54f30bf01" %} +{% set version = "0.3.0" %} +{% set sha256 = "0d2099172bbf006dc0eb21c0c0eb720f0681ed5e77d3e7194f13025c66ccd373" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('idemuxcpp', max_pin="x") }} @@ -40,5 +40,8 @@ about: summary: "A Lexogen tool for demultiplexing and index error correcting fastq files. Works with Lexogen i7, i5 and i1 barcodes." extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - entzian diff --git a/recipes/igv-reports/meta.yaml b/recipes/igv-reports/meta.yaml index 1e69cef3c08a1..3dad6f0d57606 100644 --- a/recipes/igv-reports/meta.yaml +++ b/recipes/igv-reports/meta.yaml @@ -1,5 +1,5 @@ {% set name = "igv-reports" %} -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 2a4bb08945e7872108a83037468249581b2fb42b2934cf33446971443175611d + sha256: edc03797c90b91dc0ac35b8352b316b11dc71c380f94ff3802e784baa971b19a build: noarch: python diff --git a/recipes/im2deep/meta.yaml b/recipes/im2deep/meta.yaml index 80ba742c8e0f8..8d186c0704c2b 100644 --- a/recipes/im2deep/meta.yaml +++ b/recipes/im2deep/meta.yaml @@ -1,6 +1,6 @@ {% set name = "im2deep" %} -{% set version = "0.1.8" %} -{% set sha256 = "cd671e843c850f8deb8682872890f0555e9d250ef5351239e4f29f2b49d519ee" %} +{% set version = "0.2.0" %} +{% set sha256 = "51678cfa2af905af196176e37e694c8629d9d8f2c4a1848185b5794697e0544b" %} package: name: {{ name|lower }} diff --git a/recipes/impg/build.sh b/recipes/impg/build.sh index d70db500fe871..0b47a91666337 100644 --- a/recipes/impg/build.sh +++ b/recipes/impg/build.sh @@ -1,8 +1,6 @@ #!/bin/bash -euo -# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. -# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. -export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" +set -xe # build statically linked binary with Rust RUST_BACKTRACE=1 diff --git a/recipes/impg/meta.yaml b/recipes/impg/meta.yaml index 04999b4407314..0d323eb9e9ac2 100644 --- a/recipes/impg/meta.yaml +++ b/recipes/impg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "impg" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: ad2f4f4ea68e0c3feb5ecef5b408bb8649c4a67f5203ca7320434ed9a070c7ee + sha256: 6b7a8786c1bfcc663c5154b11965d7b5fe31454a6363f6448a07ae935ea8c085 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} @@ -31,5 +31,8 @@ about: dev_url: https://github.com/pangenome/{{ name }} extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - AndreaGuarracino diff --git a/recipes/infernal/build.sh b/recipes/infernal/build.sh index 96e0f326ebabc..712789d396a1e 100644 --- a/recipes/infernal/build.sh +++ b/recipes/infernal/build.sh @@ -2,9 +2,13 @@ set -ex +export M4="${BUILD_PREFIX}/bin/m4" +export INCLUDE_PATH="${PREFIX}/include" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + grep -l -r "/usr/bin/perl" . | xargs sed -i.bak -e 's/usr\/bin\/perl/usr\/bin\/env perl/g' -autoreconf -i +autoreconf -if case $(uname -m) in "x86_64") @@ -19,6 +23,6 @@ case $(uname -m) in ;; esac -./configure --prefix="${PREFIX}" "${ARCH_OPTS}" +./configure --prefix="${PREFIX}" CC="${CC}" CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" "${ARCH_OPTS}" make -j${CPU_COUNT} make install diff --git a/recipes/infernal/meta.yaml b/recipes/infernal/meta.yaml index 0bb3322d57752..78a8740143bd8 100644 --- a/recipes/infernal/meta.yaml +++ b/recipes/infernal/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -26,6 +26,9 @@ requirements: - libgomp # [linux] - llvm-openmp # [osx] - wget + run: + - libgomp # [linux] + - llvm-openmp # [osx] test: commands: @@ -41,18 +44,19 @@ test: - cmstat -h about: - home: http://eddylab.org/infernal - license: BSD-3-Clause + home: 'http://eddylab.org/infernal' + license: "BSD-3-Clause" license_family: BSD license_file: LICENSE - summary: Infernal is for searching DNA sequence databases for RNA structure and sequence similarities. - description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. - doc_url: http://eddylab.org/infernal/Userguide.pdf - dev_url: https://github.com/EddyRivasLab/infernal + summary: "Infernal is for searching DNA sequence databases for RNA structure and sequence similarities." + description: "Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities." + doc_url: "http://eddylab.org/infernal/Userguide.pdf" + dev_url: "https://github.com/EddyRivasLab/infernal" extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - doi:10.1093/bioinformatics/btt509 - biotools:infernal diff --git a/recipes/inspector/meta.yaml b/recipes/inspector/meta.yaml index 25408db41b8b1..81d97fd7ce491 100644 --- a/recipes/inspector/meta.yaml +++ b/recipes/inspector/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2" %} +{% set version = "1.3.1" %} package: name: inspector @@ -6,20 +6,24 @@ package: source: url: https://github.com/ChongLab/Inspector/archive/refs/tags/inspector-v{{ version }}.tar.gz - sha256: 6d7ca6b22053d06105a549a064cf9a26efaf5c4a2a1a4502f2f36a4eb248ec4a + sha256: 2f1fa14ed4f504909183de09161681ae1a2dcfb3463b15fec09d227b69c51d0f build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage('inspector', max_pin="x") }} requirements: run: - python - - minimap2 =2.15 - - pysam =0.16.0.1 - - statsmodels =0.10.1 - - samtools =1.9 - - flye =2.8.3 + - minimap2 >=2.28 + - pysam >=0.22.1 + - statsmodels >=0.14.2 + - numpy >=2.1.0 + - pandas >=2.2.2 + - samtools >=1.20 + - flye >=2.9.5 test: commands: diff --git a/recipes/intarna/meta.yaml b/recipes/intarna/meta.yaml index 2fd80c6850890..534cc11818644 100644 --- a/recipes/intarna/meta.yaml +++ b/recipes/intarna/meta.yaml @@ -1,5 +1,5 @@ -{% set INTARNA_VERSION = "3.4.0" %} -{% set INTARNA_SHA256 = "4b0c53472dad49f3fbe6f0d3b1613d22d7b438bf650936da6a351a25fa9d535c" %} +{% set INTARNA_VERSION = "3.4.1" %} +{% set INTARNA_SHA256 = "4fd338a9a7a62f4398a27f41783120abaad9bccdecd39387c436adb0601f0ed8" %} {% set VRNA_VERSION = "2.4.14" %} package: @@ -12,7 +12,7 @@ about: summary: Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('intarna', max_pin="x.x") }} diff --git a/recipes/ipyrad/meta.yaml b/recipes/ipyrad/meta.yaml index 9b46a7831e71e..e03997c92935e 100644 --- a/recipes/ipyrad/meta.yaml +++ b/recipes/ipyrad/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ipyrad" %} -{% set version = "0.9.96" %} -{% set sha256 = "88bbaa820ad8b3626553c9d114a3a3f09fb35b15bff33b4b9a5b3d4e69ddb8cd" %} +{% set version = "0.9.102" %} +{% set sha256 = "2a8dc210d69cdedd34ac92715f23a9c3b7b4593a97b0d16851a566eacf33ef42" %} package: name: {{ name }} diff --git a/recipes/irescue/meta.yaml b/recipes/irescue/meta.yaml index d03df028c954e..009fc1d48346a 100644 --- a/recipes/irescue/meta.yaml +++ b/recipes/irescue/meta.yaml @@ -1,25 +1,29 @@ {% set name = "irescue" %} -{% set version = "1.0.3" %} +{% set version = "1.1.2" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/IRescue-{{ version }}.tar.gz - sha256: 9d68f42cd70c1ee9151699201319a3c879a3400b51a1224ccd66191ae5bb16ae + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/irescue-{{ version }}.tar.gz + sha256: 49a47a8859b3435cc94b171625c8c8c3b7bd7026498a0fd616dd48adb511e38c build: noarch: python - script: {{ PYTHON }} -m pip install . -vv - number: 1 + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + number: 0 + entry_points: + - irescue = irescue.main:main + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - - python >=3.7 + - python >=3.8 - pip run: - - python >=3.7 + - python >=3.8 - numpy >=1.20.2 - requests >=2.27.1 - gawk >=5.0.1 @@ -28,6 +32,7 @@ requirements: - pysam >=0.16.0.1 - bedtools >=2.30.0 - samtools >=1.12 + - networkx >=3.1 test: imports: @@ -37,10 +42,15 @@ test: about: home: https://github.com/bodegalab/irescue - summary: A tool to quantify transposable elements expression in scRNA-seq. + summary: "A tool to quantify transposable elements expression in scRNA-seq." license: MIT + license_family: MIT license_file: LICENSE + dev_url: https://github.com/bodegalab/irescue + doc_url: https://pypi.org/project/IRescue extra: recipe-maintainers: - bepoli + identifiers: + - doi:10.1101/2022.09.16.508229 diff --git a/recipes/irfinder/build.sh b/recipes/irfinder/build.sh index 1a87af2d43087..be08c698e0e13 100644 --- a/recipes/irfinder/build.sh +++ b/recipes/irfinder/build.sh @@ -1,8 +1,10 @@ #!/bin/sh -cd $SRC_DIR/src/irfinder && make && mv irfinder $SRC_DIR/bin/util -cd $SRC_DIR/src/trim && make && mv trim $SRC_DIR/bin/util -cd $SRC_DIR/src/winflat && make && mv winflat $SRC_DIR/bin/util +set -xe + +cd $SRC_DIR/src/irfinder && make -j ${CPU_COUNT} && mv irfinder $SRC_DIR/bin/util +cd $SRC_DIR/src/trim && make -j ${CPU_COUNT} && mv trim $SRC_DIR/bin/util +cd $SRC_DIR/src/winflat && make -j ${CPU_COUNT} && mv winflat $SRC_DIR/bin/util irfinder_home=$PREFIX/opt/irfinder-$PKG_VERSION mkdir -p $irfinder_home diff --git a/recipes/irfinder/meta.yaml b/recipes/irfinder/meta.yaml index b041a98420745..7066b218a6a5e 100644 --- a/recipes/irfinder/meta.yaml +++ b/recipes/irfinder/meta.yaml @@ -5,11 +5,13 @@ package: version: '{{ version }}' source: - url: https://github.com/williamritchie/IRFinder/archive/v{{ version }}.tar.gz + url: https://github.com/dgaolab/IRFinder/archive/refs/tags/v{{version}}.tar.gz sha256: 94fee8fdac37a5d51ae459d1b06c8d6ed0107752bf2535f207f787e3246ba8b2 build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("irfinder", max_pin="x") }} requirements: build: @@ -24,7 +26,14 @@ test: - IRFinder -v about: - home: https://github.com/williamritchie/IRFinder + home: https://github.com/dgaolab/IRFinder license: MIT license_family: MIT summary: Intron Retention Finder + dev_url: https://github.com/dgaolab/IRFinder + doc_url: https://github.com/williamritchie/IRFinder/wiki + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/iseq/meta.yaml b/recipes/iseq/meta.yaml index 2d579ced77195..193270e7e7cef 100644 --- a/recipes/iseq/meta.yaml +++ b/recipes/iseq/meta.yaml @@ -1,5 +1,5 @@ {% set name = "iSeq" %} -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/BioOmics/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: a7209fa37eaa95c1beef471a494d82d56bc4313c801d05fb7478cfa3e745a67e + sha256: de0b9f1e06842a14f0a112023b989a38f6d422d860d44b19d3ec717d3c00bc34 build: noarch: generic diff --git a/recipes/isoquant/meta.yaml b/recipes/isoquant/meta.yaml index bbc7fbd26d950..ee3930be3b942 100644 --- a/recipes/isoquant/meta.yaml +++ b/recipes/isoquant/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IsoQuant" %} -{% set version = "3.5.0" %} -{% set sha256 = "80771cc4fbe8d222b5dfa45be392942b2fdd356ebbb1d99e26d251c37bba085d" %} +{% set version = "3.6.1" %} +{% set sha256 = "6d16e47e9ca45f9a0d029940d5b84e03038d9ba3d640945e3a5087acfd7ed56d" %} package: name: {{ name | lower }} diff --git a/recipes/itolapi/meta.yaml b/recipes/itolapi/meta.yaml index 0e664d28481a5..806c0a9213404 100644 --- a/recipes/itolapi/meta.yaml +++ b/recipes/itolapi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "itolapi" %} -{% set version = "4.1.4" %} +{% set version = "4.1.5" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 68e87ba51d209da556b0e373b3b0456b644a1a732c193fedbd7785ff37b6a2cb + sha256: 8ce2f6c0560b4b3898913a61a821667ea62aca330aad008e4c71fe98ec26c874 build: noarch: python diff --git a/recipes/itsxpress/meta.yaml b/recipes/itsxpress/meta.yaml index 2ecd49b405f60..cbef171ed668d 100644 --- a/recipes/itsxpress/meta.yaml +++ b/recipes/itsxpress/meta.yaml @@ -1,8 +1,8 @@ {% set name = "itsxpress" %} -{% set version = "2.1.0" %} +{% set version = "2.1.2" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "608e5c55526d4c084f8ea552c7bd2d232505ae83751fc517c8ceabb2eb483aed" %} +{% set hash_value = "5a19ef9333ac4acacfa1da9c27ff3f713d7521661fbfe7541c58221c2ce2d08f" %} package: name: '{{ name|lower }}' diff --git a/recipes/jalview/meta.yaml b/recipes/jalview/meta.yaml index 54db0fb5834b3..d6bf758f6eb2f 100644 --- a/recipes/jalview/meta.yaml +++ b/recipes/jalview/meta.yaml @@ -1,5 +1,5 @@ {% set name = "jalview" %} -{% set version = "2.11.3.3" %} +{% set version = "2.11.4.0" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ build: source: url: https://www.jalview.org/source/jalview_{{ version|replace(".", "_") }}.tar.gz - sha256: "e41bcbb8d8e46eaed125f5bdac9f16ef443a804bb5b6c1310abd9489a862fa79" + sha256: "a128b70eb51228a02ecd47c93fa74140ffd905fbe5bf184fe405c39e78390a6d" requirements: build: diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 761afe067f7c8..821dfee562371 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.13.1" %} +{% set version = "2.15.4" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 6b2ccd796ae6c0e09e8e02fc4b7173826994b1db81bad5961fde588c6fc6964e + sha256: fa0a6163dab65d1705c1968cc41adc0f6b035a8fbc572b7ddff12721b5b58642 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: diff --git a/recipes/jclusterfunk/build.sh b/recipes/jclusterfunk/build.sh new file mode 100755 index 0000000000000..8750eb03bcab7 --- /dev/null +++ b/recipes/jclusterfunk/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu -o pipefail + +outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $outdir +mkdir -p $PREFIX/bin + +cp jclusterfunk jclusterfunk.jar $outdir/ + +ln -s $outdir/jclusterfunk $PREFIX/bin +chmod 0755 "${PREFIX}/bin/jclusterfunk" diff --git a/recipes/jclusterfunk/meta.yaml b/recipes/jclusterfunk/meta.yaml new file mode 100644 index 0000000000000..1e468afe4134c --- /dev/null +++ b/recipes/jclusterfunk/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "0.0.25" %} +{% set name = "jclusterfunk" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/snake-flu/jclusterfunk/releases/download/v{{ version }}/jclusterfunk_v{{ version }}.tgz + sha256: 333029dfcfe5d08ecb96bd31f2fed1b732547d45a1f892b9515ae28b528beee8 + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - openjdk + run: + - openjdk + +test: + commands: + - jclusterfunk --help + +about: + home: https://github.com/snake-flu/jclusterfunk + license: GPL-3.0-only + license_family: GPL3 + license_url: https://github.com/snake-flu/jclusterfunk/blob/master/LICENSE + summary: A command line tool with a bunch of functions for trees diff --git a/recipes/jvarkit/meta.yaml b/recipes/jvarkit/meta.yaml index b6f52cdbf9b3d..e396de5f8c452 100644 --- a/recipes/jvarkit/meta.yaml +++ b/recipes/jvarkit/meta.yaml @@ -1,6 +1,6 @@ {% set name = "jvarkit" %} -{% set version = "2024.08.01" %} -{% set sha256 = "5c35258898ef0c65e118e01db663489565989792d949e6a5d93965c9680250cd" %} +{% set version = "2024.08.25" %} +{% set sha256 = "1836eae5f27216a3df84d8dbb9282575955149452883d5f86ba1aebb57b59cbf" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin=None) }} # it's date based (yyyy.mm.dd) there's no real semantic pinning, and breaking changes happen (e.g.: tools / libraries being removed) @@ -26,6 +26,8 @@ requirements: - gawk run: - openjdk >=11 + - samtools >=1.20 + - bcftools >=1.20 test: commands: diff --git a/recipes/k8/build.sh b/recipes/k8/build.sh index 3b3aeda6a195d..96edeaf676cde 100644 --- a/recipes/k8/build.sh +++ b/recipes/k8/build.sh @@ -1,9 +1,29 @@ -#!/usr/bin/env bash +#!/bin/bash set -x +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + DEFAULT_LINUX_VERSION="cos7" -NODE_VERSION="18.19.1" +# * k8 is only compatible with Node.js v18.x, not more recent node versions +# * node-18.19.x can be compiled on CentOS 7, but not on macOS with clang +# * node-18.20.x can be compiled on MacOS but not on CentOS 7 because it +# includes an updated c-ares library which is incompatible with glibc on CentOS 7 +if [[ "$(uname)" == "Darwin" ]]; then + NODE_VERSION="18.20.4" + export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" +else + NODE_VERSION="18.19.1" +fi + +case $(uname -m) in + x86_64) + THREADS="-j2" + ;; + *) + THREADS="-j3" + ;; +esac wget -O- https://nodejs.org/dist/v${NODE_VERSION}/node-v${NODE_VERSION}.tar.gz | tar -zxf - pushd node-v${NODE_VERSION} @@ -15,17 +35,20 @@ pushd node-v${NODE_VERSION} # 2024-03-19T13:32:27.9241412Z 13:32:27 BIOCONDA INFO (OUT) cc1plus: some warnings being treated as errors patch -p0 < ${RECIPE_DIR}/nodejs-x86_64.patch -./configure --without-node-snapshot --without-etw --without-npm --without-inspector --without-dtrace -make -j3 +# The provided configure script is a sh/python hybrid which boils down to one line of Python +python -c "import configure" --without-node-snapshot --without-etw --without-npm --without-inspector --without-dtrace +make "${THREADS}" popd # make it possible to set conda build's CXXFLAGS and point to the Node sources sed -i.bak 's/CXXFLAGS=/CXXFLAGS?=/' Makefile sed -i.bak 's/NODE_SRC=/NODE_SRC?=/' Makefile sed -i.bak 's/LIBS=/LIBS?=/' Makefile +rm -rf *.bak # Then compile k8 NODE_SRC="node-v${NODE_VERSION}" CXXFLAGS="${CXXFLAGS} -std=c++17 -g -O3 -Wall" LIBS="${LDFLAGS} -pthread" make mkdir -p $PREFIX/bin -cp -f k8 $PREFIX/bin/k8 +chmod 0755 k8 +cp -f k8 $PREFIX/bin/ diff --git a/recipes/k8/meta.yaml b/recipes/k8/meta.yaml index bd8884f37dc2f..98f026709acd1 100644 --- a/recipes/k8/meta.yaml +++ b/recipes/k8/meta.yaml @@ -10,7 +10,8 @@ source: sha256: 4157aa86066eb0a7874de194893c4544ac772d009cc1148377c9c346f9fc6d07 build: - number: 1 + number: 3 + skip: True # [osx and x86_64] run_exports: - {{ pin_subpackage('k8', max_pin="x") }} @@ -20,7 +21,8 @@ requirements: - make - sysroot_linux-64 >=2.17 # [linux and x86_64] host: - - python ==3.8 + - python >=3.8 + - setuptools - zlib - wget - tar @@ -38,9 +40,11 @@ about: license: MIT license_family: MIT license_file: "LICENSE.txt" - summary: "Lightweight JavaScript shell based on Google's V8 JavaScript engine" + summary: "Lightweight JavaScript shell based on Google's V8 JavaScript engine." dev_url: "https://github.com/attractivechaos/k8" + doc_url: "https://github.com/attractivechaos/k8/blob/v{{ version }}/README.md" extra: additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/kallisto/build.sh b/recipes/kallisto/build.sh index 99c91effdd6c4..5f7b7f92b140d 100644 --- a/recipes/kallisto/build.sh +++ b/recipes/kallisto/build.sh @@ -1,13 +1,38 @@ #!/bin/bash +mkdir -p "${PREFIX}/bin" +export M4="${BUILD_PREFIX}/bin/m4" + cd ext/htslib || exit 1 -export M4=${BUILD_PREFIX}/bin/m4 autoreconf --force --install --verbose ./configure cd ../.. || exit 1 -mkdir -p "${PREFIX}/bin" -mkdir -p build -cd build || exit 1 -cmake -DCMAKE_INSTALL_PREFIX:PATH="$PREFIX" .. -DUSE_HDF5=ON -make -make install + +case $(uname -m) in + x86_64) + ARCH_OPTS="-DENABLE_AVX2=OFF -DCOMPILATION_ARCH=OFF" + ;; + aarch64) + ARCH_OPTS="-DCOMPILATION_ARCH=OFF" + ;; + arm64) + ARCH_OPTS="-DENABLE_AVX2=OFF -DCOMPILATION_ARCH=OFF" + ;; + *) + ;; +esac + +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + +cmake -S. -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DUSE_HDF5=ON -DUSE_BAM=ON -DBUILD_FUNCTESTING=ON -DMAX_KMER_SIZE=64 \ + -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \ + "${ARCH_OPTS}" \ + "${CONFIG_ARGS}" + +cmake --build build --target install -v diff --git a/recipes/kallisto/meta.yaml b/recipes/kallisto/meta.yaml index 489c0d5c2a274..49b6ca8115b6e 100644 --- a/recipes/kallisto/meta.yaml +++ b/recipes/kallisto/meta.yaml @@ -1,12 +1,13 @@ -{% set version = "0.51.0" %} +{% set name = "kallisto" %} +{% set version = "0.51.1" %} package: - name: kallisto + name: {{ name }} version: {{ version }} source: - url: https://github.com/pachterlab/kallisto/archive/V{{ version }}.tar.gz - sha256: efeb0191c1a6a0d6de69111fb66f4bda51ff31fb40c513280f072bd44556f80d + url: https://github.com/pachterlab/kallisto/archive/refs/tags/v{{ version }}.tar.gz + sha256: a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516 build: number: 0 @@ -21,36 +22,34 @@ requirements: - autoconf - automake host: + - libcurl - bzip2 - hdf5 - xz - zlib run: - - bzip2 - hdf5 - - xz - - zlib test: commands: - kallisto cite about: - home: "http://pachterlab.github.io/kallisto" - license: BSD-2-Clause + home: "https://pachterlab.github.io/kallisto" + license: "BSD-2-Clause" license_family: BSD - summary: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. - dev_url: https://github.com/pachterlab/kallisto + summary: "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads." + dev_url: "https://github.com/pachterlab/kallisto" doc_url: "https://pachterlab.github.io/kallisto/manual.html" extra: identifiers: - biotools:kallisto - doi:10.1038/nbt.3519 + - usegalaxy-eu:kallisto_pseudo + - usegalaxy-eu:kallisto_quant recipe-maintainers: - mjsteinbaugh - skip-lints: - - missing_tests additional-platforms: - linux-aarch64 - osx-arm64 diff --git a/recipes/kegalign-full/meta.yaml b/recipes/kegalign-full/meta.yaml new file mode 100644 index 0000000000000..85047fe074c54 --- /dev/null +++ b/recipes/kegalign-full/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "0.1.2.7" %} + +package: + name: kegalign-full + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_compatible('kegalign-full', max_pin='x.x') }} + +requirements: + run: + - kegalign ={{ version }} + - lastz + - mbuffer + - samtools + - ucsc-fatotwobit + +test: + commands: + - kegalign --help + - lastz --version 2>&1 | grep released + - which faToTwoBit + +about: + home: https://github.com/galaxyproject/KegAlign + summary: 'KegAlign: A Scalable GPU-Based Whole Genome Aligner' + description: | + KegAlign is a Scalable GPU System for Pairwise Whole Genome + Alignments based on LASTZ's seed-filter-extend paradigm. + license: MIT + license_family: MIT + license_url: https://github.com/galaxyproject/KegAlign/blob/main/LICENSE + doc_url: https://github.com/galaxyproject/KegAlign/blob/main/README.md + dev_url: https://github.com/galaxyproject/KegAlign diff --git a/recipes/kleborate/build.sh b/recipes/kleborate/build.sh deleted file mode 100644 index 2ce65676732d8..0000000000000 --- a/recipes/kleborate/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -#! /bin/bash - -$PYTHON -m pip install . --ignore-installed --no-deps -vv - -# Make blastdbs of Kleborate data -# Allows containters to be usable - $PREFIX/bin/kleborate -a kleborate/data/Klebsiella_pneumoniae.fasta --all diff --git a/recipes/kleborate/fix_get_kaptive_path.patch b/recipes/kleborate/fix_get_kaptive_path.patch deleted file mode 100644 index 4b751f16ef396..0000000000000 --- a/recipes/kleborate/fix_get_kaptive_path.patch +++ /dev/null @@ -1,41 +0,0 @@ -From e897aa05e7981515ce4f34f46f1103c44c97844a Mon Sep 17 00:00:00 2001 -From: "Robert A. Petit III" -Date: Sat, 17 Jul 2021 01:44:51 -0600 -Subject: [PATCH] Update kaptive.py - ---- - kleborate/kaptive.py | 11 +++++------ - 1 file changed, 5 insertions(+), 6 deletions(-) - -diff --git a/kleborate/kaptive.py b/kleborate/kaptive.py -index 53c2fa8..729a84d 100644 ---- a/kleborate/kaptive.py -+++ b/kleborate/kaptive.py -@@ -15,22 +15,21 @@ - import os - import subprocess - import sys -+import shutil - import tempfile - - - def get_kaptive_paths(): -- this_file = os.path.realpath(__file__) -- kaptive_dir = os.path.join(os.path.dirname(os.path.dirname(this_file)), 'kaptive') -+ kaptive_py = shutil.which('kaptive.py') -+ kaptive_dir = os.path.join(os.path.dirname(os.path.dirname(kaptive_py)), 'opt/kaptive_reference_database') - if not os.path.isdir(kaptive_dir): - sys.exit('Error: could not find Kaptive directory. Did you git clone with --recursive?') -- kaptive_py = os.path.join(kaptive_dir, 'kaptive.py') - if not os.path.isfile(kaptive_py): - sys.exit('Error: could not find kaptive.py') -- db_dir = os.path.join(kaptive_dir, 'reference_database') -- kaptive_k_db = os.path.join(db_dir, 'Klebsiella_k_locus_primary_reference.gbk') -+ kaptive_k_db = os.path.join(kaptive_dir, 'Klebsiella_k_locus_primary_reference.gbk') - if not os.path.isfile(kaptive_k_db): - sys.exit('Error: could not find Klebsiella_k_locus_primary_reference.gbk') -- kaptive_o_db = os.path.join(db_dir, 'Klebsiella_o_locus_primary_reference.gbk') -+ kaptive_o_db = os.path.join(kaptive_dir, 'Klebsiella_o_locus_primary_reference.gbk') - if not os.path.isfile(kaptive_o_db): - sys.exit('Error: could not find Klebsiella_o_locus_primary_reference.gbk') - return kaptive_py, kaptive_k_db, kaptive_o_db diff --git a/recipes/kleborate/meta.yaml b/recipes/kleborate/meta.yaml index f245e9ce9cba7..8f40f1665c01c 100644 --- a/recipes/kleborate/meta.yaml +++ b/recipes/kleborate/meta.yaml @@ -1,47 +1,59 @@ -{% set name = "Kleborate" %} -{% set version = "2.3.2" %} +{% set name = "kleborate" %} +{% set version = "3.0.9" %} package: - name: {{ name|lower }} - version: {{ version }} + name: "{{ name|lower }}" + version: "{{ version }}" source: - url: https://github.com/katholt/{{ name }}/archive/v{{ version }}.tar.gz - sha256: da7cb9a27ddba4e5440063e2d4a0c4a9f9e668a65ae9f019db126dc5b10d7002 - patches: - - fix_get_kaptive_path.patch + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/kleborate-{{ version }}.tar.gz" + sha256: 9c1757aa4994a9bb5f3b7356cc8f0d54b99a2d633f33531d35d9137b835e5db2 build: - noarch: python number: 0 + noarch: python + entry_points: + - kleborate = kleborate.__main__:main + script: + - {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('kleborate', max_pin='x') }} requirements: host: - - python >=3.7 - - biopython >=1.73,<1.78 - - kaptive - - blast >=2.2.31 - - mash + - pip + - python >=3.9 run: - - python >=3.7 - - biopython >=1.73,<1.78 - - kaptive - - blast >=2.2.31 + - python >=3.9 + - biopython >=1.83 + - numpy >=1.22 + - dna_features_viewer + - minimap2 - mash + - kaptive test: + imports: + - kleborate commands: - - kaptive.py -h - - kleborate -h - - kleborate -a $(which kleborate | sed 's=bin/kleborate=opt/kaptive_reference_database/exact_match.fasta=') + - kaptive --help + - minimap2 --help + - kleborate --help about: - home: https://github.com/katholt/Kleborate - license: GNU General Public License v3 or later (GPLv3+) - license_file: LICENSE - summary: 'Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest' - long_summary: 'A tool to screen Klebsiella genome assembiles for: MLST sequence type, - species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), - ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2), antimicrobial resistance genes, including quinolone resistance SNPs and colistin resistance truncations, - and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive.' + home: "https://kleboratemodular.readthedocs.io" + dev_url: "https://github.com/klebgenomics/KleborateModular" + summary: "Kleborate: a tool for typing and screening pathogen genome assemblies" + license: "GPL-3.0-or-later" license_family: GPL3 + license_file: LICENSE + doc_url: "https://kleboratemodular.readthedocs.io" + +extra: + recipe-maintainers: + - Marysteph + identifiers: + - doi:10.1038/s41467-021-24448-3 + - doi:10.1099/mgen.0.000102 + - biotools:kleborate + - usegalaxy-eu:kleborate diff --git a/recipes/kmertools/build.sh b/recipes/kmertools/build.sh index 9a40edcacf2d1..472a714ec66c5 100644 --- a/recipes/kmertools/build.sh +++ b/recipes/kmertools/build.sh @@ -4,4 +4,34 @@ cargo build --release # Install the binaries -cargo install --path kmertools --root $PREFIX +cargo install --verbose --path kmertools --root "${PREFIX}" + +# Check if the system is macOS +if [[ "$(uname)" == "Darwin" ]]; then + # Get the architecture + arch=$(uname -m) + + # Set MACOSX_DEPLOYMENT_TARGET based on architecture + if [[ "$arch" == "x86_64" ]]; then + # For Intel Macs + export MACOSX_DEPLOYMENT_TARGET=10.12 + elif [[ "$arch" == "arm64" ]]; then + # For Apple Silicon Macs + export MACOSX_DEPLOYMENT_TARGET=11.0 + else + echo "Unknown architecture: $arch" + exit 1 + fi + + echo "Set MACOSX_DEPLOYMENT_TARGET to $MACOSX_DEPLOYMENT_TARGET for $arch" +else + echo "Not running on macOS, skipping MACOSX_DEPLOYMENT_TARGET" +fi + +# Build statically linked binary with Rust +RUST_BACKTRACE=1 +# Build with maturin +maturin build -m ./conda/Cargo.toml -b pyo3 --interpreter "${PYTHON}" --release --strip + +# Install the wheel file +${PYTHON} -m pip install ./target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/kmertools/meta.yaml b/recipes/kmertools/meta.yaml index 0e97b0c0e1d13..f8b6450da96f0 100644 --- a/recipes/kmertools/meta.yaml +++ b/recipes/kmertools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.1.0" %} +{% set version = "0.1.4" %} {% set name = "kmertools" %} -{% set sha256 = "3c8cf78c95ab0baf0f69e7bc631ea52a54733bed0122b9d20e76d49df5639a4c" %} +{% set sha256 = "457ffdbe2cc34b9faf63d06124d6d68ffc9b8c83825fc800d171899dc3a8b0d9" %} package: name: {{ name }} @@ -8,6 +8,7 @@ package: build: number: 0 + skip: True # [py < 39] run_exports: - {{ pin_subpackage('kmertools', max_pin="x.x") }} @@ -18,6 +19,11 @@ source: requirements: build: - {{ compiler("rust") }} + - python + host: + - maturin >=1.7,<2.0 + - python + - pip test: commands: @@ -33,6 +39,9 @@ about: dev_url: https://github.com/anuradhawick/kmertools extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - anuradhawick - Vini2 diff --git a/recipes/kraken2/build.sh b/recipes/kraken2/build.sh index c526a455c2265..3cb65dd41091f 100644 --- a/recipes/kraken2/build.sh +++ b/recipes/kraken2/build.sh @@ -15,10 +15,13 @@ if [[ "$(uname)" == Darwin ]]; then fi ./install_kraken2.sh "${outdir}/libexec" -for bin in kraken2 kraken2-build kraken2-inspect; do +for bin in kraken2 kraken2-build kraken2-inspect k2; do chmod +x "${outdir}/libexec/$bin" ln -s "${outdir}/libexec/$bin" "${PREFIX}/bin/$bin" # Change from double quotes to single in case of special chars - sed -i.bak "s#my \$KRAKEN_DIR = \"${outdir}/libexec\";#my \$KRAKEN_DIR = '${outdir}/libexec';#g" "${outdir}/libexec/${bin}" - rm -rf "${outdir}/libexec/${bin}.bak" + # we don't do the following for the k2 binariy + if [[ $bin != "k2" ]]; then + sed -i.bak "s#my \$KRAKEN_DIR = \"${outdir}/libexec\";#my \$KRAKEN_DIR = '${outdir}/libexec';#g" "${outdir}/libexec/${bin}" + rm -rf "${outdir}/libexec/${bin}.bak" + fi done diff --git a/recipes/kraken2/meta.yaml b/recipes/kraken2/meta.yaml index f772a6e069e1b..8d2baa946852b 100644 --- a/recipes/kraken2/meta.yaml +++ b/recipes/kraken2/meta.yaml @@ -13,8 +13,9 @@ source: - Makefile.patch build: - number: 1 - run_exports: '{{ pin_subpackage("kraken2", max_pin="x.x") }}' + number: 2 + run_exports: + - '{{ pin_subpackage(name, max_pin="x.x") }}' requirements: build: @@ -35,12 +36,14 @@ requirements: - tar - rsync - zlib + - python test: commands: - kraken2 --version - kraken2-build --version - kraken2-inspect --version + - k2 --help about: home: "https://ccb.jhu.edu/software/kraken2/" diff --git a/recipes/lambda/meta.yaml b/recipes/lambda/meta.yaml index e87ddb3cc388c..882b493ea719d 100644 --- a/recipes/lambda/meta.yaml +++ b/recipes/lambda/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.0.0" %} +{% set version = "3.1.0" %} package: name: lambda @@ -6,7 +6,7 @@ package: source: url: https://github.com/seqan/lambda/releases/download/lambda-v{{ version }}/lambda3-{{ version }}-SourceWithSubmodules.tar.xz - sha256: 48b4b72007ffc86c4aad59634721e89a990fb42cb90f2cd17f52edc60d0c6482 + sha256: fb3388e8b5a9f33f7423699803eaef4e6b9838c11017bd5b0d2b07f66491f191 build: number: 0 diff --git a/recipes/last/build.sh b/recipes/last/build.sh index cdda4074d43e1..a00115fb43b2e 100644 --- a/recipes/last/build.sh +++ b/recipes/last/build.sh @@ -1,9 +1,12 @@ #!/bin/bash -xe +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + ARCH=$(uname -m) case ${ARCH} in x86_64) ARCH_FLAGS="-msse4" ;; *) ARCH_FLAGS="" ;; esac -make install CXXFLAGS="${CXXFLAGS} -O3 ${ARCH_FLAGS} -pthread -I${PREFIX}/include" prefix="${PREFIX}" +make install CXXFLAGS="${CXXFLAGS} -O3 ${ARCH_FLAGS} -pthread -I${PREFIX}/include ${LDFLAGS}" \ + prefix="${PREFIX}" -j"${CPU_COUNT}" diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index fa4b3bc69aad2..e4ced42950a1a 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1550" %} +{% set version = "1584" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.tar.gz" - sha256: 34a2d62bba74e6f2dad593b1c3997151617fb86a89a7d689e47a3a5e9377a07d + sha256: 5ed143d7311a1e2ea1fe2be87a2484612689a1498420e2a454762a6b3ab38ba3 build: number: 0 @@ -25,7 +25,6 @@ requirements: - python - pillow - parallel - - zlib test: commands: diff --git a/recipes/lastz/build.sh b/recipes/lastz/build.sh index 73bb1de4ce1cc..182e1c8acd239 100644 --- a/recipes/lastz/build.sh +++ b/recipes/lastz/build.sh @@ -1,11 +1,13 @@ #!/bin/sh +set -xe + mkdir -p $PREFIX/bin # Build lastz and lastz_D (lastz_D uses floating-point scores -make CC="${CC}" +make -j ${CPU_COUNT} CC="${CC}" # Build lastz_32, which uses 32-bit positions index and can handle genomes larger than 2Gb -make CC="${CC}" lastz_32 +make -j ${CPU_COUNT} CC="${CC}" lastz_32 chmod +x src/lastz chmod +x src/lastz_D diff --git a/recipes/lastz/meta.yaml b/recipes/lastz/meta.yaml index 5068cec65d04c..64807a95534e7 100644 --- a/recipes/lastz/meta.yaml +++ b/recipes/lastz/meta.yaml @@ -6,12 +6,13 @@ package: version: "{{ version }}" build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('lastz', max_pin='x') }} source: url: https://github.com/lastz/lastz/archive/refs/tags/{{ version }}.tar.gz sha256: 4c829603ba4aed7ddf64255b528cd88850e4557382fca29580d3576c25c5054a - patches: - makefile.patch @@ -20,6 +21,7 @@ requirements: - make - {{ compiler('c') }} run: + test: commands: - lastz --version 2>&1 | grep {{ version }} > /dev/null @@ -30,5 +32,8 @@ about: summary: LASTZ is a program for aligning DNA sequences, a pairwise aligner. extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - biotools:lastz diff --git a/recipes/leviosam2/build.sh b/recipes/leviosam2/build.sh index 03747c4c0a3e9..a752a5cf3518c 100644 --- a/recipes/leviosam2/build.sh +++ b/recipes/leviosam2/build.sh @@ -1,5 +1,22 @@ -mkdir -p build; -cd build; -cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} ${SRC_DIR} -make; -make install +#!/bin/bash + +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" + +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + +cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_LIBRARY_PATH="${PREFIX}/lib" \ + -DCMAKE_INCLUDE_PATH="${PREFIX}/include" \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + "${CONFIG_ARGS}" + +cmake --build build --target install -j "${CPU_COUNT}" -v diff --git a/recipes/leviosam2/meta.yaml b/recipes/leviosam2/meta.yaml index b039512101d06..d833f8fd73168 100644 --- a/recipes/leviosam2/meta.yaml +++ b/recipes/leviosam2/meta.yaml @@ -1,12 +1,13 @@ -{% set version = "0.4.2" %} +{% set name = "leviosam2" %} +{% set version = "0.5.0" %} package: - name: leviosam2 + name: {{ name }} version: {{ version }} source: - url: https://github.com/milkschen/leviosam2/archive/refs/tags/v{{ version }}.tar.gz - sha256: c0901f7e78e092058116a0b013286d4c452caeeaee778a24eb13301d08e56e30 + url: https://github.com/milkschen/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 5829b1565702887aefab78aaba06687724fb229e27e5d7f1244746d9e1744163 build: number: 0 @@ -21,6 +22,7 @@ requirements: host: - htslib >=1.11 - sdsl-lite >=2.1.1 + - zlib >=1.2.11,<1.3.0a0 run: - python >=3.6 - htslib >=1.11 @@ -29,16 +31,20 @@ requirements: test: commands: - - leviosam2 -h + - leviosam2 -h + about: home: "https://github.com/milkschen/leviosam2" license: MIT license_family: MIT license_file: LICENSE - summary: "Fast and accurate coordinate conversion between assemblies" - doc_url: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" + summary: "Fast and accurate coordinate conversion between assemblies." + doc_url: "https://github.com/milkschen/leviosam2/blob/v{{ version }}/README.md" + dev_url: "https://github.com/milkschen/leviosam2" extra: identifiers: - doi:10.1093/bioinformatics/btab396 - doi:10.1101/2022.04.27.489683 + additional-platforms: + - linux-aarch64 diff --git a/recipes/lexicmap/build.sh b/recipes/lexicmap/build.sh new file mode 100644 index 0000000000000..fcf25512b98e6 --- /dev/null +++ b/recipes/lexicmap/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +cp lexicmap $PREFIX/bin diff --git a/recipes/lexicmap/meta.yaml b/recipes/lexicmap/meta.yaml new file mode 100644 index 0000000000000..d5488f59fd7f7 --- /dev/null +++ b/recipes/lexicmap/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.4.0" %} + +package: + name: lexicmap + version: {{ version }} + +source: + url: https://github.com/shenwei356/LexicMap/releases/download/v{{ version }}/lexicmap_darwin_amd64.tar.gz # [osx] + md5: 631f54c4ddb655522728f7818778d080 # [osx] + + url: https://github.com/shenwei356/LexicMap/releases/download/v{{ version }}/lexicmap_darwin_arm64.tar.gz # [arm64] + md5: 2afe68c7d0f074291dd615d79bc5bc09 # [arm64] + + url: https://github.com/shenwei356/LexicMap/releases/download/v{{ version }}/lexicmap_linux_amd64.tar.gz # [linux] + md5: c2fca1f71e99b8e78d7b043ff82aa4e5 # [linux] + + url: https://github.com/shenwei356/LexicMap/releases/download/v{{ version }}/lexicmap_linux_arm64.tar.gz # [aarch64] + md5: ba006e38889489198fa703a5f7ebb805 # [aarch64] + +build: + number: 0 + run_exports: + - {{ pin_subpackage('lexicmap', max_pin='x.x') }} + +test: + commands: + - lexicmap version --help + +about: + home: https://github.com/shenwei356/LexicMap + summary: efficient sequence alignment against millions of prokaryotic genomes + license: MIT + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/medaka/LICENSE.md b/recipes/lib-pod5/LICENSE.md similarity index 95% rename from recipes/medaka/LICENSE.md rename to recipes/lib-pod5/LICENSE.md index 56dddbbdb5f2d..9f3e082df8e44 100644 --- a/recipes/medaka/LICENSE.md +++ b/recipes/lib-pod5/LICENSE.md @@ -1,8 +1,8 @@ This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this -file, You can obtain one at http://mozilla.org/MPL/2.0/. +file, You can obtain one at https://mozilla.org/MPL/2.0/. -(c) 2016 Oxford Nanopore Technologies Ltd. +©2021 Oxford Nanopore Technologies PLC. Mozilla Public License Version 2.0 @@ -10,24 +10,24 @@ Mozilla Public License Version 2.0 ### 1. Definitions -**1.1. “Contributor”** +**1.1. “Contributor”** means each individual or legal entity that creates, contributes to the creation of, or owns Covered Software. -**1.2. “Contributor Version”** +**1.2. “Contributor Version”** means the combination of the Contributions of others (if any) used by a Contributor and that particular Contributor's Contribution. -**1.3. “Contribution”** +**1.3. “Contribution”** means Covered Software of a particular Contributor. -**1.4. “Covered Software”** +**1.4. “Covered Software”** means Source Code Form to which the initial Contributor has attached the notice in Exhibit A, the Executable Form of such Source Code Form, and Modifications of such Source Code Form, in each case including portions thereof. -**1.5. “Incompatible With Secondary Licenses”** +**1.5. “Incompatible With Secondary Licenses”** means * **(a)** that the initial Contributor has attached the notice described @@ -36,22 +36,22 @@ Mozilla Public License Version 2.0 version 1.1 or earlier of the License, but not also under the terms of a Secondary License. -**1.6. “Executable Form”** +**1.6. “Executable Form”** means any form of the work other than Source Code Form. -**1.7. “Larger Work”** - means a work that combines Covered Software with other material, in +**1.7. “Larger Work”** + means a work that combines Covered Software with other material, in a separate file or files, that is not Covered Software. -**1.8. “License”** +**1.8. “License”** means this document. -**1.9. “Licensable”** +**1.9. “Licensable”** means having the right to grant, to the maximum extent possible, whether at the time of the initial grant or subsequently, any and all of the rights conveyed by this License. -**1.10. “Modifications”** +**1.10. “Modifications”** means any of the following: * **(a)** any file in Source Code Form that results from an addition to, @@ -60,7 +60,7 @@ Mozilla Public License Version 2.0 * **(b)** any new file in Source Code Form that contains any Covered Software. -**1.11. “Patent Claims” of a Contributor** +**1.11. “Patent Claims” of a Contributor** means any patent claim(s), including without limitation, method, process, and apparatus claims, in any patent Licensable by such Contributor that would be infringed, but for the grant of the @@ -68,16 +68,16 @@ Mozilla Public License Version 2.0 made, import, or transfer of either its Contributions or its Contributor Version. -**1.12. “Secondary License”** +**1.12. “Secondary License”** means either the GNU General Public License, Version 2.0, the GNU Lesser General Public License, Version 2.1, the GNU Affero General Public License, Version 3.0, or any later versions of those licenses. -**1.13. “Source Code Form”** +**1.13. “Source Code Form”** means the form of the work preferred for making modifications. -**1.14. “You” (or “Your”)** +**1.14. “You” (or “Your”)** means an individual or a legal entity exercising rights under this License. For legal entities, “You” includes any entity that controls, is controlled by, or is under common control with You. For @@ -347,7 +347,7 @@ notice described in Exhibit B of this License must be attached. This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this - file, You can obtain one at http://mozilla.org/MPL/2.0/. + file, You can obtain one at https://mozilla.org/MPL/2.0/. If it is not possible or desirable to put the notice in a particular file, then You may include the notice in a location (such as a LICENSE @@ -360,5 +360,3 @@ You may add additional accurate notices of copyright ownership. This Source Code Form is "Incompatible With Secondary Licenses", as defined by the Mozilla Public License, v. 2.0. - - diff --git a/recipes/lib-pod5/meta.yaml b/recipes/lib-pod5/meta.yaml new file mode 100644 index 0000000000000..72786148d5074 --- /dev/null +++ b/recipes/lib-pod5/meta.yaml @@ -0,0 +1,58 @@ +{% set name = "lib-pod5" %} +{% set version = "0.3.15" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/nanoporetech/pod5-file-format/releases/download/{{ version }}/pod5-{{ version }}.tar.gz + sha256: 85e3196bfc375b7d6eb36787a312af5276b19829ceded551b55e9e193939e8f4 + +build: + number: 0 + noarch: python + script: + - {{ PYTHON }} -m pip install https://files.pythonhosted.org/packages/9a/34/4ade92cc2e2690a52473a4c8a62c32b8364a81ed803d6096ab43d0fd3dcb/lib_pod5-{{ version }}-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -vvv --no-deps --no-build-isolation --no-cache-dir # [linux and x86_64] + - {{ PYTHON }} -m pip install https://files.pythonhosted.org/packages/fd/e4/e4d33770ecdeff95a1475153b3d0342041a2fc17279bd140c3502073cc16/lib_pod5-{{ version }}-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl -vvv --no-deps --no-build-isolation --no-cache-dir # [linux and aarch64] + - {{ PYTHON }} -m pip install https://files.pythonhosted.org/packages/64/af/a549fea23785b064f95da916d4e086fa52a07ba83dae6e3ee9309299bb17/lib_pod5-{{ version }}-cp312-cp312-macosx_10_15_universal2.whl -vvv --no-deps --no-build-isolation --no-cache-dir # [osx and x86_64] + - {{ PYTHON }} -m pip install https://files.pythonhosted.org/packages/ab/8c/5c0ca9d60a26bb02823201853d9214a8e75238c4f08cc54996300f671a16/lib_pod5-{{ version }}-cp312-cp312-macosx_11_0_arm64.whl -vvv --no-deps --no-build-isolation --no-cache-dir # [osx and arm64] + run_exports: + - {{ pin_subpackage('lib-pod5', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pybind11 >=2.10.0 + - pip + run: + - python >=3.8 + - numpy >=1.21.0 + +test: + imports: + - lib_pod5 + +about: + home: https://github.com/nanoporetech/pod5-file-format + summary: "Python bindings for the POD5 file format." + license: "MPL-2.0" + license_family: OTHER + license_file: "LICENSE.md" + dev_url: https://github.com/nanoporetech/pod5-file-format + doc_url: https://pod5-file-format.readthedocs.io/en/latest + description: | + [![Documentation Status](https://readthedocs.org/projects/pod5-file-format/badge/?version=latest)](https://pod5-file-format.readthedocs.io/) + + **Python bindings for the POD5 file format** + + What does this project contain + ------------------------------ + + This project contains the low-level core library (extension modules) for reading and writing POD5 files. + This project forms the basis of the pure-python [pod5 package](https://github.com/nanoporetech/pod5-file-format) which is probably the project you want. + + Documentation + ------------- + + Full documentation is found at https://pod5-file-format.readthedocs.io diff --git a/recipes/libcifpp/build.sh b/recipes/libcifpp/build.sh index fd0933e91291d..62f983f67c85c 100644 --- a/recipes/libcifpp/build.sh +++ b/recipes/libcifpp/build.sh @@ -1,8 +1,15 @@ #!/bin/bash -mkdir build -cd build +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" -cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF -DCIFPP_DOWNLOAD_CCD=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCIFPP_INSTALL_UPDATE_SCRIPT=OFF .. -cmake --build . --config Release -cmake --install . --prefix ${PREFIX} +cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DBUILD_TESTING=OFF -DCIFPP_DOWNLOAD_CCD=OFF \ + -DCIFPP_INSTALL_UPDATE_SCRIPT=OFF + +cmake --build build/ --target install -j "${CPU_COUNT}" -v diff --git a/recipes/libcifpp/meta.yaml b/recipes/libcifpp/meta.yaml index 7b8ec21e655f2..a6ec1b44e2dbc 100644 --- a/recipes/libcifpp/meta.yaml +++ b/recipes/libcifpp/meta.yaml @@ -1,6 +1,6 @@ {% set name = "libcifpp" %} -{% set version = "7.0.4" %} -{% set sha256 = "324eda2f6874df32671cd984c7249bfae025ca3fe1bfd875cbef35b046408b88" %} +{% set version = "7.0.6" %} +{% set sha256 = "bbdd3a7ae0e2925a56dbb6dcc2b2a53d0a72774078545f10c5de2389414a9971" %} package: name: {{ name|lower }} @@ -11,8 +11,8 @@ source: sha256: {{ sha256 }} build: + number: 0 skip: True # [osx] - number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} @@ -26,7 +26,6 @@ requirements: - zlib - boost-cpp run: - - zlib - boost-cpp test: @@ -34,14 +33,16 @@ test: - test -e $PREFIX/lib/libcifpp.a about: - home: https://github.com/PDB-REDO/libcifpp + home: "https://github.com/PDB-REDO/libcifpp" license: BSD-2-Clause license_file: LICENSE license_family: BSD - summary: Library containing code to manipulate mmCIF and PDB files - doc_url: https://pdb-redo.github.io/libcifpp/ - dev_url: https://github.com/PDB-REDO/libcifpp + summary: "Library containing code to manipulate mmCIF and PDB files." + doc_url: "https://pdb-redo.github.io/libcifpp" + dev_url: "https://github.com/PDB-REDO/libcifpp" extra: recipe-maintainers: - multimeric + additional-platforms: + - linux-aarch64 diff --git a/recipes/libsbml/LICENSE.txt b/recipes/libsbml/LICENSE.txt new file mode 100644 index 0000000000000..91d790aa62342 --- /dev/null +++ b/recipes/libsbml/LICENSE.txt @@ -0,0 +1,167 @@ + Licensing and Distribution Terms for libSBML + +The majority of libSBML is copyrighted as follows: + +* Copyright (C) 2013-2018 jointly by the following organizations: + 1. California Institute of Technology, Pasadena, CA, USA + 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK + 3. University of Heidelberg, Heidelberg, Germany + +* Copyright (C) 2009-2013 jointly by the following organizations: + 1. California Institute of Technology, Pasadena, CA, USA + 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK + +* Copyright (C) 2006-2008 by the California Institute of Technology, + Pasadena, CA, USA + +* Copyright (C) 2002-2005 jointly by the following organizations: + 1. California Institute of Technology, Pasadena, CA, USA + 2. Japan Science and Technology Agency, Japan + +Portions of the source code comprising libSBML were copyrighted +and contributed by third parties, and placed under the same LGPL +2.1 license as the rest of libSBML. The following are their +copyright statements: + +* Copyright (C) 2004-2008 by European Media Laboratories Research + gGmbH, Heidelberg, Germany. (For the "SBML Layout" code.) + +LibSBML is free software; you can redistribute it and/or modify +it under the terms of the GNU Lesser General Public License as +published by the Free Software Foundation; either version 2.1 of +the License, or any later version. + +This software is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF +MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software +and documentation provided hereunder is on an "as is" basis, and +the copyright holders have no obligations to provide maintenance, +support, updates, enhancements or modifications. In no event +shall the copyright holders be liable to any party for direct, +indirect, special, incidental or consequential damages, including +lost profits, arising out of the use of this software and its +documentation, even if the copyright holders have been advised of +the possibility of such damage. See the GNU Lesser General Public +License for more details. + +You should have received a copy of the GNU Lesser General Public +License along with this library in the file named "COPYING.txt" +included with the software distribution. A copy is also +available online at the Internet address +http://sbml.org/software/libsbml/COPYING.html for your +convenience. You may also write to obtain a copy from the Free +Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, +MA 02110-1301, USA. + + + Third-party software incorporated into both the libSBML + binary and source-code distributions + +LibSBML incorporates an open-source compression library written by +a third party. The following is information about the copyright +and distribution terms of this library: + +* MiniZip 1.01e, copyright (C) 1998-2005 Gilles Vollant, released + under terms compatible with the LGPL. Please see the file + src/sbml/compress/00README.txt for more information about + MiniZip 1.01e and its license terms. + + + Additional third-party software incorporated only + into the libSBML source code distribution + +Additional software is used to produce the documentation of +libSBML. The binary distributions of libSBML do not include this +software; they are only present in the source code distribution +and the libSBML documentation archives. + +* Argparse 1.2.1, copyright (C) 2006-2009 Steven J. Bethard + and distributed under the Python Software + Foundation License version 2. Code downloaded from + http://code.google.com/p/argparse/ on 2012-02-10. + +* Google Code Prettify, distributed under the terms of the + Apache License Version 2.0, January 2004. Code downloaded from + http://code.google.com/p/google-code-prettify/ on 2013-10-16. + +* PrettyTable, copyright (C) 2009-2013 Luke Maurits, distributed + under the following BSD-derivative license: + + Copyright (c) 2009-2013 Luke Maurits + All rights reserved. + With contributions from: + * Chris Clark + * Christoph Robbert + * Klein Stephane + * "maartendb" + + Redistribution and use in source and binary forms, with or + without modification, are permitted provided that the + following conditions are met: + + * Redistributions of source code must retain the above + copyright notice, this list of conditions and the + following disclaimer. + + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the + following disclaimer in the documentation and/or other + materials provided with the distribution. + + * The name of the author may not be used to endorse or + promote products derived from this software without + specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND + CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, + INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF + MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT + NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) + HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN + CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR + OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +* ExcludeDoclet, copyright (C) 2004 by Sun Microsystems, Inc., and + distributed under the following open-source terms: + + Copyright 2004 Sun Microsystems, Inc. All Rights Reserved. + + Redistribution and use in source and binary forms, with or + without modification, are permitted provided that the + following conditions are met: + + - Redistribution of source code must retain the above + copyright notice, this list of conditions and the following + disclaimer. + + - Redistribution in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. Neither the name of Sun Microsystems, + Inc. nor the names of contributors may be used to endorse or + promote products derived from this software without specific + prior written permission. + + This software is provided "AS IS," without a warranty of any + kind. ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND + WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE + HEREBY EXCLUDED. SUN MICROSYSTEMS, INC. ("SUN") AND ITS + LICENSORS SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED BY + LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THIS + SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS + LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR + FOR DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR + PUNITIVE DAMAGES, HOWEVER CAUSED AND REGARDLESS OF THE THEORY + OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY TO USE + THIS SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE POSSIBILITY + OF SUCH DAMAGES. + + You acknowledge that this software is not designed, licensed + or intended for use in the design, construction, operation or + maintenance of any nuclear facility. diff --git a/recipes/libsbml/build.sh b/recipes/libsbml/build.sh index 7b3b0d2884b8b..dbb0f2e1daee1 100644 --- a/recipes/libsbml/build.sh +++ b/recipes/libsbml/build.sh @@ -1,21 +1,39 @@ #!/bin/bash + +set -xe + mkdir build cd build + +declare -a CMAKE_LIBXML_LIBRARY +if [[ ${target_platform} == osx-*64 ]]; then + CMAKE_LIBXML_LIBRARY+=(-DLIBXML_LIBRARY="${PREFIX}"/lib/libxml2.dylib) +elif [[ ${target_platform} == linux-*64 ]]; then + CMAKE_LIBXML_LIBRARY+=(-DLIBXML_LIBRARY="${PREFIX}"/lib/libxml2.so) +fi + cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} \ -DCMAKE_INSTALL_LIBDIR=${PREFIX}/lib \ -DCMAKE_CXX_COMPILER=${CXX} \ -DCMAKE_C_COMPILER=${CC} \ + -DCMAKE_CXX_STANDARD_LIBRARIES=-lxml2 \ -DWITH_SWIG=OFF \ - -DLIBSBML_DEPENDENCY_DIR="${PREFIX}" \ + "${CMAKE_LIBXML_LIBRARY[@]}" \ -DLIBXML_INCLUDE_DIR=${PREFIX}/include/libxml2 \ -DENABLE_COMP=ON \ -DENABLE_FBC=ON \ -DENABLE_GROUPS=ON \ - -DENABLE_L3V2EXTENDEDMATH=ON \ -DENABLE_LAYOUT=ON \ -DENABLE_MULTI=ON \ -DENABLE_QUAL=ON \ -DENABLE_RENDER=ON \ + -DENABLE_DISTRIB=ON \ + -DENABLE_ARRAYS=ON \ + -DENABLE_DYN=ON \ + -DENABLE_REQUIREDELEMENTS=ON \ + -DENABLE_SPATIAL=ON \ + -DWITH_CPP_NAMESPACE=ON \ .. + make -j"${CPU_COUNT}" make install diff --git a/recipes/libsbml/build_failure.linux-64.yaml b/recipes/libsbml/build_failure.linux-64.yaml deleted file mode 100644 index 7172757f203aa..0000000000000 --- a/recipes/libsbml/build_failure.linux-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 11a10c25d366c5890bbb2c3d3c0f43403d43e7af7937559a8b3e620fc3593de8 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error -log: |2- - | ^~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/FunctionDefinition.h:136, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/Model.h:449, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/validator/constraints/UniqueVarsInRules.cpp:39: - /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/ListOf.h:111:27: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 111 | struct IdEq : public std::unary_function - | ^~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/libsbml_1718134461495/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/string:48, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/Model.h:447: - /opt/conda/conda-bld/libsbml_1718134461495/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/FunctionDefinition.h:136, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/Model.h:449, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/validator/constraints/UnitsBase.cpp:39: - /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/ListOf.h:111:27: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 111 | struct IdEq : public std::unary_function - | ^~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/libsbml_1718134461495/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/string:48, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/Model.h:447: - /opt/conda/conda-bld/libsbml_1718134461495/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ - [ 95%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/CompressCommon.cpp.o - [ 95%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/InputDecompressor.cpp.o - [ 95%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/bzfstream.cpp.o - [ 95%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/OutputCompressor.cpp.o - In file included from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/FunctionDefinition.h:136, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/Model.h:449, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/validator/constraints/ValidCnUnitsValue.cpp:39: - /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/ListOf.h:111:27: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 111 | struct IdEq : public std::unary_function - | ^~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/libsbml_1718134461495/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/string:48, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/Model.h:447: - /opt/conda/conda-bld/libsbml_1718134461495/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ - [ 95%] Building C object src/CMakeFiles/sbml-static.dir/sbml/compress/zip.c.o - [ 95%] Building C object src/CMakeFiles/sbml-static.dir/sbml/compress/unzip.c.o - [ 95%] Building C object src/CMakeFiles/sbml-static.dir/sbml/compress/ioapi.c.o - [ 96%] Building C object src/CMakeFiles/sbml-static.dir/sbml/compress/ioapi_mem.c.o - [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/zfstream.cpp.o - [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/compress/zipfstream.cpp.o - [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLAttributes.cpp.o - [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLBuffer.cpp.o - [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLConstructorException.cpp.o - [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLError.cpp.o - [ 96%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLErrorLog.cpp.o - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLLogOverride.cpp.o - /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/xml/XMLErrorLog.cpp:98:24: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 98 | struct Delete : public unary_function - | ^~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/libsbml_1718134461495/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/functional:49, - from /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/xml/XMLErrorLog.cpp:38: - /opt/conda/conda-bld/libsbml_1718134461495/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLFileBuffer.cpp.o - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLHandler.cpp.o - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLInputStream.cpp.o - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLMemoryBuffer.cpp.o - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLNamespaces.cpp.o - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLNode.cpp.o - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLOutputStream.cpp.o - [ 97%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLParser.cpp.o - [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLToken.cpp.o - [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLTokenizer.cpp.o - [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/XMLTriple.cpp.o - [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/LibXMLAttributes.cpp.o - [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/LibXMLHandler.cpp.o - [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/LibXMLNamespaces.cpp.o - [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/LibXMLParser.cpp.o - [ 98%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/xml/LibXMLTranscode.cpp.o - /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/xml/LibXMLParser.cpp: In member function 'virtual bool LibXMLParser::parseNext()': - /opt/conda/conda-bld/libsbml_1718134461495/work/src/sbml/xml/LibXMLParser.cpp:422:46: error: invalid conversion from 'const xmlError*' {aka 'const _xmlError*'} to 'xmlErrorPtr' {aka '_xmlError*'} [-fpermissive] - 422 | xmlErrorPtr libxmlError = xmlGetLastError(); - | ~~~~~~~~~~~~~~~^~ - | | - | const xmlError* {aka const _xmlError*} - make[2]: *** [src/CMakeFiles/sbml-static.dir/build.make:6082: src/CMakeFiles/sbml-static.dir/sbml/xml/LibXMLParser.cpp.o] Error 1 - make[2]: *** Waiting for unfinished jobs.... - make[1]: *** [CMakeFiles/Makefile2:242: src/CMakeFiles/sbml-static.dir/all] Error 2 - make: *** [Makefile:156: all] Error 2 - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/libsbml_1718134461495/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/libsbml/conda_build_config.yaml b/recipes/libsbml/conda_build_config.yaml new file mode 100644 index 0000000000000..8c1d84a5c606c --- /dev/null +++ b/recipes/libsbml/conda_build_config.yaml @@ -0,0 +1,7 @@ +libxml2: + - 2.9 # [linux] + - 2.10 + - 2.11 + - 2.12 +pin_run_as_build: + libxml2: x.x diff --git a/recipes/libsbml/meta.yaml b/recipes/libsbml/meta.yaml index 45ced1405a863..1f1cc5e0af27c 100644 --- a/recipes/libsbml/meta.yaml +++ b/recipes/libsbml/meta.yaml @@ -1,18 +1,17 @@ -{% set version = "5.18.0" %} -{% set sha256 = "6c01be2306ec0c9656b59cb082eb7b90176c39506dd0f912b02e08298a553360" %} +{% set version = "5.20.4" %} +{% set sha256 = "02c225d3513e1f5d6e3c0168456f568e67f006eddaab82f09b4bdf0d53d2050e" %} package: name: libsbml version: {{ version }} build: - number: 11 - skip: True # [osx] + number: 1 run_exports: - {{ pin_subpackage('libsbml', max_pin='x.x') }} source: - url: https://sourceforge.net/projects/sbml/files/libsbml/{{ version }}/stable/libSBML-{{ version }}-core-plus-packages-src.tar.gz + url: https://github.com/sbmlteam/libsbml/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: @@ -26,16 +25,20 @@ requirements: - libxml2 - zlib run: - - bzip2 - libxml2 - - zlib - + test: commands: - - test -f "${PREFIX}/lib/libsbml${SHLIB_EXT-.so}" + - test -f "${PREFIX}/lib/libsbml${SHLIB_EXT-.so}" # [linux] + - test -f "${PREFIX}/lib/libsbml${SHLIB_EXT-.dylib}" # [osx] about: home: http://sbml.org/Software/libSBML license: LGPL license_file: 'LICENSE.txt' summary: LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml index 444882115ee1a..c9c450090f4ed 100644 --- a/recipes/locityper/meta.yaml +++ b/recipes/locityper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "locityper" %} -{% set version = "0.16.8" %} +{% set version = "0.16.12" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz - sha256: 45676912a3a7a8d164f0e6c0c71697d21878baa476cd45b8bf4a2c9d9e5f018f + sha256: 0bd3a82c1df6de921ed477edfca4ffb5017cf194807e358e482b49afba867dd7 build: number: 0 diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml index 0856d2ca4d10a..bc46dd5be022e 100644 --- a/recipes/lotus2/meta.yaml +++ b/recipes/lotus2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "lotus2" %} -{% set version = "2.32" %} -{% set sha256 = "5c1c4e6e0cb6cd7277be6a163d184ea4dd30eac3b03b171deede8ce85509fb4e" %} +{% set version = "2.34.1" %} +{% set sha256 = "fdda62d3ab02e37e160c0b1c36aeee43247838c271c99733be71d0bfbeb77419" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -39,9 +39,10 @@ requirements: - r-dplyr - rdp_classifier - rtk - - sdm ==2.17 + - sdm ==2.18 - swarm - unzip + - usearch >=12.0_beta,<13 - vsearch - wget - zip # workaround for the Galaxy wrapper (mulled conda env creation fails) diff --git a/recipes/lsabgc/meta.yaml b/recipes/lsabgc/meta.yaml index f55c6fb0d327f..2f794a8713fad 100644 --- a/recipes/lsabgc/meta.yaml +++ b/recipes/lsabgc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "lsabgc" %} -{% set version = "1.0.5" %} +{% set version = "1.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/lsaBGC-Pan/archive/refs/tags/v{{ version }}.tar.gz - sha256: c6354a39e64238d42c9f5d3e1464d78545f91d5231de2306d162cee6b36eb85f + sha256: 04eadeadd7887883d48112624dd23496c19e2a038605e29fb0102c79badab5f4 build: number: 0 diff --git a/recipes/ltr_retriever/meta.yaml b/recipes/ltr_retriever/meta.yaml index fab51c19ad426..a2e668b82c87b 100644 --- a/recipes/ltr_retriever/meta.yaml +++ b/recipes/ltr_retriever/meta.yaml @@ -1,6 +1,6 @@ {% set name = "LTR_retriever" %} -{% set version = "2.9.9" %} -{% set sha256 = "ef7d59349c0cbb3c819a102e68488b85cb116c099a4512d72d8a70293f13c7c8" %} +{% set version = "3.0.1" %} +{% set sha256 = "a3ca3bd8d81f3a8260e1386d03bd7f8a7aa42882f92ccbaa1a4fb1d8120658a8" %} package: name: "{{ name|lower }}" diff --git a/recipes/macrel/meta.yaml b/recipes/macrel/meta.yaml index 9c9a48f2f5a66..7df1b4dc7941c 100644 --- a/recipes/macrel/meta.yaml +++ b/recipes/macrel/meta.yaml @@ -1,6 +1,6 @@ {% set name = "macrel" %} -{% set version = "1.4.0" %} -{% set sha256 = "323d21a43965af912ca2165a28aa5c0f25851afbc4dc32ecf805b3da5e265376" %} +{% set version = "1.5.0" %} +{% set sha256 = "d2a4e3ba756af530f0fb66e95530a6e29c0c4074c40c7e55246dec0fc68c5296" %} package: name: {{ name }} diff --git a/recipes/macs3/meta.yaml b/recipes/macs3/meta.yaml index 844a8d9e8a0e7..7fcee4f154187 100644 --- a/recipes/macs3/meta.yaml +++ b/recipes/macs3/meta.yaml @@ -1,21 +1,21 @@ {% set name = "MACS3" %} -{% set version = "3.0.1" %} -{% set sha256 = "9e1a63685629852e6128a3270d264f990790538f48610aac7fd2fd139ef8fe12" %} +{% set version = "3.0.2" %} +{% set sha256 = "1605d11dc2470516c070deab4e32b60e6d06e02d1be93d1e4c40981a404b8f40" %} package: name: {{ name|lower }} version: {{ version }} source: - git_url: https://github.com/macs3-project/MACS.git - git_rev: 34f9a81398ec2af78317cd0b128f3a1e52a68f17 + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/macs3-{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 3 + number: 1 skip: True # [py < 39] - script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: - - {{ pin_subpackage('macs3', max_pin="x.x") }} + - {{ pin_subpackage('macs3', max_pin="x") }} requirements: build: @@ -27,14 +27,14 @@ requirements: - numpy >=1.25 - scipy >=1.12 - cython >=3.0 - - hmmlearn 0.3 + - hmmlearn >=0.3.2 - scikit-learn >=1.3 - cykhash >=2.0,<3.0 run: - python - numpy >=1.25 - scipy >=1.12 - - hmmlearn 0.3 + - hmmlearn >=0.3.2 - scikit-learn >=1.3 - cykhash >=2.0,<3.0 @@ -45,19 +45,28 @@ test: - macs3 -h about: - dev_url: https://github.com/macs3-project/MACS/ - doc_url: https://macs3-project.github.io/MACS/ - home: https://pypi.org/project/MACS3/ + dev_url: "https://github.com/macs3-project/MACS" + doc_url: "https://macs3-project.github.io/MACS" + home: "https://github.com/macs3-project/MACS" license: BSD-3-Clause license_family: BSD license_file: LICENSE - summary: Model Based Analysis for ChIP-Seq data + summary: "Model Based Analysis for ChIP-Seq data." extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - biotools:macs - doi:10.1186/gb-2008-9-9-r137 - usegalaxy-eu:peakcalling_macs - skip-lints: - - uses_vcs_url - - missing_hash + - usegalaxy-eu:macs2_bdgbroadcall + - usegalaxy-eu:macs2_bdgcmp + - usegalaxy-eu:macs2_bdgdiff + - usegalaxy-eu:macs2_bdgpeakcall + - usegalaxy-eu:macs2_callpeak + - usegalaxy-eu:macs2_filterdup + - usegalaxy-eu:macs2_predictd + - usegalaxy-eu:macs2_randsample + - usegalaxy-eu:macs2_refinepeak diff --git a/recipes/maegatk/meta.yaml b/recipes/maegatk/meta.yaml index a7a26ecda678c..f0101130ca332 100644 --- a/recipes/maegatk/meta.yaml +++ b/recipes/maegatk/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fce1ec287914e03ce2b317a4f6a338f1806cd82e5c77f4e4cb1efbd48c87bdda build: - number: 1 + number: 2 noarch: python entry_points: - maegatk = maegatk.cli:main @@ -32,9 +32,9 @@ requirements: - biopython - optparse-pretty - regex - - ruamel.yaml + - ruamel.yaml 0.16.12 - openjdk - - fgbio + - fgbio-minimal - bwa - samtools - freebayes @@ -52,13 +52,17 @@ test: - maegatk --help about: - home: https://github.com/caleblareau/maegatk - summary: Mitochondrial Alteration Enrichment and Genome Analysis Toolkit + home: "https://github.com/caleblareau/maegatk" + summary: "Mitochondrial Alteration Enrichment and Genome Analysis Toolkit." license: MIT license_family: MIT license_file: LICENSE.txt description: Processing and quality control of mitochondrial genome variants from MAESTER data. + dev_url: "https://github.com/caleblareau/maegatk" + doc_url: "https://github.com/caleblareau/maegatk/wiki" extra: recipe-maintainers: - mencian + identifiers: + - doi:10.1038/s41587-022-01210-8 diff --git a/recipes/mashpit/meta.yaml b/recipes/mashpit/meta.yaml index 16a7f9b314a25..299fe006c885d 100644 --- a/recipes/mashpit/meta.yaml +++ b/recipes/mashpit/meta.yaml @@ -1,47 +1,49 @@ -{% set version = "0.9.6" %} - -package: - name: mashpit - version: '{{ version }}' - -source: - url: https://github.com/tongzhouxu/mashpit/archive/refs/tags/v{{ version }}.tar.gz - sha256: 94754449251e51fff771c5d9579ef7016cf1d2984dfcdc5f01a558ceac772d14 - -build: - noarch: python - script: python -m pip install --no-deps --ignore-installed . - number: 0 - run_exports: - - {{ pin_subpackage("mashpit", max_pin="x.x") }} - -requirements: - host: - - python >=3.8 - - pip - run: - - biopython =1.78 - - dask >=2024.1 - - flask >=3.0 - - ncbi-datasets-cli >=16.10 - - ncbi-datasets-pylib >=16.6.0 - - numpy >=1.19.5 - - python >=3.8 - - pandas >=1.1.5 - - requests - - scikit-bio - - scipy >=1.0 - - screed >=1.0.5 - - sourmash >=4.6.1 - - tqdm - -test: - commands: - - mashpit --help - -about: - home: https://github.com/tongzhouxu/mashpit - license: GPL-2 - license_family: GPL - license_file: LICENSE - summary: Sketch-based surveillance platform +{% set version = "0.9.7" %} + +package: + name: mashpit + version: '{{ version }}' + +source: + url: https://github.com/tongzhouxu/mashpit/archive/refs/tags/v{{ version }}.tar.gz + sha256: 4f93e00f8ff5cdb1eb81bc5cf01db824dbb8f54e67dbe9aab910b21fdd38fbed + +build: + noarch: python + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv + number: 0 + run_exports: + - {{ pin_subpackage("mashpit", max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - biopython =1.78 + - dask >=2024.1 + - flask >=3.0 + - ncbi-datasets-cli >=16.10 + - ncbi-datasets-pylib >=16.6.0 + - numpy >=1.19.5 + - python >=3.8 + - pandas >=1.1.5 + - requests + - scikit-bio + - scipy >=1.0 + - screed >=1.0.5 + - sourmash >=4.6.1 + - tqdm + - phytreeviz + +test: + commands: + - mashpit --help + +about: + home: https://github.com/tongzhouxu/mashpit + license: "GPL-2.0-or-later" + license_family: GPL2 + license_file: LICENSE + summary: Sketch-based surveillance platform + dev_url: https://github.com/tongzhouxu/mashpit diff --git a/recipes/matchtigs/build.sh b/recipes/matchtigs/build.sh index b6cbf0da5ee0e..fb79714e8ab7f 100755 --- a/recipes/matchtigs/build.sh +++ b/recipes/matchtigs/build.sh @@ -1,9 +1,3 @@ -#!/bin/bash -e - -# TODO: Remove the following export when pinning is updated and we use -# {{ compiler('rust') }} in the recipe. -export \ - CARGO_NET_GIT_FETCH_WITH_CLI=true \ - CARGO_HOME="${BUILD_PREFIX}/.cargo" +#!/bin/bash -ex cargo install --no-track --verbose --root "${PREFIX}" --path . diff --git a/recipes/matchtigs/build_failure.linux-64.yaml b/recipes/matchtigs/build_failure.linux-64.yaml deleted file mode 100644 index 7efc8e897a32f..0000000000000 --- a/recipes/matchtigs/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 02efdfc2f9abb5a0a1b47ed3022a17ded394809c39b45eb88ed5f9cb82af9995 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - Running rustc --crate-name time --edition=2021 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/time-0.3.21/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="formatting"' --cfg 'feature="local-offset"' --cfg 'feature="macros"' --cfg 'feature="std"' -C metadata=cd91c07161414263 -C extra-filename=-cd91c07161414263 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern itoa=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libitoa-62c89c15c3dfb3bd.rmeta --extern libc=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/liblibc-24109b92b56898e0.rmeta --extern num_threads=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libnum_threads-29052a9a6bdcc9a0.rmeta --extern time_core=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtime_core-2e91ef91f00946ce.rmeta --extern time_macros=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtime_macros-9ef2748d38fa3eaa.so --cap-lints allow - Compiling bigraph v2.1.1 - Running rustc --crate-name bigraph --edition=2021 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/bigraph-2.1.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 -C metadata=d48072365ca04b7e -C extra-filename=-d48072365ca04b7e --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern bitvector=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libbitvector-86c69f343ae8ebe4.rmeta --extern traitgraph=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtraitgraph-9d144d98ec7b776d.rmeta --extern traitgraph_algo=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtraitgraph_algo-0da65161844e678e.rmeta --cap-lints allow - Compiling compact-genome v1.3.1 - Running rustc --crate-name compact_genome --edition=2021 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/compact-genome-1.3.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 -C metadata=f1dacdb0e642ea1d -C extra-filename=-f1dacdb0e642ea1d --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern bitvec=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libbitvec-15d630b4c5e43590.rmeta --extern itertools=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libitertools-ef1bbdf2dc7723ca.rmeta --extern lazy_static=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/liblazy_static-fb705ce03f437159.rmeta --extern ref_cast=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libref_cast-42ca62cc9a853eb0.rmeta --extern traitsequence=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtraitsequence-1a990810ce5d3411.rmeta --cap-lints allow - Running rustc --crate-name error_chain /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/error-chain-0.12.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="backtrace"' --cfg 'feature="default"' --cfg 'feature="example_generated"' -C metadata=de91467585a0f101 -C extra-filename=-de91467585a0f101 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern backtrace=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libbacktrace-af4cf630bdf33906.rmeta --cap-lints allow --cfg has_error_source --cfg has_error_description_deprecated --cfg 'build="release"' - Running rustc --crate-name crossbeam_queue --edition=2018 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crossbeam-queue-0.3.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="alloc"' --cfg 'feature="std"' -C metadata=a9a20555b2200c9e -C extra-filename=-a9a20555b2200c9e --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcfg_if-1f0e8aa877c8070d.rmeta --extern crossbeam_utils=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_utils-469504b851c5f146.rmeta --cap-lints allow - Compiling crossbeam-deque v0.8.3 - Running rustc --crate-name crossbeam_deque --edition=2018 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crossbeam-deque-0.8.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="crossbeam-epoch"' --cfg 'feature="crossbeam-utils"' --cfg 'feature="std"' -C metadata=09b8b5d6c6489017 -C extra-filename=-09b8b5d6c6489017 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcfg_if-1f0e8aa877c8070d.rmeta --extern crossbeam_epoch=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_epoch-03a2a8c23802678b.rmeta --extern crossbeam_utils=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_utils-469504b851c5f146.rmeta --cap-lints allow - Running rustc --crate-name crc32fast /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crc32fast-1.3.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=1b5dbef380751fbb -C extra-filename=-1b5dbef380751fbb --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcfg_if-1f0e8aa877c8070d.rmeta --cap-lints allow --cfg crc32fast_stdarchx86 - Compiling crossbeam-channel v0.5.8 - Running rustc --crate-name crossbeam_channel --edition=2018 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crossbeam-channel-0.5.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="crossbeam-utils"' --cfg 'feature="std"' -C metadata=4ec529cb6862f4cf -C extra-filename=-4ec529cb6862f4cf --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcfg_if-1f0e8aa877c8070d.rmeta --extern crossbeam_utils=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_utils-469504b851c5f146.rmeta --cap-lints allow - Compiling miniz_oxide v0.7.1 - Running rustc --crate-name miniz_oxide --edition=2018 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/miniz_oxide-0.7.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="with-alloc"' -C metadata=d4b698deea0ed15d -C extra-filename=-d4b698deea0ed15d --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern adler=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libadler-bc2939b95ebef4b5.rmeta --cap-lints allow - Compiling clap_derive v4.3.0 - Running rustc --crate-name clap_derive --edition=2021 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/clap_derive-4.3.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' -C metadata=e5c04879dc24b4de -C extra-filename=-e5c04879dc24b4de --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern heck=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libheck-ce3c1226d2131855.rlib --extern proc_macro2=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libproc_macro2-28704a5d3a30d148.rlib --extern quote=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libquote-5e1d4707a1044434.rlib --extern syn=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libsyn-6909a0153da8cd82.rlib --extern proc_macro --cap-lints allow - Compiling termcolor v1.1.3 - Running rustc --crate-name termcolor --edition=2018 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/termcolor-1.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 -C metadata=bda75f15087c6830 -C extra-filename=-bda75f15087c6830 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --cap-lints allow - Compiling disjoint-sets v0.4.2 - Running rustc --crate-name disjoint_sets /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/disjoint-sets-0.4.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 -C metadata=cdef6477d36b0c69 -C extra-filename=-cdef6477d36b0c69 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --cap-lints allow - Compiling genome-graph v5.2.0 - Running rustc --crate-name genome_graph --edition=2021 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/genome-graph-5.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="traitgraph-algo"' -C metadata=f1f9f43eca9c0cbc -C extra-filename=-f1f9f43eca9c0cbc --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libanyhow-970e725c20f36b78.rmeta --extern bigraph=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libbigraph-d48072365ca04b7e.rmeta --extern bio=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libbio-428bb18d1e5e7978.rmeta --extern compact_genome=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcompact_genome-f1dacdb0e642ea1d.rmeta --extern disjoint_sets=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libdisjoint_sets-cdef6477d36b0c69.rmeta --extern error_chain=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/liberror_chain-de91467585a0f101.rmeta --extern log=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/liblog-222ce67e5627d39a.rmeta --extern num_traits=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libnum_traits-91ac9ff4e716de54.rmeta --extern regex=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libregex-e8f29f1319bd1bf9.rmeta --extern traitgraph_algo=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtraitgraph_algo-0da65161844e678e.rmeta --cap-lints allow - Compiling clap v4.3.0 - Running rustc --crate-name clap --edition=2021 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.3.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="cargo"' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="error-context"' --cfg 'feature="help"' --cfg 'feature="std"' --cfg 'feature="suggestions"' --cfg 'feature="usage"' -C metadata=62f315ad00245630 -C extra-filename=-62f315ad00245630 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern clap_builder=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libclap_builder-8be52c6c0fae3a91.rmeta --extern clap_derive=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libclap_derive-e5c04879dc24b4de.so --extern once_cell=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libonce_cell-1af048d720dc90db.rmeta --cap-lints allow - Compiling simplelog v0.12.1 - Running rustc --crate-name simplelog --edition=2018 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/simplelog-0.12.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="default"' --cfg 'feature="local-offset"' --cfg 'feature="termcolor"' -C metadata=570deb8a8d99c61b -C extra-filename=-570deb8a8d99c61b --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern log=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/liblog-222ce67e5627d39a.rmeta --extern termcolor=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtermcolor-bda75f15087c6830.rmeta --extern time=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtime-cd91c07161414263.rmeta --cap-lints allow - Compiling flate2 v1.0.26 - Running rustc --crate-name flate2 --edition=2018 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/flate2-1.0.26/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="default"' --cfg 'feature="miniz_oxide"' --cfg 'feature="rust_backend"' -C metadata=e28aebe213d35db0 -C extra-filename=-e28aebe213d35db0 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern crc32fast=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrc32fast-1b5dbef380751fbb.rmeta --extern miniz_oxide=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libminiz_oxide-d4b698deea0ed15d.rmeta --cap-lints allow - Compiling crossbeam v0.8.2 - Running rustc --crate-name crossbeam --edition=2018 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crossbeam-0.8.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 --cfg 'feature="alloc"' --cfg 'feature="crossbeam-channel"' --cfg 'feature="crossbeam-deque"' --cfg 'feature="crossbeam-epoch"' --cfg 'feature="crossbeam-queue"' --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=e0ba050ad89c9cc4 -C extra-filename=-e0ba050ad89c9cc4 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcfg_if-1f0e8aa877c8070d.rmeta --extern crossbeam_channel=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_channel-4ec529cb6862f4cf.rmeta --extern crossbeam_deque=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_deque-09b8b5d6c6489017.rmeta --extern crossbeam_epoch=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_epoch-03a2a8c23802678b.rmeta --extern crossbeam_queue=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_queue-a9a20555b2200c9e.rmeta --extern crossbeam_utils=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam_utils-469504b851c5f146.rmeta --cap-lints allow - Compiling memory-stats v1.1.0 - Running rustc --crate-name memory_stats --edition=2021 /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/memory-stats-1.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 -C metadata=0abaf08295d64751 -C extra-filename=-0abaf08295d64751 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern libc=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/liblibc-24109b92b56898e0.rmeta --cap-lints allow - Compiling permutation v0.4.1 - Running rustc --crate-name permutation /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/permutation-0.4.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 -C metadata=cbccced583c33429 -C extra-filename=-cbccced583c33429 --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --cap-lints allow - Compiling atomic-counter v1.0.1 - Running rustc --crate-name atomic_counter /opt/conda/conda-bld/matchtigs_1685352493749/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/atomic-counter-1.0.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C debuginfo=2 -C metadata=83828d0b73047a5b -C extra-filename=-83828d0b73047a5b --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --cap-lints allow - Compiling matchtigs v1.5.5 (/opt/conda/conda-bld/matchtigs_1685352493749/work) - Running rustc --crate-name libmatchtigs --edition=2021 src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type rlib --crate-type dylib --emit=dep-info,link -C opt-level=3 -C debuginfo=2 -C metadata=c59794c42c2e5d2c --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern atomic_counter=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libatomic_counter-83828d0b73047a5b.rlib --extern clap=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libclap-62f315ad00245630.rlib --extern crossbeam=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam-e0ba050ad89c9cc4.rlib --extern disjoint_sets=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libdisjoint_sets-cdef6477d36b0c69.rlib --extern flate2=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libflate2-e28aebe213d35db0.rlib --extern genome_graph=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libgenome_graph-f1f9f43eca9c0cbc.rlib --extern hashbrown=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libhashbrown-8db72db2c593f85e.rlib --extern itertools=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libitertools-ef1bbdf2dc7723ca.rlib --extern log=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/liblog-222ce67e5627d39a.rlib --extern memory_stats=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libmemory_stats-0abaf08295d64751.rlib --extern permutation=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libpermutation-cbccced583c33429.rlib --extern simplelog=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libsimplelog-570deb8a8d99c61b.rlib --extern traitgraph_algo=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtraitgraph_algo-0da65161844e678e.rlib - error[E0277]: the trait bound hashbrown::HashMap<_, _>: NodeWeightArray is not satisfied - --> src/implementation/greedytigs/mod.rs:153:17 - | - 153 | hashbrown::HashMap<_, _>, - | ^^^^^^^^^^^^^^^^^^^^^^^^ the trait NodeWeightArray is not implemented for hashbrown::HashMap<_, _> - | - = help: the following other types implement trait NodeWeightArray: - EpochNodeWeightArray - Vec - hashbrown::map::HashMap - note: required by a bound in compute_greedytigs_choose_dijkstra_performance_type - --> src/implementation/greedytigs/mod.rs:171:30 - | - 159 | fn compute_greedytigs_choose_dijkstra_performance_type< - | --------------------------------------------------- required by a bound in this function - ... - 171 | DijkstraNodeWeightArray: NodeWeightArray, - | ^^^^^^^^^^^^^^^^^^^^^^ required by this bound in compute_greedytigs_choose_dijkstra_performance_type - - error[E0277]: the trait bound hashbrown::HashMap<_, _>: NodeWeightArray is not satisfied - --> src/implementation/matchtigs/mod.rs:127:66 - | - 127 | compute_matchtigs::<_, _, _, _, _, DijkstraHeapType, hashbrown::HashMap<_, _>>( - | ^^^^^^^^^^^^^^^^^^^^^^^^ the trait NodeWeightArray is not implemented for hashbrown::HashMap<_, _> - | - = help: the following other types implement trait NodeWeightArray: - EpochNodeWeightArray - Vec - hashbrown::map::HashMap - note: required by a bound in compute_matchtigs - --> src/implementation/matchtigs/mod.rs:152:30 - | - 138 | fn compute_matchtigs< - | ----------------- required by a bound in this function - ... - 152 | DijkstraNodeWeightArray: NodeWeightArray, - | ^^^^^^^^^^^^^^^^^^^^^^ required by this bound in compute_matchtigs - - For more information about this error, try rustc --explain E0277. - error: could not compile matchtigs due to 2 previous errors - - Caused by: - process didn't exit successfully: rustc --crate-name libmatchtigs --edition=2021 src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type rlib --crate-type dylib --emit=dep-info,link -C opt-level=3 -C debuginfo=2 -C metadata=c59794c42c2e5d2c --out-dir /opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps -C linker=/opt/conda/conda-bld/matchtigs_1685352493749/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps --extern atomic_counter=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libatomic_counter-83828d0b73047a5b.rlib --extern clap=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libclap-62f315ad00245630.rlib --extern crossbeam=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libcrossbeam-e0ba050ad89c9cc4.rlib --extern disjoint_sets=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libdisjoint_sets-cdef6477d36b0c69.rlib --extern flate2=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libflate2-e28aebe213d35db0.rlib --extern genome_graph=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libgenome_graph-f1f9f43eca9c0cbc.rlib --extern hashbrown=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libhashbrown-8db72db2c593f85e.rlib --extern itertools=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libitertools-ef1bbdf2dc7723ca.rlib --extern log=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/liblog-222ce67e5627d39a.rlib --extern memory_stats=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libmemory_stats-0abaf08295d64751.rlib --extern permutation=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libpermutation-cbccced583c33429.rlib --extern simplelog=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libsimplelog-570deb8a8d99c61b.rlib --extern traitgraph_algo=/opt/conda/conda-bld/matchtigs_1685352493749/work/target/release/deps/libtraitgraph_algo-0da65161844e678e.rlib (exit status: 1) - error: failed to compile matchtigs v1.5.5 (/opt/conda/conda-bld/matchtigs_1685352493749/work), intermediate artifacts can be found at /opt/conda/conda-bld/matchtigs_1685352493749/work/target - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/matchtigs_1685352493749/work/conda_build.sh']' returned non-zero exit status 101. -# Last 100 lines of the build log. diff --git a/recipes/matchtigs/build_failure.osx-64.yaml b/recipes/matchtigs/build_failure.osx-64.yaml deleted file mode 100644 index c1ec0d0846ab8..0000000000000 --- a/recipes/matchtigs/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 02efdfc2f9abb5a0a1b47ed3022a17ded394809c39b45eb88ed5f9cb82af9995 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - Running rustc --crate-name time --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/time-0.3.21/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="formatting"' --cfg 'feature="local-offset"' --cfg 'feature="macros"' --cfg 'feature="std"' -C metadata=cff33a254c499774 -C extra-filename=-cff33a254c499774 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern itoa=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libitoa-b6b1c1e87a00a932.rmeta --extern libc=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/liblibc-5ccb4aa1e1d2bd7b.rmeta --extern num_threads=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libnum_threads-89b9574ec870b2e7.rmeta --extern time_core=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtime_core-efbc93ef8285afaf.rmeta --extern time_macros=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtime_macros-bdc1a6b7f4a5cf89.dylib --cap-lints allow - Compiling bigraph v2.1.1 - Running rustc --crate-name bigraph --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/bigraph-2.1.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=d2bd8a69f23852a3 -C extra-filename=-d2bd8a69f23852a3 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern bitvector=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libbitvector-62c20adfe03e270b.rmeta --extern traitgraph=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtraitgraph-bc9e80d37d1ec123.rmeta --extern traitgraph_algo=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtraitgraph_algo-51afa055a65fcde9.rmeta --cap-lints allow - Compiling compact-genome v1.3.1 - Running rustc --crate-name compact_genome --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/compact-genome-1.3.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=e9d7ac380993b77d -C extra-filename=-e9d7ac380993b77d --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern bitvec=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libbitvec-14901b094009aee9.rmeta --extern itertools=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libitertools-8b37b4be1693c850.rmeta --extern lazy_static=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/liblazy_static-8edbd0d7e87fd514.rmeta --extern ref_cast=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libref_cast-cc0d3a2bee0d0e12.rmeta --extern traitsequence=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtraitsequence-a531d7f6a4e1fe1e.rmeta --cap-lints allow - Running rustc --crate-name error_chain /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/error-chain-0.12.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="backtrace"' --cfg 'feature="default"' --cfg 'feature="example_generated"' -C metadata=6c9568dbb57bc607 -C extra-filename=-6c9568dbb57bc607 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern backtrace=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libbacktrace-570fe45a369c67f4.rmeta --cap-lints allow --cfg has_error_source --cfg has_error_description_deprecated --cfg 'build="release"' - Running rustc --crate-name crc32fast /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crc32fast-1.3.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=7811e7ccc03c41a3 -C extra-filename=-7811e7ccc03c41a3 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern cfg_if=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcfg_if-339ca62e89c174cb.rmeta --cap-lints allow --cfg crc32fast_stdarchx86 - Compiling crossbeam-deque v0.8.3 - Running rustc --crate-name crossbeam_deque --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crossbeam-deque-0.8.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="crossbeam-epoch"' --cfg 'feature="crossbeam-utils"' --cfg 'feature="std"' -C metadata=7865db6c4e96116f -C extra-filename=-7865db6c4e96116f --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern cfg_if=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcfg_if-339ca62e89c174cb.rmeta --extern crossbeam_epoch=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_epoch-a10e430ec7b298ce.rmeta --extern crossbeam_utils=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_utils-bf65195b665feb14.rmeta --cap-lints allow - Running rustc --crate-name crossbeam_queue --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crossbeam-queue-0.3.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="alloc"' --cfg 'feature="std"' -C metadata=b41cf3aebcf055e5 -C extra-filename=-b41cf3aebcf055e5 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern cfg_if=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcfg_if-339ca62e89c174cb.rmeta --extern crossbeam_utils=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_utils-bf65195b665feb14.rmeta --cap-lints allow - Compiling crossbeam-channel v0.5.8 - Running rustc --crate-name crossbeam_channel --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crossbeam-channel-0.5.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="crossbeam-utils"' --cfg 'feature="std"' -C metadata=7bd094e4aa0096a2 -C extra-filename=-7bd094e4aa0096a2 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern cfg_if=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcfg_if-339ca62e89c174cb.rmeta --extern crossbeam_utils=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_utils-bf65195b665feb14.rmeta --cap-lints allow - Compiling miniz_oxide v0.7.1 - Running rustc --crate-name miniz_oxide --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/miniz_oxide-0.7.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="with-alloc"' -C metadata=3da386d2fb157607 -C extra-filename=-3da386d2fb157607 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern adler=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libadler-754d0b764340dbd6.rmeta --cap-lints allow - Compiling clap_derive v4.3.0 - Running rustc --crate-name clap_derive --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/clap_derive-4.3.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C split-debuginfo=unpacked -C debug-assertions=off --cfg 'feature="default"' -C metadata=0f55988242712f27 -C extra-filename=-0f55988242712f27 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern heck=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libheck-62756755ed2fbfaa.rlib --extern proc_macro2=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libproc_macro2-40d3bbe8601e6cec.rlib --extern quote=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libquote-6701b06942490b47.rlib --extern syn=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libsyn-74574b7852e8dedb.rlib --extern proc_macro --cap-lints allow - Compiling disjoint-sets v0.4.2 - Running rustc --crate-name disjoint_sets /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/disjoint-sets-0.4.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=d6b88b013a3f602b -C extra-filename=-d6b88b013a3f602b --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --cap-lints allow - Compiling termcolor v1.1.3 - Running rustc --crate-name termcolor --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/termcolor-1.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=a4346f1bb9e6cd9d -C extra-filename=-a4346f1bb9e6cd9d --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --cap-lints allow - Compiling simplelog v0.12.1 - Running rustc --crate-name simplelog --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/simplelog-0.12.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="default"' --cfg 'feature="local-offset"' --cfg 'feature="termcolor"' -C metadata=049ab829b27b68bc -C extra-filename=-049ab829b27b68bc --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern log=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/liblog-9e6b74f49674def0.rmeta --extern termcolor=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtermcolor-a4346f1bb9e6cd9d.rmeta --extern time=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtime-cff33a254c499774.rmeta --cap-lints allow - Compiling clap v4.3.0 - Running rustc --crate-name clap --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.3.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="cargo"' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="error-context"' --cfg 'feature="help"' --cfg 'feature="std"' --cfg 'feature="suggestions"' --cfg 'feature="usage"' -C metadata=74d7a9ce665f4d0a -C extra-filename=-74d7a9ce665f4d0a --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern clap_builder=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libclap_builder-a116f0451cad590b.rmeta --extern clap_derive=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libclap_derive-0f55988242712f27.dylib --extern once_cell=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libonce_cell-5097ed0257a50681.rmeta --cap-lints allow - Compiling genome-graph v5.2.0 - Running rustc --crate-name genome_graph --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/genome-graph-5.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="traitgraph-algo"' -C metadata=161e13b62f7e18c3 -C extra-filename=-161e13b62f7e18c3 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern anyhow=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libanyhow-1bd97613d181b76f.rmeta --extern bigraph=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libbigraph-d2bd8a69f23852a3.rmeta --extern bio=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libbio-bc9df6df28031d3a.rmeta --extern compact_genome=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcompact_genome-e9d7ac380993b77d.rmeta --extern disjoint_sets=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libdisjoint_sets-d6b88b013a3f602b.rmeta --extern error_chain=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/liberror_chain-6c9568dbb57bc607.rmeta --extern log=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/liblog-9e6b74f49674def0.rmeta --extern num_traits=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libnum_traits-268c3fdbd8502ef9.rmeta --extern regex=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libregex-0703bb8ce6a2ee23.rmeta --extern traitgraph_algo=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtraitgraph_algo-51afa055a65fcde9.rmeta --cap-lints allow - Compiling flate2 v1.0.26 - Running rustc --crate-name flate2 --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/flate2-1.0.26/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="default"' --cfg 'feature="miniz_oxide"' --cfg 'feature="rust_backend"' -C metadata=e088f03a9f7cc483 -C extra-filename=-e088f03a9f7cc483 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern crc32fast=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrc32fast-7811e7ccc03c41a3.rmeta --extern miniz_oxide=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libminiz_oxide-3da386d2fb157607.rmeta --cap-lints allow - Compiling crossbeam v0.8.2 - Running rustc --crate-name crossbeam --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/crossbeam-0.8.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 --cfg 'feature="alloc"' --cfg 'feature="crossbeam-channel"' --cfg 'feature="crossbeam-deque"' --cfg 'feature="crossbeam-epoch"' --cfg 'feature="crossbeam-queue"' --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=2b10bb12540e959a -C extra-filename=-2b10bb12540e959a --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern cfg_if=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcfg_if-339ca62e89c174cb.rmeta --extern crossbeam_channel=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_channel-7bd094e4aa0096a2.rmeta --extern crossbeam_deque=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_deque-7865db6c4e96116f.rmeta --extern crossbeam_epoch=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_epoch-a10e430ec7b298ce.rmeta --extern crossbeam_queue=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_queue-b41cf3aebcf055e5.rmeta --extern crossbeam_utils=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam_utils-bf65195b665feb14.rmeta --cap-lints allow - Compiling memory-stats v1.1.0 - Running rustc --crate-name memory_stats --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/memory-stats-1.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=c00b1209dafae645 -C extra-filename=-c00b1209dafae645 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern libc=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/liblibc-5ccb4aa1e1d2bd7b.rmeta --cap-lints allow - Compiling permutation v0.4.1 - Running rustc --crate-name permutation /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/permutation-0.4.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=b54a1338bdf1876c -C extra-filename=-b54a1338bdf1876c --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --cap-lints allow - Compiling atomic-counter v1.0.1 - Running rustc --crate-name atomic_counter /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/atomic-counter-1.0.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=421a189e98cc8a78 -C extra-filename=-421a189e98cc8a78 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --cap-lints allow - Compiling matchtigs v1.5.5 (/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work) - Running rustc --crate-name libmatchtigs --edition=2021 src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type rlib --crate-type dylib --emit=dep-info,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=bd40b947ed26e03b --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern atomic_counter=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libatomic_counter-421a189e98cc8a78.rlib --extern clap=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libclap-74d7a9ce665f4d0a.rlib --extern crossbeam=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam-2b10bb12540e959a.rlib --extern disjoint_sets=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libdisjoint_sets-d6b88b013a3f602b.rlib --extern flate2=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libflate2-e088f03a9f7cc483.rlib --extern genome_graph=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libgenome_graph-161e13b62f7e18c3.rlib --extern hashbrown=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libhashbrown-f4ec59303b295fb7.rlib --extern itertools=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libitertools-8b37b4be1693c850.rlib --extern log=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/liblog-9e6b74f49674def0.rlib --extern memory_stats=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libmemory_stats-c00b1209dafae645.rlib --extern permutation=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libpermutation-b54a1338bdf1876c.rlib --extern simplelog=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libsimplelog-049ab829b27b68bc.rlib --extern traitgraph_algo=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtraitgraph_algo-51afa055a65fcde9.rlib - error[E0277]: the trait bound hashbrown::HashMap<_, _>: NodeWeightArray is not satisfied - --> src/implementation/greedytigs/mod.rs:153:17 - | - 153 | hashbrown::HashMap<_, _>, - | ^^^^^^^^^^^^^^^^^^^^^^^^ the trait NodeWeightArray is not implemented for hashbrown::HashMap<_, _> - | - = help: the following other types implement trait NodeWeightArray: - EpochNodeWeightArray - Vec - hashbrown::map::HashMap - note: required by a bound in compute_greedytigs_choose_dijkstra_performance_type - --> src/implementation/greedytigs/mod.rs:171:30 - | - 159 | fn compute_greedytigs_choose_dijkstra_performance_type< - | --------------------------------------------------- required by a bound in this function - ... - 171 | DijkstraNodeWeightArray: NodeWeightArray, - | ^^^^^^^^^^^^^^^^^^^^^^ required by this bound in compute_greedytigs_choose_dijkstra_performance_type - - error[E0277]: the trait bound hashbrown::HashMap<_, _>: NodeWeightArray is not satisfied - --> src/implementation/matchtigs/mod.rs:127:66 - | - 127 | compute_matchtigs::<_, _, _, _, _, DijkstraHeapType, hashbrown::HashMap<_, _>>( - | ^^^^^^^^^^^^^^^^^^^^^^^^ the trait NodeWeightArray is not implemented for hashbrown::HashMap<_, _> - | - = help: the following other types implement trait NodeWeightArray: - EpochNodeWeightArray - Vec - hashbrown::map::HashMap - note: required by a bound in compute_matchtigs - --> src/implementation/matchtigs/mod.rs:152:30 - | - 138 | fn compute_matchtigs< - | ----------------- required by a bound in this function - ... - 152 | DijkstraNodeWeightArray: NodeWeightArray, - | ^^^^^^^^^^^^^^^^^^^^^^ required by this bound in compute_matchtigs - - For more information about this error, try rustc --explain E0277. - error: could not compile matchtigs due to 2 previous errors - - Caused by: - process didn't exit successfully: rustc --crate-name libmatchtigs --edition=2021 src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type rlib --crate-type dylib --emit=dep-info,link -C opt-level=3 -C split-debuginfo=unpacked -C debuginfo=2 -C metadata=bd40b947ed26e03b --out-dir /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps --extern atomic_counter=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libatomic_counter-421a189e98cc8a78.rlib --extern clap=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libclap-74d7a9ce665f4d0a.rlib --extern crossbeam=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libcrossbeam-2b10bb12540e959a.rlib --extern disjoint_sets=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libdisjoint_sets-d6b88b013a3f602b.rlib --extern flate2=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libflate2-e088f03a9f7cc483.rlib --extern genome_graph=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libgenome_graph-161e13b62f7e18c3.rlib --extern hashbrown=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libhashbrown-f4ec59303b295fb7.rlib --extern itertools=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libitertools-8b37b4be1693c850.rlib --extern log=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/liblog-9e6b74f49674def0.rlib --extern memory_stats=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libmemory_stats-c00b1209dafae645.rlib --extern permutation=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libpermutation-b54a1338bdf1876c.rlib --extern simplelog=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libsimplelog-049ab829b27b68bc.rlib --extern traitgraph_algo=/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target/release/deps/libtraitgraph_algo-51afa055a65fcde9.rlib (exit status: 1) - error: failed to compile matchtigs v1.5.5 (/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work), intermediate artifacts can be found at /opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/target - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/matchtigs_1685352902295/work/conda_build.sh']' returned non-zero exit status 101. -# Last 100 lines of the build log. diff --git a/recipes/matchtigs/meta.yaml b/recipes/matchtigs/meta.yaml index 34e9b0af46499..c27476b2c0647 100644 --- a/recipes/matchtigs/meta.yaml +++ b/recipes/matchtigs/meta.yaml @@ -1,19 +1,22 @@ -{% set version = "2.1.5" %} +{% set name = "matchtigs" %} +{% set version = "2.1.7" %} package: - name: matchtigs + name: {{ name }} version: {{ version }} build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('matchtigs', max_pin="x") }} source: - url: https://github.com/algbio/matchtigs/archive/refs/tags/v{{ version }}.tar.gz - sha256: b01f2e3582801eda2f7003a2bf5843c4d4788e71c178eb226e70775aeaf48370 + url: https://github.com/algbio/matchtigs/archive/b809cc85986d4339bd45705e40df9e802816ff80.zip + sha256: 14079f983631b2ba5a41a01f8afd5786e6351722aba3da6b46ccd4cb46c03656 requirements: build: - - rust >=1.65 + - {{ compiler('rust') }} - {{ compiler('c') }} test: @@ -21,10 +24,18 @@ test: - matchtigs --help about: - home: https://github.com/algbio/matchtigs.git + home: "https://github.com/algbio/matchtigs" license: MIT + license_family: MIT summary: | - Different algorithms for computing small and minimum plain text representations of kmer sets. + "Different algorithms for computing small and minimum plain text representations of kmer sets." + dev_url: "https://github.com/algbio/matchtigs" + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - sebschmi + identifiers: + - doi:10.1186/s13059-023-02968-z diff --git a/recipes/maxit/build.sh b/recipes/maxit/build.sh new file mode 100644 index 0000000000000..ba58162b48c94 --- /dev/null +++ b/recipes/maxit/build.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +set -exo pipefail + +# Disable parallel build +export CPU_COUNT=1 + +export RCSBROOT="${SRC_DIR}" + +# To pass CI test on Linux-x86_64 platform +if [[ "$(uname -s)" == "Linux" && "$(uname -m)" == "x86_64" ]]; then + ulimit -v 2097152 +fi + +ln -s "${CC_FOR_BUILD}" "${BUILD_PREFIX}/bin/gcc" +ln -s "${CXX_FOR_BUILD}" "${BUILD_PREFIX}/bin/g++" + +cd ${SRC_DIR}/maxit-v10.1/src && \ +sed -i.bak "s|rcsbroot = getenv(\"RCSBROOT\")|rcsbroot = \"${RCSBROOT}\"|g" maxit.C process_entry.C generate_assembly_cif_file.C + +cd "${SRC_DIR}/cifparse-obj-v7.0" && sed -i.bak 's|mv |cp |g' Makefile +cd "${SRC_DIR}" && sed -i.bak "s|./data/binary|${RCSBROOT}/data/binary|g" binary.sh +cd "${SRC_DIR}" && make binary -j${CPU_COUNT} + +unlink "${BUILD_PREFIX}/bin/gcc" +unlink "${BUILD_PREFIX}/bin/g++" + +install -d "${PREFIX}/bin" +install ${SRC_DIR}/bin/* "${PREFIX}/bin" + +install -d "${PREFIX}/data" +find "${SRC_DIR}/data" -type d -exec install -d "${PREFIX}/data/{}" \; +find "${SRC_DIR}/data" -type f -exec install -m 644 "{}" "${PREFIX}/data/{}" \; diff --git a/recipes/maxit/meta.yaml b/recipes/maxit/meta.yaml new file mode 100644 index 0000000000000..6ad2a788c5d33 --- /dev/null +++ b/recipes/maxit/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "MAXIT" %} +{% set version = "11.200" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://sw-tools.rcsb.org/apps/{{ name }}/{{ name|lower }}-v{{ version }}-prod-src.tar.gz + sha256: 658e236c6310cf7e55218a0500f82050ef86074f5d5b3f61d2a161b04a38cc39 + patches: + - platform.sh.patch # [osx] + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + - bison + - flex + - coreutils + +test: + commands: + - output=$(maxit 2>&1 || true) && echo ${output} | grep -q 'maxit -input inputfile' + +about: + home: https://sw-tools.rcsb.org/apps/MAXIT + doc_url: https://sw-tools.rcsb.org/apps/MAXIT/README-source + license: "RCSB PDB Software License" + license_family: OTHER + summary: "MAXIT assists in the processing and curation of macromolecular structure data." + description: | + MAXIT assists in the processing and curation of macromolecular structure data. MAXIT can: + - Read and write PDB and mmCIF format files, and translate between file formats. + - Perform consistency checks on coordinates, sequence, and crystal data. + - Automatically construct, transform, and merge information between formats + - Align residue numbering in the coordinates with the sequence + - Reorder and rename atoms in standard and nonstandard residues and ligands according to the Chemical Component Dictionary + - Assign ligands the same chain IDs as the adjacent polymers + - Detect missing or additional atoms + +extra: + recipe-maintainers: + - eunos-1128 + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/maxit/platform.sh.patch b/recipes/maxit/platform.sh.patch new file mode 100644 index 0000000000000..4cedc77a96aae --- /dev/null +++ b/recipes/maxit/platform.sh.patch @@ -0,0 +1,50 @@ +diff --git a/etc/platform.sh b/etc/platform.sh +index 1607685..e5f3573 100755 +--- a/etc/platform.sh ++++ b/etc/platform.sh +@@ -6,7 +6,7 @@ + # Copy the platform specific section of the Makefile in + # the current directory to: + # +-# Makefile.platform. ++# Makefile.platform. + # + # + sysid="unknown" +@@ -29,10 +29,10 @@ case $(uname -s) in + + # Check if it is a Mac OS platform + Darwin) +-# First check if it is clang-xxxx +- clang_ver=$(gcc --version | grep -e "clang-") ++# First check if it is clang ++ clang_ver=$(clang --version | grep -e "clang version") + if [ ! -z "$clang_ver" ] +- then ++ then + sysid="darwin4" + else + # Check if it is GCC version 4.x +@@ -61,7 +61,7 @@ case $(uname -s) in + # It is GCC version 4.x + sysid="darwin4" + fi +- fi ++ fi + ;; + + # Check if it is a Linux platform +@@ -85,11 +85,11 @@ case $(uname -s) in + fi + # + if [ -z "$gcc_ver" ] +- then ++ then + # Check if it is GCC version 5.x + gcc_ver=$(gcc --version | grep -e " 5\.") + if [ -z "$gcc_ver" ] +- then ++ then + # If not GCC version 5.x + gcc_ver=$(gcc --version | grep -e " 4\.") + if [ -z "$gcc_ver" ] diff --git a/recipes/mcl/build.sh b/recipes/mcl/build.sh index 066d521961a67..e8c845e3701b6 100644 --- a/recipes/mcl/build.sh +++ b/recipes/mcl/build.sh @@ -6,20 +6,23 @@ export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CFLAGS="${CFLAGS} -O3 -fcommon" -export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" +export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" +export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" cd cimfomfa +autoupdate +autoreconf -if ./configure --prefix="${PREFIX}" \ CC="${CC}" CFLAGS="${CFLAGS}" \ CPPFLAGS="${CPPFLAGS}" \ LDFLAGS="${LDFLAGS}" \ - --enable-shared + --disable-shared make -j"${CPU_COUNT}" make install make clean cd .. +autoupdate ./configure --prefix="${PREFIX}" \ CC="${CC}" CFLAGS="${CFLAGS}" \ CPPFLAGS="${CPPFLAGS}" \ @@ -32,4 +35,4 @@ make clean # Add back in the mcl/blast scripts. # Remove this once the next release re-incorporates them. # See https://github.com/micans/mcl/discussions/25 -cp $RECIPE_DIR/scripts/mc* $PREFIX/bin/ +cp -rf $RECIPE_DIR/scripts/mc* $PREFIX/bin/ diff --git a/recipes/mcl/meta.yaml b/recipes/mcl/meta.yaml index 30a984029b69c..34eb97e7fe060 100644 --- a/recipes/mcl/meta.yaml +++ b/recipes/mcl/meta.yaml @@ -14,7 +14,7 @@ source: folder: cimfomfa build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('mcl', max_pin=None) }} @@ -22,11 +22,13 @@ requirements: build: - make - {{ compiler('c') }} + - autoconf + - automake + - libtool host: - perl run: - perl - - blast test: commands: @@ -43,13 +45,13 @@ test: - mcxsubs --version about: - home: https://micans.org/mcl/ - license: GPL-3.0-only + home: "https://micans.org/mcl" + license: "GPL-3.0-only" license_family: GPL license_file: LICENSE - summary: MCL - a cluster algorithm for graphs - dev_url: https://github.com/micans/mcl - doc_url: https://micans.org/mcl/man/mcl.html + summary: "MCL - a cluster algorithm for graphs." + dev_url: "https://github.com/micans/mcl" + doc_url: "https://micans.org/mcl/man/mcl.html" extra: identifiers: @@ -57,3 +59,5 @@ extra: - doi:10.1093/nar/30.7.1575 - biotools:mcl - usegalaxy-eu:mcl + additional-platforms: + - linux-aarch64 diff --git a/recipes/medaka/build.sh b/recipes/medaka/build.sh index a17d134c7c243..5dc2e9c7995bd 100644 --- a/recipes/medaka/build.sh +++ b/recipes/medaka/build.sh @@ -1,10 +1,10 @@ -#!/bin/bash +#!/bin/bash -euo export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CFLAGS="-I${PREFIX}/include ${LDFLAGS}" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" # disable Makefile driven build of htslib.a sed -i.bak "s/'build_ext': HTSBuild//" setup.py @@ -13,4 +13,6 @@ sed -i.bak "s/'build_ext': HTSBuild//" setup.py sed -i.bak 's/extra_objects.*//' build.py sed -i.bak 's/^libraries=\[/libraries=\["hts",/' build.py -$PYTHON -m pip install . --no-deps --ignore-installed -vvv +rm -rf *.bak + +${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/medaka/build_failure.linux-64.yaml b/recipes/medaka/build_failure.linux-64.yaml deleted file mode 100644 index 362238bbedeef..0000000000000 --- a/recipes/medaka/build_failure.linux-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: fe8244e36e00fce9b146f015c871e6714fe382a6b7375f652967216782b9cb0f # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue -log: |2- - - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("tensorflow==2.10.0=cuda112py310he87a039_0"), MatchSpec("__cuda"), MatchSpec("pysam==0.16.0.1=py27ha863e18_1"), MatchSpec("python_abi=2.7[build=*_cp27mu]")} - Encountered problems while solving: - - package pysam-0.16.0.1-py27ha863e18_1 requires python_abi 2.7.* *_cp27mu, but none of the providers can be installed - - nothing provides __cuda needed by tensorflow-2.10.0-cuda112py310he87a039_0 - - Could not solve for environment specs - The following packages are incompatible - [32mopenssl >=1.1.1w,<1.1.2a [0m is requested and can be installed; - [32mpysam >=0.16.0.1 [0m is installable with the potential options - [32mpysam [0.16.0.1|0.17.0|...|0.20.0][0m would require - [32mpython_abi 2.7.* *_cp27mu[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.21.0][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.21.0][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.21.0][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.21.0][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam [0.19.1|0.20.0|0.21.0][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [31mpysam 0.21.0[0m would require - [31mopenssl >=3.1.0,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpysam 0.22.0[0m would require - [31mopenssl >=3.1.3,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpysam [0.22.0|0.22.1][0m would require - [31mopenssl >=3.2.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpysam 0.22.1[0m would require - [31mopenssl >=3.3.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython >=3.11,<3.12.0a0 [0m is not installable because there are no viable options - [31mpython 3.11.0[0m would require - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.0[0m would require - [31mopenssl >=3.0.5,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.0[0m would require - [31mopenssl >=3.0.7,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython [3.11.1|3.11.2|3.11.3][0m would require - [31mopenssl >=3.1.0,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.4[0m would require - [31mopenssl >=3.1.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.5[0m would require - [31mopenssl >=3.1.2,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.6[0m would require - [31mopenssl >=3.1.3,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.7[0m would require - [31mopenssl >=3.2.0,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython [3.11.8|3.11.9][0m would require - [31mopenssl >=3.2.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython_abi 3.11.* *_cp311[0m is not installable because it conflicts with any installable versions previously reported; - [32mtensorflow >=2.10,<2.11 [0m is installable with the potential options - [32mtensorflow 2.10.0[0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32mtensorflow 2.10.0[0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mtensorflow 2.10.0[0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mtensorflow 2.10.0[0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [31mtensorflow 2.10.0[0m would require - [31m__cuda[0m, which is missing on the system. -# Last 100 lines of the build log. diff --git a/recipes/medaka/build_failure.osx-64.yaml b/recipes/medaka/build_failure.osx-64.yaml deleted file mode 100644 index 382a5d84d4aa9..0000000000000 --- a/recipes/medaka/build_failure.osx-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: fe8244e36e00fce9b146f015c871e6714fe382a6b7375f652967216782b9cb0f # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue -log: |2- - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("openssl[version='>=3.0.0,<4.0a0']"), MatchSpec("libcurl==7.79.1=h97da3c1_1")} - Encountered problems while solving: - - package libcurl-7.79.1-h97da3c1_1 requires openssl >=3.0.0,<4.0a0, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - htslib >=1.14 is installable with the potential options - htslib [1.14|1.15|1.15.1] would require - libcurl [>=7.79.1,<8.0a0 |>=7.81.0,<8.0a0 |>=7.82.0,<8.0a0 ] with the potential options - libcurl [7.79.1|7.80.0|7.81.0|7.82.0] would require - openssl >=3.0.0,<4.0a0 , which can be installed; - libcurl [7.79.1|7.80.0|7.81.0|7.82.0] would require - openssl >=1.1.1l,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl 7.83.0 would require - openssl >=3.0.2,<4.0a0 , which can be installed; - libcurl 7.83.0 would require - openssl >=1.1.1n,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl 7.83.1 would require - openssl >=3.0.3,<4.0a0 , which can be installed; - libcurl 7.83.1 would require - openssl >=1.1.1o,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl [7.85.0|7.86.0] would require - openssl >=1.1.1q,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl [7.85.0|7.86.0] would require - openssl >=3.0.5,<4.0a0 , which can be installed; - libcurl 7.86.0 would require - openssl >=3.0.7,<4.0a0 , which can be installed; - libcurl [7.86.0|7.87.0] would require - krb5 >=1.20.1,<1.21.0a0 with the potential options - krb5 1.20.1 would require - openssl >=1.1.1s,<1.1.2a , which conflicts with any installable versions previously reported; - krb5 1.20.1 would require - openssl >=3.0.7,<4.0a0 , which can be installed; - openssl >=3.0.7,<4.0a0 , which can be installed; - libcurl [7.86.0|7.87.0] would require - openssl >=1.1.1s,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl [7.88.0|7.88.1] would require - openssl >=3.0.8,<4.0a0 , which can be installed; - libcurl 7.88.1 would require - openssl >=3.1.0,<4.0a0 , which can be installed; - htslib [1.15.1|1.16] would require - libcurl >=7.83.1,<8.0a0 with the potential options - libcurl 7.83.1, which can be installed (as previously explained); - libcurl 7.83.1, which cannot be installed (as previously explained); - libcurl [7.85.0|7.86.0], which cannot be installed (as previously explained); - libcurl [7.85.0|7.86.0], which can be installed (as previously explained); - libcurl 7.86.0, which can be installed (as previously explained); - libcurl [7.86.0|7.87.0], which can be installed (as previously explained); - libcurl [7.86.0|7.87.0], which cannot be installed (as previously explained); - libcurl [7.88.0|7.88.1], which can be installed (as previously explained); - libcurl 7.88.1, which can be installed (as previously explained); - htslib 1.17 would require - libcurl >=8.0.1,<9.0a0 , which conflicts with any installable versions previously reported; - htslib 1.17 would require - libcurl >=7.88.1,<8.0a0 , which can be installed (as previously explained); - htslib 1.18 would require - libcurl >=8.2.0,<9.0a0 , which conflicts with any installable versions previously reported; - htslib [1.19|1.19.1] would require - libcurl >=8.5.0,<9.0a0 , which conflicts with any installable versions previously reported; - htslib 1.20 would require - libcurl >=8.7.1,<9.0a0 , which conflicts with any installable versions previously reported; - htslib 1.20 would require - libcurl >=8.8.0,<9.0a0 , which conflicts with any installable versions previously reported; - libcurl 7.* is installable with the potential options - libcurl [7.79.1|7.80.0|7.81.0|7.82.0], which can be installed (as previously explained); - libcurl [7.79.1|7.80.0|7.81.0|7.82.0], which cannot be installed (as previously explained); - libcurl 7.83.0, which can be installed (as previously explained); - libcurl 7.83.0, which cannot be installed (as previously explained); - libcurl 7.83.1, which can be installed (as previously explained); - libcurl 7.83.1, which cannot be installed (as previously explained); - libcurl [7.85.0|7.86.0], which cannot be installed (as previously explained); - libcurl [7.85.0|7.86.0], which can be installed (as previously explained); - libcurl 7.86.0, which can be installed (as previously explained); - libcurl [7.86.0|7.87.0], which can be installed (as previously explained); - libcurl [7.86.0|7.87.0], which cannot be installed (as previously explained); - libcurl [7.88.0|7.88.1], which can be installed (as previously explained); - libcurl 7.88.1, which can be installed (as previously explained); - libcurl [7.61.1|7.62.0|...|7.78.0], which can be installed; - openssl 1.1.1.* is not installable because it conflicts with any installable versions previously reported; - python 3.12.* *_cpython is installable with the potential options - python 3.12.0 would require - openssl >=3.1.3,<4.0a0 , which can be installed; - python 3.12.0rc3 would require - _python_rc, which does not exist (perhaps a missing channel); - python 3.12.1 would require - openssl >=3.2.0,<4.0a0 , which can be installed; - python [3.12.2|3.12.3] would require - openssl >=3.2.1,<4.0a0 , which can be installed. -# Last 100 lines of the build log. diff --git a/recipes/medaka/conda_build_config.yaml b/recipes/medaka/conda_build_config.yaml deleted file mode 100644 index f45b292d8ac64..0000000000000 --- a/recipes/medaka/conda_build_config.yaml +++ /dev/null @@ -1,9 +0,0 @@ -# Required to support Tensorflow v2.10, which is the only version -# supported by Medaka. The pinning of older versions of libcurl and -# openssl will cause installation of outdated packages and likely -# lead solver conflicts in the future. Please review this on future -# releases, especially if support for TensorFlow 2.11+ is added. -libcurl: - - 7 -openssl: - - 1.1.1 diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 2b96f89fbca10..95068e0465bbb 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,20 +1,21 @@ -{% set name = "Medaka" %} -{% set version = "1.11.3" %} -{% set sha256 = "940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9" %} +{% set name = "medaka" %} +{% set version = "2.0.0" %} +{% set sha256 = "8089c4b3966a096bb0fedab7538f02d625fe0a5c0396c42856dde2f0a2ad1627" %} # Bot PRs - Always review requirements.txt for new release package: - name: {{ name|lower }} + name: {{ name }} version: {{ version }} source: - url: https://github.com/nanoporetech/medaka/releases/download/v{{ version }}/medaka-{{ version }}.tar.gz + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/medaka-{{ version }}.tar.gz sha256: {{ sha256 }} patches: - patch build: - number: 1 + number: 0 + skip: True # [osx or py < 38 or py > 311] entry_points: - medaka = medaka.medaka:main - medaka_counts = medaka.medaka_counts:main @@ -26,11 +27,12 @@ build: requirements: build: - {{ compiler('c') }} - - coreutils + - cmake + - make host: - python - pip - - cffi >=1.15.0 + - cffi - htslib >=1.14 - libcurl - openssl @@ -39,14 +41,12 @@ requirements: - zlib run: - python - - cffi >=1.15.0 + - cffi - grpcio - h5py - intervaltree - # Please review the need for the conda_build_config.yaml - # if a more recent version of Tensorflow is supported. - - tensorflow >=2.10,<2.11 - - numpy >=1.21.6 + - pytorch >=2.3,<2.4 + - numpy >=1.21.0,<2.0.0 - nomkl # [osx] - mappy - ont-fast5-api @@ -60,8 +60,7 @@ requirements: - bcftools >=1.14 - minimap2 >=2.17 - htslib >=1.14 - - libcurl - - openssl + - tqdm - wurlitzer test: @@ -69,19 +68,23 @@ test: - medaka commands: - medaka --help - - medaka consensus --help + - medaka inference --help - medaka_data_path - medaka_version_report about: - home: https://github.com/nanoporetech/medaka - summary: Neural network sequence error correction. - license: MPL-2.0 + home: "https://github.com/nanoporetech/medaka" + summary: "A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks." + license: "MPL-2.0" license_family: OTHER - license_file: LICENSE.md - dev_url: https://github.com/nanoporetech/medaka + license_file: "LICENSE" + dev_url: "https://github.com/nanoporetech/medaka" + doc_url: "https://github.com/nanoporetech/medaka/blob/v{{ version }}/README.md" extra: identifiers: - usegalaxy-eu:medaka_consensus + - usegalaxy-eu:medaka_consensus_pipeline + - usegalaxy-eu:medaka_variant + - usegalaxy-eu:medaka_variant_pipeline - biotools:medaka diff --git a/recipes/medicc2/build_failure.osx-64.yaml b/recipes/medicc2/build_failure.osx-64.yaml deleted file mode 100644 index d85b0fa5a17f6..0000000000000 --- a/recipes/medicc2/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 21d3865430842e65e74a078a26c2e14e555ea2c30cb3d453e0b42d65d25d1072 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - python_abi 3.7.* *_cp37m, which can be installed; - ncls [0.0.63|0.0.64|0.0.65|0.0.66] would require - python_abi 3.8.* *_cp38, which can be installed; - ncls [0.0.63|0.0.64|0.0.65|0.0.66] would require - python_abi 3.9.* *_cp39, which can be installed; - ncls [0.0.65|0.0.66] would require - python_abi 3.10.* *_cp310, which can be installed; - sorted_nearest >=0.0.33 , which can be installed (as previously explained); - python >=3.11,<3.12.0a0 is not installable because it requires - python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported. - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("pyranges==0.0.39=py37h1de35cc_0"), MatchSpec("python[version='>=3.7,<3.8.0a0']")} - Encountered problems while solving: - - package pyranges-0.0.39-py37h1de35cc_0 requires python >=3.7,<3.8.0a0, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - pyranges is installable with the potential options - pyranges [0.0.39|0.0.40|...|0.0.52] would require - python >=3.7,<3.8.0a0 , which can be installed; - pyranges [0.0.51|0.0.52] would require - python >=3.6,<3.7.0a0 , which can be installed; - pyranges [0.0.100|0.0.101|...|0.0.99] would require - sorted_nearest [>=0.0.28 |>=0.0.30 ] with the potential options - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=2.7,<2.8.0a0 , which can be installed; - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=3.6,<3.7.0a0 , which can be installed; - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=3.7,<3.8.0a0 , which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 2.7.* *_cp27m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 3.6.* *_cp36m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 3.7.* *_cp37m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37|0.0.39] would require - python_abi 3.8.* *_cp38, which can be installed; - sorted_nearest [0.0.32|0.0.33|0.0.37|0.0.39] would require - python_abi 3.9.* *_cp39, which can be installed; - sorted_nearest [0.0.37|0.0.39] would require - python_abi 3.10.* *_cp310, which can be installed; - pyranges [0.0.125|0.0.127|0.0.128|0.0.129] would require - ncls >=0.0.63 with the potential options - ncls [0.0.63|0.0.64|0.0.65|0.0.66] would require - python_abi 2.7.* *_cp27m, which can be installed; - ncls [0.0.63|0.0.64|0.0.65|0.0.66] would require - python_abi 3.6.* *_cp36m, which can be installed; - ncls [0.0.63|0.0.64|0.0.65|0.0.66] would require - python_abi 3.7.* *_cp37m, which can be installed; - ncls [0.0.63|0.0.64|0.0.65|0.0.66] would require - python_abi 3.8.* *_cp38, which can be installed; - ncls [0.0.63|0.0.64|0.0.65|0.0.66] would require - python_abi 3.9.* *_cp39, which can be installed; - ncls [0.0.65|0.0.66] would require - python_abi 3.10.* *_cp310, which can be installed; - sorted_nearest >=0.0.33 , which can be installed (as previously explained); - python >=3.11,<3.12.0a0 is not installable because it requires - python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported. -# Last 100 lines of the build log. diff --git a/recipes/medicc2/meta.yaml b/recipes/medicc2/meta.yaml index 34c7f0f7d235e..a994a9c9b558f 100644 --- a/recipes/medicc2/meta.yaml +++ b/recipes/medicc2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "medicc2" %} -{% set version = "1.0.4" %} -{% set hash = "ed890c608b5d6ad08ea1e459af93a844242c1e12a02bd0f03b542a3654dcc720" %} +{% set version = "1.1.2" %} +{% set hash = "13cb58099d5e4b79b4169b8ccc8f2543863b1dab0a43fafb5e146bfd9d9adc97" %} package: @@ -13,47 +13,53 @@ source: build: number: 0 + skip: True # [py < 38 or py >= 311] run_exports: - {{ pin_subpackage("medicc2", max_pin="x") }} - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv requirements: build: - {{ compiler('c') }} - {{ compiler("cxx") }} host: - - python >=3.8,<3.11 + - python - pip # The following are needed for building the Cython extension - numpy >=1.20.1 - openfst ==1.8.2 - setuptools - cython ==0.29.* + - pathlib2 run: - - python >=3.8,<3.11 + - python - numpy >=1.20.1,<2.0 - pyyaml >=5.4.1 - {{ pin_compatible('openfst', max_pin='x.x.x') }} - - pandas >=1.2.2,<2.1 + - pandas >=1.2,<2.1 - joblib >=1.0.1 - biopython >=1.78 - scipy >=1.7 - - matplotlib-base >=3.3 + - matplotlib-base >=3.3.4 - pyranges test: commands: - medicc2 --help -extra: - recipe-maintainers: - - tlkaufmann - about: home: https://bitbucket.org/schwarzlab/medicc2 - license: GPL-3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Whole-genome doubling-aware copy number phylogenies for cancer evolution description: | For more information see the accompanying biorxiv preprint "Kaufmann et al. Whole-genome doubling-aware copy number phylogenies for cancer evolution with MEDICC2." + dev_url: https://bitbucket.org/schwarzlab/medicc2 + +extra: + recipe-maintainers: + - tlkaufmann + identifiers: + - doi:10.1186/s13059-022-02794-9 diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 407cffb19171f..6584018563bc8 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.26.0" %} -{% set sha256 = "b70c46074b8b2cadf20664cbea7f4c1e4628db531068d0f08c955c747540be32" %} +{% set version = "0.28.1" %} +{% set sha256 = "b1bb238782036c05795b74fbb7e97ff998e234fd89f4501234b052d3f2a0d683" %} package: name: mehari diff --git a/recipes/meme/build.sh b/recipes/meme/build.sh index d421c84749228..30440594b5d6a 100644 --- a/recipes/meme/build.sh +++ b/recipes/meme/build.sh @@ -1,13 +1,10 @@ -#!/bin/bash -set -e +#!/bin/bash -ex -export MEME_ETC_DIR=${PREFIX}/etc -#HOME=/tmp cpanm CGI::Application -#HOME=/tmp cpanm XML::Parser::Expat --configure-args "EXPATLIBPATH=$PREFIX/lib" --configure-args "EXPATHINCPATH=$PREFIX/include" +export MEME_ETC_DIR="${PREFIX}/etc" +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" -autoreconf -i - -perl scripts/dependencies.pl +autoreconf -if ./configure CC="${CC}" \ CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include" \ @@ -16,14 +13,7 @@ perl scripts/dependencies.pl --enable-build-libxml2 \ --enable-build-libxslt -make AM_CFLAGS='-DNAN="(0.0/0.0)"' -j4 - -# tests will only work inside the build dir, but -# https://github.com/conda/conda-build/issues/1453 -# so you need `conda build --prefix-length 1` -# for it to work properly -# make test - +make AM_CFLAGS='-DNAN="(0.0/0.0)"' -j"${CPU_COUNT}" make install make clean @@ -35,6 +25,5 @@ if [ ${PY3K}==1 ]; then sed -i.bak '994s/dreme/dreme-py3/' ${PREFIX}/bin/meme-chip rm ${PREFIX}/bin/meme-chip.bak # Fix for dreme - cp scripts/*py3.py ${PREFIX}/lib/${PKG_NAME}-${PKG_VERSION}/python/ + cp -rf scripts/*py3.py ${PREFIX}/lib/${PKG_NAME}-${PKG_VERSION}/python/ fi - diff --git a/recipes/meme/meta.yaml b/recipes/meme/meta.yaml index 5e542248cf755..b44bef89008de 100644 --- a/recipes/meme/meta.yaml +++ b/recipes/meme/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MEME" %} -{% set version = "5.5.5" %} -{% set sha256 = "bebb4a176e72d62e3a2d5ba5f22439185bbc4bbf4769604fbca12dff8e1f739f" %} +{% set version = "5.5.7" %} +{% set sha256 = "1dca8d0e6d1d36570c1a88ab8dbe7e4b177733fbbeacaa2e8c4674febf57aaf4" %} package: name: {{ name|lower }} @@ -11,8 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 - detect_binary_files_with_prefix: True + number: 0 run_exports: - {{ pin_subpackage("meme", max_pin="x") }} @@ -25,12 +24,11 @@ requirements: - libtool host: - nodejs >=16.4.1 - - openmpi - - yaml - - icu >=72.1,<73.0a0 + - libgomp # [linux] + - llvm-openmp # [osx] + - icu - ghostscript - zlib - - xz - libxslt - libxml2 - expat @@ -74,15 +72,14 @@ test: - dreme -version about: - home: https://meme-suite.org + home: "https://meme-suite.org" license: Custom license_file: COPYING - summary: Motif-based sequence analysis tools + summary: "Motif-based sequence analysis tools." + doc_url: "https://meme-suite.org/meme/doc/overview.html" extra: - container: - # openmpi needs ssh/rsh - extended-base: true identifiers: - biotools:meme_suite - usegalaxy-eu:meme_dreme + - doi:10.1093/nar/gkv416 diff --git a/recipes/mess/meta.yaml b/recipes/mess/meta.yaml index e95fe08460b76..79e6e64a7263c 100644 --- a/recipes/mess/meta.yaml +++ b/recipes/mess/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MeSS" %} -{% set version = "0.8.3" %} +{% set version = "0.9.0" %} package: name: "{{ name|lower }}" @@ -7,14 +7,14 @@ package: source: url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0f33dad4c2a90ed5e7d573c5cdb878150d63e99cfdbf83504f72c557eb075d74 + sha256: a0bb9d8dc81548cfad1cc45d43c82d41b28a399dd8f6bad4c5588a8201196f1a build: number: 0 noarch: python entry_points: - mess=mess.__main__:main - script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: - {{ pin_subpackage('mess', max_pin="x.x") }} @@ -26,8 +26,8 @@ requirements: run: - python >=3.10 - - snakemake-minimal >=7.32.4 - - pulp <2.8 + - mamba >=1.5.8 + - snakemake-minimal >=8.0.0 - snaketool-utils >=0.0.5 - attrmap >=0.0.7 - pyyaml >=6.0.1 @@ -55,4 +55,6 @@ extra: recipe-maintainers: - farchaab - tpillone + identifiers: + - biotools:mess diff --git a/recipes/metabinner/build.sh b/recipes/metabinner/build.sh index 5ea0e225a2eb9..34888d0a58586 100644 --- a/recipes/metabinner/build.sh +++ b/recipes/metabinner/build.sh @@ -6,3 +6,8 @@ chmod a+x run_metabinner.sh cp run_metabinner.sh $PREFIX/bin/ cp -r auxiliary $PREFIX/bin/ cp -r scripts $PREFIX/bin/ + +## Original build by author just placed directories in bin, not scripts themsleves +## To ensure backwards compatibility, we additionally symlink the scripts to the bin directory +ln -s $PREFIX/bin/auxiliary/* $PREFIX/bin/ +ln -s $PREFIX/bin/scripts/* $PREFIX/bin/ diff --git a/recipes/metabinner/meta.yaml b/recipes/metabinner/meta.yaml index e0987b3a72b74..bd2fc3e2824a7 100644 --- a/recipes/metabinner/meta.yaml +++ b/recipes/metabinner/meta.yaml @@ -7,8 +7,10 @@ source: sha256: 087a28aeb8fe218a3a2a6dd53b3bc5cad4cf33353fde3eebb8ee992461a99119 build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage("metabinner", max_pin="x") }} requirements: run: @@ -30,10 +32,12 @@ requirements: test: commands: - - which run_metabinner.sh - + - "gen_coverage_file.sh 2> /dev/null | grep 'Usage: bash gen_coverage_file.sh'" + - which gen_kmer.py + - Filter_tooshort.py --help + - "run_metabinner.sh 2> /dev/null | grep 'Usage: bash run_metabinner.sh'" + about: home: "https://github.com/ziyewang/MetaBinner" license: BSD summary: "Ensemble binning method to recover individual genomes from complex microbial communities" - diff --git a/recipes/metabolabpy/meta.yaml b/recipes/metabolabpy/meta.yaml index 738dbbfb7fdea..1ebc73d558377 100644 --- a/recipes/metabolabpy/meta.yaml +++ b/recipes/metabolabpy/meta.yaml @@ -1,6 +1,6 @@ {% set name = "metabolabpy" %} -{% set version = "0.9.46" %} -{% set sha256 = "e48ae83d423f290e4e55d64fbea97032e3f7a1c0e8942d177a5da755cabff7fa" %} +{% set version = "0.9.53" %} +{% set sha256 = "33a3b653bc876908948578abb0354d146ab796cb234640a90a7ec1cadee19427" %} package: name: {{ name|lower }} diff --git a/recipes/metabolights-utils/meta.yaml b/recipes/metabolights-utils/meta.yaml index eb899c33eb3da..f12e37a1a9786 100644 --- a/recipes/metabolights-utils/meta.yaml +++ b/recipes/metabolights-utils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metabolights-utils" %} -{% set version = "1.1.5" %} +{% set version = "1.1.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz - sha256: eafde551191dac729435067b37acefbd9c2b921f661a4f8253e6a618413a2c27 + sha256: 1e50774a4d4ab15d47e8274773f400fec3c09fc508bddd16dd30fb9c2626716c build: entry_points: diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml index 0d6ed66393dbf..474fe1ebaeca8 100644 --- a/recipes/metabuli/meta.yaml +++ b/recipes/metabuli/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.0.5" %} -{% set sha256 = "c84a4e2436904f0cbea7126abf2a5f665a870735c8af786883e10f3f872bda28" %} +{% set version = "1.0.8" %} +{% set sha256 = "cc7e496ff82f00b56ef59aa2a04fa572a2025225b0558e0df144f166fade82d4" %} package: name: metabuli version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('metabuli', max_pin="x") }} diff --git a/recipes/metacache/build.sh b/recipes/metacache/build.sh index d598c1db19aeb..148f16909d068 100644 --- a/recipes/metacache/build.sh +++ b/recipes/metacache/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -set -e +set -xe export CPATH=${PREFIX}/include export CXXPATH=${PREFIX}/include @@ -11,7 +11,7 @@ sed -i.bak "s|LDFLAGS = -pthread|LDFLAGS = -pthread -L$PREFIX/lib|" mkdir -p $PREFIX/bin -make +make -j ${CPU_COUNT} chmod +x metacache download-ncbi-genomes download-ncbi-taxmaps download-ncbi-taxonomy metacache-build-refseq metacache-db-info metacache-partition-genomes summarize-results mv metacache $PREFIX/bin mv download-ncbi-genomes $PREFIX/bin diff --git a/recipes/metacache/meta.yaml b/recipes/metacache/meta.yaml index f37fdf17c598b..c2067924f2f8b 100644 --- a/recipes/metacache/meta.yaml +++ b/recipes/metacache/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.4.2" %} +{% set version = "2.4.3" %} package: name: metacache @@ -6,7 +6,7 @@ package: source: url: https://github.com/muellan/metacache/archive/refs/tags/v{{ version }}.tar.gz - sha256: 2062de4c13cc9ed3962c8903b81dca05ccabd5820305362229bc446c11c9b111 + sha256: 2b43aa1ac051d6cbaa4d29c3ed7d9593e226e7e2b35cdd0b2e513e465456a7b2 build: number: 1 @@ -39,6 +39,10 @@ test: about: home: https://github.com/muellan/metacache - license: GPL-3.0 + license: GPL-3.0-or-later license_file: LICENSE summary: MetaCache is a classification system for mapping genomic sequences (short reads, long reads, contigs, ...) from metagenomic samples to their most likely taxon of origin. + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/metacerberus-lite/meta.yaml b/recipes/metacerberus-lite/meta.yaml index 3888274b58bec..1ac5cf12771ec 100644 --- a/recipes/metacerberus-lite/meta.yaml +++ b/recipes/metacerberus-lite/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MetaCerberus-lite" %} -{% set version = "1.3.2" %} +{% set version = "1.4.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/raw-lab/MetaCerberus/archive/refs/tags/v{{version}}.tar.gz" - sha256: 678929f58b38fafc635dfb35e248b5c76b4cd682b9e2d3499fe953ee3b974d68 + sha256: 0651000d6b9a3ed4fb8301ccc2508befdd32e39be6bbeb3bb29bdc0142816be3 build: number: 0 @@ -36,6 +36,7 @@ requirements: - configargparse - metaomestats - psutil + - hydrampp test: diff --git a/recipes/metacerberus/meta.yaml b/recipes/metacerberus/meta.yaml index 8ecc533811481..10e9b5464d1ae 100644 --- a/recipes/metacerberus/meta.yaml +++ b/recipes/metacerberus/meta.yaml @@ -1,13 +1,13 @@ {% set name = "MetaCerberus" %} -{% set version = "1.3.1" %} +{% set version = "1.4.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 725be35a0e9b2a3867791e1cb8284ec95a09d3479516e9b265e3751659ce7935 + url: "https://github.com/raw-lab/MetaCerberus/archive/refs/tags/v{{version}}.tar.gz" + sha256: 0651000d6b9a3ed4fb8301ccc2508befdd32e39be6bbeb3bb29bdc0142816be3 build: number: 0 @@ -24,7 +24,6 @@ requirements: run: - python >=3.8 - setuptools <70.0.0 - - grpcio =1.43 - pandas - fastqc - flash2 @@ -36,10 +35,6 @@ requirements: - phanotate - trnascan-se - pyhmmer - - ray-default <=2.6.3 - - ray-core <=2.6.3 - - ray-tune <=2.6.3 - - ray-dashboard <=2.6.3 - plotly - scikit-learn - dominate @@ -47,6 +42,7 @@ requirements: - configargparse - metaomestats - psutil + - hydrampp test: diff --git a/recipes/metacoag/meta.yaml b/recipes/metacoag/meta.yaml index 1f40236ed4268..0ca99928a9650 100644 --- a/recipes/metacoag/meta.yaml +++ b/recipes/metacoag/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MetaCoAG" %} -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: "{{ name|lower }}" @@ -7,11 +7,10 @@ package: source: url: "https://github.com/metagentools/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: 5962a92e49842f55db50b7a7bede8dc33b9508a08d395a796b3f4fa78fed70b9 + sha256: 1a8d91cb02fdad9ba15c636eeaf167e34f118bc4d12f57366e107ebf160781c7 build: number: 0 - noarch: python entry_points: - metacoag = metacoag.cli:main - combine_cov = metacoag.metacoag_utils.support.combine_cov:main @@ -56,6 +55,8 @@ about: dev_url: "https://github.com/metagentools/MetaCoAG" extra: + skip-lints: + - should_be_noarch_generic recipe-maintainers: - Vini2 identifiers: diff --git a/recipes/metamdbg/build.sh b/recipes/metamdbg/build.sh index 6ca4ef93a91f9..70ccacb85cb1e 100644 --- a/recipes/metamdbg/build.sh +++ b/recipes/metamdbg/build.sh @@ -1,5 +1,6 @@ #!/bin/bash +set -xe mkdir -p $PREFIX/bin @@ -9,6 +10,6 @@ mkdir build cd build cmake .. -make +make -j ${CPU_COUNT} cp ./bin/metaMDBG $PREFIX/bin diff --git a/recipes/metamdbg/meta.yaml b/recipes/metamdbg/meta.yaml index 3d46090812f17..1465c0636bde5 100644 --- a/recipes/metamdbg/meta.yaml +++ b/recipes/metamdbg/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('metamdbg', max_pin="x.x") }} @@ -21,11 +21,11 @@ requirements: - make host: - zlib - - openmp + - libgomp run: - zlib - - openmp - - minimap2 =2.24 + - libgomp + - minimap2 =2.28 - time =1.8 test: @@ -37,3 +37,6 @@ about: license: MIT summary: 'MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.' +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/metav/meta.yaml b/recipes/metav/meta.yaml index 3423876580db3..5c61f129ddc50 100644 --- a/recipes/metav/meta.yaml +++ b/recipes/metav/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metav" %} -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f1cbf33630a26e9c34276244e08e2d56fa7128aca2553347700065f6536cdd65 + sha256: 54c59f9d72aff1a2129a7e02c1cb10a1f14196d87242c8fd6ea18de30a771612 build: number: 0 diff --git a/recipes/meteor/meta.yaml b/recipes/meteor/meta.yaml index fbc183ab78ca8..d69075ed31f23 100644 --- a/recipes/meteor/meta.yaml +++ b/recipes/meteor/meta.yaml @@ -1,6 +1,6 @@ {% set name = "meteor" %} -{% set version = "2.0.14" %} -{% set sha256 = "0f70351c94b5a2290fb5bfe7bbb671771c607d704565ce73a2a2a0b69beb1e23" %} +{% set version = "2.0.16" %} +{% set sha256 = "ac059e87ac6b66eb15ac9e5826fdbcd1d3b4726736ae02f46508236080d202b0" %} package: name: {{ name }} @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 0 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv entry_points: - meteor = meteor.meteor:main @@ -33,10 +33,9 @@ requirements: - ete3 - packaging - cogent3 + - py-bgzip - biom-format - - bcftools >=1.19 - - raxml-ng >=1.0.1 - - bedtools >=2.18.0 + - freebayes >=1.3.6 test: commands: diff --git a/recipes/methbat/meta.yaml b/recipes/methbat/meta.yaml index 33388fb2c43a5..3a568f5b18909 100644 --- a/recipes/methbat/meta.yaml +++ b/recipes/methbat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "methbat" %} -{% set version = "0.13.1" %} -{% set sha256 = "79e3e48edda49d31601a58252a5e4b5a0d2d35900208df97f16de66712d6ba56" %} +{% set version = "0.13.2" %} +{% set sha256 = "3a3a6374170e8b2acdc5e2c160eaabdafe5d613139d0c798438794ea35bff6c5" %} package: name: {{ name }} diff --git a/recipes/methylartist/meta.yaml b/recipes/methylartist/meta.yaml index 13807dcfdbdd1..f26e3db2fa3b5 100644 --- a/recipes/methylartist/meta.yaml +++ b/recipes/methylartist/meta.yaml @@ -1,5 +1,5 @@ {% set name = "methylartist" %} -{% set version = "1.3.0" %} +{% set version = "1.3.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 955f2ca5b0ba0d2c28e7421140e90555a8ef867ecedb41788c83132b29410329 + sha256: a720ca9367edcb9e2b7cd7980064f6c814235e41e057f7f78567d27f04d95884 build: noarch: python diff --git a/recipes/methylmap/meta.yaml b/recipes/methylmap/meta.yaml index 2deb96f13c1c9..8278a62a0e8c6 100644 --- a/recipes/methylmap/meta.yaml +++ b/recipes/methylmap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "methylmap" %} -{% set version = "0.4.6" %} +{% set version = "0.5.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: ff94b6d5b75c704af8ced7b0c0187c1a4d8bfb7cf3565bde09ea46d2c9e44963 + sha256: 774fca972d16efbc1cce5b1f7a0b2876cb9526f24c6ba2e886a59f4006b11679 build: number: 0 @@ -29,10 +29,12 @@ requirements: - plotly >=5.4.0 - pyranges >=0.0.77 - tabix -# - modbam2bed ## not available in bioconda, only through epi2me-labs - scipy - dash - + - dash-bootstrap-components + - tqdm + - ont-modkit + test: imports: - methylmap diff --git a/recipes/mgatk/meta.yaml b/recipes/mgatk/meta.yaml index 3a641253df822..a7f891da24de7 100644 --- a/recipes/mgatk/meta.yaml +++ b/recipes/mgatk/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f42f5eb8fcfd38dd6ef3db853764071311cb70d841a73ff2f40f0a0c9e9d7de9 build: - number: 1 + number: 2 noarch: python entry_points: - mgatk = mgatk.cli:main @@ -36,7 +36,7 @@ requirements: - pandas - optparse-pretty - regex - - ruamel.yaml + - ruamel.yaml 0.16.12 - openjdk - picard-slim - r-base diff --git a/recipes/mgems/build.sh b/recipes/mgems/build.sh index 6ba573ff2b226..df3e14ac25675 100644 --- a/recipes/mgems/build.sh +++ b/recipes/mgems/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + mkdir -p $PREFIX/bin mkdir build diff --git a/recipes/mgems/meta.yaml b/recipes/mgems/meta.yaml index f49f8b26161b7..be00e71ac1a41 100644 --- a/recipes/mgems/meta.yaml +++ b/recipes/mgems/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mGEMS" %} -{% set version = "1.3.2" %} +{% set version = "1.3.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/PROBIC/{{ name }}/archive/v{{ version }}.tar.gz - sha256: d655553643200754cbb5c76f1b8d161bece8cb45a8b6e86fea4da65d4f437f9e + sha256: c16db45f575d039ca5219b9bc7b7a4dc4bc3ceb3239b2a61085106d3d666b57a build: number: 1 @@ -41,6 +41,9 @@ about: dev_url: https://github.com/PROBIC/mGEMS extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - doi:10.1099/mgen.0.000691 recipe-maintainers: diff --git a/recipes/mgikit/meta.yaml b/recipes/mgikit/meta.yaml index 900126f1a46ed..c519032f8deb4 100644 --- a/recipes/mgikit/meta.yaml +++ b/recipes/mgikit/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "0.1.5" %} +{% set version = "0.1.6" %} package: name: mgikit version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('mgikit', max_pin="x.x") }} source: url: https://github.com/sagc-bioinformatics/mgikit/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3f079452f3d2b2734843ae1fc821e956d45949cb3d7f8c3ce99d259af9eb2ac0 + sha256: 6f94322108cb8ac62a7dbd213d95949b6ac82eddb6ff07221e62820461be3d9d requirements: build: diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml index 35cb14a8d7e3a..7be89ec5a1ba8 100644 --- a/recipes/mgnify-pipelines-toolkit/meta.yaml +++ b/recipes/mgnify-pipelines-toolkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mgnify-pipelines-toolkit" %} -{% set version = "0.1.4" %} +{% set version = "0.1.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz - sha256: ad7862883b901b5aad2e542f0ff3ba86733a99e46d95abe8483b63c525a584bf + sha256: a89ad126b2b3e57552dddd1ddd935ed5a269376cd351328712eb30fb92006fc9 build: entry_points: diff --git a/recipes/mhcflurry/meta.yaml b/recipes/mhcflurry/meta.yaml index cf51e883c801f..768e19e92eb7b 100644 --- a/recipes/mhcflurry/meta.yaml +++ b/recipes/mhcflurry/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mhcflurry" %} -{% set version = "2.1.2" %} +{% set version = "2.1.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 95f7b23abde2838118190307096d84c795f373646d231ddf07969cdb4a5138de + sha256: 5f8a4e743bf6e5a17ad4e6fe79be7755b45a5005d048fbf3d8eb90762236c68e build: number: 0 diff --git a/recipes/micom/meta.yaml b/recipes/micom/meta.yaml index 952d0e627826a..b3ba642623eec 100644 --- a/recipes/micom/meta.yaml +++ b/recipes/micom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "micom" %} -{% set version = "0.36.3" %} +{% set version = "0.37.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7fca46cd7886683d1e19587703b0f8ac80deea051f0d010c824e99e1c21b695d + sha256: 26539e8243f6b2366f266f8d4af78a3312d70d815fb1a8f00a5cc64be86d5b82 build: number: 0 diff --git a/recipes/microhapulator/meta.yaml b/recipes/microhapulator/meta.yaml index 311ce5aa3802a..7b5cff8ef3082 100644 --- a/recipes/microhapulator/meta.yaml +++ b/recipes/microhapulator/meta.yaml @@ -1,6 +1,6 @@ {% set name = "microhapulator" %} -{% set version = "0.8" %} -{% set sha256 = "7415985d6dc7147bec0cf97e1bdf707d72033ccc3fdd0a1c332014da637d35fe" %} +{% set version = "0.8.4" %} +{% set sha256 = "215ddd41c8506a20c076bcf765e49646fd9d759a6f511495cc697e7fc2ad51cb" %} package: name: {{ name }} @@ -25,7 +25,6 @@ requirements: - pip run: - biopython - - bwa >=0.7.17 - fastqc >=0.11.9 - flash >=1.2 - happer >=0.1 @@ -33,6 +32,7 @@ requirements: - jsonschema >=4.0 - matplotlib-base >=3.0 - microhapdb >=0.10.1 + - minimap2 >=2.25 - multiqc >=1.14 - nbformat >=5.0,<5.6 - numpy >=1.19 diff --git a/recipes/mimsi/meta.yaml b/recipes/mimsi/meta.yaml index ff1db577f609a..afbe48b18ac7d 100755 --- a/recipes/mimsi/meta.yaml +++ b/recipes/mimsi/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.4" %} +{% set version = "0.4.5" %} package: @@ -7,10 +7,12 @@ package: source: url: https://github.com/mskcc/mimsi/archive/refs/tags/v{{ version }}.tar.gz - sha256: fcf866629615550f30ce63d065036370141a050ae5643c0bcd3751ae0f5696aa + sha256: 3bbca89b5592911c92f5e18c3d490f85914ccf64101b8dabb35c196668f6e3bd build: number: 0 + run_exports: + - {{ pin_subpackage('mimsi', max_pin='x.x') }} noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir " diff --git a/recipes/minigraph/build.sh b/recipes/minigraph/build.sh index 36a34c892d737..4391a7aaca22f 100644 --- a/recipes/minigraph/build.sh +++ b/recipes/minigraph/build.sh @@ -1,9 +1,11 @@ #!/bin/bash +set -xe + mkdir -p $PREFIX/bin export C_INCLUDE_PATH="${PREFIX}/include" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -make CC="${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" +make -j ${CPU_COUNT} CC="${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" cp minigraph $PREFIX/bin diff --git a/recipes/minigraph/meta.yaml b/recipes/minigraph/meta.yaml index 6a1a93b243c54..456963ae6b205 100644 --- a/recipes/minigraph/meta.yaml +++ b/recipes/minigraph/meta.yaml @@ -8,9 +8,11 @@ package: source: url: https://github.com/lh3/minigraph/archive/refs/tags/v{{ version }}.tar.gz sha256: 4272447393f0ae1e656376abe144de96cbafc777414d4c496f735dd4a6d3c06a + patches: + - minigraph-aarch64.patch # [aarch64 or arm64] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('minigraph', max_pin="x.x") }} @@ -35,5 +37,7 @@ about: dev_url: https://github.com/lh3/minigraph extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1186/s13059-020-02168-z diff --git a/recipes/minigraph/minigraph-aarch64.patch b/recipes/minigraph/minigraph-aarch64.patch new file mode 100644 index 0000000000000..8223b8cc34900 --- /dev/null +++ b/recipes/minigraph/minigraph-aarch64.patch @@ -0,0 +1,11 @@ +diff --git c/Makefile i/Makefile +index 4dd33e6..8c49614 100644 +--- c/Makefile ++++ i/Makefile +@@ -1,5 +1,5 @@ + CC= gcc +-CFLAGS= -g -Wall -Wc++-compat -std=c99 -msse4 -O3 ++CFLAGS= -g -Wall -Wc++-compat -std=c99 -O3 + CPPFLAGS= + INCLUDES= + OBJS= kalloc.o kthread.o algo.o sys.o gfa-base.o gfa-io.o gfa-aug.o gfa-bbl.o gfa-ed.o \ diff --git a/recipes/minimap2/build.sh b/recipes/minimap2/build.sh index b6f518c35e81b..8cb728cd50339 100644 --- a/recipes/minimap2/build.sh +++ b/recipes/minimap2/build.sh @@ -2,23 +2,26 @@ set -xe -mkdir -p ${PREFIX}/bin ${PREFIX}/lib ${PREFIX}/include +mkdir -p ${PREFIX}/bin ${PREFIX}/lib ${PREFIX}/include $PREFIX/share/man/man1 case $(uname -m) in aarch64) ARCH_OPTS="aarch64=1" ;; + arm64) + ARCH_OPTS="aarch64=1" + ;; *) ARCH_OPTS="" ;; esac -make CFLAGS="-g -Wall -O2 -Wc++-compat -I${PREFIX}/include -L${PREFIX}/lib" \ - ${ARCH_OPTS} -j${CPU_COUNT} minimap2 sdust +make CFLAGS="${CFLAGS} -g -Wall -O3 -Wc++-compat -I${PREFIX}/include -L${PREFIX}/lib" \ + "${ARCH_OPTS}" -j"${CPU_COUNT}" minimap2 sdust chmod 755 minimap2 && chmod 755 sdust -cp minimap2 misc/paftools.js ${PREFIX}/bin -cp sdust ${PREFIX}/bin -cp libminimap2.a ${PREFIX}/lib -cp *.h ${PREFIX}/include +cp -rf minimap2 misc/paftools.js ${PREFIX}/bin +cp -rf sdust ${PREFIX}/bin +cp -rf libminimap2.a ${PREFIX}/lib +cp -rf *.h ${PREFIX}/include diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index 7c2bc89fb1520..bcfd16f66dfac 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -12,7 +12,7 @@ source: - override-makefile.patch build: - number: 1 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -24,7 +24,6 @@ requirements: - zlib run: - k8 - - zlib test: commands: @@ -46,7 +45,8 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - biotools:{{ name| lower }} - usegalaxy-eu:{{ name| lower }} - - doi:10.1093/bioinformatics/bty191 \ No newline at end of file + - doi:10.1093/bioinformatics/bty191 diff --git a/recipes/minimizers/meta.yaml b/recipes/minimizers/meta.yaml new file mode 100644 index 0000000000000..eaba48148df54 --- /dev/null +++ b/recipes/minimizers/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "minimizers" %} +{% set version = "0.1.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 41757d81ec6a2872f947ec568eb521bdd40170832bee21b748d48b1778f817bf + +build: + number: 0 + noarch: python + entry_points: + - minimizers=minimizers.minimizers:main + run_exports: + - {{ pin_subpackage('minimizers', max_pin="x.x") }} + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + +requirements: + host: + - pip + - python >=3.6 + - bio + run: + - biopython >=1.83 + - python >=3.6 + - bio + +test: + imports: + - minimizers + commands: + - minimizers --version + +about: + home: https://github.com/cumbof/minimizers + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Minimizers extraction from fasta files." + description: | + A Python package for extracting minimizers from fasta files + dev_url: https://github.com/cumbof/minimizers + +extra: + recipe-maintainers: + - cumbof diff --git a/recipes/miniprot-boundary-scorer/build.sh b/recipes/miniprot-boundary-scorer/build.sh new file mode 100644 index 0000000000000..91d45589b3f93 --- /dev/null +++ b/recipes/miniprot-boundary-scorer/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +set -xe + +make -j ${CPU_COUNT} CC="${CXX}" LDFLAGS="-L${PREFIX}/lib" + +mkdir -p ${PREFIX}/bin +cp miniprot_boundary_scorer ${PREFIX}/bin \ No newline at end of file diff --git a/recipes/miniprot-boundary-scorer/meta.yaml b/recipes/miniprot-boundary-scorer/meta.yaml new file mode 100644 index 0000000000000..cb7ef5acd15e7 --- /dev/null +++ b/recipes/miniprot-boundary-scorer/meta.yaml @@ -0,0 +1,36 @@ +{% set name = "miniprot-boundary-scorer" %} +{% set version = "1.0.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/tomasbruna/miniprot-boundary-scorer/releases/download/v{{ version }}/{{ name }}.tgz + sha256: 9a5f3babd6db07b673589f2bb8de9436fd9a9c844483ce893d27de0d79ed79e8 + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + + +requirements: + build: + - make + - {{ compiler('cxx') }} + +test: + commands: + - miniprot_boundary_scorer 2>&1 | grep "^Usage:" > /dev/null + +about: + home: https://github.com/tomasbruna/miniprot-boundary-scorer + license: Artistic-1.0 + summary: Miniprot boundary scorer parses introns, starts, stops and exons from miniprot's alignment output and scores them + dev_url: https://github.com/tomasbruna/miniprot-boundary-scorer + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/minute/meta.yaml b/recipes/minute/meta.yaml index 7de1dc0076d35..8ce2b630e521a 100644 --- a/recipes/minute/meta.yaml +++ b/recipes/minute/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.6.0" %} +{% set version = "0.9.0" %} package: name: minute version: {{ version }} source: - url: https://github.com/NBISweden/minute/archive/refs/tags/v{{ version }}.tar.gz - sha256: 168077b9bc369d8e4bbda51133d00a344dc33716e2a070311cfacaf792b131d7 + url: https://github.com/elsasserlab/minute/archive/refs/tags/v{{ version }}.tar.gz + sha256: bac0252f635ff015d80abd35375407ccf48b12babd947f900889d6475f2cac13 build: number: 0 @@ -18,22 +18,22 @@ build: requirements: host: - pip - - python >=3.7 + - python >=3.8 run: - - python >=3.7 - - importlib-metadata # [py==37] + - python >=3.8 - ruamel.yaml - snakemake-minimal >=7.22.0 - samtools >=1.13 - cutadapt >=3.7 - - bowtie2 >=2.4.4 + - bowtie2 >=2.5.3 + - strobealign >=0.13.0 - je-suite >=2.0.RC - igvtools >=2.5.3 - deeptools >=3.5.0 - picard >=2.26.0 - fastqc >=0.11.9 - bedtools >=2.30.0 - - multiqc =1.13 + - multiqc =1.17 - xopen >=1.2.0 - sra-tools >=2.11.0 - r-base >=4.0.0 @@ -48,7 +48,7 @@ test: - minute --version about: - home: https://github.com/NBISweden/minute/ + home: https://github.com/elsasserlab/minute/ license: MIT summary: MINUTE-ChIP data analysis workflow diff --git a/recipes/mirtop/meta.yaml b/recipes/mirtop/meta.yaml index 560bde94eae09..327cbfd86b4c0 100644 --- a/recipes/mirtop/meta.yaml +++ b/recipes/mirtop/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.4.25" %} +{% set version = "0.4.28" %} package: name: mirtop @@ -6,24 +6,21 @@ package: source: url: https://github.com/miRTop/mirtop/archive/v{{ version }}.tar.gz - sha256: 309377c432bf3d45c24659d4a9d2cd6ad61b928122bbc1e392e921b29bef3282 + sha256: 1937ee0e90dd8f00071ebd8f4449709367396bdeb8236dc831122141717438d6 build: - script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 noarch: python entry_points: - mirtop=mirtop.command_line:main + run_exports: + - {{ pin_subpackage('mirtop', max_pin="x.x") }} requirements: host: - python - - setuptools - - pysam - - pybedtools - - pandas - - biopython - + - pip run: - python - pysam @@ -43,10 +40,13 @@ test: - mirtop --help about: - home: http://github.com/mirtop/mirtop - license: MIT License + home: "https://github.com/mirtop/mirtop" + license: MIT license_family: MIT - summary: 'Small RNA-seq annotation' + license_file: LICENSE + summary: 'Small RNA-seq annotation.' + dev_url: "https://github.com/mirtop/mirtop" + doc_url: "https://mirtop.readthedocs.io/en/latest" extra: identifiers: diff --git a/recipes/mkdesigner/meta.yaml b/recipes/mkdesigner/meta.yaml index e00b2fa6ba705..7c89662a1d4a4 100644 --- a/recipes/mkdesigner/meta.yaml +++ b/recipes/mkdesigner/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mkdesigner" %} -{% set version = "0.4.3" %} +{% set version = "0.4.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mkdesigner-{{ version }}.tar.gz - sha256: b56c5fd1f60e300e2bfefb4997e3af7bfd5a37ed6643138114ba810a83250e1a + sha256: 29513140681b1f667764081bf981c1a548be3cf877bab4ffe551df96b1efbd9d build: entry_points: diff --git a/recipes/moni/build.sh b/recipes/moni/build.sh new file mode 100644 index 0000000000000..455d5bf7c0861 --- /dev/null +++ b/recipes/moni/build.sh @@ -0,0 +1,18 @@ +#!/bin/bash + +set -xe + +export CPATH=$PREFIX/include:$CPATH +export LIBRARY_PATH=$PREFIX/lib:$LIBRARY_PATH +export LD_LIBRARY_PATH=$PREFIX/lib:$LD_LIBRARY_PATH + +mkdir build +cd build +cmake -DCMAKE_INSTALL_PREFIX=$PREFIX \ + -DCMAKE_PREFIX_PATH=$PREFIX \ + -DCMAKE_INCLUDE_PATH=$PREFIX/include \ + -DCMAKE_LIBRARY_PATH=$PREFIX/lib \ + -DZLIB_ROOT=$PREFIX \ + .. +make -j ${CPU_COUNT} VERBOSE=1 +make install diff --git a/recipes/r-stitch/conda_build_config.yaml b/recipes/moni/conda_build_config.yaml similarity index 50% rename from recipes/r-stitch/conda_build_config.yaml rename to recipes/moni/conda_build_config.yaml index 4f2dcf10e9f82..f62708b887406 100644 --- a/recipes/r-stitch/conda_build_config.yaml +++ b/recipes/moni/conda_build_config.yaml @@ -1,4 +1,5 @@ c_compiler_version: - - 12 + - 9.3.0 # [linux] + cxx_compiler_version: - - 12 \ No newline at end of file + - 9.3.0 # [linux] diff --git a/recipes/moni/meta.yaml b/recipes/moni/meta.yaml new file mode 100644 index 0000000000000..b5da94ad049f8 --- /dev/null +++ b/recipes/moni/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "moni" %} +{% set version = "0.2.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/maxrossi91/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 638cd590e0c91218a9c7c0bf5aac6289d445a5a1b3ad91aa0cf62d7ff57ce0ce + +build: + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + build: + - {{ compiler('cxx') }} + - cmake + - make + - git + host: + - zlib + - python + run: + - zlib + - python + +test: + commands: + - moni -h + - moni build -h + - moni ms -h + - moni mems -h + - moni extend -h + +about: + home: https://github.com/maxrossi91/moni + license: MIT + license_family: MIT + license_file: LICENSE + summary: 'A Pangenomics Index for Finding MEMs' + description: | + MONI (Multi) is a Pangenomics Index for Finding Maximal Exact Matches (MEMs). + It uses the prefix-free parsing of the text to build the Burrows-Wheeler Transform (BWT) + of the reference genomes, the suffix array (SA) samples at the beginning and at the end + of each run of the BWT, and the threshold positions. + +extra: + recipe-maintainers: + - AndreaGuarracino + - maxrossi91 \ No newline at end of file diff --git a/recipes/monsda/meta.yaml b/recipes/monsda/meta.yaml index c6342c5d30b90..a0454d15ae606 100644 --- a/recipes/monsda/meta.yaml +++ b/recipes/monsda/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MONSDA" %} -{% set version = "1.2.7" %} -{% set sha256 = "6a3b15a4c5eb3ab74d7bad0313cfbc59bb7af22b02994de38c6440a0e0071cba" %} +{% set version = "1.2.8" %} +{% set sha256 = "dcfb363649328568fef304d25bb0278155f94e954b207d8f841a452fdaf67024" %} package: name: "{{ name|lower }}" diff --git a/recipes/moods/build.sh b/recipes/moods/build.sh index 689926c02722e..c2f64e2904e62 100644 --- a/recipes/moods/build.sh +++ b/recipes/moods/build.sh @@ -7,11 +7,11 @@ cat > setup.py.patch << EOF common_includes = ["core/"] -common_compile_args = ['-O3', '-fPIC', '--std=c++11'] -+common_compile_args = ['-mtune=generic', '-O3', '-fPIC', '--std=c++11'] ++common_compile_args = ['-mtune=generic', '-O3', '-fPIC', '--std=c++14'] tools_mod = Extension('MOODS._tools', sources=['core/tools_wrap.cxx', EOF patch setup.py setup.py.patch rm setup.py.patch -${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir diff --git a/recipes/moods/meta.yaml b/recipes/moods/meta.yaml index 27913e29ea5a3..36ffbea571da0 100644 --- a/recipes/moods/meta.yaml +++ b/recipes/moods/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e694e37c7487286801bffcda3e0576157960007919dd5ceb8b5a1626dc2968e1 build: - number: 1 + number: 2 skip: True # [py < 36] run_exports: - {{ pin_subpackage('moods', max_pin="x") }} @@ -29,14 +29,18 @@ test: - MOODS.scan about: - home: https://www.cs.helsinki.fi/group/pssmfind/ + home: "https://www.cs.helsinki.fi/group/pssmfind" summary: 'MOODS: Motif Occurrence Detection Suite' - license: GPL-3.0-or-later + license: "GPL-3.0-or-later" license_family: GPL3 license_file: COPYING.GPLv3 - dev_url: https://github.com/jhkorhonen/MOODS + dev_url: "https://github.com/jhkorhonen/MOODS" + doc_url: "https://github.com/jhkorhonen/MOODS/wiki" extra: identifiers: - biotools:MOODS - doi:10.1109/TCBB.2009.35 + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/mquad/meta.yaml b/recipes/mquad/meta.yaml new file mode 100644 index 0000000000000..1e58632d7b083 --- /dev/null +++ b/recipes/mquad/meta.yaml @@ -0,0 +1,58 @@ +{% set name = "mquad" %} +{% set version = "0.1.8b" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + git_url: https://github.com/single-cell-genetics/MQuad.git + git_rev: c2d750c + sha256: unused + +build: + number: 0 + noarch: python + entry_points: + - mquad = mquad.mquad_CLI:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('mquad', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - numpy >=1.9.0 + - scipy >=1.4.0 + - matplotlib-base + - bbmix >=0.2.2 + - vireosnp + - kneed + - pandas + - seaborn-base + - scikit-learn + +test: + imports: + - mquad + commands: + - mquad --help + +about: + home: "https://github.com/aaronkwc/MQuad" + summary: "MQuad: Mixture Model for Mitochondrial Mutation detection in single-cell omics data." + license: "Apache-2.0" + license_family: APACHE + license_file: LICENSE + dev_url: "https://github.com/aaronkwc/MQuad" + doc_url: "https://github.com/single-cell-genetics/MQuad/blob/main/README.rst" + +extra: + identifiers: + - doi:10.1038/s41467-022-28845-0 + - biotools:mquad + skip-lints: + - uses_vcs_url diff --git a/recipes/ms2pip/meta.yaml b/recipes/ms2pip/meta.yaml index 095eb5313e4db..df283caa45a97 100644 --- a/recipes/ms2pip/meta.yaml +++ b/recipes/ms2pip/meta.yaml @@ -1,17 +1,18 @@ -{% set version = "4.0.0.dev8" %} +{% set version = "4.0.0" %} {% set name = "ms2pip" %} -{% set sha256 = "2a464e00135c875c12c98f6853a4487e193a0730b5bd94f82a44e8d5fb21a7bb" %} +{% set sha256 = "b2329700e8c2af5c64d8fa0ef62dbc6ee52c60d7b18e5d860a4d9194c225ec29" %} package: - name: "ms2pip" + name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://pypi.io/packages/source/m/ms2pip/ms2pip-{{ version }}.tar.gz + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: {{ sha256 }} build: - number: 1 + number: 0 + skip: true # [py >= 312] run_exports: - {{ pin_subpackage(name, max_pin="x") }} entry_points: @@ -34,21 +35,22 @@ requirements: run: - python >=3.8 - {{ pin_compatible('numpy') }} - - pandas >=1.0 - - pyteomics >=3.5 + - pandas >=1.0,<2 + - pyteomics >=3.5,<5 - tqdm >=4 - pytables >=3.4 - - tomlkit >=0.5 - - click >=7 - - xgboost >=1.3 + - tomlkit >=0.5,<1 + - click >=7,<9 + - xgboost >=1.3,<2 - matplotlib-base >=3.0 - lxml >=4 - rich >=13 - - pydantic >=1.10,<2 - - psm-utils + - pydantic >=2 + - psm-utils >=0.9 - werkzeug >=2 - pyarrow - pyopenms + - ms2rescore-rs test: imports: diff --git a/recipes/ms2query/meta.yaml b/recipes/ms2query/meta.yaml index 7e0654830d053..36e618ab5adb8 100644 --- a/recipes/ms2query/meta.yaml +++ b/recipes/ms2query/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ms2query" %} -{% set version = "1.5.0" %} -{% set sha256 = "7f72a7b2f4a6bf4b8d73e99e6708184decf34d36afe359fc38b3678561a44772" %} +{% set version = "1.5.3" %} +{% set sha256 = "d1e79994e2bdee9317d2dc87a8f9360a86ff406a103558024e1f93e0261cd535" %} package: name: {{ name|lower }} diff --git a/recipes/msisensor-pro/build.sh b/recipes/msisensor-pro/build.sh index 8c7cabd77d629..1651e36191fd5 100644 --- a/recipes/msisensor-pro/build.sh +++ b/recipes/msisensor-pro/build.sh @@ -1,2 +1,7 @@ -make -C cpp CC=$CC CXX=$CXX -cp cpp/msisensor-pro $PREFIX/bin +#!/bin/bash + +mkdir -p ${PREFIX}/bin + +make -C cpp CC="${CC}" CXX="${CXX}" -j"${CPU_COUNT}" +chmod 0755 cpp/msisensor-pro +mv cpp/msisensor-pro ${PREFIX}/bin diff --git a/recipes/msisensor-pro/build_failure.linux-64.yaml b/recipes/msisensor-pro/build_failure.linux-64.yaml deleted file mode 100644 index 966f52c6572e2..0000000000000 --- a/recipes/msisensor-pro/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 78ea6e46bf2985f75436cac4d34088dd710099309f3507510a45d90f36f68972 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - patching file cpp/makefile - Patch analysis gives: - [[ RA-MD1LOVE ]] - [[ buildfixes.patch ]] - - Key: - - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/conda/conda-bld/msisensor-pro_1717781420099/work - export PREFIX=/opt/conda/conda-bld/msisensor-pro_1717781420099/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold - export BUILD_PREFIX=/opt/conda/conda-bld/msisensor-pro_1717781420099/_build_env - export SRC_DIR=/opt/conda/conda-bld/msisensor-pro_1717781420099/work - INFO: activate-binutils_linux-64.sh made the following environmental changes: - ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line - AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar - AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as - CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt - ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit - GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof - LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld - LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold - NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm - OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy - OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump - RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib - READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf - SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size - STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings - STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip - INFO: activate-gcc_linux-64.sh made the following environmental changes: - BUILD=x86_64-conda-linux-gnu - CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr - CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot - CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu - CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu - CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp - CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include - DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include - GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc - GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar - GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm - GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib - HOST=x86_64-conda-linux-gnu - LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu - build_alias=x86_64-conda-linux-gnu - host_alias=x86_64-conda-linux-gnu - -BUILD=x86_64-conda_cos6-linux-gnu - -CONDA_BUILD_SYSROOT= - INFO: activate-gxx_linux-64.sh made the following environmental changes: - CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g - make: Entering directory '$SRC_DIR/cpp' - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c cmds.cpp -o cmds.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c scan.cpp -o scan.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c distribution.cpp -o distribution.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c refseq.cpp -o refseq.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c polyscan.cpp -o polyscan.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c param.cpp -o param.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c utilities.cpp -o utilities.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c homo.cpp -o homo.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c window.cpp -o window.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c bamreader.cpp -o bamreader.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c sample.cpp -o sample.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c chi.cpp -o chi.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -c somatic.cpp -o somatic.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 cmds.o scan.o distribution.o refseq.o polyscan.o param.o utilities.o homo.o window.o bamreader.o sample.o chi.o somatic.o -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/msisensor-pro-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -fopenmp -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -lm -lz -lpthread -lhts -o msisensor-pro - /opt/conda/conda-bld/msisensor-pro_1717781420099/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory - collect2: error: ld returned 1 exit status - make: *** [makefile:27: msisensor-pro] Error 1 - make: Leaving directory '$SRC_DIR/cpp' - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/msisensor-pro_1717781420099/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/msisensor-pro/buildfixes.patch b/recipes/msisensor-pro/buildfixes.patch index 2bffe10bdc6e3..f72ef3a7c4e7f 100644 --- a/recipes/msisensor-pro/buildfixes.patch +++ b/recipes/msisensor-pro/buildfixes.patch @@ -4,24 +4,31 @@ index 321a56b..dc541fc 100755 +++ b/cpp/bamreader.cpp @@ -27,6 +27,7 @@ unsigned int g_CloseMappedPlus = 0; unsigned int g_CloseMappedMinus = 0; - + //init hash/maps for read pairing on the fly +#define register KSORT_INIT_GENERIC(uint32_t) KHASH_MAP_INIT_STR(read_name, bam1_t *) struct fetch_func_data_SR { diff --git a/cpp/makefile b/cpp/makefile -index 78da629..98daf27 100755 +index 88639e1..c1f6bb6 100644 --- a/cpp/makefile +++ b/cpp/makefile -@@ -6,8 +6,8 @@ HTSLIB=$(realpath ../vendor/htslib-1.11) +@@ -1,13 +1,13 @@ +-CXX=g++ ++CXX=${CXX} + + HTSLIB=$(realpath ../vendor/htslib-1.11) + # HTSLIB_CPPFLAGS=-I$(realpath $(HTSLIB_ROOT)) + # echo $(HTSLIB_CPPFLAGS) # HTSLIB_LDFLAGS=-L/mnt/project/Project_Pindel/pindel_update/pindel/htslib/ -Wl,-rpath CPP_ROOT=cpp - CXXFLAGS+= -O2 -fopenmp +-CXXFLAGS+= -O2 -fopenmp -LDFLAGS+= -L${HTSLIB} -INCLUDES+= -I${HTSLIB} -+LDFLAGS+= -+INCLUDES+= ++CXXFLAGS+= -O3 -fopenmp -I${PREFIX}/include ++LDFLAGS+= -L${PREFIX}/lib ++INCLUDES+= -I${PREFIX}/include LIBS+= -lm -lz -lpthread -lhts LD_LIBRARY_PATH+= -L${HTSLIB} export LD_LIBRARY_PATH=${HTSLIB_ROOT} @@ -30,7 +37,7 @@ index 78da629..98daf27 100755 %.o:%.cpp - $(CXX) -L ${HTSLIB} -std=c++11 $(CXXFLAGS) $(INCLUDES) -c $< -o $@ -+ $(CXX) -std=c++11 $(CXXFLAGS) $(INCLUDES) -c $< -o $@ ++ $(CXX) -std=c++14 $(CXXFLAGS) $(INCLUDES) -c $< -o $@ -all: htsfile msisensor-pro +all: msisensor-pro @@ -40,7 +47,7 @@ index 78da629..98daf27 100755 msisensor-pro: $(OBJS) - $(CXX) -std=c++11 $^ $(CXXFLAGS) $(LDFLAGS) $(LIBS) -Wl,-rpath=${HTSLIB} -o $@ -+ $(CXX) -std=c++11 $^ $(CXXFLAGS) $(LDFLAGS) $(LIBS) -o $@ - # $(CXX) -std=c++11 $^ $(CXXFLAGS) $(INCLUDES) $(LDFLAGS) $(LIBS) -o $@ ++ $(CXX) -std=c++14 $^ $(CXXFLAGS) $(LDFLAGS) $(LIBS) -o $@ + # $(CXX) -std=c++11 $^ $(CXXFLAGS) $(INCLUDES) $(LDFLAGS) $(LIBS) -o $@ clean: diff --git a/recipes/msisensor-pro/meta.yaml b/recipes/msisensor-pro/meta.yaml index 66291f742cde5..fd05528df5614 100644 --- a/recipes/msisensor-pro/meta.yaml +++ b/recipes/msisensor-pro/meta.yaml @@ -1,34 +1,42 @@ -{% set version = "1.2.0" %} +{% set name = "msisensor-pro" %} +{% set version = "1.3.0" %} package: - name: msisensor-pro + name: {{ name }} version: "{{ version }}" -build: - number: 7 - source: - url: https://github.com/xjtu-omics/msisensor-pro/archive/v{{ version }}.tar.gz - sha256: 0b6de043bf7ee7322814a8c805f8abdc19ac746cba9f0dbe0d687b556c473f25 + url: https://github.com/xjtu-omics/{{ name }}/archive/v{{ version }}.tar.gz + sha256: 30d03841abfe12daee57984bb97687222534b18aeaa17ff7f4d1116dc31cc9c1 patches: - buildfixes.patch +build: + number: 0 + run_exports: + - {{ pin_subpackage('msisensor-pro', max_pin="x") }} + requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] - - libgomp # [linux] host: - htslib + - llvm-openmp # [osx] + - libgomp # [linux] + - libcurl + - bzip2 + - zlib run: - htslib + about: - home: https://github.com/xjtu-omics/msisensor-pro + home: "https://github.com/xjtu-omics/msisensor-pro" license: "Custom Licence" license_file: LICENSE - summary: Microsatellite Instability (MSI) detection using high-throughput sequencing data. + summary: "Microsatellite Instability (MSI) detection using high-throughput sequencing data." + dev_url: "https://github.com/xjtu-omics/msisensor-pro" + doc_url: "https://github.com/xjtu-omics/msisensor-pro/wiki" test: commands: @@ -36,3 +44,11 @@ test: - "msisensor-pro baseline -h 2>&1 | grep Usage" - "msisensor-pro pro -h 2>&1 | grep Usage" - "msisensor-pro msi -h 2>&1 | grep Usage" + +extra: + identifiers: + - biotools:msisensor-pro + - doi:10.1016/j.gpb.2020.02.001 + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/msisensor-rna/meta.yaml b/recipes/msisensor-rna/meta.yaml new file mode 100644 index 0000000000000..015cb396c6e46 --- /dev/null +++ b/recipes/msisensor-rna/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "msisensor-rna" %} +{% set version = "0.1.6" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/xjtu-omics/msisensor-rna/archive/{{ version }}.tar.gz + sha256: 69a420f5850aa412244d252451cc98071a4a410e51ff40e5cf676e7560f89d0c + +build: + number: 0 + noarch: python + entry_points: + - msisensor-rna = msisensor_rna.msisensor_rna:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('msisensor-rna', max_pin="x.x") }} + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - pandas >=1.0 + - numpy >=1.16 + - scikit-learn >=0.24 + - imbalanced-learn >=0.8.0 + +test: + imports: + - msisensor_rna + commands: + - msisensor-rna --help + +about: + home: https://github.com/xjtu-omics/msisensor-rna + summary: "MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data." + license: Community-Spec-1.0 + license_file: LICENSE + dev_url: https://github.com/xjtu-omics/msisensor-rna + +extra: + identifiers: + - doi:10.1093/gpbjnl/qzae004 diff --git a/recipes/msweep/meta.yaml b/recipes/msweep/meta.yaml index 270f718e0e07e..c3f6dfbac8a1b 100644 --- a/recipes/msweep/meta.yaml +++ b/recipes/msweep/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mSWEEP" %} -{% set version = "2.1.0" %} -{% set sha256 = "8654eefab5f1fa9fb483ac5bef5b46f22c7bc3e9f2023e77c7f15ebd2c176930" %} +{% set version = "2.2.0" %} +{% set sha256 = "9f2cbaaa877466a59171a4e74fe26d462657b62ae0e3b464672e44490a6f3d73" %} {% set user = "PROBIC" %} package: @@ -24,9 +24,9 @@ requirements: - git >=2.10.0 - cmake >=3.0.0 - make + host: - llvm-openmp # [osx] - libgomp # [linux] - host: - zlib >=1.2.0 - xz >=5.2.0 - bzip2 >=1.0.6 @@ -42,5 +42,7 @@ about: summary: 'mSWEEP - bacterial community composition estimation from pseudoalignments' extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.12688/wellcomeopenres.15639.2 diff --git a/recipes/mtgrasp/meta.yaml b/recipes/mtgrasp/meta.yaml index 08bdd491afede..5f957b450f1ba 100644 --- a/recipes/mtgrasp/meta.yaml +++ b/recipes/mtgrasp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.4" %} +{% set version = "1.1.6" %} {% set name = "mtGrasp" %} package: @@ -7,10 +7,10 @@ package: source: url: https://github.com/bcgsc/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 0145d9153153f58ff3e7a28f20bf238f7b8ead71700fb1add1aced6e0dbb0214 + sha256: 07c558d607df8d250e181439f08a4d13e2930afc566a060ea5b11b59e18c721a build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage('mtgrasp', max_pin="x") }} diff --git a/recipes/mtnucratio/LICENSE b/recipes/mtnucratio/LICENSE new file mode 100644 index 0000000000000..9cecc1d4669ee --- /dev/null +++ b/recipes/mtnucratio/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/mtnucratio/meta.yaml b/recipes/mtnucratio/meta.yaml index 22ffc4a354171..316b6a40e19a0 100644 --- a/recipes/mtnucratio/meta.yaml +++ b/recipes/mtnucratio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7" %} +{% set version = "0.7.1" %} package: name: mtnucratio @@ -6,11 +6,13 @@ package: source: url: https://github.com/apeltzer/MTNucRatioCalculator/releases/download/{{ version }}/MTNucRatioCalculator-{{ version }}.jar - sha256: 6e1e648f0de63448ad3b3015417fce4046da15a07338e4f10433e373acdc9bd7 + sha256: 4ba78973ba16a53f2e5197fdd9836c672cf73a6a77238dfa17566d55ff75d80d build: noarch: generic - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('mtnucratio', max_pin="x") }} requirements: run: @@ -24,4 +26,5 @@ test: about: home: https://github.com/apeltzer/MTNucRatioCalculator license: GPLv3 + license_file: LICENSE summary: "A small tool to determine MT to Nuclear ratios for NGS data." diff --git a/recipes/mtnucratio/mtnucratio.py b/recipes/mtnucratio/mtnucratio.py index 3bd1029be10bc..bed939c5f2653 100755 --- a/recipes/mtnucratio/mtnucratio.py +++ b/recipes/mtnucratio/mtnucratio.py @@ -11,7 +11,7 @@ import sys import subprocess from os import access, getenv, X_OK -jar_file = 'MTNucRatioCalculator-0.7.jar' +jar_file = 'MTNucRatioCalculator-0.7.1.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 05c07f9b53a31..1dea0f11dda30 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "multiqc" %} -{% set version = "1.23" %} +{% set version = "1.25.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/MultiQC/MultiQC/archive/v{{ version }}.tar.gz - sha256: 1f874e3bdaf3f183ff474126e76791e420732764c2988d8074b826d92aa7282a + sha256: 829a08f44e0183224ef1d8c0ecb163c6acc54f1a1d85445ed62857f5603ee7cb build: number: 0 diff --git a/recipes/mummer/build.sh b/recipes/mummer/build.sh index 4b86465dad6b2..b6253f4c51f63 100644 --- a/recipes/mummer/build.sh +++ b/recipes/mummer/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + BINARY=mummer BINARY_HOME=$PREFIX/bin MUMMER_HOME=$PREFIX/opt/mummer-$PKG_VERSION @@ -47,7 +49,14 @@ for i in exact-tandems dnadiff mapview mummerplot nucmer promer run-mummer1 run- perl -i -pe 's/(envs\/\_\_.*)(\K\@)/\\@/' $i done +# fix hashbang lines to use conda's perl +for i in dnadiff mapview mummerplot nucmer promer; do + sed -i.bak '1 s|^#!/.*/perl -w$|#!/usr/bin/env perl|g' $MUMMER_HOME/$i + rm -rf $MUMMER_HOME/$i.bak +done + for i in $binaries; do + # ensure executable and setup symlink for binary chmod +x $MUMMER_HOME/$i ln -s "$MUMMER_HOME/$i" "$BINARY_HOME/$i" done diff --git a/recipes/mummer/meta.yaml b/recipes/mummer/meta.yaml index 9c8ecd737d370..231fd29aec1a8 100644 --- a/recipes/mummer/meta.yaml +++ b/recipes/mummer/meta.yaml @@ -11,10 +11,14 @@ source: sha256: {{ sha256 }} patches: - patches/gnuplot_mouse_clipboardformat.patch + - patches/linkloc_explicit.patch + - patches/addleafcount_explicit.patch + - patches/findmumcand_explicit.patch + - patches/findmaxmat_explicit.patch + - patches/procmaxmat_explicit.patch build: - number: 18 - skip: True # [osx] + number: 20 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} @@ -24,24 +28,24 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - perl # [not osx] + - perl run: - - perl # [not osx] + - perl test: commands: - "mummer -h &> /dev/null" - #- "delta-filter -h &> /dev/null" - #- "dnadiff -h &> /dev/null" - #- "mapview -h &> /dev/null" + - "delta-filter -h &> /dev/null" + - "dnadiff -h &> /dev/null" + - "mapview -h &> /dev/null" - "mummerplot -h &> /dev/null" - "nucmer -h &> /dev/null" - "promer -h &> /dev/null" - "show-aligns -h &> /dev/null" - #- "show-coords -h &> /dev/null" - #- "show-diff -h &> /dev/null" - #- "show-snps -h &> /dev/null" - #- "show-tiling -h &> /dev/null" + - "show-coords -h &> /dev/null" + - "show-diff -h &> /dev/null" + - "show-snps -h &> /dev/null" + - "show-tiling -h &> /dev/null" about: home: 'http://mummer.sourceforge.net/' @@ -52,5 +56,7 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - biotools:mummer + diff --git a/recipes/mummer/patches/addleafcount_explicit.patch b/recipes/mummer/patches/addleafcount_explicit.patch new file mode 100644 index 0000000000000..c697f885c4361 --- /dev/null +++ b/recipes/mummer/patches/addleafcount_explicit.patch @@ -0,0 +1,19 @@ +--- MUMmer3.23/src/kurtz/streesrc/addleafcount.c.old 2024-08-07 13:34:49 ++++ MUMmer3.23/src/kurtz/streesrc/addleafcount.c 2024-08-07 13:48:50 +@@ -13,6 +13,16 @@ + #include "spacedef.h" + #include "arraydef.h" + ++void getbranchinfostree(Suffixtree *stree,Uint whichinfo, ++ Branchinfo *branchinfo,Bref btptr); ++ ++Sint depthfirststree(Suffixtree *stree,Reference *startnode, ++ Sint (*processleaf)(Uint,Bref,void *), ++ BOOL (*processbranch1)(Bref,void *), ++ Sint (*processbranch2)(Bref,void *), ++ BOOL (*stoptraversal)(void *), ++ void *stopinfo,void *info); ++ + typedef struct + { + Suffixtree *stree; // suffix tree info diff --git a/recipes/mummer/patches/findmaxmat_explicit.patch b/recipes/mummer/patches/findmaxmat_explicit.patch new file mode 100644 index 0000000000000..78ceb0e257981 --- /dev/null +++ b/recipes/mummer/patches/findmaxmat_explicit.patch @@ -0,0 +1,34 @@ +--- MUMmer3.23/src/kurtz/mm3src/findmaxmat.c.old 2024-08-07 13:55:45 ++++ MUMmer3.23/src/kurtz/mm3src/findmaxmat.c 2024-08-07 14:03:39 +@@ -14,7 +14,31 @@ + #include "debugdef.h" + #include "spacedef.h" + #include "maxmatdef.h" ++ ++void linklocstree(Suffixtree *stree,Location *outloc,Location *inloc); ++ ++SYMBOL *scanprefixstree(Suffixtree *stree,Location *outloc, ++ Location *inloc,SYMBOL *left, ++ SYMBOL *right,Uint rescanlength); ++ ++SYMBOL *findprefixpathstree(Suffixtree *stree, ++ ArrayPathinfo *path, ++ Location *outloc, ++ Location *inloc, ++ SYMBOL *left,SYMBOL *right, ++ Uint rescanlength); + ++Sint depthfirststree(Suffixtree *stree,Reference *startnode, ++ Sint (*processleaf)(Uint,Bref,void *), ++ BOOL (*processbranch1)(Bref,void *), ++ Sint (*processbranch2)(Bref,void *), ++ BOOL (*stoptraversal)(void *), ++ void *stopinfo,void *info); ++ ++SYMBOL *scanprefixfromnodestree(Suffixtree *stree,Location *loc, ++ Bref btptr,SYMBOL *left, ++ SYMBOL *right,Uint rescanlength); ++ + //} + + /*EE diff --git a/recipes/mummer/patches/findmumcand_explicit.patch b/recipes/mummer/patches/findmumcand_explicit.patch new file mode 100644 index 0000000000000..141b3164973c4 --- /dev/null +++ b/recipes/mummer/patches/findmumcand_explicit.patch @@ -0,0 +1,19 @@ +--- MUMmer3.23/src/kurtz/mm3src/findmumcand.c.old 2024-08-07 13:42:47 ++++ MUMmer3.23/src/kurtz/mm3src/findmumcand.c 2024-08-07 13:54:04 +@@ -15,6 +15,16 @@ + #include "spacedef.h" + #include "maxmatdef.h" + ++void linklocstree(Suffixtree *stree,Location *outloc,Location *inloc); ++ ++SYMBOL *scanprefixfromnodestree(Suffixtree *stree,Location *loc, ++ Bref btptr,SYMBOL *left, ++ SYMBOL *right,Uint rescanlength); ++ ++SYMBOL *scanprefixstree(Suffixtree *stree,Location *outloc, ++ Location *inloc,SYMBOL *left, ++ SYMBOL *right,Uint rescanlength); ++ + //} + + /*EE diff --git a/recipes/mummer/patches/linkloc_explicit.patch b/recipes/mummer/patches/linkloc_explicit.patch new file mode 100644 index 0000000000000..96ad6ea4cb176 --- /dev/null +++ b/recipes/mummer/patches/linkloc_explicit.patch @@ -0,0 +1,12 @@ +--- MUMmer3.23/src/kurtz/streesrc/linkloc.c.old 2024-08-07 12:45:16 ++++ MUMmer3.23/src/kurtz/streesrc/linkloc.c 2024-08-07 13:48:38 +@@ -11,6 +11,9 @@ + #include "debugdef.h" + #include "streeacc.h" + ++void getbranchinfostree(Suffixtree *stree,Uint whichinfo, ++ Branchinfo *branchinfo,Bref btptr); ++ + void rescanstree(Suffixtree *stree,Location *loc, + Bref btptr,SYMBOL *left,SYMBOL *right) + { diff --git a/recipes/mummer/patches/procmaxmat_explicit.patch b/recipes/mummer/patches/procmaxmat_explicit.patch new file mode 100644 index 0000000000000..87252e37230ba --- /dev/null +++ b/recipes/mummer/patches/procmaxmat_explicit.patch @@ -0,0 +1,19 @@ +--- MUMmer3.23/src/kurtz/mm3src/procmaxmat.c.old 2024-08-07 14:05:17 ++++ MUMmer3.23/src/kurtz/mm3src/procmaxmat.c 2024-08-07 14:07:03 +@@ -19,6 +19,16 @@ + #include "spacedef.h" + #include "streedef.h" + #include "maxmatdef.h" ++ ++Uint getmaxtextlenstree(void); ++ ++Sint constructprogressstree(Suffixtree *stree,SYMBOL *text, ++ Uint textlen, ++ void (*progress)(Uint,void *), ++ void (*finalprogress)(void *), ++ void *info); ++ ++void freestree(Suffixtree *stree); + + //} + diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml index 16e21de4c8ff2..9953f38bd5c3e 100644 --- a/recipes/muscle/meta.yaml +++ b/recipes/muscle/meta.yaml @@ -12,7 +12,7 @@ source: - support-linux-aarch64.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -35,5 +35,6 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - biotools:muscle diff --git a/recipes/mview/build.sh b/recipes/mview/build.sh new file mode 100644 index 0000000000000..6b9c4344b742e --- /dev/null +++ b/recipes/mview/build.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +set -exuo pipefail + +sed -i.bak \ + -e "s|\$MVIEW_HOME = \"/home/brown/HOME/work/MView/dev\";|\$MVIEW_HOME = \$ENV{'CONDA_PREFIX'} if exists \$ENV{'CONDA_PREFIX'};|" \ + -e 's|$MVIEW_LIB = "$MVIEW_HOME/lib";|$MVIEW_LIB = "$MVIEW_HOME/lib/mview'${PKG_VERSION}'";|' \ + ${SRC_DIR}/bin/mview + +LIB_INSTALL_DIR=${PREFIX}/lib/mview${PKG_VERSION} + +mkdir -p ${LIB_INSTALL_DIR}/Bio +cp -r ${SRC_DIR}/lib/Bio/{MView,Parse,Util} ${LIB_INSTALL_DIR}/Bio/ + +install -D -m 755 ${SRC_DIR}/bin/mview ${PREFIX}/bin/ diff --git a/recipes/mview/meta.yaml b/recipes/mview/meta.yaml new file mode 100644 index 0000000000000..0704c98853b8e --- /dev/null +++ b/recipes/mview/meta.yaml @@ -0,0 +1,57 @@ +{% set name = "MView" %} +{% set version = "1.68" %} +{% set author = "desmid" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/{{ author }}/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 4c3c75ba7f3cead82e641a83f3ad43b38169fef16aa8b9c8414e35f1eb1081c7 + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + noarch: generic + + +requirements: + host: + - perl >=5.0,<6.0 + run: + - perl >=5.0,<6.0 + +test: + requires: + - wget + commands: + - wget https://rest.uniprot.org/uniprotkb/Q16602.fasta + - mview -in fasta Q16602.fasta -width 77 + +about: + home: https://{{ author }}.github.io/{{ name|lower }} + doc_url: https://{{ author }}.github.io/{{ name|lower }}/contents.html + dev_url: https://github.com/{{ author }}/{{ name|lower }} + license: GPL-2.0-or-later + license_family: GPL2 + license_file: LICENSE.md + summary: "MView extracts and reformats the results of a sequence database search or multiple alignment." + description: | + MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, + optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats. + + Inputs: + - Sequence database search: BLAST, FASTA suites. + - Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF. + + Outputs: + - HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated). + + The tool is used in molecular biology and biomedical research for data analyses and as a component in various bioinformatics web services. + Research papers citing MView are indexed on [Google Scholar](https://scholar.google.com/citations?user=4ughzM0AAAAJ&hl=en). + +extra: + recipe-maintainers: + - eunos-1128 diff --git a/recipes/mvip/meta.yaml b/recipes/mvip/meta.yaml index f0f8bbd911427..613e0bbbd9bb8 100644 --- a/recipes/mvip/meta.yaml +++ b/recipes/mvip/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mvip" %} -{% set version = "1.1.1" %} +{% set version = "1.1.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 53e82ef6b4ffddba5c14d19d267c148a6d41432c5833a2b4750bb4ccdadcf0f3 + sha256: ca056513e45714c5988aba02572aa179055b17100a0c4192a274324a02e8cc46 build: number: 0 diff --git a/recipes/mycotools/meta.yaml b/recipes/mycotools/meta.yaml index 13bac43437c45..e67804eb73353 100644 --- a/recipes/mycotools/meta.yaml +++ b/recipes/mycotools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mycotools" %} -{% set version = "0.31.45" %} +{% set version = "0.32.3" %} package: name: {{ name|lower }} @@ -7,9 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mycotools-{{ version }}.tar.gz - sha256: 6754e065060db21fb68296bbe3ab008010eaf3b5c464664db737dd37e3fc02c5 + sha256: 598caafca226eeb485759c88ff9ab3c05c0d9803e900c2cea7c191cb4df7c77e build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir entry_points: - mtdb = mycotools.mtdb:main - acc2fa = mycotools.acc2fa:cli @@ -42,19 +45,18 @@ build: - predb2mtdb = mycotools.predb2mtdb:cli - s2subs = mycotools.s2subs:cli - update_mtdb = mycotools.update_mtdb:cli - noarch: python - script: python -m pip install . -vv --no-deps --no-build-isolation - number: 0 + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} run_exports: - {{ pin_subpackage('mycotools', max_pin="x.x") }} requirements: host: + - python >=3 - setuptools-scm - pip - - cython run: - - python >=3.0,<4.0 + - python >=3 - biopython - pandas - requests @@ -70,23 +72,24 @@ requirements: - fasttree - diamond - ete3 + - ncbi-datasets-cli test: imports: - mycotools commands: - - pip check - mtdb --help - predb2mtdb --help - update_mtdb --help - requires: - - pip about: - home: https://github.com/xonq/mycotools - summary: Comparative genomics automation and standardization software - license: BSD-3-Clause + home: "https://github.com/xonq/mycotools" + summary: "Comparative genomics automation and standardization software." + license: "BSD-3-Clause" + license_family: BSD license_file: LICENSE + dev_url: "https://github.com/xonq/mycotools" + doc_url: "https://github.com/xonq/mycotools/wiki" extra: recipe-maintainers: diff --git a/recipes/nanocount/meta.yaml b/recipes/nanocount/meta.yaml new file mode 100644 index 0000000000000..90fbda93b8280 --- /dev/null +++ b/recipes/nanocount/meta.yaml @@ -0,0 +1,59 @@ +{% set name = "NanoCount" %} +{% set version = "1.0.0.post6" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/NanoCount-{{ version }}.tar.gz + sha256: 0f24e8526ce9a0df9894cacaac957f285c90bf1d2f98507bb183981cb0ea346e + +build: + entry_points: + - NanoCount=NanoCount.__main__:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('nanocount', max_pin='x') }} + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - tqdm >=4.51.0 + - numpy >=1.19.4 + - pysam >=0.16.0 + - pandas >=1.1.4 + - colorlog >=4.1.0 + +test: + imports: + - NanoCount + - NanoCount.NanoCount + commands: + - pip check + - NanoCount --help + requires: + - pip + +about: + home: https://github.com/a-slide/NanoCount/ + doc_url: https://a-slide.github.io/NanoCount/ + summary: Transcript abundance estimation from Nanopore *direct-RNA sequencing* datasets + description: NanoCount estimates transcripts abundance from Oxford Nanopore *direct-RNA sequencing* datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads + license: MIT + licence_url: https://mit-license.org/ + license_file: LICENSE + +extra: + recipe-maintainers: + - corneliusroemer + identifiers: + - doi:10.1093/nar/gkab1129 + author: Adrien Leger + author_email: aleg@ebi.ac.uk + author_url: https://adrienleger.com diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index aa336929dc77c..05bde9e5c9da5 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.4.11" %} +{% set version = "0.4.13" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: 822a74f70748cdb0539dd990955adeceb76c8e4e858ecee5e0097a31fac34ceb + sha256: 76189a75edccd511e2641318aa80957aea7beb126ddf0a5cd0bdefce5de33a45 build: entry_points: diff --git a/recipes/nanoplot/meta.yaml b/recipes/nanoplot/meta.yaml index b40260be1a127..af69dc565bfdf 100644 --- a/recipes/nanoplot/meta.yaml +++ b/recipes/nanoplot/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.42.0" %} +{% set version = "1.43.0" %} package: name: nanoplot version: {{ version }} source: - url: https://pypi.io/packages/source/n/nanoplot/NanoPlot-{{ version }}.tar.gz - sha256: 0f8fd2cffd33a346b3306716058c6cb4091c931e8ab502f10b17a28749e8b6d9 + url: https://pypi.io/packages/source/n/nanoplot/nanoplot-{{ version }}.tar.gz + sha256: 0f94096d689b552c32fd7246ad87cb6d5e5e2499dad5acc551091e0ff67f48df build: entry_points: - NanoPlot=nanoplot.NanoPlot:main - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage("nanoplot", max_pin="x.x") }} @@ -28,8 +28,7 @@ requirements: - scipy - python-dateutil - libpng - - nanoget >=1.18.1 - - nanomath >=1.0.0 + - nanoget >=1.19.1 - plotly >=5.4.0 - pyarrow - python-kaleido diff --git a/recipes/nanosim/build.sh b/recipes/nanosim/build.sh index 87b317b6f8ecc..fdeb10cd57daf 100644 --- a/recipes/nanosim/build.sh +++ b/recipes/nanosim/build.sh @@ -2,7 +2,8 @@ set -eu -o pipefail mkdir -p ${PREFIX}/bin -cp src/*.py ${PREFIX}/bin/ +cp -rf src/*.py ${PREFIX}/bin/ +cp -rf src/*lua ${PREFIX}/bin/ chmod 0755 "${PREFIX}/bin/read_analysis.py" chmod 0755 "${PREFIX}/bin/simulator.py" diff --git a/recipes/nanosim/meta.yaml b/recipes/nanosim/meta.yaml index c61ceb870abb8..8562cc8a2044d 100644 --- a/recipes/nanosim/meta.yaml +++ b/recipes/nanosim/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.1.0" %} -{% set sha256 = "6b994fc545b80f7a30a426837eb023c4c03c3ffb5807f8513b7e176c3dd5f5ba" %} +{% set version = "3.2.1" %} +{% set sha256 = "49a0608e9fa8ce78b497b2fbe08b82194f5b4e6670e4b2275baccf4e7b3017d8" %} package: name: nanosim @@ -11,7 +11,9 @@ source: build: noarch: generic - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('nanosim', max_pin="x") }} requirements: run: @@ -24,10 +26,13 @@ requirements: - pybedtools >=0.7.10 - pysam >=0.13 - htseq >=0.9.1 - - minimap2 + - minimap2 >=2.18 - last - samtools - genometools-genometools + - regex + - piecewise-regression + - sam2pairwise test: commands: @@ -36,11 +41,11 @@ test: about: home: https://github.com/bcgsc/NanoSim - license: GPL-3.0 - license_file: - - COPYRIGHT - - LICENSE + license: "GPL-3.0-only" + license_family: GPL3 + license_file: LICENSE summary: 'NanoSim is a fast and scalable read simulator for Nanopore sequencing data.' + dev_url: https://github.com/bcgsc/NanoSim extra: identifiers: diff --git a/recipes/nanovar/meta.yaml b/recipes/nanovar/meta.yaml index ec3526daa2127..1e0dbbfc3bd97 100644 --- a/recipes/nanovar/meta.yaml +++ b/recipes/nanovar/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.1" %} +{% set version = "1.8.1" %} package: name: nanovar @@ -6,11 +6,11 @@ package: source: url: https://pypi.io/packages/source/n/nanovar/nanovar-{{ version }}.tar.gz - sha256: 5b189ff18958be0e7406752f7700e0c70d464ae64b70ed278fd32a2fe61280a4 + sha256: c75159f86a4043f5ba37c4ea16b9c5953e44d7a1c1dd854de7928464bed83bc9 build: skip: True # [py2k or osx or py > 39] - number: 1 + number: 0 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv run_exports: - {{ pin_subpackage('nanovar', max_pin="x") }} @@ -23,18 +23,18 @@ requirements: - python run: - python - - biopython >=1.78 + - numpy >=1.17.3, <2.0.0 + - scipy >=1.2.1 + - biopython >=1.82 + - pybedtools >=0.8.2 - matplotlib-base >=2.2.3 + - tensorflow-cpu >=2.0.0, <=2.15.1 - natsort >=6.2.0 - - numpy >=1.17.3 - - progress >=1.4 - - pybedtools >=0.8.2 - - scipy >=1.2.1 - - tensorflow-mkl >=2.0.0 + - pysam >=0.15.3 + - bs4 >=0.0.2 - bedtools >=2.26.0 - minimap2 >=2.17 - samtools >=1.3 - - pysam >=0.15.3 test: imports: diff --git a/recipes/ncbi-stxtyper/build.sh b/recipes/ncbi-stxtyper/build.sh new file mode 100755 index 0000000000000..34aa84ada3b2d --- /dev/null +++ b/recipes/ncbi-stxtyper/build.sh @@ -0,0 +1,23 @@ +#!/bin/bash + +# fix error because of gnu++17 features. Suggested by https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk +# CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" + +echo +echo "Starting build.sh" +echo +echo "SRC_DIR=$SRC_DIR" +echo "pwd -P" +pwd -P +echo "ls -l" +ls -l + +# note that for version 3.7 the make command should be: +make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS" PREFIX="$PREFIX" + +#echo "make CXX=\"$CXX $LDFLAGS\" CPPFLAGS=\"$CXXFLAGS\" PREFIX=\"$PREFIX\" DEFAULT_DB_DIR=\"$PREFIX/share/amrfinderplus/data\"" + +#make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS" PREFIX=$PREFIX DEFAULT_DB_DIR="$PREFIX/share/amrfinderplus/data" +make install bindir=$PREFIX/bin + +echo "build.sh done" diff --git a/recipes/ncbi-stxtyper/meta.yaml b/recipes/ncbi-stxtyper/meta.yaml new file mode 100644 index 0000000000000..22955929e7a18 --- /dev/null +++ b/recipes/ncbi-stxtyper/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.0.24" %} +{% set sha256 = "54ddeb7ec1a052c141c32eea402c816f0515f47b7f0a5afeb054e410f9a4576f" %} + +package: + name: ncbi-stxtyper + version: {{ version }} + +source: + url: https://github.com/ncbi/stxtyper/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_compatible('ncbi-amrfinderplus', max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + - coreutils + run: + - blast >=2.9 + +test: + commands: + - echo "PREFIX=$PREFIX CONDA_PREFIX=$CONDA_PREFIX SRC_DIR=$SRC_DIR" # for debugging + - stxtyper --help + - fasta_check -help + - fasta_extract -help + +about: + home: https://github.com/ncbi/stxtyper + license: Public Domain + license_file: LICENSE + summary: StxTyper identifies and types Stx operons from assembled genomic sequence. + description: | + This software and the included database use a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence + doc_url: https://github.com/ncbi/stxtyper + +extra: + recipe-maintainers: + - evolarjun diff --git a/recipes/ncbi-vdb/build.sh b/recipes/ncbi-vdb/build.sh index 9b73fbb271b0e..f1b45b55eedd6 100644 --- a/recipes/ncbi-vdb/build.sh +++ b/recipes/ncbi-vdb/build.sh @@ -22,20 +22,25 @@ end-of-patch } | patch -p0 -i- -# Execute Make commands from a separate subdirectory. Else: -# ERROR: In source builds are not allowed -#BUILD_DIR="${SRC_DIR}/build_vdb" -#mkdir -p "${BUILD_DIR}" -#cd "${BUILD_DIR}" +if [[ "$(uname)" == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include -O3 -D_FILE_OFFSET_BITS=64 -DH5_USE_110_API" cmake -S ncbi-vdb/ -B build_vdb \ -DNGS_INCDIR="${PREFIX}" \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ -DCMAKE_BUILD_TYPE=Release \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_INSTALL_LIBDIR="${PREFIX}/lib" \ -DCMAKE_CXX_COMPILER="${CXX}" \ -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ - -DCMAKE_LIBRARY_PATH="${PREFIX}/lib" + "${CONFIG_ARGS}" -cmake --build build_vdb/ --target install -j 4 -v +cmake --build build_vdb/ --target install -j "${CPU_COUNT}" -v diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml index 3afafe6901532..68b395345f2bf 100644 --- a/recipes/ncbi-vdb/meta.yaml +++ b/recipes/ncbi-vdb/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('ncbi-vdb', max_pin='x') }} @@ -26,19 +26,19 @@ requirements: - make about: - home: https://github.com/ncbi/ncbi-vdb + home: "https://github.com/ncbi/ncbi-vdb" license: Public Domain - summary: SRA tools database engine + summary: "SRA tools database engine." description: | - VDB is the database engine that all SRA tools use. It is a columnar database - system with a number of unique features. All SRA objects are stored in VDB. - dev_url: https://github.com/ncbi/ncbi-vdb - doc_url: https://github.com/ncbi/ncbi-vdb/wiki + "VDB is the database engine that all SRA tools use. It is a columnar database + system with a number of unique features. All SRA objects are stored in VDB." + dev_url: "https://github.com/ncbi/ncbi-vdb" + doc_url: "https://github.com/ncbi/ncbi-vdb/wiki" test: commands: - - test -e ${PREFIX}/lib64/libncbi-vdb.so # [not osx] - - test -e ${PREFIX}/lib64/libncbi-vdb.dylib # [osx] + - test -e ${PREFIX}/lib/libncbi-vdb.so # [not osx] + - test -e ${PREFIX}/lib/libncbi-vdb.dylib # [osx] extra: additional-platforms: diff --git a/recipes/neat/meta.yaml b/recipes/neat/meta.yaml index d79c967a7fb41..0387300d88ae8 100644 --- a/recipes/neat/meta.yaml +++ b/recipes/neat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "NEAT" %} -{% set version = "4.2.3" %} +{% set version = "4.2.5" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/ncsa/{{ name }}/archive/{{ version }}.tar.gz - sha256: 915d297842d4f775a79f59f37aac729ade742676f37473dbdbbedab64e81a046 + sha256: ba3ef6233f236a89fd41af8a52a922e04b48c596d8573675c52da2682aaa4752 build: diff --git a/recipes/nedbit-features-calculator/build.sh b/recipes/nedbit-features-calculator/build.sh new file mode 100644 index 0000000000000..b57e9cfb29d0e --- /dev/null +++ b/recipes/nedbit-features-calculator/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash +mkdir -p ${PREFIX}/bin + +cd src + +$CC -o $PREFIX/bin/nedbit-features-calculator nedbit_features_calculator.c -lm + +chmod u+x ${PREFIX}/bin/nedbit-features-calculator diff --git a/recipes/nedbit-features-calculator/meta.yaml b/recipes/nedbit-features-calculator/meta.yaml new file mode 100644 index 0000000000000..390e2826acadf --- /dev/null +++ b/recipes/nedbit-features-calculator/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.2" %} + +package: + name: nedbit-features-calculator + version: {{ version }} + +source: + url: https://github.com/anuprulez/NIAPU/archive/refs/tags/{{ version }}.tar.gz + sha256: 50424bf7df99b51dc71a4121beae89ef69b2bb4eaba559c99643baecb8544806 + +build: + number: 1 + run_exports: + - {{ pin_subpackage('nedbit-features-calculator', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + +test: + commands: + - nedbit-features-calculator + +about: + home: https://github.com/AndMastro/NIAPU + license: MIT + summary: Network diffusion and biology-informed topological features + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/nextpolish2/build.sh b/recipes/nextpolish2/build.sh index 5e20a67b60e44..4c85d7f615175 100644 --- a/recipes/nextpolish2/build.sh +++ b/recipes/nextpolish2/build.sh @@ -1,4 +1,4 @@ -#!/bin/bash -euo +#!/bin/bash -exuo # build statically linked binary with Rust RUST_BACKTRACE=1 cargo install --verbose --path . --root "${PREFIX}" diff --git a/recipes/nextpolish2/meta.yaml b/recipes/nextpolish2/meta.yaml index c90c5f20d41d2..714e5aab5d652 100644 --- a/recipes/nextpolish2/meta.yaml +++ b/recipes/nextpolish2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 5f94cfabae5d38397a33c118f572246070707aa23f7b2ab831fd255710f50280 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('nextpolish2', max_pin="x.x") }} @@ -40,6 +40,9 @@ about: doc_url: "https://github.com/Nextomics/NextPolish2/blob/{{ version }}/README.md" extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - moold identifiers: diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index 6d6f19923748b..88f19b53e3497 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.5.1" %} +{% set version = "8.5.3" %} package: name: nextstrain-cli @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain_cli-{{ version }}.tar.gz - sha256: 5318296512acc4e47fe7d0ffa11b0654ec47ad7822006be3b75864f17b94ea67 + sha256: 5401fd3f1b60479cb3b8c0519917fa5df43fdaddd6007e158888283a5c872428 build: number: 0 diff --git a/recipes/ngs-bits/meta.yaml b/recipes/ngs-bits/meta.yaml index a0cfd0e03364c..5a2b865428cdb 100644 --- a/recipes/ngs-bits/meta.yaml +++ b/recipes/ngs-bits/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2024_07" %} +{% set version = "2024_08" %} package: name: ngs-bits @@ -12,7 +12,7 @@ build: source: url: https://github.com/imgag/ngs-bits/releases/download/{{ version }}/ngs-bits-{{ version }}.tgz - sha256: c1f78b59d87516c5fba44a1375da561b8b1577b4ef949ce63b9a042bbf7f1853 + sha256: 615e61360eafdfdb923336e7c985e7a599c80ad56e534b30bbe97e4b524bc55d # Note: pinning of sysroot_linux-64 =2.17 enforces cos7 and is currently needed to prevent an memcpy@GLIBC2.14 error requirements: diff --git a/recipes/nohuman/build.sh b/recipes/nohuman/build.sh index 98067b0d04217..29a06029e6302 100644 --- a/recipes/nohuman/build.sh +++ b/recipes/nohuman/build.sh @@ -1,17 +1,8 @@ #!/bin/bash set -ex -RUST_BACKTRACE=full +cargo-bundle-licenses --format yaml --output THIRDPARTY.yml -if [ "$(uname)" == "Darwin" ]; then - # apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory - export HOME="/Users/distiller" - export HOME=`pwd` - echo "HOME is $HOME" +RUST_BACKTRACE=full cargo install -v --locked --no-track --root "$PREFIX" --path . - # according to https://github.com/rust-lang/cargo/issues/2422#issuecomment-198458960 removing circle ci default configuration solves cargo trouble downloading crates - #git config --global --unset url.ssh://git@github.com.insteadOf -fi - -cargo install -v --locked --root "$PREFIX" --path . "$STRIP" "$PREFIX/bin/nohuman" \ No newline at end of file diff --git a/recipes/nohuman/meta.yaml b/recipes/nohuman/meta.yaml index f084e962a765c..faca6ca3f3f18 100644 --- a/recipes/nohuman/meta.yaml +++ b/recipes/nohuman/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.1" %} +{% set version = "0.3.0" %} {% set name = "nohuman" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 73a79909e487e0669e1604407024c8f1db1a3a0adf2fb3d76d80987823d85fd2 + sha256: 3503a0e8b6fcbf92832fe4bfcfb3d5a071536a8ebe3230cac1ee4e053de3cf6a build: number: 0 @@ -17,22 +17,23 @@ build: requirements: build: - {{ compiler('c') }} - host: - - rust >=1.70 - - openssl + - {{ compiler('rust') }} + - cargo-bundle-licenses run: - kraken2 =2.1 test: commands: - nohuman --help + - nohuman --check about: home: https://github.com/mbhall88/nohuman license: MIT - license_family: MIT + license_file: + - LICENSE + - THIRDPARTY.yml summary: Remove human reads from a sequencing run - license_file: LICENSE extra: recipe-maintainers: diff --git a/recipes/ntedit/meta.yaml b/recipes/ntedit/meta.yaml index 0c4fd19bd40e6..381a1d7165671 100644 --- a/recipes/ntedit/meta.yaml +++ b/recipes/ntedit/meta.yaml @@ -1,18 +1,18 @@ {% set name = "ntedit" %} -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x") }} source: url: https://github.com/bcgsc/ntEdit/releases/download/v{{ version }}/ntEdit-{{ version }}.tar.gz - sha256: 314bc1a39c2d382786ee64d83a1b8c4519e5c9feb0203b1b7f4ab0d9087cf6c5 + sha256: fc4ee277a66bd90fd5fce8806c394efc07bb955499acea7591973e60df2399ea requirements: build: diff --git a/recipes/ntjoin/meta.yaml b/recipes/ntjoin/meta.yaml index a369b9bf428cc..bd29bd4215cb8 100644 --- a/recipes/ntjoin/meta.yaml +++ b/recipes/ntjoin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.4" %} +{% set version = "1.1.5" %} package: name: ntjoin @@ -6,7 +6,7 @@ package: source: url: https://github.com/bcgsc/ntJoin/releases/download/v{{ version }}/ntJoin-{{ version }}.tar.gz - sha256: ec24330e11ea63948d1b124273dae79e80088d672f7e536e7d97787f0c2bb644 + sha256: 808260e3e8c25121f4b7b88a0dd1766c9da0b59d5ebf843a5ec84efb13944009 build: number: 1 @@ -32,6 +32,7 @@ requirements: - zlib - make - btllib + - packaging test: commands: diff --git a/recipes/ntm-profiler/meta.yaml b/recipes/ntm-profiler/meta.yaml index d920b448d61cc..deab8d25ca9f4 100644 --- a/recipes/ntm-profiler/meta.yaml +++ b/recipes/ntm-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ntm-profiler" %} -{% set version = "0.4.0" %} -{% set sha256 = "6d9625d3b0ad2ee8a757cf6ab69381fd8d63c7d9adde76e56076b616f3039deb" %} +{% set version = "0.5.0" %} +{% set sha256 = "6dafd31f7a5ccf7b770481c0fffeb09509287a402ca4023ee88e0620d440c85b" %} package: name: {{name}} diff --git a/recipes/ntroot/meta.yaml b/recipes/ntroot/meta.yaml index ab1636a060e4c..2227aa091d3e1 100644 --- a/recipes/ntroot/meta.yaml +++ b/recipes/ntroot/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ntRoot" %} -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bcgsc/ntRoot/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: 0b1cfb7008e1bb7efeea400fab9da4f73e297357ee83ae23904b21d9a91d5c81 + sha256: 455aca749834edf866fd159dfbf9facc7769edc74f932cea611c4401cde4f6d5 build: number: 0 diff --git a/recipes/ntsynt/meta.yaml b/recipes/ntsynt/meta.yaml index 1229bf07bc8b3..96b331202d4a4 100644 --- a/recipes/ntsynt/meta.yaml +++ b/recipes/ntsynt/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ntSynt" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/bcgsc/ntSynt/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: 71fa06c73481313518a504586b86a2a32cd49006ce6728b40eef0d455b9bb409 + sha256: 6ada92dfe51dec8cd47900a5c41ee3c649cc95777eb81fe860e10748ce04e133 build: - number: 3 + number: 0 run_exports: - {{ pin_subpackage("ntsynt", max_pin="x") }} diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 7f05f8d15b67a..021ea4f7df913 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.11.3" %} -{% set sha256 = "2d79d3b313338ad22ba32588261e0795567c9687b951746472ca46e8ee6e61dd" %} +{% set version = "2.11.9" %} +{% set sha256 = "9721f4a3383b7e4354058b6755dcffdf753fb86fcb0a83a5dd8b81acf5aeb4e0" %} package: name: {{ name|lower }} diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml index ad46a7b90f03d..41e7e84dcf8ce 100644 --- a/recipes/oarfish/meta.yaml +++ b/recipes/oarfish/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.1" %} +{% set version = "0.6.2" %} package: name: oarfish @@ -11,13 +11,17 @@ build: source: url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz - sha256: 83fe964065c1068be8085eaf36ce436d8199577d2647fa52138046ccc253d62b + sha256: 78b523fc459fec5ae3680395925862b4d367bd56d051120f28c689dd387e1758 requirements: build: + - make - {{ compiler('rust') }} + - {{ compiler('c') }} host: + - zlib run: + - zlib test: commands: diff --git a/recipes/olivar/meta.yaml b/recipes/olivar/meta.yaml index 5cda48e56fae5..76c2f242c2d65 100644 --- a/recipes/olivar/meta.yaml +++ b/recipes/olivar/meta.yaml @@ -1,5 +1,5 @@ {% set name = "olivar" %} -{% set version = "1.1.5" %} +{% set version = "1.2.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/treangenlab/Olivar/archive/refs/tags/v{{version}}.tar.gz - sha256: 7ead97763b448fbf9c7cad5f25c08b5e5063e92bfd8fc069604f05d76cf071f2 + sha256: 51940193397a97950fe6d8c0076bfe9cc891fbe048d952fe73ed9cef67d2c03f build: number: 0 diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index af34fb5a538b7..f6a36fb5d4699 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ont-modkit" %} -{% set version = "0.3.1" %} -{% set sha256 = "f780f60411bf8a94f2b4dc7383c14a0c04050cca8b1d3e2763c480d72026b3ba" %} +{% set version = "0.4.1" %} +{% set sha256 = "45cd7d4ee69092db7412a15f02799c3118bf5fa4e40e193e30e8c65c4f762f79" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("ont-modkit", max_pin="x.x") }} diff --git a/recipes/open-cravat/meta.yaml b/recipes/open-cravat/meta.yaml index 4575700fc40ea..7d59bcaab5edc 100644 --- a/recipes/open-cravat/meta.yaml +++ b/recipes/open-cravat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "open-cravat" %} -{% set version = "2.7.3" %} +{% set version = "2.9.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e052ab00c04c1db9f45cd1ec2d7d774279fb1fe4d5763ab13d6fcb7e6d1d7df9 + sha256: 816484cd30196659d85b0e4705815ae06749f13f9524eb48ac07942b3ed92f08 build: number: 0 diff --git a/recipes/openms-meta/build.sh b/recipes/openms-meta/build.sh index 54dd40136fce4..82f6b8c86d1f9 100644 --- a/recipes/openms-meta/build.sh +++ b/recipes/openms-meta/build.sh @@ -46,6 +46,6 @@ cmake .. \ -DBUILD_EXAMPLES=OFF # limit concurrent build jobs due to memory usage on CI -make -j2 OpenMS TOPP +make -j1 OpenMS TOPP # The subpackages will do the installing of the parts #make install diff --git a/recipes/openms-meta/meta.yaml b/recipes/openms-meta/meta.yaml index cbc167c08c8cc..32c28922e024f 100644 --- a/recipes/openms-meta/meta.yaml +++ b/recipes/openms-meta/meta.yaml @@ -1,5 +1,5 @@ {% set name = "OpenMS" %} -{% set version = "3.1.0" %} # if ends with 'dev' it is considered a development release and pulled from GitHub +{% set version = "3.2.0" %} # if ends with 'dev' it is considered a development release and pulled from GitHub package: name: {{ name|lower }}-meta version: {{ version }} @@ -11,8 +11,8 @@ source: git_depth: 1 # (Defaults to -1/not shallow) {% else %} source: - url: https://github.com/OpenMS/OpenMS/releases/download/Release{{ version }}/OpenMS-{{ version }}-src.tar.gz - md5: 6a60ef1a95c7ce915cc3a02e5bccd593 + url: https://github.com/OpenMS/OpenMS/releases/download/release%2F3.2.0/OpenMS-3.2.tar.gz # since we discarded the trailing 0 during the GHA we have to hard code this, fix it next release + md5: 60ebfe8a45f7e1fb5566d21231b460e8 {% endif %} build: @@ -46,6 +46,7 @@ requirements: - libsvm - coinmp - sysroot_linux-64 =2.17 # [linux] + - yaml-cpp test: commands: @@ -77,6 +78,8 @@ outputs: - libsvm - coinmp - sysroot_linux-64 =2.17 # [linux] + - yaml-cpp + build: run_exports: - {{ pin_compatible('llvm-openmp', max_pin='x.x') }} # [osx] @@ -118,6 +121,8 @@ outputs: - libsvm - coinmp - sysroot_linux-64 =2.17 # [linux] + - yaml-cpp + run: - {{ pin_subpackage('libopenms', exact=True) }} - {{ pin_compatible('llvm-openmp', max_pin='x.x') }} # [osx] diff --git a/recipes/orthanq/meta.yaml b/recipes/orthanq/meta.yaml index 61374a7b9a177..4b7782c61727f 100644 --- a/recipes/orthanq/meta.yaml +++ b/recipes/orthanq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.7.1" %} +{% set version = "1.7.8" %} package: name: orthanq @@ -12,7 +12,7 @@ build: source: url: https://github.com/orthanq/orthanq/archive/v{{ version }}.tar.gz - sha256: 1e918960bd307cdd7d21ef341d1f0827abe8bb243bb4c15266c957dc5b70c07b + sha256: bc4036a3d058263c8a49319573d1ef926e807a1d6b4bf845d09d686556c0d893 requirements: build: diff --git a/recipes/orthologer/build.sh b/recipes/orthologer/build.sh new file mode 100644 index 0000000000000..0741cbebb9195 --- /dev/null +++ b/recipes/orthologer/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +# flag installer that no external packages should be installed +# they are all installed by conda dependencies +export SKIP_EXTERNAL=1 + +# install ORTHOLOGER and BRHCLUS +./install_pkg.sh diff --git a/recipes/orthologer/meta.yaml b/recipes/orthologer/meta.yaml new file mode 100644 index 0000000000000..029292417924b --- /dev/null +++ b/recipes/orthologer/meta.yaml @@ -0,0 +1,68 @@ +{% set name = "orthologer" %} +{% set version = "3.4.1" %} +{% set sha256 = "b4d6504ea75899d3e13facc4232efdfe79c66283cccfe5d5ea8996f7905f346d" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('orthologer', max_pin="x") }} + +source: + url: https://data.orthodb.org/current/download/software/orthologer_{{ version }}.tgz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler('cxx') }} + - {{ compiler('c') }} + - cmake + - make + - bash >=4.1 + host: + - llvm-openmp # [osx] + - libgomp # [linux] + - rsync + - wget + - bash >=4.1 + run: + - bash >=4.1 + - python >=3.4 + - llvm-openmp # [osx] + - libgomp # [linux] + - rsync + - wget + - blast + - mmseqs2 + - cd-hit + - diamond + - biopython + - numpy + +test: + commands: + - ALLOW_RUNAS_ROOT=1 orthologer -h + +about: + home: https://orthologer.ezlab.org + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Assessment of assembly completeness using Universal Single Copy Orthologs." + description: compute orthology + dev_url: https://gitlab.com/ezlab/orthologer_container + doc_url: https://orthologer.ezlab.org/#on-orthodb-data + +extra: + container: + # Necessary to allow Orthologer to download files from the internet when used with Singularity + # and default bind paths (see also https://github.com/bioconda/bioconda-recipes/issues/11583). + # Should be removed again when the base container is fixed. Not yet... + extended-base: True + identifiers: + - biotools:orthologer + recipe-maintainers: + - ftegenfe diff --git a/recipes/palikiss/meta.yaml b/recipes/palikiss/meta.yaml index 6d375b44938c5..556c317057398 100644 --- a/recipes/palikiss/meta.yaml +++ b/recipes/palikiss/meta.yaml @@ -1,19 +1,20 @@ -{% set version = "2.3.1" %} +{% set fold_grammars_version = "2.3.1" %} +{% set palikiss_version = "1.1.0" %} {% set packagename = "palikiss" %} {% set sha256 = "0c5b7d91893d0a23189f4af3602e18f110f030eac49a3658f7acede23596fde0" %} package: name: {{ packagename }} - version: 1.1.0 + version: {{ palikiss_version }} source: sha256: {{ sha256 }} # the repository "fold-grammars" contains sources for several programs, i.e. pKiss, RNAshapes, ... # thus, the version number does not correspond to the {{ packagename }} version number - url: https://github.com/jlab/fold-grammars/archive/{{ version }}.tar.gz + url: https://github.com/jlab/fold-grammars/archive/{{ fold_grammars_version }}.tar.gz build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('palikiss', max_pin="x") }} diff --git a/recipes/panacus/build.sh b/recipes/panacus/build.sh index f2c10555de8f5..76104b6f15c94 100644 --- a/recipes/panacus/build.sh +++ b/recipes/panacus/build.sh @@ -1,7 +1,7 @@ #!/bin/bash -euo -RUST_BACKTRACE=1 CARGO_HOME="${BUILD_PREFIX}/.cargo" cargo build --release - mkdir -p $PREFIX/bin -cp target/release/panacus $PREFIX/bin + +RUST_BACKTRACE=1 cargo install --no-track --verbose --root "${PREFIX}" --path . + cp scripts/panacus-visualize.py $PREFIX/bin/panacus-visualize diff --git a/recipes/panacus/meta.yaml b/recipes/panacus/meta.yaml index d5ada5ff55534..af5bddd58cb9b 100644 --- a/recipes/panacus/meta.yaml +++ b/recipes/panacus/meta.yaml @@ -1,5 +1,5 @@ {% set name = "panacus" %} -{% set version = "0.2.3" %} +{% set version = "0.2.4" %} package: name: {{ name|lower }} @@ -7,17 +7,19 @@ package: source: url: https://github.com/marschall-lab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 969eaed515a9679f5a74632986240f7afd0558b2a2914281dc783ac1fa1b6f9e + sha256: e4709c5e3e4b5c445789406a0ebf06a2052e24bc5fcc3b540cacf8064c2ab478 build: - number: 0 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: - {{ compiler('c') }} - - rust >=1.68 + - {{ compiler('rust') }} + - cmake + - make run: - python - matplotlib-base @@ -25,7 +27,7 @@ requirements: - pandas - scikit-learn - scipy - - seaborn + - seaborn-base test: commands: @@ -37,8 +39,13 @@ about: license: MIT license_family: MIT license_file: LICENSE - summary: panacus is a tool for computing counting statistics for GFA files + summary: "panacus is a tool for computing counting statistics for GFA files." + dev_url: https://github.com/marschall-lab/{{ name }} extra: + additional-platforms: + - osx-arm64 + - linux-aarch64 recipe-maintainers: - danydoerr + - heringerp diff --git a/recipes/panfeed/meta.yaml b/recipes/panfeed/meta.yaml index ecb21dbb39dd6..833ba2d123065 100644 --- a/recipes/panfeed/meta.yaml +++ b/recipes/panfeed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.6.1" %} +{% set version = "1.6.2" %} {% set name = "panfeed" %} package: @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 427bf671c6edfb57e3671a83cd941f5ac894d2b9ed9e7df60f6615d6c911949c + sha256: 71e6e97b29784396421b59511dbca27103acfe31a3f392324d4d0419179340be build: entry_points: diff --git a/recipes/pango-collapse/meta.yaml b/recipes/pango-collapse/meta.yaml new file mode 100644 index 0000000000000..f5b8cdbfd43bd --- /dev/null +++ b/recipes/pango-collapse/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "pango-collapse" %} +{% set version = "0.8.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name | replace("-","_") }}-{{ version }}.tar.gz + sha256: 8bf215c09cb04732726c7e9064dd7d087faa9d1fc3d4e42b8d5803738247f532 + +build: + run_exports: + - {{ pin_subpackage('pango-collapse', max_pin="x.x") }} + entry_points: + - pango-collapse = pango_collapse.main:app + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.8,<4.0 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.8,<4.0 + - typer >=0.6.1,<0.7.0 + - pango_aliasor >=0.3.0,<0.4.0 + - pandas >=1.3,<=1.5.3 + - numpy >=1.19.5,<1.27.0 + +test: + imports: + - pango_collapse + commands: + - pip check + - pango-collapse --help + requires: + - pip + +about: + home: https://github.com/MDU-PHL/pango-collapse + summary: Collapse Pango sublineages up to user defined parent lineages. + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - Wytamma + + + diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index 8f8eef806262b..8c9f30d0327ae 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.29" %} +{% set version = "1.30" %} package: name: pango-designation @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: 884b4de47169323f711d02f9801ddb31bb3e383ac1b4eab93aed9d435cb15c6a + sha256: 835075a7410d4d3a59003105a993358ce20f4ee744231f9728092756a8f2e8d6 build: number: 0 diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index d1b23dc48e60a..2e6b8d042674d 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.29" %} +{% set version = "1.30" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9f0e8ebab54ff1933f9abffb60cbc577df79b0d0ebfa51b8265b7d72720802d6 + sha256: e289ee774c133238294aa2bfa5d331ed89047ffc67af8e3614c01a51ffd46b43 build: number: 0 diff --git a/recipes/parafly/build.sh b/recipes/parafly/build.sh index 14413e4aa02ca..11933133c32cf 100644 --- a/recipes/parafly/build.sh +++ b/recipes/parafly/build.sh @@ -1,4 +1,7 @@ #!/bin/bash + +set -xe + ./configure --prefix=$PREFIX -make install +make -j ${CPU_COUNT} CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated" install cp $PREFIX/bin/ParaFly $PREFIX diff --git a/recipes/parafly/meta.yaml b/recipes/parafly/meta.yaml index 8ed8685215b79..bb7fa4c6d6d1b 100644 --- a/recipes/parafly/meta.yaml +++ b/recipes/parafly/meta.yaml @@ -5,15 +5,22 @@ package: source: url: http://downloads.sourceforge.net/project/parafly/parafly-r2013-01-21.tgz sha256: 64cf7ac2d4af0801b78d58f4057a1489d76b2b8ae59c78997f434d1239fa4abe + patches: + - parafly-aarch64.patch # [aarch64 or arm64] build: - number: 2 + skip: True # [osx] + number: 3 + run_exports: + - {{ pin_subpackage("parafly", max_pin=None) }} requirements: build: - make - - {{ compiler('c') }} + - {{ compiler('cxx') }} host: + - llvm-openmp # [osx] + - libgomp # [linux] - zlib run: - zlib @@ -26,3 +33,7 @@ about: home: http://parafly.sourceforge.net/ license: The Broad Institute (own license thingy) summary: Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. Success/failure is captured, and failed commands are retained and reported. + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/parafly/parafly-aarch64.patch b/recipes/parafly/parafly-aarch64.patch new file mode 100644 index 0000000000000..d6336c05dcde2 --- /dev/null +++ b/recipes/parafly/parafly-aarch64.patch @@ -0,0 +1,11 @@ +--- a/configure 2024-08-06 18:16:49.448814938 +0300 ++++ b/configure 2024-08-06 18:17:03.665713668 +0300 +@@ -3016,7 +3016,7 @@ + + + #AC_OPENMP # requires autoconf >= 2.62 +-AM_CXXFLAGS=-m64 ++AM_CXXFLAGS= + + case $CXX in + g++*) AM_CXXFLAGS="-pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated $AM_CXXFLAGS" diff --git a/recipes/parascopy/meta.yaml b/recipes/parascopy/meta.yaml index 5bc435f33fb96..2befb97a039a4 100644 --- a/recipes/parascopy/meta.yaml +++ b/recipes/parascopy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "parascopy" %} -{% set version = "1.16.2" %} +{% set version = "1.17.1" %} package: name: {{ name|lower }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/tprodanov/{{ name }}/archive/v{{ version }}.tar.gz - sha256: f1fa85349f49a504cc49afa93a2f8aab6600f6edaea3bdf7be21adca973ebe50 + sha256: 3b6871a198e60b76a0d1f94dd219134c8662547d3a98fb20786443916e964a5b requirements: build: diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index d99dc6f3bfb79..893029bbcf967 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.5" %} +{% set version = "2.0.6" %} package: name: parsnp @@ -6,7 +6,7 @@ package: source: url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" - sha256: 1d23695d0d624fa17e02c43b1d730200e526c17a48615593f75ee8fc35402489 + sha256: cde5fb488418764e87942afa747002d01d35e80d7c3a44a71bb2d1bd4d69ed0c build: number: 0 diff --git a/recipes/pasta/meta.yaml b/recipes/pasta/meta.yaml index 4392437dfa127..03ae3152eaa67 100644 --- a/recipes/pasta/meta.yaml +++ b/recipes/pasta/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.9.0" %} -{% set sha256 = "6f816aebe00b7b6bb78a250ad45f5aa2aa8eff0f9719736f05b0597dd3b1f9a1" %} +{% set version = "1.9.2" %} +{% set sha256 = "06c20f022765d2c1daab13a916ec2ea2277c5ef43afcf3e54c6a7ade7aed0944" %} package: name: pasta @@ -22,7 +22,7 @@ requirements: host: - python - setuptools - - dendropy <=4.5.1 + - dendropy - wget - openjdk - pcre @@ -32,12 +32,12 @@ requirements: - raxml - muscle <4 # later versions expects other cmd argument names - mafft - - hmmer ==3.1b2 + - hmmer - prank run: - python - - dendropy <=4.5.1 # later version do not expose _convert_node_to_root_polytomy + - dendropy - openjdk - pcre - pymongo >=3.3.0 @@ -46,7 +46,7 @@ requirements: - raxml - muscle <4 # later versions expects other cmd argument names - mafft - - hmmer ==3.1b2 + - hmmer - prank test: diff --git a/recipes/pastml/meta.yaml b/recipes/pastml/meta.yaml index 18087182c28db..e985066b7448c 100644 --- a/recipes/pastml/meta.yaml +++ b/recipes/pastml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pastml" %} -{% set version = "1.9.46" %} +{% set version = "1.9.49" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: cf127cb64693edf587dc3472de87c876d6603cf2215ca7b0bdf4d879df6223ff + sha256: 421f3be11dd0bd09615aeaba0026b8cc749115c7d72b87576c55e652ac943949 build: number: 0 diff --git a/recipes/pasty/meta.yaml b/recipes/pasty/meta.yaml index c0ac5731107c1..69cec8609056a 100644 --- a/recipes/pasty/meta.yaml +++ b/recipes/pasty/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pasty" %} -{% set version = "2.0.0" %} +{% set version = "2.2.1" %} package: name: {{ name | lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/rpetit3/pasty/archive/v{{ version }}.tar.gz - sha256: f1d6d38c1a797b88249c896030192901ea1e399387a30cda0612537387619cc8 + sha256: e407107082aadbbbc4d650dfbe965b6b9421c9fd384ee7e2ab380e7eca8991cc build: number: 0 @@ -17,7 +17,7 @@ build: requirements: run: - - camlhmp >=0.2.2 + - camlhmp >=1.1.0 test: commands: diff --git a/recipes/pathogen-embed/meta.yaml b/recipes/pathogen-embed/meta.yaml index 585b65b93e761..6686d0251dbaa 100644 --- a/recipes/pathogen-embed/meta.yaml +++ b/recipes/pathogen-embed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.3.0" %} +{% set version = "3.1.0" %} {% set name = "pathogen-embed" %} package: @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pathogen_embed-{{ version }}.tar.gz - sha256: 47ef737b7609593c6de143c17f54bc1e526aaa615773aad73bb6464de67cbff1 + sha256: 27c4a048c7e3c6bafc753ec297252f214a41d75a2c55ebb02542b8f37b19a897 build: number: 0 diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml index 404ee9ae14a9d..db629d9a89746 100644 --- a/recipes/pathogen-profiler/meta.yaml +++ b/recipes/pathogen-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pathogen-profiler" %} -{% set version = "4.3.0" %} -{% set sha256 = "ca6d579308a045c7d433c71c6951293c2f7f7d4952ca37e80b1830a6e9be7fd4" %} +{% set version = "4.4.0" %} +{% set sha256 = "42a82777c01f26f1a5c85185960873e173329f9f84e081a1eef0fe66ac940f2e" %} package: name: {{name}} diff --git a/recipes/pathphynder/meta.yaml b/recipes/pathphynder/meta.yaml index 7a6159c41ce7e..9fac48b8890f8 100644 --- a/recipes/pathphynder/meta.yaml +++ b/recipes/pathphynder/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pathphynder" %} -{% set version = "1.2.1" %} -{% set sha256="8cecb2cddc6e7783a28281aa006341f642c0799c31a78bf1c1cda05308019f81" %} +{% set version = "1.2.3" %} +{% set sha256="2c2acd0c15e9403f5506980121551654c5072fb62edc02846600f7902087e2ca" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 0 noarch: generic run_exports: - {{ pin_subpackage( 'pathphynder', max_pin='x.x') }} diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml index 7eb2b16bcdfc7..8d3f1cf875a11 100644 --- a/recipes/pbstarphase/meta.yaml +++ b/recipes/pbstarphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbstarphase" %} -{% set version = "0.13.1" %} -{% set sha256 = "1808901a0c3c29093733046ec343122905980566423773e64e8df29060ae6721" %} +{% set version = "0.14.2" %} +{% set sha256 = "c8694b47f164db08074cee118238694d8383c0df526637ec1068ae8e93494b75" %} package: name: {{ name }} diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 726942da286dc..7759666dc9ca5 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.4" %} -{% set sha256 = "39e9b2fb3370ee584fbeed8522260c44bb6053489819057f1a232267a526f72a" %} +{% set version = "0.4.5" %} +{% set sha256 = "d420e1a35d1d27c0854c9d81118ecd4de3402d658715c282da3b372565bdf6d6" %} package: @@ -11,7 +11,7 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('pcaone', max_pin="x") }} diff --git a/recipes/pdbx/build.sh b/recipes/pdbx/build.sh new file mode 100644 index 0000000000000..0ba07c5223114 --- /dev/null +++ b/recipes/pdbx/build.sh @@ -0,0 +1,7 @@ +#!/bin/sh + +mkdir -p build +cd build +cmake ${SRC_DIR} ${CMAKE_ARGS} +make +make install diff --git a/recipes/pdbx/meta.yaml b/recipes/pdbx/meta.yaml new file mode 100644 index 0000000000000..c28ff53effdf5 --- /dev/null +++ b/recipes/pdbx/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "pdbx" %} +{% set org = "soedinglab" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/eunos-1128/pdbx/archive/refs/tags/v{{ version }}.tar.gz + sha256: 6b2c9e632b9b9ad1ac7a2683f9e3a50c778dda559507072839924ae0b2bea6a3 + +build: + number: 1 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - make + - cmake + - {{ compiler('c') }} + - {{ compiler('cxx') }} # [linux] + host: + - python >=3.7,<3.12 + run: + - python >=3.7,<3.12 + +test: + imports: + - {{ name }} + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/{{ org }}/{{ name }} + summary: pdbx is a parser module in python for structures of the protein data bank in the mmcif format + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + description: | + Proper recognition to the [Protein Data Bank](http://mmcif.wwpdb.org/docs/sw-examples/python/html/index.html) + where this library for protein structures in the mmCIF format initially came from. + We modified the original library to support python3. + This fork is used by scripts in the HHsuite [on GitHub](https://github.com/soedinglab/hh-suite). + doc_url: https://github.com/{{ org }}/{{ name }}#readme + dev_url: https://github.com/{{ org }}/{{ name }} + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - eunos-1128 diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml index 3d0de3bfbe81d..f4cbb24469e75 100644 --- a/recipes/peaks2utr/meta.yaml +++ b/recipes/peaks2utr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "peaks2utr" %} -{% set version = "1.2.6" %} +{% set version = "1.3.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz - sha256: ba17dd81b942e6b846804b03154358e331c489d7bc12573711c551faece11fed + sha256: ddf7c44725124aabcc4541e567f493de9658b2036a0a804d997376a7bf6b0828 build: number: 0 diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 13a1eb134f708..66ede8a61bc99 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the peptide-shaker.py file {% set name = "PeptideShaker" %} -{% set version = "3.0.8" %} -{% set sha256 = "d7bd1bc9d7f30961da6eb19f8370d2853f5b254857de953eeb34b735ff04aa99" %} +{% set version = "3.0.11" %} +{% set sha256 = "8893de0b068b3adc0c45b1139374a08ecbd8661e1fa087e5aec950d1091e2dec" %} package: name: peptide-shaker @@ -31,14 +31,15 @@ test: about: home: "https://compomics.github.io/projects/peptide-shaker.html" dev_url: "https://github.com/compomics/peptide-shaker" - license: Apache-2.0 + license: "Apache-2.0" license_family: APACHE - summary: Independent platform for interpretation of proteomics identification results + summary: "Independent platform for interpretation of proteomics identification results." description: PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, Metamorpheus, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data! + doc_url: "https://github.com/compomics/peptide-shaker/blob/master/README.md" extra: notes: diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index d41c0b5831e05..4860d508ad6e0 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'PeptideShaker-3.0.8.jar' +jar_file = 'PeptideShaker-3.0.11.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] diff --git a/recipes/peptides/meta.yaml b/recipes/peptides/meta.yaml index f9c435c64005c..b07809680fac3 100644 --- a/recipes/peptides/meta.yaml +++ b/recipes/peptides/meta.yaml @@ -1,5 +1,5 @@ {% set name = "peptides" %} -{% set version = "0.3.1" %} +{% set version = "0.3.4" %} package: name: "{{ name }}" @@ -7,18 +7,20 @@ package: source: url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: d813fdfa74cb3d9087420d9e9c12faa35366ad1cd37ab4fb57236da8f7dd1776 + sha256: e4cd95c7aec68a1876d85bd544478d2d0106e1d884b515c861979dbe00e14a39 build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - python - pip - - setuptools >=39.2 + - setuptools >=46.4 - wheel >=0.30 - astor >=0.6 run: diff --git a/recipes/percolator/build.sh b/recipes/percolator/build.sh index 5dc597f961637..433b421c79df6 100644 --- a/recipes/percolator/build.sh +++ b/recipes/percolator/build.sh @@ -8,7 +8,7 @@ cmake -S . -B percobuild \ -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_INSTALL_PREFIX="$PREFIX" -DXML_SUPPORT=ON \ -DCMAKE_PREFIX_PATH="$PREFIX;$PREFIX/lib" -DCMAKE_CXX_COMPILER="${CXX}" \ - -DCMAKE_CXX_FLAGS="-std=c++14 -O3 -I{PREFIX}/include" + -DCMAKE_CXX_FLAGS="${CXXFLAGS} -std=c++14 -O3 -I{PREFIX}/include" cmake --build percobuild/ --target install -j ${CPU_COUNT} -v # First make sure we dont get problems with truncated PREFIX due to null terminators: @@ -19,7 +19,7 @@ cmake -S ${SRC_DIR}/src/converters -B converterbuild \ -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_INSTALL_PREFIX="$PREFIX" -DBOOST_ROOT="$PREFIX" \ -DBOOST_LIBRARYDIR="$PREFIX/lib" -DSERIALIZE="Boost" \ - -DCMAKE_CXX_FLAGS="-std=c++11 -O3 -I{PREFIX}/include" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS} -std=c++14 -O3 -I{PREFIX}/include" \ -DCMAKE_PREFIX_PATH="$PREFIX" -DCMAKE_CXX_COMPILER="${CXX}" cmake --build converterbuild/ --target install -j ${CPU_COUNT} -v diff --git a/recipes/percolator/meta.yaml b/recipes/percolator/meta.yaml index c3a9540cf1790..263639be02075 100644 --- a/recipes/percolator/meta.yaml +++ b/recipes/percolator/meta.yaml @@ -1,13 +1,13 @@ {% set name = "percolator" %} -{% set version = "3.6.5" %} +{% set version = "3.7.1" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/percolator/percolator/archive/refs/tags/rel-3-06-05.tar.gz - sha256: e386998046f59c34be01b1b0347709751d92f3a98e9a0079f8e7c5af5e2dcc8f + url: https://github.com/percolator/percolator/archive/refs/tags/rel-3-07-01.tar.gz + sha256: f1c9833063cb4e99c51a632efc3f80c6b8f48a43fd440ea3eb0968af5c84b97a build: number: 0 @@ -33,19 +33,19 @@ requirements: test: commands: - - sqt2pin -o testsqt.txt $PREFIX/testdata/target.sqt $PREFIX/testdata/target.sqt - - tandem2pin -o testtandem.txt $PREFIX/testdata/target.t.xml $PREFIX/testdata/target.t.xml - - msgf2pin -o testmzid.txt $PREFIX/testdata/target.mzid $PREFIX/testdata/target.mzid + #- sqt2pin -o testsqt.txt $PREFIX/testdata/target.sqt $PREFIX/testdata/target.sqt + #- tandem2pin -o testtandem.txt $PREFIX/testdata/target.t.xml $PREFIX/testdata/target.t.xml + #- msgf2pin -o testmzid.txt $PREFIX/testdata/target.mzid $PREFIX/testdata/target.mzid - percolator -X test.xml $PREFIX/testdata/percolatorTab about: - home: https://github.com/percolator/percolator + home: "https://github.com/percolator/percolator" license: Apache-2.0 license_family: APACHE - license_file: license.txt - summary: Semi-supervised learning for peptide identification from shotgun proteomics datasets - dev_url: https://github.com/percolator/percolator - doc_url: http://percolator.ms/ + license_file: "license.txt" + summary: "Semi-supervised learning for peptide identification from shotgun proteomics datasets." + dev_url: "https://github.com/percolator/percolator" + doc_url: "http://percolator.ms" extra: container: diff --git a/recipes/perl-convert-binary-c/build.sh b/recipes/perl-convert-binary-c/build.sh index acdfe24e65034..c6548a2e84767 100644 --- a/recipes/perl-convert-binary-c/build.sh +++ b/recipes/perl-convert-binary-c/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + # If it has Build.PL use that, otherwise use Makefile.PL if [ -f Build.PL ]; then perl Build.PL @@ -10,7 +12,7 @@ if [ -f Build.PL ]; then elif [ -f Makefile.PL ]; then # Make sure this goes in site perl Makefile.PL INSTALLDIRS=site - make + make -j ${CPU_COUNT} make test make install else diff --git a/recipes/perl-convert-binary-c/build_failure.osx-64.yaml b/recipes/perl-convert-binary-c/build_failure.osx-64.yaml deleted file mode 100644 index 988d5d7e4f623..0000000000000 --- a/recipes/perl-convert-binary-c/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b029f79f91254b89c13e5479ef25482a5d686dfd473a858727180255bcdcb8e6 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - } STMT_END - ^ - cbc/util.c:655:13: note: ')' token is here - DUMP_INDENT; - ^~~~~~~~~~~ - cbc/util.c:577:11: note: expanded from macro 'DUMP_INDENT' - } STMT_END - ^~~~~~~~ - ./ppport.h:3814:20: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - cbc/util.c:670:11: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - DUMP_INDENT; - ^~~~~~~~~~~ - cbc/util.c:574:9: note: expanded from macro 'DUMP_INDENT' - STMT_START { \ - ^~~~~~~~~~ - ./ppport.h:3813:28: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - cbc/util.c:670:11: note: '{' token is here - DUMP_INDENT; - ^~~~~~~~~~~ - cbc/util.c:574:20: note: expanded from macro 'DUMP_INDENT' - STMT_START { \ - ^ - cbc/util.c:670:11: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - DUMP_INDENT; - ^~~~~~~~~~~ - cbc/util.c:577:9: note: expanded from macro 'DUMP_INDENT' - } STMT_END - ^ - cbc/util.c:670:11: note: ')' token is here - DUMP_INDENT; - ^~~~~~~~~~~ - cbc/util.c:577:11: note: expanded from macro 'DUMP_INDENT' - } STMT_END - ^~~~~~~~ - ./ppport.h:3814:20: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 114 warnings generated. - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/bitfields.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/byteorder.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/cterror.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/ctparse.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/cttags.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/cttype.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/fileinfo.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/layout.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/y_parser.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ctlib/y_pragma.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ucpp/assert.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ucpp/cpp.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ucpp/eval.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ucpp/lexer.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ucpp/macro.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ucpp/mem.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] ucpp/nhash.c - ucpp/nhash.c:464:11: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] - action(arg, pnode); - ^ - ucpp/nhash.c:466:11: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] - action(pnode); - ^ - ucpp/nhash.c:478:10: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] - action(arg, node); - ^ - ucpp/nhash.c:480:10: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] - action(node); - ^ - 4 warnings generated. - Compiling [x86_64-apple-darwin13.4.0-clang -O3] util/hash.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] util/list.c - Compiling [x86_64-apple-darwin13.4.0-clang -O3] util/memalloc.c - rm -f blib/arch/auto/Convert/Binary/C/C.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong C.o cbc/basic.o cbc/dimension.o cbc/hook.o cbc/idl.o cbc/init.o cbc/macros.o cbc/member.o cbc/object.o cbc/option.o cbc/pack.o cbc/sourcify.o cbc/tag.o cbc/type.o cbc/typeinfo.o cbc/util.o ctlib/bitfields.o ctlib/byteorder.o ctlib/cterror.o ctlib/ctparse.o ctlib/cttags.o ctlib/cttype.o ctlib/fileinfo.o ctlib/layout.o ctlib/y_parser.o ctlib/y_pragma.o ucpp/assert.o ucpp/cpp.o ucpp/eval.o ucpp/lexer.o ucpp/macro.o ucpp/mem.o ucpp/nhash.o util/hash.o util/list.o util/memalloc.o -o blib/arch/auto/Convert/Binary/C/C.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:561: blib/arch/auto/Convert/Binary/C/C.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-convert-binary-c_1685353575548/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-convert-binary-c/meta.yaml b/recipes/perl-convert-binary-c/meta.yaml index f4812fb74c229..94f4002d4df60 100644 --- a/recipes/perl-convert-binary-c/meta.yaml +++ b/recipes/perl-convert-binary-c/meta.yaml @@ -1,26 +1,26 @@ {% set name = "perl-convert-binary-c" %} -{% set version = "0.84" %} -{% set sha256 = "a99ce7a8e60b8c6fe1cf73f290e423bd206e8721e3588ed125eebf7c39be3fb0" %} +{% set version = "0.85" %} +{% set sha256 = "c4cf42e00ea429ae3db276755b922282b4e8e9419d0eaf094aaa24107abc50e5" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/M/MH/MHX/Convert-Binary-C-0.84.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MH/MHX/Convert-Binary-C-0.85.tar.gz sha256: {{ sha256 }} build: - number: 3 + number: 1 + run_exports: + - {{ pin_subpackage('perl-convert-binary-c', max_pin="x.x") }} requirements: build: - make - {{ compiler('cxx') }} - host: - perl - run: - perl @@ -33,3 +33,8 @@ about: home: http://search.cpan.org/~mhx/Convert-Binary-C/ license: perl_5 summary: 'Binary Data Conversion using C Types' + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/perl-graph/meta.yaml b/recipes/perl-graph/meta.yaml index 951fae7d30fb1..802d75eb81ba1 100644 --- a/recipes/perl-graph/meta.yaml +++ b/recipes/perl-graph/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-graph - version: "0.9729" + version: "0.9732" source: - url: https://cpan.metacpan.org/authors/id/E/ET/ETJ/Graph-0.9729.tar.gz - sha256: 3efbed46ca82f78f25253d034232b0cc9cfadfbd867437e63f9275850f85abb0 + url: https://cpan.metacpan.org/authors/id/E/ET/ETJ/Graph-0.9732.tar.gz + sha256: eafc9e519a04ac0a61a3eb34b6e18709411e5abde4bf1d9019c2e371aedf6c50 build: noarch: generic diff --git a/recipes/perl-mce-shared/meta.yaml b/recipes/perl-mce-shared/meta.yaml index c37471eabc40c..94bbf9efe458b 100644 --- a/recipes/perl-mce-shared/meta.yaml +++ b/recipes/perl-mce-shared/meta.yaml @@ -1,14 +1,14 @@ {% set name = "perl-mce-shared" %} -{% set version = "1.891" %} -{% set sha256 = "f65459bd04f5e41bbf3ba82d74af3e0fc6c992cfc245dc403b6ce4cc24904cb5" %} +{% set version = "1.893" %} +{% set sha256 = "fa4c487adfb0db3c8f2b6aa274d33d8f827fa234c631bb3af3d94fa4a3c9462f" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-Shared-1.891.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-Shared-1.893.tar.gz sha256: {{ sha256 }} build: diff --git a/recipes/perl-mce/meta.yaml b/recipes/perl-mce/meta.yaml index 724ef988ccc24..eb7e0cfee892a 100644 --- a/recipes/perl-mce/meta.yaml +++ b/recipes/perl-mce/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-mce" %} -{% set version = "1.897" %} -{% set sha256 = "673d337d14fc2d7a12576ca6615c729821dc616ee76e0ecc9c0f32de8a9f9c39" %} +{% set version = "1.900" %} +{% set sha256 = "f83132da7a993a4700464cdbf1665bab8ec8ec120beb86e607cd983d207fc935" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-1.897.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-1.900.tar.gz sha256: {{ sha256 }} build: diff --git a/recipes/perl-minion/meta.yaml b/recipes/perl-minion/meta.yaml index f072af8962b1d..0dc5647826631 100644 --- a/recipes/perl-minion/meta.yaml +++ b/recipes/perl-minion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-minion" %} -{% set version = "10.30" %} -{% set sha256 = "b704bd66ec4af1c03394689f02c0ac0480ebd06ce9cca17291501b9202c6ed1c" %} +{% set version = "10.31" %} +{% set sha256 = "3068f99033e69df08145b584a91ee224f4e97dc6242e102221e8220a3f28503b" %} package: name: {{ name }} diff --git a/recipes/perl-parallel-forkmanager/meta.yaml b/recipes/perl-parallel-forkmanager/meta.yaml index 538bd3c4c8a96..bba5e7ed46bfe 100644 --- a/recipes/perl-parallel-forkmanager/meta.yaml +++ b/recipes/perl-parallel-forkmanager/meta.yaml @@ -1,14 +1,16 @@ package: name: perl-parallel-forkmanager - version: "2.02" + version: "2.03" source: - url: https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-2.02.tar.gz - sha256: c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404 + url: https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-2.03.tar.gz + sha256: c0e0bead458224b9ac5bb32ed2b1fa088963b565521c1bb1a6a3566d522c2e35 build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('perl-parallel-forkmanager', max_pin='x') }} requirements: build: diff --git a/recipes/perl-term-table/meta.yaml b/recipes/perl-term-table/meta.yaml index f2e5c6f439f5b..90c7601d8941b 100644 --- a/recipes/perl-term-table/meta.yaml +++ b/recipes/perl-term-table/meta.yaml @@ -1,18 +1,20 @@ {% set name = "perl-term-table" %} -{% set version = "0.016" %} -{% set sha256 = "8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf" %} +{% set version = "0.022" %} +{% set sha256 = "b9dbdacfa7362846e3c4a100081832db9da74b7356828ef9d92869c44642e0b8" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.016.tar.gz + url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.022.tar.gz sha256: {{ sha256 }} build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: diff --git a/recipes/pgenlib/meta.yaml b/recipes/pgenlib/meta.yaml index 6310a5f8d966f..a5786127871dc 100644 --- a/recipes/pgenlib/meta.yaml +++ b/recipes/pgenlib/meta.yaml @@ -1,16 +1,16 @@ {% set name = "pgenlib" %} -{% set version = "0.90.2" %} +{% set version = "0.91.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://pypi.io/packages/source/P/Pgenlib/Pgenlib-{{ version }}.tar.gz" - sha256: 09825be43ffb25bc68b6e243b98989a5bc35a8aa22cd749fd9f602d778dd6bd0 + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 32992274214d2e6735b721544abfd0ae0c76906c4193120f7091065b88f68dfa build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" run_exports: - {{ pin_subpackage('pgenlib', max_pin="x.x") }} @@ -21,12 +21,13 @@ requirements: host: - python - pip - - cython - - numpy + - cython + - numpy >=2.0.0 # [py >= 39] + - numpy # [py < 39] - zlib run: - python - - {{ pin_compatible('numpy') }} + - numpy >=1.19.0 test: imports: @@ -46,3 +47,6 @@ extra: - chrchang identifiers: - doi:10.1186/s13742-015-0047-8 + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/pgrc/build.sh b/recipes/pgrc/build.sh new file mode 100644 index 0000000000000..b71b6c3f55249 --- /dev/null +++ b/recipes/pgrc/build.sh @@ -0,0 +1,23 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin + +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + +cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + "${CONFIG_ARGS}" +cmake --build build --target PgRC -j "${CPU_COUNT}" -v + +chmod 0755 build/PgRC +cp -rf build/PgRC $PREFIX/bin diff --git a/recipes/pgrc/meta.yaml b/recipes/pgrc/meta.yaml new file mode 100644 index 0000000000000..c497ed99c87e7 --- /dev/null +++ b/recipes/pgrc/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "2.0" %} +{% set sha256 = "b4f7c1020dcf83428ee04663e2d68e81b08ba5853c9edffb3d5d00ac0f361b92" %} + +package: + name: pgrc + version: {{ version }} + +build: + number: 1 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('pgrc', max_pin="x") }} + +source: + url: https://github.com/kowallus/PgRC/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler('cxx') }} + - cmake >=3.5 + - make + host: + - llvm-openmp # [osx] + - libgomp # [linux] + run: + - llvm-openmp # [osx] + - libgomp # [linux] + +test: + commands: + - PgRC -v 2>&1 | grep -F {{ version }} + +about: + home: https://github.com/kowallus/PgRC + license: "GPL-3.0-or-later" + license_file: LICENSE + license_family: GPL3 + summary: "A tool for compressing the DNA stream of FASTQ datasets." + dev_url: https://github.com/kowallus/PgRC + +extra: + additional-platforms: + - linux-aarch64 + recipe-maintainers: + - kowallus + identifiers: + - doi:10.1093/bioinformatics/btz919 diff --git a/recipes/phables/meta.yaml b/recipes/phables/meta.yaml index 2d16b2857d523..b27d85947317e 100644 --- a/recipes/phables/meta.yaml +++ b/recipes/phables/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phables" %} -{% set version = "1.4.0" %} +{% set version = "1.4.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 09b843141ab32cda5016741b7f31ccefcb659448f0fd4aa55697c509680e16e9 + sha256: f456260bf710073986ecd524975e09083c5cf7d0ad3a0e6808ba48a2b7dc0ee4 build: number: 0 - noarch: python + noarch: false entry_points: - phables=phables.__main__:main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" @@ -48,5 +48,7 @@ about: dev_url: "https://github.com/Vini2/phables" extra: + skip-lints: + - should_be_noarch_generic recipe-maintainers: - Vini2 diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index 9f0478e642922..23e84b018047c 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.19.9" %} +{% set version = "2.0.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d8378135c89a9c957fe3236ce8a2f1ff2846100a4aa207d7cacec8500237e4dd + sha256: 32358dc24e564860ce56fa71772599a00d12dc746b6ca2fb046fbca9f4c1e2c3 build: noarch: python diff --git a/recipes/phyloacc/build.sh b/recipes/phyloacc/build.sh index b2034f66d9414..eb6412c7bc712 100644 --- a/recipes/phyloacc/build.sh +++ b/recipes/phyloacc/build.sh @@ -1,11 +1,13 @@ #!/bin/bash +set -xe + mkdir -p ${PREFIX}/bin mkdir -p ${SP_DIR} -make install CXX=${CXX} +make -j ${CPU_COUNT} install CXX=${CXX} cp src/PhyloAcc-interface/phyloacc.py ${PREFIX}/bin/ ln -s ${PREFIX}/bin/phyloacc.py ${PREFIX}/bin/phyloacc cp src/PhyloAcc-interface/phyloacc_post.py ${PREFIX}/bin/ -cp -R src/PhyloAcc-interface/phyloacc_lib ${SP_DIR}/ +cp -R src/PhyloAcc-interface/phyloacc_lib ${SP_DIR}/ \ No newline at end of file diff --git a/recipes/phyloacc/meta.yaml b/recipes/phyloacc/meta.yaml index 5c9be1dcd5e59..d8b30dff74689 100644 --- a/recipes/phyloacc/meta.yaml +++ b/recipes/phyloacc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PhyloAcc" %} -{% set version = "2.3.3" %} -{% set sha256 = "9fd75cae7015dd35d516ec040a331fcb6cb5377644d0d7864b488fda2f288d60" %} +{% set version = "2.4.1" %} +{% set sha256 = "919203dc541c172f9e835b0568f6abd49999a24734957fec020b01161479282c" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: build: number: 1 - skip: True # [py < 38] + skip: True # [py < 311] run_exports: - {{ pin_subpackage('phyloacc', max_pin="x") }} @@ -35,7 +35,8 @@ requirements: - matplotlib-base >=3.5 - biopython >=1.79 - numpy >=1.22 - - snakemake-minimal >=7.3 + - snakemake-minimal >=8.0 + - snakemake-executor-plugin-slurm - libgomp # [linux] - llvm-openmp # [osx] @@ -56,5 +57,7 @@ about: dev_url: https://github.com/phyloacc/PhyloAcc extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - gwct diff --git a/recipes/phyloaln/build.sh b/recipes/phyloaln/build.sh new file mode 100644 index 0000000000000..1832c18446a37 --- /dev/null +++ b/recipes/phyloaln/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +set -xe + +mkdir -p $PREFIX/bin +cp -rf $SRC_DIR/lib $PREFIX/bin +cp $SRC_DIR/PhyloAln $PREFIX/bin +cp -rf $SRC_DIR/scripts/* $PREFIX/bin diff --git a/recipes/phyloaln/meta.yaml b/recipes/phyloaln/meta.yaml new file mode 100644 index 0000000000000..59022155f358e --- /dev/null +++ b/recipes/phyloaln/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set sha256 = "e10ed2b344bff8b10a4334fd8d1d9d108104f6d1395bb50828edd78b82cdca5b" %} + +package: + name: phyloaln + version: "{{ version }}" +source: + url: https://github.com/huangyh45/PhyloAln/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('phyloaln', max_pin='x') }} + +requirements: + run: + - biopython >=1.77 + - ete3 >=3.1.2 + - hmmer >=3.1 + - mafft >=7.467 + - perl >=5.26.2 + - perl-bioperl >=1.7.2 + - perl-parallel-forkmanager >=2.02 + - python >=3.7.4 + +test: + commands: + - PhyloAln -h + - hmmbuild -h + - hmmsearch -h + - merge_seqs.py -h + - root_tree.py -h + - select_seqs.py -h + - test_effect.py -h + - trim_matrix.py -h + - perl -MBio::SeqIO -e 1 + - perl -MBio::DB::Fasta -e 1 + - perl -MParallel::ForkManager -e 1 + - mafft --version + +about: + home: https://github.com/huangyh45/PhyloAln + license: MIT + license_file: LICENSE + summary: "PhyloAln: a reference-based multiple sequence alignment tool for phylogeny" + +extra: + identifiers: + - doi:10.1093/molbev/msae150 diff --git a/recipes/phylodeep/meta.yaml b/recipes/phylodeep/meta.yaml new file mode 100644 index 0000000000000..52c3e29e478dd --- /dev/null +++ b/recipes/phylodeep/meta.yaml @@ -0,0 +1,63 @@ +{% set name = "phylodeep" %} +{% set version = "0.9" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 123365b279c706b9b2c0f4c8b215bc3f9943b8c52a02f76bb0e9a2bc91cf5d47 + +build: + number: 0 + noarch: python + entry_points: + - checkdeep = phylodeep.checkdeep:main + - modeldeep = phylodeep.modeldeep:main + - paramdeep = phylodeep.paramdeep:main + - subtree_picker = phylodeep.tree_utilities:subtree_picker_main + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir" + run_exports: + - {{ pin_subpackage('phylodeep', max_pin="x.x") }} + +requirements: + host: + - pip + - python >=3.6 + run: + - python >=3.6 + - scikit-learn >=1.0,<1.3.0 + - tensorflow >=2.0.0 + - ete3 >=3.1.1,<=3.1.3 + - pandas >=1.0.0,<1.4.0 + - matplotlib-base >=3.0.2,<3.7.0 + - keras ==2.2.4 + - phylodeep_data_bd >=0.6 + - phylodeep_data_bdei >=0.4 + - phylodeep_data_bdss >=0.4 + +test: + imports: + - phylodeep + commands: + - checkdeep --help + - modeldeep --help + - paramdeep --help + - subtree_picker --help + +about: + home: "https://github.com/evolbioinfo/phylodeep" + summary: "Deep-learning parameter estimation and model selection from phylogenetic trees." + description: | + PhyloDeep is a python library for parameter estimation and model selection from phylogenetic trees, + based on deep learning. + license: "GPL-3.0-or-later" + license_family: GPL3 + license_file: LICENSE + doc_url: "https://github.com/evolbioinfo/phylodeep/blob/{{ version }}/README.md" + dev_url: "https://github.com/evolbioinfo/phylodeep" + +extra: + recipe-maintainers: + - annazhukova diff --git a/recipes/phylodeep_data_bdss/meta.yaml b/recipes/phylodeep_data_bdss/meta.yaml index 7116090176840..e38d67480cc16 100644 --- a/recipes/phylodeep_data_bdss/meta.yaml +++ b/recipes/phylodeep_data_bdss/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phylodeep_data_bdss" %} -{% set version = "0.3" %} +{% set version = "0.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2af2db81208ac169ace415d0b4e68405a680283b744c450115f340e4bfa7071e + sha256: 2b97fb01e3babb969e786ba85074ab6799466903bbd351b3675b7099c3e17277 build: number: 0 diff --git a/recipes/phylofisher/meta.yaml b/recipes/phylofisher/meta.yaml index 29979d4e64b53..c95b2662fea79 100644 --- a/recipes/phylofisher/meta.yaml +++ b/recipes/phylofisher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PhyloFisher" %} -{% set version = "1.2.13" %} +{% set version = "1.2.14" %} package: name: "{{ name|lower }}" @@ -7,12 +7,12 @@ package: source: url: "https://github.com/TheBrownLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 0003e1820bbf84453edbf3cba68e01e2bd1c24a12608fe02bc01b1168efb5a1b + sha256: fd2c46cf1a49eb0fb83348dd280292f5f6b3a2541d76dd21f7e377e90be9dde5 build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vvv" + script: "{{ PYTHON }} -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('phylofisher', max_pin='x') }} @@ -30,7 +30,7 @@ requirements: - hmmer =3.3 - diamond =2.0.15 - fasttree =2.1.10 - - mafft =7.520 + - mafft =7.525 - trimal =1.4.1 - blast - cd-hit =4.8.1 @@ -47,7 +47,7 @@ about: home: "https://github.com/TheBrownLab/PhyloFisher" license: MIT license_family: MIT - license_file: LICENSE.txt + license_file: "LICENSE.txt" summary: "A package for the creation, analysis, and visualization of eukaryotic phylogenomic datasets." - doc_url: https://thebrownlab.github.io/phylofisher-pages/ - dev_url: https://github.com/TheBrownLab/PhyloFisher + doc_url: "https://thebrownlab.github.io/phylofisher-pages" + dev_url: "https://github.com/TheBrownLab/PhyloFisher" diff --git a/recipes/pia/meta.yaml b/recipes/pia/meta.yaml index 83c9eb152c594..039016c4488e9 100644 --- a/recipes/pia/meta.yaml +++ b/recipes/pia/meta.yaml @@ -8,7 +8,7 @@ package: build: noarch: generic - number: 0 + number: 2 run_exports: - {{ pin_subpackage('pia', max_pin="x") }} @@ -18,7 +18,7 @@ source: requirements: run: - - openjdk >=21 + - openjdk =21 test: commands: diff --git a/recipes/piawka/build.sh b/recipes/piawka/build.sh new file mode 100644 index 0000000000000..036594907f2e1 --- /dev/null +++ b/recipes/piawka/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# increase verbosity for debugging +set -x + +mkdir -p $PREFIX/bin + +# Replace `mawk -f` shebangs with "polyglot shebangs" +# as per https://unix.stackexchange.com/a/361796/605705 +# not to rely on non-standard `env -S` option +polyglot1='#!/bin/sh'; polyglot2='"exec" "mawk" "-f" "$0" "$@" && 0 {}' +for f in $SRC_DIR/scripts/*; do + t="$PREFIX/bin/$(basename $f)" + head -n 1 $f | grep awk && ( echo "$polyglot1" > $t && echo "$polyglot2" >> $t ) + cat $f >> $t +done + +chmod +x $PREFIX/bin/* + diff --git a/recipes/piawka/meta.yaml b/recipes/piawka/meta.yaml new file mode 100644 index 0000000000000..46510a8351bc5 --- /dev/null +++ b/recipes/piawka/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "piawka" %} +{% set version = "0.7.10" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/novikovalab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz + sha256: 511859b69525db7dc988ae55556e6fd31e2709f0e3a4de404f87abfadb97a273 + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('piawka', max_pin="x.x") }} + +requirements: + run: + - mawk =1.3.4 + - parallel + - bash + - tabix + +test: + commands: + - piawka_par.sh -h + +about: + home: https://github.com/novikovalab/piawka + license: MIT + license_family: MIT + license_file: LICENSE + summary: 'The powerful AWK script to calculate population statistics in VCF files with support for varying ploidy and missing data' + description: | + The powerful awk script to calculate π, Dxy (or πxy, or Nei's D) + and some more simple stats (Fst, Tajima's D, Ronfort's rho) in VCF files in the command line. + Developed to analyze arbitrary-ploidy groups with substantial amounts of missing data. + Largely inspired by https://github.com/ksamuk/pixy + dev_url: https://github.com/novikovalab/piawka + doc_url: https://github.com/novikovalab/piawka/wiki + doc_source_url: https://github.com/novikovalab/piawka/blob/main/README.md + +extra: + recipe-maintainers: + - taprs diff --git a/recipes/picrust2/meta.yaml b/recipes/picrust2/meta.yaml index 0a197f6654f6b..f2b495f7e56f6 100644 --- a/recipes/picrust2/meta.yaml +++ b/recipes/picrust2/meta.yaml @@ -1,15 +1,17 @@ {% set name = "picrust2" %} -{% set version = "2.5.2" %} +{% set version = "2.5.3" %} package: name: "{{ name|lower }}" version: "{{ version | replace('-', '_') }}" source: - url: https://github.com/picrust/picrust2/archive/refs/tags/v2.5.2.tar.gz - sha256: a8c3832bf759233b52b41c56a0ffef72491e431fee347a7c05695596c76a1a4c + url: https://github.com/picrust/picrust2/archive/refs/tags/v2.5.3.tar.gz + sha256: b8dfab3b961d7bafd9ceafaeb3ce95cc66c61d3c5e51325e79574d6e0c2b1e40 build: + run_exports: + - {{ pin_subpackage('picrust2', max_pin="x.x") }} number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " @@ -18,26 +20,28 @@ requirements: host: - cython - pip - - python >=3.5,<3.9 + - python >=3.5 run: - biom-format >=2.1.10 + - dendropy 4.5.2 - epa-ng 0.3.8 - - gappa 0.8.0 + - gappa >=0.8.0,<=0.8.5 - glpk >=4.65 - h5py >=2.10.0 - hmmer >=3.1b2,<=3.2.1 + - jinja2 >=2.11.3 - joblib >=1.0.1 - numpy >=1.19.5 - pandas >=1.1.5 - - python >=3.5,<3.9 + - python >=3.5 - pytest >=4.4.1 - pytest-cov >=2.6.1 - r-base >=3.5.1 - r-castor >=1.7.2 - scipy >=1.2.1 - - sepp 4.3.10 + - sepp 4.4.0 - wget - + test: commands: - add_descriptions.py -h > /dev/null diff --git a/recipes/picrust2/post-link.sh b/recipes/picrust2/post-link.sh index c84fa20b56125..e7ffd8b392170 100644 --- a/recipes/picrust2/post-link.sh +++ b/recipes/picrust2/post-link.sh @@ -1,9 +1,9 @@ #!/bin/bash -FN="v2.5.2.tar.gz" -TARBALL_DIR="picrust2-2.5.2" -URL="https://github.com/picrust/picrust2/archive/v2.5.2.tar.gz" -SHA256="a8c3832bf759233b52b41c56a0ffef72491e431fee347a7c05695596c76a1a4c" +FN="v2.5.3.tar.gz" +TARBALL_DIR="picrust2-2.5.3" +URL="https://github.com/picrust/picrust2/archive/v2.5.3.tar.gz" +SHA256="b8dfab3b961d7bafd9ceafaeb3ce95cc66c61d3c5e51325e79574d6e0c2b1e40" # Create staging area. STAGING=$PREFIX/staging diff --git a/recipes/piper/meta.yaml b/recipes/piper/meta.yaml index cf3d8030e4a85..ba86bbdf68bdf 100644 --- a/recipes/piper/meta.yaml +++ b/recipes/piper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "piper" %} -{% set version = "0.14.2" %} +{% set version = "0.14.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "fff74a6e7cbf188a3ce023913a9ce63098e7c3acfa73833fd9e4c4096a578035" + sha256: "fec31dd795de95ee88e6019e0c8402aa3a37f8e03213f01f348c8ee50ce8570e" build: number: 0 diff --git a/recipes/pipits/meta.yaml b/recipes/pipits/meta.yaml index 8cb0fa5c54ccf..0c32e5afba401 100644 --- a/recipes/pipits/meta.yaml +++ b/recipes/pipits/meta.yaml @@ -1,14 +1,16 @@ package: name: pipits - version: "3.0" + version: "3.1" source: - url: https://github.com/hsgweon/pipits/archive/refs/tags/3.0.tar.gz - sha256: ee9f142e473e57b186760d940131610c16bdfe57eefca935df35779fd85377bd + url: https://github.com/hsgweon/pipits/archive/refs/tags/3.1.tar.gz + sha256: a51bdaf4ec22487b9ed6f9111568d370ce0f9732afc010a5d0de0e642af758d7 build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('pipits', max_pin="x") }} requirements: host: diff --git a/recipes/piranha-polio/meta.yaml b/recipes/piranha-polio/meta.yaml index 679fe76aa8c46..8e3b1be9c9df3 100644 --- a/recipes/piranha-polio/meta.yaml +++ b/recipes/piranha-polio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.5" %} +{% set version = "1.3.1" %} package: name: piranha-polio @@ -6,7 +6,7 @@ package: source: url: https://github.com/polio-nanopore/piranha/archive/refs/tags/{{ version }}.tar.gz - sha256: c6b9f8fdaab085bfbe75b2839d29dceb3e40c8af100379123f40eeebeb83c8fb + sha256: a2786e24459e4d9d5a45cc7c7b76853b433944bc5d17929fa12c0c99e2d89b22 build: number: 0 diff --git a/recipes/pkiss/meta.yaml b/recipes/pkiss/meta.yaml index 6e05c89596ce9..5bef440d7e10c 100644 --- a/recipes/pkiss/meta.yaml +++ b/recipes/pkiss/meta.yaml @@ -1,19 +1,20 @@ -{% set version = "2.3.1" %} +{% set fold_grammars_version = "2.3.1" %} +{% set pkiss_version = "2.3.0" %} {% set packagename = "pkiss" %} {% set sha256 = "0c5b7d91893d0a23189f4af3602e18f110f030eac49a3658f7acede23596fde0" %} package: name: {{ packagename }} - version: 2.3.0 + version: {{ pkiss_version }} source: sha256: {{ sha256 }} # the repository "fold-grammars" contains sources for several programs, i.e. pKiss, RNAshapes, ... # thus, the version number does not correspond to the {{ packagename }} version number - url: https://github.com/jlab/fold-grammars/archive/{{ version }}.tar.gz + url: https://github.com/jlab/fold-grammars/archive/{{ fold_grammars_version }}.tar.gz build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('pkiss', max_pin="x") }} diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index e37d7821ced54..ea46961af1b4f 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.24" %} -{% set sha256 = "a0ee1ace9b5e2a9bf17c735d3b95236e9756921eded7cd9847717dd0adff6e42" %} +{% set version = "0.75.26" %} +{% set sha256 = "3f71b17ef9590de1c82db7ff4e8e2e05ca63fd1f5bfea0b7ee077b378bed7037" %} package: name: {{ name|lower }} diff --git a/recipes/plasnet/meta.yaml b/recipes/plasnet/meta.yaml index 82a185e403c37..c210d46bcaf0e 100644 --- a/recipes/plasnet/meta.yaml +++ b/recipes/plasnet/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} {% set name = "plasnet" %} package: @@ -7,11 +7,11 @@ package: source: url: https://github.com/leoisl/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: ca8d17649d59dbf0b5ce20d8c687a9f3a17804007b0fdb59654156b665149285 + sha256: 2afc3e7c91265d3605860e70cffcbe366ba36e0dd5da08331b83fd20883af392 build: - number: 0 - noarch: generic + number: 1 + noarch: python script: python -m pip install . --no-deps --ignore-installed -vvv entry_points: - plasnet = plasnet.plasnet_main:main diff --git a/recipes/pling/meta.yaml b/recipes/pling/meta.yaml new file mode 100644 index 0000000000000..61c2193346c7e --- /dev/null +++ b/recipes/pling/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "2.0.0" %} +{% set name = "pling" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/iqbal-lab-org/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 9e00b70239dcefdcfbaf3089757f1d6505428d71e1ef612fa3e3a230b368ce44 + +build: + number: 0 + noarch: python + script: "pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + entry_points: + - pling = pling.run_pling:main + run_exports: + - {{ pin_subpackage("pling", max_pin="x") }} + +requirements: + host: + - python >=3.9,<3.12 + - pip + run: + - python >=3.9,<3.12 + - sourmash >=4.4.0,<5.0.0 + - pandas >=1.5.3 + - numpy >=1.26.0 + - intervaltree >=3.0.2 + - mummer >=3.23 + - glpk >=5.0 + - snakemake >=7.25.4,<8.0.0 + - plasnet >=0.6.0 + - dingII +test: + imports: + - pling + + commands: + - pling --help + +about: + home: https://github.com/iqbal-lab-org/pling + license: LICENSE + license_family: MIT + summary: 'Pling computes the rearrangement distance between plasmids and clusters on their basis ' + diff --git a/recipes/pod5/LICENSE.md b/recipes/pod5/LICENSE.md new file mode 100644 index 0000000000000..9f3e082df8e44 --- /dev/null +++ b/recipes/pod5/LICENSE.md @@ -0,0 +1,362 @@ +This Source Code Form is subject to the terms of the Mozilla Public +License, v. 2.0. If a copy of the MPL was not distributed with this +file, You can obtain one at https://mozilla.org/MPL/2.0/. + +©2021 Oxford Nanopore Technologies PLC. + + +Mozilla Public License Version 2.0 +================================== + +### 1. Definitions + +**1.1. “Contributor”** + means each individual or legal entity that creates, contributes to + the creation of, or owns Covered Software. + +**1.2. “Contributor Version”** + means the combination of the Contributions of others (if any) used + by a Contributor and that particular Contributor's Contribution. + +**1.3. “Contribution”** + means Covered Software of a particular Contributor. + +**1.4. “Covered Software”** + means Source Code Form to which the initial Contributor has attached + the notice in Exhibit A, the Executable Form of such Source Code + Form, and Modifications of such Source Code Form, in each case + including portions thereof. + +**1.5. “Incompatible With Secondary Licenses”** + means + +* **(a)** that the initial Contributor has attached the notice described + in Exhibit B to the Covered Software; or +* **(b)** that the Covered Software was made available under the terms of + version 1.1 or earlier of the License, but not also under the + terms of a Secondary License. + +**1.6. “Executable Form”** + means any form of the work other than Source Code Form. + +**1.7. “Larger Work”** + means a work that combines Covered Software with other material, in + a separate file or files, that is not Covered Software. + +**1.8. “License”** + means this document. + +**1.9. “Licensable”** + means having the right to grant, to the maximum extent possible, + whether at the time of the initial grant or subsequently, any and + all of the rights conveyed by this License. + +**1.10. “Modifications”** + means any of the following: + +* **(a)** any file in Source Code Form that results from an addition to, + deletion from, or modification of the contents of Covered + Software; or +* **(b)** any new file in Source Code Form that contains any Covered + Software. + +**1.11. “Patent Claims” of a Contributor** + means any patent claim(s), including without limitation, method, + process, and apparatus claims, in any patent Licensable by such + Contributor that would be infringed, but for the grant of the + License, by the making, using, selling, offering for sale, having + made, import, or transfer of either its Contributions or its + Contributor Version. + +**1.12. “Secondary License”** + means either the GNU General Public License, Version 2.0, the GNU + Lesser General Public License, Version 2.1, the GNU Affero General + Public License, Version 3.0, or any later versions of those + licenses. + +**1.13. “Source Code Form”** + means the form of the work preferred for making modifications. + +**1.14. “You” (or “Your”)** + means an individual or a legal entity exercising rights under this + License. For legal entities, “You” includes any entity that + controls, is controlled by, or is under common control with You. For + purposes of this definition, “control” means **(a)** the power, direct + or indirect, to cause the direction or management of such entity, + whether by contract or otherwise, or **(b)** ownership of more than + fifty percent (50%) of the outstanding shares or beneficial + ownership of such entity. + + +### 2. License Grants and Conditions + +#### 2.1. Grants + +Each Contributor hereby grants You a world-wide, royalty-free, +non-exclusive license: + +* **(a)** under intellectual property rights (other than patent or trademark) + Licensable by such Contributor to use, reproduce, make available, + modify, display, perform, distribute, and otherwise exploit its + Contributions, either on an unmodified basis, with Modifications, or + as part of a Larger Work; and +* **(b)** under Patent Claims of such Contributor to make, use, sell, offer + for sale, have made, import, and otherwise transfer either its + Contributions or its Contributor Version. + +#### 2.2. Effective Date + +The licenses granted in Section 2.1 with respect to any Contribution +become effective for each Contribution on the date the Contributor first +distributes such Contribution. + +#### 2.3. Limitations on Grant Scope + +The licenses granted in this Section 2 are the only rights granted under +this License. No additional rights or licenses will be implied from the +distribution or licensing of Covered Software under this License. +Notwithstanding Section 2.1(b) above, no patent license is granted by a +Contributor: + +* **(a)** for any code that a Contributor has removed from Covered Software; + or +* **(b)** for infringements caused by: **(i)** Your and any other third party's + modifications of Covered Software, or **(ii)** the combination of its + Contributions with other software (except as part of its Contributor + Version); or +* **(c)** under Patent Claims infringed by Covered Software in the absence of + its Contributions. + +This License does not grant any rights in the trademarks, service marks, +or logos of any Contributor (except as may be necessary to comply with +the notice requirements in Section 3.4). + +#### 2.4. Subsequent Licenses + +No Contributor makes additional grants as a result of Your choice to +distribute the Covered Software under a subsequent version of this +License (see Section 10.2) or under the terms of a Secondary License (if +permitted under the terms of Section 3.3). + +#### 2.5. Representation + +Each Contributor represents that the Contributor believes its +Contributions are its original creation(s) or it has sufficient rights +to grant the rights to its Contributions conveyed by this License. + +#### 2.6. Fair Use + +This License is not intended to limit any rights You have under +applicable copyright doctrines of fair use, fair dealing, or other +equivalents. + +#### 2.7. Conditions + +Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted +in Section 2.1. + + +### 3. Responsibilities + +#### 3.1. Distribution of Source Form + +All distribution of Covered Software in Source Code Form, including any +Modifications that You create or to which You contribute, must be under +the terms of this License. You must inform recipients that the Source +Code Form of the Covered Software is governed by the terms of this +License, and how they can obtain a copy of this License. You may not +attempt to alter or restrict the recipients' rights in the Source Code +Form. + +#### 3.2. Distribution of Executable Form + +If You distribute Covered Software in Executable Form then: + +* **(a)** such Covered Software must also be made available in Source Code + Form, as described in Section 3.1, and You must inform recipients of + the Executable Form how they can obtain a copy of such Source Code + Form by reasonable means in a timely manner, at a charge no more + than the cost of distribution to the recipient; and + +* **(b)** You may distribute such Executable Form under the terms of this + License, or sublicense it under different terms, provided that the + license for the Executable Form does not attempt to limit or alter + the recipients' rights in the Source Code Form under this License. + +#### 3.3. Distribution of a Larger Work + +You may create and distribute a Larger Work under terms of Your choice, +provided that You also comply with the requirements of this License for +the Covered Software. If the Larger Work is a combination of Covered +Software with a work governed by one or more Secondary Licenses, and the +Covered Software is not Incompatible With Secondary Licenses, this +License permits You to additionally distribute such Covered Software +under the terms of such Secondary License(s), so that the recipient of +the Larger Work may, at their option, further distribute the Covered +Software under the terms of either this License or such Secondary +License(s). + +#### 3.4. Notices + +You may not remove or alter the substance of any license notices +(including copyright notices, patent notices, disclaimers of warranty, +or limitations of liability) contained within the Source Code Form of +the Covered Software, except that You may alter any license notices to +the extent required to remedy known factual inaccuracies. + +#### 3.5. Application of Additional Terms + +You may choose to offer, and to charge a fee for, warranty, support, +indemnity or liability obligations to one or more recipients of Covered +Software. However, You may do so only on Your own behalf, and not on +behalf of any Contributor. You must make it absolutely clear that any +such warranty, support, indemnity, or liability obligation is offered by +You alone, and You hereby agree to indemnify every Contributor for any +liability incurred by such Contributor as a result of warranty, support, +indemnity or liability terms You offer. You may include additional +disclaimers of warranty and limitations of liability specific to any +jurisdiction. + + +### 4. Inability to Comply Due to Statute or Regulation + +If it is impossible for You to comply with any of the terms of this +License with respect to some or all of the Covered Software due to +statute, judicial order, or regulation then You must: **(a)** comply with +the terms of this License to the maximum extent possible; and **(b)** +describe the limitations and the code they affect. Such description must +be placed in a text file included with all distributions of the Covered +Software under this License. Except to the extent prohibited by statute +or regulation, such description must be sufficiently detailed for a +recipient of ordinary skill to be able to understand it. + + +### 5. Termination + +**5.1.** The rights granted under this License will terminate automatically +if You fail to comply with any of its terms. However, if You become +compliant, then the rights granted under this License from a particular +Contributor are reinstated **(a)** provisionally, unless and until such +Contributor explicitly and finally terminates Your grants, and **(b)** on an +ongoing basis, if such Contributor fails to notify You of the +non-compliance by some reasonable means prior to 60 days after You have +come back into compliance. Moreover, Your grants from a particular +Contributor are reinstated on an ongoing basis if such Contributor +notifies You of the non-compliance by some reasonable means, this is the +first time You have received notice of non-compliance with this License +from such Contributor, and You become compliant prior to 30 days after +Your receipt of the notice. + +**5.2.** If You initiate litigation against any entity by asserting a patent +infringement claim (excluding declaratory judgment actions, +counter-claims, and cross-claims) alleging that a Contributor Version +directly or indirectly infringes any patent, then the rights granted to +You by any and all Contributors for the Covered Software under Section +2.1 of this License shall terminate. + +**5.3.** In the event of termination under Sections 5.1 or 5.2 above, all +end user license agreements (excluding distributors and resellers) which +have been validly granted by You or Your distributors under this License +prior to termination shall survive termination. + + +### 6. Disclaimer of Warranty + +> Covered Software is provided under this License on an “as is” +> basis, without warranty of any kind, either expressed, implied, or +> statutory, including, without limitation, warranties that the +> Covered Software is free of defects, merchantable, fit for a +> particular purpose or non-infringing. The entire risk as to the +> quality and performance of the Covered Software is with You. +> Should any Covered Software prove defective in any respect, You +> (not any Contributor) assume the cost of any necessary servicing, +> repair, or correction. This disclaimer of warranty constitutes an +> essential part of this License. No use of any Covered Software is +> authorized under this License except under this disclaimer. + +### 7. Limitation of Liability + +> Under no circumstances and under no legal theory, whether tort +> (including negligence), contract, or otherwise, shall any +> Contributor, or anyone who distributes Covered Software as +> permitted above, be liable to You for any direct, indirect, +> special, incidental, or consequential damages of any character +> including, without limitation, damages for lost profits, loss of +> goodwill, work stoppage, computer failure or malfunction, or any +> and all other commercial damages or losses, even if such party +> shall have been informed of the possibility of such damages. This +> limitation of liability shall not apply to liability for death or +> personal injury resulting from such party's negligence to the +> extent applicable law prohibits such limitation. Some +> jurisdictions do not allow the exclusion or limitation of +> incidental or consequential damages, so this exclusion and +> limitation may not apply to You. + + +### 8. Litigation + +Any litigation relating to this License may be brought only in the +courts of a jurisdiction where the defendant maintains its principal +place of business and such litigation shall be governed by laws of that +jurisdiction, without reference to its conflict-of-law provisions. +Nothing in this Section shall prevent a party's ability to bring +cross-claims or counter-claims. + + +### 9. Miscellaneous + +This License represents the complete agreement concerning the subject +matter hereof. If any provision of this License is held to be +unenforceable, such provision shall be reformed only to the extent +necessary to make it enforceable. Any law or regulation which provides +that the language of a contract shall be construed against the drafter +shall not be used to construe this License against a Contributor. + + +### 10. Versions of the License + +#### 10.1. New Versions + +Mozilla Foundation is the license steward. Except as provided in Section +10.3, no one other than the license steward has the right to modify or +publish new versions of this License. Each version will be given a +distinguishing version number. + +#### 10.2. Effect of New Versions + +You may distribute the Covered Software under the terms of the version +of the License under which You originally received the Covered Software, +or under the terms of any subsequent version published by the license +steward. + +#### 10.3. Modified Versions + +If you create software not governed by this License, and you want to +create a new license for such software, you may create and use a +modified version of this License if you rename the license and remove +any references to the name of the license steward (except to note that +such modified license differs from this License). + +#### 10.4. Distributing Source Code Form that is Incompatible With Secondary Licenses + +If You choose to distribute Source Code Form that is Incompatible With +Secondary Licenses under the terms of this version of the License, the +notice described in Exhibit B of this License must be attached. + +## Exhibit A - Source Code Form License Notice + + This Source Code Form is subject to the terms of the Mozilla Public + License, v. 2.0. If a copy of the MPL was not distributed with this + file, You can obtain one at https://mozilla.org/MPL/2.0/. + +If it is not possible or desirable to put the notice in a particular +file, then You may include the notice in a location (such as a LICENSE +file in a relevant directory) where a recipient would be likely to look +for such a notice. + +You may add additional accurate notices of copyright ownership. + +## Exhibit B - “Incompatible With Secondary Licenses” Notice + + This Source Code Form is "Incompatible With Secondary Licenses", as + defined by the Mozilla Public License, v. 2.0. diff --git a/recipes/pod5/meta.yaml b/recipes/pod5/meta.yaml new file mode 100644 index 0000000000000..11c50c7d4c37c --- /dev/null +++ b/recipes/pod5/meta.yaml @@ -0,0 +1,73 @@ +{% set name = "pod5" %} +{% set version = "0.3.15" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/nanoporetech/pod5-file-format/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz + sha256: 85e3196bfc375b7d6eb36787a312af5276b19829ceded551b55e9e193939e8f4 + +build: + number: 0 + noarch: python + entry_points: + - pod5 = pod5.tools.main:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('pod5', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - lib-pod5 =={{ version }} + - iso8601 + - importlib-metadata # [py < 38] + - more-itertools + - numpy >=1.21.0 + - typing-extensions # [py < 310] + - pyarrow >=16.1.0,<16.2.dev0 # [not osx or py < 312] + - pytz + - packaging + - polars >=0.19,<1.dev0 + - h5py >=3.11.0,<3.12.dev0 # [py > 38] + #- vbz_h5py_plugin + - tqdm + +test: + imports: + - pod5 + commands: + - pod5 --help + +about: + summary: "Oxford Nanopore Technologies Pod5 File Format Python API and Tools." + license: "MPL-2.0" + license_family: OTHER + license_file: "LICENSE.md" + home: "https://github.com/nanoporetech/pod5-file-format" + dev_url: "https://github.com/nanoporetech/pod5-file-format" + doc_url: "https://pod5-file-format.readthedocs.io/en/latest" + description: + + POD5 File Format + ---------------- + + POD5 is a file format for storing nanopore dna data in an easily accessible way. + The format is able to be written in a streaming manner which allows a sequencing instrument to directly write the format. + + Data in POD5 is stored using Apache Arrow, allowing users to consume data in many languages using standard tools. + + What does this project contain + ------------------------------ + + This project contains a core library for reading and writing POD5 data, and a toolkit for accessing this data in other languages. + + Documentation + ------------- + + Full documentation is found at https://pod5-file-format.readthedocs.io diff --git a/recipes/veryfasttree/LICENSE b/recipes/polap/LICENSE similarity index 97% rename from recipes/veryfasttree/LICENSE rename to recipes/polap/LICENSE index 357d4c5614dee..f288702d2fa16 100644 --- a/recipes/veryfasttree/LICENSE +++ b/recipes/polap/LICENSE @@ -1,18 +1,3 @@ - -VeryFastTree -- speeding up the estimation of phylogenies for large alignments - through parallelization and vectorization strategies - -VeryFastTree: - César P. Pomar: https://citius.usc.es/v/cesar-alfredo-pineiro-pomar - Juan C. Pichel: https://citius.usc.es/v/juan-carlos-pichel-campos - -Based on FastTree: - Morgan N. Price: http://www.microbesonline.org/fasttree/ - -Copyright (C) 2008-2015 The Regents of the University of California -Copyright (C) 2018-2019 Universidade de Santiago de Compostela - - GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 @@ -646,8 +631,8 @@ to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. - Copyright (C) 2008-2015 The Regents of the University of California - Copyright (C) 2018-2019 Universidade de Santiago de Compostela + + Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -667,9 +652,7 @@ Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: - Fasttree Copyright (C) 2008-2015 The Regents of the University of California - VeryFastTree Copyright (C) 2018-2019 Universidade de Santiago de Compostela - + Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. diff --git a/recipes/polap/build.sh b/recipes/polap/build.sh new file mode 100644 index 0000000000000..343b7d9d0f89f --- /dev/null +++ b/recipes/polap/build.sh @@ -0,0 +1,24 @@ +#!/usr/bin/env bash + +mkdir -p $PREFIX/bin + +files=(polap + polap-conda-environment-fmlrc.yaml + polap-conda-environment.yaml + polap-mt.1.c70.3.faa + polap-parsing.sh + polap-pt.2.c70.3.faa + polap.sh + run-polap-genes.R + run-polap-jellyfish.R + run-polap-mtcontig.R + run-polap-ncbitools + run-polap-pairs.R) + +for i in "${files[@]}"; do + cp src/$i $PREFIX/bin +done + +chmod +x $PREFIX/bin/polap +chmod +x $PREFIX/bin/polap.sh +chmod +x $PREFIX/bin/run-polap-* diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml new file mode 100644 index 0000000000000..eacc9680c84a3 --- /dev/null +++ b/recipes/polap/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "polap" %} +{% set version = "0.2.6" %} +{% set sha256 = "6d9b5ffc26ce6feeaa6119d0dda57e07af9e9def55e5510b0ddf237699b15948" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: https://github.com/goshng/{{ name }}/archive/refs/tags/{{ version }}.tar.gz + sha256: "{{ sha256 }}" + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('polap', max_pin="x.x") }} + +requirements: + run: + - python + - flye >=2.9.2 + - seqkit + - minimap2 >=2.24 + - blast + - bedtools + - seqtk + - bioawk + - entrez-direct + - sra-tools + - csvtk + - gfastats + - kmer-jellyfish + - clustalw + - samtools + - assembly-stats + - orthofinder + - bioconductor-ggtree + - perl-xml-libxml + - icu + - libxml2 + - perl + - r-base + - r-dplyr + - r-readr + - r-optparse + - r-stringr + - r-tidyr + - parallel + +test: + commands: + - polap + +about: + home: https://github.com/goshng/polap + license: GPL-3.0-or-later + license_family: GPL + license_file: LICENSE + summary: "POLAP: plant organelle long-read assembly pipeline" + dev_url: https://github.com/goshng/polap + doc_url: https://goshng.github.io/polap/polap.html + +extra: + recipe-maintainers: + - goshng diff --git a/recipes/poolsnp/meta.yaml b/recipes/poolsnp/meta.yaml index 5f92f96931557..b477040292487 100644 --- a/recipes/poolsnp/meta.yaml +++ b/recipes/poolsnp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "poolsnp" %} -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} {% set github = "https://github.com/capoony/PoolSNP" %} package: @@ -8,7 +8,7 @@ package: source: url: "{{ github }}/archive/refs/tags/v.{{ version }}.tar.gz" - sha256: a73c61c7ef49be9bd1212ea8049fe617296b0a82b80e0338e2b78dc55105438f + sha256: a98003758e2f93f2c7dc907ad990594e7fa85ca5f3fd5a7b3bcbc6363fbb9571 requirements: host: @@ -37,4 +37,4 @@ about: extra: recipe-maintainers: - - abhilesh \ No newline at end of file + - abhilesh diff --git a/recipes/poplddecay/build.sh b/recipes/poplddecay/build.sh new file mode 100644 index 0000000000000..da285f1095326 --- /dev/null +++ b/recipes/poplddecay/build.sh @@ -0,0 +1,20 @@ +#!/bin/bash -euo + +mkdir -p ${PREFIX}/bin + +export M4="${BUILD_PREFIX}/bin/m4" +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" + +autoreconf -if +./configure CXX="${CXX}" \ + CXXFLAGS="${CXXFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + --prefix="${PREFIX}" + +make -j"${CPU_COUNT}" + +chmod 0755 PopLDdecay +cp -rf PopLDdecay ${PREFIX}/bin diff --git a/recipes/poplddecay/meta.yaml b/recipes/poplddecay/meta.yaml new file mode 100644 index 0000000000000..6c2d6e9728491 --- /dev/null +++ b/recipes/poplddecay/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "PopLDdecay" %} +{% set version = "3.43" %} +{% set sha256 = "ce5b89005ac063e590d02f4a5922da646651fb2086c5708b280feda84c84dd72" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/BGI-shenzhen/PopLDdecay/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 1 + run_exports: + - {{ pin_subpackage('poplddecay', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - autoconf + - automake + - libtool + host: + - zlib + +test: + commands: + - 'PopLDdecay 2>&1 | grep "Usage: PopLDdecay"' + +about: + home: "https://github.com/BGI-shenzhen/PopLDdecay" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format (VCF) files." + dev_url: "https://github.com/BGI-shenzhen/PopLDdecay" + doc_url: "https://github.com/BGI-shenzhen/PopLDdecay/blob/v{{ version }}/README.md" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + identifiers: + - doi:10.1093/bioinformatics/bty875 + - biotools:PopLDdecay diff --git a/recipes/popoolation2/build.sh b/recipes/popoolation2/build.sh new file mode 100644 index 0000000000000..0d2faf8de0be4 --- /dev/null +++ b/recipes/popoolation2/build.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +outdir=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM} +mkdir -p ${PREFIX}/bin ${outdir} + +chmod +x *.pl export/*.pl indel_filtering/*.pl +cp -R *.pl export Modules indel_filtering ${PREFIX}/bin +cp mpileup2sync.jar ${outdir} +cp ${RECIPE_DIR}/mpileup2sync.py ${outdir}/mpileup2sync + +ln -s ${outdir}/mpileup2sync ${PREFIX}/bin + +for f in cmh2gwas.pl pwc2igv.pl subsample_sync2fasta.pl subsample_sync2GenePop.pl + do + ln -s ${PREFIX}/bin/export/${f} ${PREFIX}/bin +done + +for f in filter-sync-by-gtf.pl identify-indel-regions.pl + do + ln -s ${PREFIX}/bin/indel_filtering/${f} ${PREFIX}/bin +done diff --git a/recipes/popoolation2/meta.yaml b/recipes/popoolation2/meta.yaml new file mode 100644 index 0000000000000..6f33895b378fc --- /dev/null +++ b/recipes/popoolation2/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "popoolation2" %} +{% set version = "1.201" %} +{% set sha256 = "7f45353a211ec88d36fd1beed1d128673f3ff911b731211eb5a39f8602bddd42" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://downloads.sourceforge.net/project/popoolation2/popoolation2_1201.zip + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('popoolation2', max_pin="x") }} + +requirements: + host: + - perl + run: + - perl + - perl-text-nsp + - r-base + - bwa + - samtools + - igv + - openjdk + - python + +test: + commands: + - page -V 2>&1 | grep page + - snp-frequency-diff.pl --help 2>&1 | grep SNP-frequency-diff.pl + - fst-sliding.pl --help 2>&1 | grep fst-sliding.pl + - fisher-test.pl --help 2>&1 | grep fisher-test.pl + - pwc2igv.pl --help 2>&1 | grep pwc2igv + - cmh2gwas.pl --help 2>&1 | grep cmh2gwas + - identify-indel-regions.pl 2>&1 | grep identify-indel-regions + - filter-sync-by-gtf.pl 2>&1 | grep filter-sync-by-gtf + - mpileup2sync --help 2>&1 | grep mpileup2sync + - subsample_sync2fasta.pl 2>&1 | grep subsample_sync2fasta + - subsample_sync2GenePop.pl 2>&1 | grep subsample_sync2GenePop + - filter-sync-by-gtf.pl 2>&1 | grep filter-sync-by-gtf + +about: + home: "https://sourceforge.net/projects/popoolation2" + summary: "PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences." + license: BSD-3 + license_family: BSD + +extra: + identifiers: + - doi:10.1093/bioinformatics/btr589 diff --git a/recipes/popoolation2/mpileup2sync.py b/recipes/popoolation2/mpileup2sync.py new file mode 100644 index 0000000000000..2629cf831876a --- /dev/null +++ b/recipes/popoolation2/mpileup2sync.py @@ -0,0 +1,123 @@ +#! /usr/bin/env python +# +# Wrapper script for Java Conda packages that ensures that the java runtime +# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). + +# +# Program Parameters +# +import os +import subprocess +import sys +import shutil +from os import access +from os import getenv +from os import X_OK + +jar_file = 'mpileup2sync.jar' + + +default_jvm_mem_opts = ['-Xms2g', '-Xmx7g'] + +# !!! End of parameter section. No user-serviceable code below this line !!! + + +def real_dirname(path): + """Return the symlink-resolved, canonicalized directory-portion of path.""" + return os.path.dirname(os.path.realpath(path)) + + +def java_executable(): + """Return the executable name of the Java interpreter.""" + java_home = getenv('JAVA_HOME') + java_bin = os.path.join('bin', 'java') + + if java_home and access(os.path.join(java_home, java_bin), X_OK): + return os.path.join(java_home, java_bin) + else: + return 'java' + + +def jvm_opts(argv): + """Construct list of Java arguments based on our argument list. + + The argument list passed in argv must not include the script name. + The return value is a 3-tuple lists of strings of the form: + (memory_options, prop_options, passthrough_options) + """ + mem_opts = [] + prop_opts = [] + pass_args = [] + exec_dir = None + + for arg in argv: + if arg.startswith('-D'): + prop_opts.append(arg) + elif arg.startswith('-XX'): + prop_opts.append(arg) + elif arg.startswith('-Xm'): + mem_opts.append(arg) + elif arg.startswith('--exec_dir='): + exec_dir = arg.split('=')[1].strip('"').strip("'") + if not os.path.exists(exec_dir): + shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) + else: + pass_args.append(arg) + + # In the original shell script the test coded below read: + # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] + # To reproduce the behaviour of the above shell code fragment + # it is important to explictly check for equality with None + # in the second condition, so a null envar value counts as True! + + if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: + mem_opts = default_jvm_mem_opts + + return (mem_opts, prop_opts, pass_args, exec_dir) + + +def def_temp_log_opts(args): + """ + Establish default temporary and log folders. + """ + TEMP = os.getenv("TEMP") + + if TEMP is not None: + if '-log' not in args: + args.append('-log') + args.append(TEMP+'/logs') + + if '-temp_folder' not in args : + args.append('-temp_folder') + args.append(TEMP) + + return args + + +def main(): + java = java_executable() + """ + PeptideShaker updates files relative to the path of the jar file. + In a multiuser setting, the option --exec_dir="exec_dir" + can be used as the location for the peptide-shaker distribution. + If the exec_dir dies not exist, + we copy the jar file, lib, and resources to the exec_dir directory. + """ + (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) + pass_args = def_temp_log_opts(pass_args) + jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) + + if pass_args != [] and pass_args[0].startswith('eu'): + jar_arg = '-cp' + else: + jar_arg = '-jar' + + jar_path = os.path.join(jar_dir, jar_file) + + java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args + + sys.exit(subprocess.call(java_args)) + + +if __name__ == '__main__': + main() diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index fb5756890a9fc..802e0ca68a124 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.7" %} +{% set version = "2.7.0" %} {% set name = "PopPUNK" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: faa11756c6c7acc0df2ef50a1deaf27432f1e510219a7484cc16f92e44b2e179 + sha256: bba7cb9fad5027abc78fd6761755169ae999d3d86a96bdfbfe577a360f907067 build: number: 0 @@ -89,6 +89,7 @@ test: - poppunk_references --help - poppunk_mandrake --help - poppunk_info --help + - poppunk_lineages_from_strains --help about: home: https://poppunk.bacpop.org/ @@ -99,3 +100,8 @@ about: extra: identifiers: - doi:10.1101/gr.241455.118 + # enabling this would require arm64 packages for: mandrake, pp-sketchlib, + # rapidnj + # additional-platforms: + # - linux-aarch64 + # - osx-arm64 diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index 3a1b063442689..0f5d28be758ff 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1.0" %} +{% set version = "2.1.2" %} package: name: ppanggolin @@ -6,11 +6,10 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: f0f81d57e571619438a558895de750bb02f4728cfb2eb1928431dadb22fd49d1 + sha256: ecb5cc4bc4db3a1e842a4085d6aec3a25a12513215523797723e325f96d1158d build: - number: 0 - skip: True # [py<37] + number: 1 run_exports: - {{ pin_subpackage("ppanggolin", max_pin="x") }} @@ -23,7 +22,7 @@ requirements: - pip - cython <3 run: - - python + - python >=3.8,<=3.12 - tqdm =4 - pytables =3 - pyrodigal =3 @@ -55,6 +54,9 @@ about: summary: "PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph" extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - axbazin - jpjarnoux + - JeanMainguy diff --git a/recipes/promotercalculator/meta.yaml b/recipes/promotercalculator/meta.yaml new file mode 100644 index 0000000000000..ef929a32415d8 --- /dev/null +++ b/recipes/promotercalculator/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "promotercalculator" %} +{% set version = "1.2.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/promotercalculator-{{ version }}.tar.gz + sha256: 8ab36fa50266b5e1fa958a7e331e6c352a68d09d255931dfa9c319fc3e856b49 + +build: + entry_points: + - promoter-calculator = promoter_calculator.cli:main + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + number: 0 + run_exports: + - {{ pin_subpackage("promotercalculator", max_pin="x") }} + +requirements: + host: + - python + - pip + run: + - python + - biopython + - numpy + - scikit-learn + - scipy + +test: + imports: + - promoter_calculator + commands: + - promoter-calculator --help + +about: + home: https://github.com/barricklab/promoter-calculator + summary: "Promoter-Calculator (Barrick Lab Fork)" + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + dev_url: https://github.com/barricklab/promoter-calculator + +extra: + recipe-maintainers: + - croots diff --git a/recipes/pronto/meta.yaml b/recipes/pronto/meta.yaml index d6d9f73830252..2c29479c7acce 100644 --- a/recipes/pronto/meta.yaml +++ b/recipes/pronto/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pronto" %} -{% set version = "2.5.7" %} +{% set version = "2.5.8" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 014a5b02064781d6edd7ca5b4f63b13342dd9b5322248f5a4740f48a98464629 + sha256: 5283ec5b35ddc12d34f2e50098b9900bb7b80172b7f769ccc93f5d82b7022799 build: noarch: python diff --git a/recipes/prot-scriber/build.sh b/recipes/prot-scriber/build.sh index 3662f6efb60db..0609d45584d5d 100644 --- a/recipes/prot-scriber/build.sh +++ b/recipes/prot-scriber/build.sh @@ -1,8 +1,6 @@ -#!/bin/bash -euo +#!/bin/bash -# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. -# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. -export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" +set -xeuo # build statically linked binary with Rust RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX diff --git a/recipes/prot-scriber/meta.yaml b/recipes/prot-scriber/meta.yaml index c74897c5d6a79..b32921251aa5a 100644 --- a/recipes/prot-scriber/meta.yaml +++ b/recipes/prot-scriber/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.1.5" %} -{% set sha256 = "75d75e7a78b631716efb25f762b18405ada70eec3558a2b721c8c633c308269e" %} +{% set version = "0.1.6" %} +{% set sha256 = "f79722ec7338b354df855b94f250f509e7742cd8cc4762a21c96905fc162f92f" %} package: name: prot-scriber version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("prot-scriber", max_pin="x") }} @@ -16,8 +16,8 @@ source: requirements: build: - - rust - {{ compiler('c') }} + - {{ compiler('rust') }} test: commands: @@ -25,6 +25,10 @@ test: about: home: https://github.com/usadellab/prot-scriber - license: GPL-3 + license: GPL-3.0-only summary: "Assigns short human readable descriptions (HRD) to query biological sequences using reference candidate descriptions." license_file: LICENSE + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/prymer/meta.yaml b/recipes/prymer/meta.yaml new file mode 100644 index 0000000000000..5302549095ed6 --- /dev/null +++ b/recipes/prymer/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "prymer" %} +{% set version = "2.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/fulcrumgenomics/{{ name }}/archive/refs/tags/{{ version }}.tar.gz + sha256: e11a09a58e9310b2ff1b89b9e36913f47c08e0b22e1d3d9ce9321e4013fb3c2e + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . -vvv --no-build-isolation --no-deps + run_exports: + - {{ pin_subpackage('prymer', max_pin="x.x") }} + +requirements: + host: + - pip + - python >=3.11 + - poetry + run: + - bwa-aln-interactive >=0.7.18 + - python >=3.11 + - pysam >=0.22.0 + - primer3 >=2.6.1 + +test: + imports: + - prymer + +about: + home: https://pypi.org/project/prymer/ + summary: Python Primer Design Library + license: MIT + license_family: MIT + license_file: LICENSE + dev_url: https://github.com/fulcrumgenomics/prymer + doc_url: https://prymer.readthedocs.io/en/latest/ + +extra: + recipe-maintainers: + - emmcauley + - geoffjentry + - nh13 + - tfenne diff --git a/recipes/psims/meta.yaml b/recipes/psims/meta.yaml index fbab7ed9f4c18..64e6ca723d030 100644 --- a/recipes/psims/meta.yaml +++ b/recipes/psims/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.3.3" %} -{% set sha256 = "d956fb6d2a42087fe35595ad452802fe115a7952c8bcb63951d19b99530b1358" %} +{% set version = "1.3.4" %} +{% set sha256 = "4cac9368616118186fe12dc137adcd12d934df5013956816615b5eaa95cb0573" %} package: name: "psims" diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index 526d07c3caedb..02b60ab80be76 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.9.0" %} -{% set sha256 = "445bb667088d237d0b78f443d184b080a9ce6b33eab3b585295ce51194950abb" %} +{% set version = "1.1.1" %} +{% set sha256 = "8926d8f5e2e05ac38d54d6ae5c89461568085b60d23414a907c820bc674a4a2b" %} package: name: {{ name|lower }} diff --git a/recipes/pyabpoa/meta.yaml b/recipes/pyabpoa/meta.yaml index a70e32f310f07..78b8f0a130346 100644 --- a/recipes/pyabpoa/meta.yaml +++ b/recipes/pyabpoa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyabpoa" %} -{% set version = "1.5.2" %} +{% set version = "1.5.3" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/yangao07/abPOA/releases/download/v{{ version }}/abPOA-v{{ version }}.tar.gz - sha256: 706f0ca0110f4974ae7b93157db560bb9beda4273d8c883fa6a03ccb19958149 + sha256: bb97de2dbdec014f2fb24beb0c85fa0b2073f717f3b68639e1edd89239729e6c build: - number: 1 + number: 0 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/pyani/meta.yaml b/recipes/pyani/meta.yaml index b615cc7c9b19b..36b375deb00aa 100644 --- a/recipes/pyani/meta.yaml +++ b/recipes/pyani/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyani" %} -{% set version = "0.2.12" %} +{% set version = "0.2.13.1" %} package: name: {{ name|lower }} @@ -7,29 +7,35 @@ package: source: url: https://github.com/widdowquinn/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 31bac50843d3af54cf273a4388f4f87bffb0688082e4e3179ea1640aa208626d + sha256: 98c2bb205eb286bd53b27d0deacd01ad25f00dd2483a91ba19765203af03d9ef build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('pyani', max_pin="x.x") }} requirements: host: - - python >3 - - setuptools - + - python >=3.7 + - pip run: - - python >3 + - python >=3.7 - biopython + - blast + - blast-legacy # [not osx] + - intervaltree - matplotlib-base + - mummer + - namedlist + - networkx + - numpy - pandas - - seaborn - scipy - - numpy - - mummer - - blast - - blast-legacy # [not osx] + - seaborn-base + - sqlalchemy + - tqdm test: imports: @@ -39,8 +45,15 @@ test: - genbank_get_genomes_by_taxon.py -h about: - home: http://widdowquinn.github.io/pyani/ + home: "https://github.com/widdowquinn/pyani" license: MIT license_file: LICENSE summary: 'pyani provides a package and script for calculation of genome-scale average nucleotide identity.' license_family: MIT + dev_url: "https://github.com/widdowquinn/pyani" + doc_url: "https://widdowquinn.github.io/pyani" + +extra: + identifiers: + - doi:10.1039/C5AY02550H + - biotools:pyani diff --git a/recipes/pybdei/meta.yaml b/recipes/pybdei/meta.yaml new file mode 100644 index 0000000000000..8b263e9ba7d22 --- /dev/null +++ b/recipes/pybdei/meta.yaml @@ -0,0 +1,68 @@ +{% set name = "pybdei" %} +{% set version = "0.13" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybdei-{{ version }}.tar.gz + sha256: 4fcd3950aa60a25538bb8716a88ed5d5b24f63b1deebf1828e2e0ea9ac45441f + +build: + script_env: + - CC=$CXX + entry_points: + - bdei_infer = pybdei.inference:main + - bdei_loglikelihood = pybdei.loglikelihood:main + - bdei_u = pybdei.u_calculator:main + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation --no-binary=pybdei + number: 0 + run_exports: + - {{ pin_subpackage('pybdei', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('cxx') }} + host: + - python >=3.9 + - setuptools + - numpy >=1.24.0 + - pip + - nlopt + run: + - python >=3.9 + - ete3 >=3.1.3 + - scipy >=1.11.1 + - six >=1.16.0 + - treesimulator >=0.1.22 + - {{ pin_compatible('numpy >=1.24.0') }} + +test: + imports: + - pybdei + commands: + - pip check + - bdei_infer --help + - bdei_loglikelihood --help + - bdei_u --help + requires: + - pip + +about: + home: "https://github.com/evolbioinfo/bdei" + summary: "Maximum likelihood estimation of Birth-Death Exposed-Infectious (BDEI) epidemiological model parameters from phylogenetic trees." + description: | + PyBDEI provides tools for fast and accurate maximum likelihood estimation + of Birth-Death Exposed-Infectious (BDEI) epidemiological model parameters + from phylogenetic trees. + license: LGPL-2.1 + license_file: LICENSE + license_family: GPL2 + dev_url: https://github.com/evolbioinfo/bdei + +extra: + recipe-maintainers: + - annazhukova + identifiers: + - doi:10.1093/sysbio/syad059 \ No newline at end of file diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 4b79d5057b32c..5b42a9cd463cf 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.2.31" %} +{% set version = "1.2.185" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 39abd33afc379d9624ff7da4f0eb38acaf7a14f5c48aa0bbce6d761ca3632e6b + sha256: 9525f0548dd11df88b33845ecf51d17ee9c2c5675a0723ebf5c25c586c58e598 build: number: 0 diff --git a/recipes/pydamage/meta.yaml b/recipes/pydamage/meta.yaml index 10d38b9c95b16..f192b2ad8e663 100644 --- a/recipes/pydamage/meta.yaml +++ b/recipes/pydamage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydamage" %} -{% set version = "0.72" %} +{% set version = "0.80" %} package: @@ -8,7 +8,7 @@ package: source: url: https://github.com/maxibor/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: a386cf89df86ea811660d93936d8153dad05ec79b1d2984dc86b14420e5ae139 + sha256: b51682e513aa3a22fcac46e22fd404a1c8b3484c2e9e0b8aeedcabaf1fddd720 build: number: 0 @@ -22,7 +22,7 @@ build: requirements: host: - pip - - python >=3.6 + - python >=3.10 run: - biopython - click @@ -31,10 +31,11 @@ requirements: - numpy - pandas - pysam >=0.13.0 - - python >=3.6 + - python >=3.10 - scipy - statsmodels - tqdm + - numba test: imports: diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index 4bcdcbc360961..466847c774fb9 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.10" %} +{% set version = "0.4.11" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: 8a296938c565035f2c219c870d8e0138e699d71b30f2add04a647b4fbd0b8b6a + sha256: 3eb9ae8fd586c04c03e0fa49f274c2db65d0fad19c91803dda09dccb7aaf598c build: noarch: python diff --git a/recipes/pydustmasker/build.sh b/recipes/pydustmasker/build.sh new file mode 100644 index 0000000000000..7da716bd0d231 --- /dev/null +++ b/recipes/pydustmasker/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +set -ex + +if [ `uname` == Darwin ]; then + export HOME=`mktemp -d` +fi + +curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y + +export PATH="$HOME/.cargo/bin:$PATH" + +export CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER="$CC" + +maturin build --interpreter python --release + +$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv diff --git a/recipes/pydustmasker/meta.yaml b/recipes/pydustmasker/meta.yaml new file mode 100644 index 0000000000000..7431828f1d333 --- /dev/null +++ b/recipes/pydustmasker/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "pydustmasker" %} +{% set version = "1.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 03f875b3cdb595394eabed823d80d4da50d687f3ade4a017ff0159ce277ae331 + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - pip + - maturin + - python + run: + - python + +test: + imports: + - pydustmasker + +about: + home: https://github.com/apcamargo/pydustmasker + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Python library for identification and masking of low-complexity regions in nucleotide sequences." + diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml index 6ec6d94b4d7c6..5cb5faa479d92 100644 --- a/recipes/pyfamsa/meta.yaml +++ b/recipes/pyfamsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyfamsa" %} -{% set version = "0.4.0" %} +{% set version = "0.5.2" %} package: name: "{{ name|lower }}" @@ -7,12 +7,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 9a09e04079b5d6401b62fed2b80886ffdd5626c30686697ff8c2b38e018e6e87 + sha256: 5715eccfaf0ac38f9eba951285de900086e10007b0e2508e3735879d7e4e5fce build: - number: 1 - skip: True # [py2k] - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" run_exports: - {{ pin_subpackage('pyfamsa', max_pin="x.x") }} @@ -41,8 +40,8 @@ about: license: GPL-3.0-or-later license_family: GPL3 license_file: COPYING - summary: Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments. - doc_url: https://pyfamsa.readthedocs.org/ + summary: "Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments." + doc_url: https://pyfamsa.readthedocs.org dev_url: https://github.com/althonos/pyfamsa extra: @@ -50,3 +49,4 @@ extra: - althonos additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/pygcap/meta.yaml b/recipes/pygcap/meta.yaml index abc14978799ed..37b05921420ad 100644 --- a/recipes/pygcap/meta.yaml +++ b/recipes/pygcap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pygcap" %} -{% set version = "1.2.5" %} +{% set version = "1.2.6" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pygcap-{{ version }}.tar.gz - sha256: caa4edf728b8cee811daf71e6fda4f3a088fcec3a6bd24a3fc37807c2ee01125 + sha256: 172aa62ec82bab05713f573e7920e65bd38ace3341f4ea4b6f8f000733c3d170 build: number: 0 diff --git a/recipes/pymochi/meta.yaml b/recipes/pymochi/meta.yaml index 7ce09a732e24f..35f5f7f435f61 100644 --- a/recipes/pymochi/meta.yaml +++ b/recipes/pymochi/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0" %} +{% set version = "1.1" %} {% set github = "https://github.com/lehner-lab/MoCHI" %} package: @@ -7,7 +7,7 @@ package: source: url: {{ github }}/archive/v{{ version }}.tar.gz - sha256: 93bd3c32b5a686d5bacecf3d48678497eeed3bf799198ab453e21accefecbae7 + sha256: d021a858a3929858c8e8d0a6d5173680aa6097d90a8f05858f9ae08cb6902c17 build: noarch: python diff --git a/recipes/pymsaviz/meta.yaml b/recipes/pymsaviz/meta.yaml index 822721aa7ffd6..55217812030cc 100644 --- a/recipes/pymsaviz/meta.yaml +++ b/recipes/pymsaviz/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pymsaviz" %} -{% set version = "0.4.2" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pymsaviz-{{ version }}.tar.gz - sha256: a6506c75b52e8e0c9f28c13f0cca2d2c5cd642c8136dbb42426ab5f19e5ff6f7 + sha256: 644a5bacfc0aa75b7c5d2c2e2b666020ac4f72e18b54a142b56d4638cfbe6764 build: entry_points: @@ -20,22 +20,19 @@ build: requirements: host: - - python >=3.8 - - poetry-core >=1.0.0 + - python >=3.9 + - hatchling - pip run: - - python >=3.8 + - python >=3.9 - biopython >=1.79 - matplotlib-base >=3.5.2 - - pytest test: imports: - pymsaviz commands: - pymsaviz --help - source_files: - - tests/ about: home: https://moshi4.github.io/pyMSAviz/ diff --git a/recipes/pymsaviz/run_test.sh b/recipes/pymsaviz/run_test.sh deleted file mode 100644 index 0afa92db35c77..0000000000000 --- a/recipes/pymsaviz/run_test.sh +++ /dev/null @@ -1 +0,0 @@ -pytest tests diff --git a/recipes/pypints/meta.yaml b/recipes/pypints/meta.yaml index b32637aeeaf6e..165eca55c2c5b 100644 --- a/recipes/pypints/meta.yaml +++ b/recipes/pypints/meta.yaml @@ -1,13 +1,13 @@ {% set name = "pyPINTS" %} -{% set version = "1.1.10" %} +{% set version = "1.1.13" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 91e4e6e8a308ad4e4e829068b96282385a0285512a2351cedd9793c50e8a7f63 + url: "https://files.pythonhosted.org/packages/df/b4/0b6ded0841b01d72c2beb676b71ea94800896ec69c937f09acee24964597/pypints-1.1.13.tar.gz" + sha256: 808fca4e7fa6ff06dffebc49c36680c872044b4babdd9e42f012fa2ff140aa3e build: number: 0 diff --git a/recipes/pyrodigal-gv/meta.yaml b/recipes/pyrodigal-gv/meta.yaml index 34996ec3ebe2b..fa9ca0b00d6c0 100644 --- a/recipes/pyrodigal-gv/meta.yaml +++ b/recipes/pyrodigal-gv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal-gv" %} -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pyrodigal_gv-{{ version }}.tar.gz - sha256: 287f0507fad25f8c148a1d93a030e1a64b0434beba62f45354526b0eeef4ca97 + sha256: aeeff43daec2c4aec7830ae2400799aa90bf273bcca86656ef239bee8d7e5ea5 build: script: {{ PYTHON }} -m pip install . --ignore-installed --use-pep517 --no-deps -vvv diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 00f628aa03c5c..76cfdde6e5ea3 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal" %} -{% set version = "3.5.1" %} +{% set version = "3.5.2" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 20af59a6d968c88910b99d5f647bb7dd22d49e440ead95fe715cdd2c49f36e9f + sha256: 2a40eb6113e720ada51c326958b295944cdc33ecee9f25d5bad4e9a8e6e6f7f5 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" entry_points: - pyrodigal = pyrodigal.cli:main diff --git a/recipes/pyseer/meta.yaml b/recipes/pyseer/meta.yaml index 1b761f3f07687..de56804f70d60 100644 --- a/recipes/pyseer/meta.yaml +++ b/recipes/pyseer/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.11" %} +{% set version = "1.3.12" %} package: name: pyseer @@ -6,10 +6,12 @@ package: source: url: https://github.com/mgalardini/pyseer/releases/download/{{ version }}/pyseer-{{ version }}.tar.gz - sha256: 384313a3a14b92f873eaad53f77a319d90b584b9253785a7ca1dfc7d9220c91e + sha256: 31a9a528f0cc6409ddb1556b533dd9631c805b1b83bce0fcc6ad85f1126c9fbe build: + run_exports: + - {{ pin_subpackage('pyseer', max_pin="x") }} number: 0 noarch: python script: python -m pip install --no-deps --ignore-installed . diff --git a/recipes/pyslow5/meta.yaml b/recipes/pyslow5/meta.yaml index 4d72ebb39ee3e..087931ecc29c0 100644 --- a/recipes/pyslow5/meta.yaml +++ b/recipes/pyslow5/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pyslow5" %} -{% set sha256 = "e756a33e2bca373dea5367af7da8db02d77d80985685566cce05cc6a711c8487" %} -{% set version = "1.2.0" %} +{% set sha256 = "2fdf091beb7e1f685d9fca70b69e406bb359d801e032d8567daf39a8833abd5a" %} +{% set version = "1.3.0" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('pyslow5', max_pin="x") }} @@ -22,6 +22,7 @@ requirements: - python - pip - cython + - setuptools - zlib - numpy run: @@ -39,3 +40,8 @@ about: license_file: thirdparty/streamvbyte/LICENSE summary: 'slow5lib Python binding' dev_url: https://github.com/hasindu2008/slow5lib + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/pysradb/meta.yaml b/recipes/pysradb/meta.yaml index 2fb096f1026c1..243922798a2e8 100644 --- a/recipes/pysradb/meta.yaml +++ b/recipes/pysradb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pysradb" %} -{% set version = "2.2.0" %} +{% set version = "2.2.1" %} package: name: '{{ name|lower }}' @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: be7c451b590045683cb8b10786fedcd622f5da76e74284e70a4b2ee65faf43e9 + sha256: 038318b70bdf6b9ff0e1c5b67a38c5832d37ed142bbeeb3c5b55eec2d51371f4 build: number: 0 noarch: python entry_points: - pysradb=pysradb.cli:parse_args - script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: - {{ pin_subpackage('pysradb', max_pin="x") }} @@ -22,12 +22,7 @@ requirements: host: - python >=3.7 - pip - - lxml >=4.6.3 - - pandas >=1.3.2 - - requests >=2.26.0 - - requests-ftp >=0.3.1 - - tqdm >=4.62.1 - - xmltodict >=0.12.0 + - hatchling run: - python >=3.7 - lxml >=4.6.3 @@ -52,6 +47,7 @@ about: summary: 'Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO' description: 'Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO' doc_url: 'https://saketkc.github.io/pysradb' + dev_url: https://github.com/saketkc/pysradb extra: recipe-maintainers: diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml index 2127906fd62dd..8a197411ebe35 100644 --- a/recipes/pyteomics/meta.yaml +++ b/recipes/pyteomics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.7.3" %} +{% set version = "4.7.4" %} package: name: pyteomics @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz - sha256: ae87f6ba02ee735b06ae56e1ac85a37051aa503e0c9dbfee650c8a7107d08f57 + sha256: cd8a9b48ea3a3075bbbc3085880b5a4f76eb7359e3c71ee3948d9bb2aa48883b build: noarch: python diff --git a/recipes/python-bioext/build.sh b/recipes/python-bioext/build.sh index 1975a26f3cea8..9ae5bff3807f0 100644 --- a/recipes/python-bioext/build.sh +++ b/recipes/python-bioext/build.sh @@ -22,7 +22,7 @@ TARGET=$PREFIX/share/$PKG_NAME/reference_data # Symlink reference data to /usr/local/share/$TARGET, since the site-packages # path may vary depending on the python version mkdir -p "$TARGET" -ln -s "$SP_DIR/BioExt/data/references" "$TARGET" +ln -sf "$SP_DIR/BioExt/data/references" "$TARGET" echo "export BEALIGN_REFERENCE_DIR=$TARGET" > "${PREFIX}/etc/conda/activate.d/${PKG_NAME}_activate.sh" echo "unset BEALIGN_REFERENCE_DIR" > "${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}_deactivate.sh" diff --git a/recipes/python-bioext/meta.yaml b/recipes/python-bioext/meta.yaml index 5292f95513bbc..0ea3844b07ae1 100644 --- a/recipes/python-bioext/meta.yaml +++ b/recipes/python-bioext/meta.yaml @@ -1,6 +1,6 @@ {% set name = "BioExt" %} -{% set version = "0.21.7" %} -{% set sha256 = "2265c9b6cb5b4a6400635a5d21f32ca1d693b97431ad188965150fc5d6b28ab6" %} +{% set version = "0.21.9" %} +{% set sha256 = "21bf30eac79c5bc553f0870a119688adaab5a040ff72f9e8fdac46fec978130f" %} package: name: python-{{ name|lower }} @@ -11,11 +11,10 @@ source: sha256: {{ sha256 }} patches: - cythonize.patch - - osx-freetype.patch # [osx] + - osx-freetype.patch # [osx] build: - number: 1 - skip: True # [py2k] + number: 0 run_exports: - {{ pin_subpackage("python-bioext", max_pin="x.x") }} @@ -24,19 +23,15 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - freetype - python - - cython >=0.28 - - setuptools - - biopython >=1.58 - - numpy >1.20.3 - - scipy - - pysam + - pip + - cython + - numpy run: - freetype - python - - biopython >=1.58 - - numpy >1.20.3 + - biopython >=1.78 + - {{ pin_compatible('numpy') }} - scipy - pysam - joblib @@ -79,6 +74,11 @@ test: about: home: https://github.com/veg/BioExt.git - license: GPL-3 + license: GPL-3.0-only license_family: GPL3 summary: 'A few handy bioinformatics tools not already in BioPython' + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/python-edlib/meta.yaml b/recipes/python-edlib/meta.yaml index aedfbb654230e..468f2b9a27044 100644 --- a/recipes/python-edlib/meta.yaml +++ b/recipes/python-edlib/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.9" %} +{% set version = "1.3.9.post1" %} package: name: python-edlib @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/e/edlib/edlib-{{ version }}.tar.gz - sha256: 64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766 + sha256: b0fb6e85882cab02208ccd6daa46f80cb9ff1d05764e91bf22920a01d7a6fbfa build: - number: 8 + number: 0 script: "EDLIB_USE_CYTHON=1 {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage("python-edlib", max_pin="x") }} diff --git a/recipes/python-hivclustering/meta.yaml b/recipes/python-hivclustering/meta.yaml index e6836779451a5..978c7db69b88c 100644 --- a/recipes/python-hivclustering/meta.yaml +++ b/recipes/python-hivclustering/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.6.8" %} +{% set version = "1.8.0" %} {% set name = "hivclustering" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/veg/{{ name }}/archive/{{ version }}.tar.gz - sha256: 63ff148ee265a273156c51b4727f5f00a07f9c3306d17f122c4c6c6ab9d41ecb + sha256: f331d44e4998149de1aa612539b15dd20c1318b411fa0a3581406a59a211adba build: noarch: python diff --git a/recipes/python-hyphy-python/build.sh b/recipes/python-hyphy-python/build.sh index b730382f43da8..b94675ce4307c 100644 --- a/recipes/python-hyphy-python/build.sh +++ b/recipes/python-hyphy-python/build.sh @@ -1,4 +1,13 @@ #!/bin/bash +if [[ `uname` == "Darwin" ]]; then + export CFLAGS="${CFLAGS} -O3 -Wno-register ${LDFLAGS} -L${PREFIX}/lib" + export CXXFLAGS="${CXXFLAGS} -O3 -Wno-register -I${PREFIX}/include" +else + export CFLAGS="${CFLAGS} -O3 ${LDFLAGS} -L${PREFIX}/lib" + export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" +fi + sed -i.bak "s#\['cc',#\['${CC}',#" setup.py -$PYTHON -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv +rm -rf *.bak +${PYTHON} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv diff --git a/recipes/python-hyphy-python/build_failure.osx-64.yaml b/recipes/python-hyphy-python/build_failure.osx-64.yaml deleted file mode 100644 index c6c2a9fdf8ffb..0000000000000 --- a/recipes/python-hyphy-python/build_failure.osx-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 9b6d23eff98464edd992ec32bd7c3ff644959f5687e570ec142d21f5676ac7eb # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Key: - - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/python-hyphy-python_1717954358254/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/python-hyphy-python_1717954358254/work/conda_build.sh']' returned non-zero exit status 1. - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/python-hyphy-python_1717954358254/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/python-hyphy-python_1717954358254/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/python-hyphy-python_1717954358254/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-hyphy-python-0.1.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-hyphy-python-0.1.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-hyphy-python-0.1.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-hyphy-python-0.1.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.11/site-packages/pip (python 3.11) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-tzf9rnlr - Initialized build tracking at /private/tmp/pip-build-tracker-tzf9rnlr - Created build tracker: /private/tmp/pip-build-tracker-tzf9rnlr - Entered build tracker: /private/tmp/pip-build-tracker-tzf9rnlr - Created temporary directory: /private/tmp/pip-install-p_4x3igj - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-16ns09mm - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-tzf9rnlr' - Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-8h0kbd0v - Preparing metadata (setup.py): started - Preparing metadata (setup.py): finished with status 'done' - Source in $SRC_DIR has version 0.1.12, which satisfies requirement hyphy-python==0.1.12 from file://$SRC_DIR - Removed hyphy-python==0.1.12 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-tzf9rnlr' - Created temporary directory: /private/tmp/pip-unpack-t7w8az6b - Building wheels for collected packages: hyphy-python - Created temporary directory: /private/tmp/pip-wheel-9pwlzrmu - Building wheel for hyphy-python (setup.py): started - Destination directory: /private/tmp/pip-wheel-9pwlzrmu - Building wheel for hyphy-python (setup.py): finished with status 'error' - Running setup.py clean for hyphy-python - Failed to build hyphy-python - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 429, in run - raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for hyphy-python, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-tzf9rnlr' -# Last 100 lines of the build log. -category: |- - compiler error diff --git a/recipes/python-hyphy-python/meta.yaml b/recipes/python-hyphy-python/meta.yaml index 363041fc44b05..6d17c7fcfe6e9 100644 --- a/recipes/python-hyphy-python/meta.yaml +++ b/recipes/python-hyphy-python/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-importlib.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('python-hyphy-python', max_pin="x.x") }} @@ -28,6 +28,8 @@ requirements: - libcurl run: - python + - llvm-openmp # [osx] + - libgomp # [linux] test: imports: @@ -40,3 +42,10 @@ about: license_file: LICENSE summary: 'HyPhy package interface library' dev_url: "https://github.com/veg/hyphy-python" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + identifiers: + - biotools:HyPhy diff --git a/recipes/pytrimal/build_failure.osx-64.yaml b/recipes/pytrimal/build_failure.osx-64.yaml deleted file mode 100644 index fd387f6646163..0000000000000 --- a/recipes/pytrimal/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: e82086ce8ce28d6bc499d24ecfe8511786c73430b331466ae2d3b51273a9ab20 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pytrimal_1717522804579/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pytrimal_1717522804579/_build_env - Traceback (most recent call last): - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/pytrimal_1717522804579/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pytrimal-0.7.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/pytrimal_1717522804579/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pytrimal-0.7.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pytrimal-0.7.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pytrimal-0.7.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.8/site-packages/pip (python 3.8) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-xa5aes5p - Initialized build tracking at /private/tmp/pip-build-tracker-xa5aes5p - Created build tracker: /private/tmp/pip-build-tracker-xa5aes5p - Entered build tracker: /private/tmp/pip-build-tracker-xa5aes5p - Created temporary directory: /private/tmp/pip-install-r7bug1kb - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-spxymxhx - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-xa5aes5p' - Created temporary directory: /private/tmp/pip-modern-metadata-qhph_27o - Preparing metadata (pyproject.toml): started - Preparing metadata (pyproject.toml): finished with status 'done' - Source in $SRC_DIR has version 0.7.0, which satisfies requirement pytrimal==0.7.0 from file://$SRC_DIR - Removed pytrimal==0.7.0 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-xa5aes5p' - Created temporary directory: /private/tmp/pip-unpack-0bkomd0_ - Building wheels for collected packages: pytrimal - Created temporary directory: /private/tmp/pip-wheel-71ufbp5h - Destination directory: /private/tmp/pip-wheel-71ufbp5h - Building wheel for pytrimal (pyproject.toml): started - Building wheel for pytrimal (pyproject.toml): finished with status 'error' - Failed to build pytrimal - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 429, in run - raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for pytrimal, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-xa5aes5p' -# Last 100 lines of the build log. diff --git a/recipes/pytrimal/meta.yaml b/recipes/pytrimal/meta.yaml index c135226ad4b8d..a1d08ae93515a 100644 --- a/recipes/pytrimal/meta.yaml +++ b/recipes/pytrimal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pytrimal" %} -{% set version = "0.7.0" %} +{% set version = "0.8.0" %} package: name: "{{ name|lower }}" @@ -7,13 +7,13 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e80df938e83a95bf81d620f5909580f3f07b661f25b8613e67037134785b91b4 + sha256: 2331e67a74f3144d82373b6a79f42198f6632bd1b5025ab01cdd3eb527ef88cf build: number: 1 - - skip: True #[py2k] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" + run_exports: + - {{ pin_subpackage('pytrimal', max_pin="x.x") }} requirements: build: @@ -23,11 +23,10 @@ requirements: - python - pip - cython - - setuptools + - scoring-matrices >=0.2.0 run: - python - - setuptools - - archspec + - scoring-matrices >=0.2.0 test: imports: @@ -37,12 +36,15 @@ test: about: home: https://github.com/althonos/pytrimal - license: GPL-3 + license: GPL-3.0-or-later license_family: GPL license_file: COPYING - summary: Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. - doc_url: https://pytrimal.readthedocs.org/ + summary: "Cython bindings and Python interface to trimAl, a tool for automated alignment trimming." + doc_url: https://pytrimal.readthedocs.org + dev_url: https://github.com/althonos/pytrimal extra: recipe-maintainers: - althonos + additional-platforms: + - linux-aarch64 diff --git a/recipes/pytximport/meta.yaml b/recipes/pytximport/meta.yaml index 698fc623fa95c..c27f43344082a 100644 --- a/recipes/pytximport/meta.yaml +++ b/recipes/pytximport/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pytximport" %} -{% set version = "0.7.0" %} +{% set version = "0.9.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pytximport-{{ version }}.tar.gz - sha256: fa4992d4fe11246941b36eadc886d34d61d6682e5cf2ad266f9f96bb0da9290a + sha256: f311705a71faa095d7e65de63235df55c805fbab4fbea10010fdae11014b3c95 build: noarch: python diff --git a/recipes/quantms-utils/meta.yaml b/recipes/quantms-utils/meta.yaml index 5f5a7c9d3c17c..0c0457e61496a 100644 --- a/recipes/quantms-utils/meta.yaml +++ b/recipes/quantms-utils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "quantms-utils" %} -{% set version = "0.0.2" %} +{% set version = "0.0.11" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/quantms_utils-{{ version }}.tar.gz - sha256: 295e4947e2cb3a4dc084854081d5e16255d422d03a7e41def531daf98317882a + sha256: f1205db7526f09d36606288782363b352546a100b4763c16d988d7cdb45bf26f build: entry_points: @@ -26,12 +26,17 @@ requirements: - python >=3.7.0,<4.0.0 - click >=7.0 - pydantic >=1.10,<2 - - sdrf-pipelines >=0.0.26 - - pyopenms >=2.6.0 - - ms2rescore ==3.0.2 - - psm-utils ==0.8.0 + - sdrf-pipelines >=0.0.29 + - pyopenms >=2.9.1 + - ms2rescore ==3.0.3 + - psm-utils ==0.8.2 + - ms2pip ==4.0.0.dev8 + - deeplc ==2.2.38 - pandas >=1.0.0 - numpy + - scipy ==1.13.1 + - scikit-learn + - deeplcretrainer test: imports: diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml index a91fb4a8cd361..d06896d5b8edc 100644 --- a/recipes/quatradis/meta.yaml +++ b/recipes/quatradis/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.3.0" %} +{% set version = "1.3.1" %} package: name: quatradis @@ -6,33 +6,32 @@ package: source: url: https://github.com/quadram-institute-bioscience/QuaTradis/archive/refs/tags/{{ version }}.tar.gz - sha256: 8634c61c93073028fc35df46b3d1337e7716924051c336a12172c65e1adb2e74 + sha256: 0c05f40e14391b5044aa014cce345e43238ff01d06edfc72258f8608d3796590 build: number: 0 - script: python -m pip install -v --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation --no-cache-dir . run_exports: - - {{ pin_subpackage('quatradis', max_pin="x.x") }} + - {{ pin_subpackage('quatradis', max_pin="x") }} requirements: build: - {{ compiler('c') }} host: - - python =3.10 - - cython >=0.20.1 + - python + - cython - pip run: - - python =3.10 - - cython + - python - setuptools # for pkg_resources + - cython - biopython - pysam >=0.18.0 - matplotlib-base - numpy - scipy - - dendropy - - seaborn - - graphviz + - dendropy ==4.6 + - seaborn-base - python-graphviz - pandas - htslib @@ -43,7 +42,7 @@ requirements: - bwa - samtools - minimap2 - - snakemake + - snakemake-minimal - snakeviz test: @@ -56,6 +55,7 @@ about: license_family: GPL3 license_file: LICENSE summary: 'A set of tools to analyse the output from TraDIS analyses' + dev_url: https://github.com/quadram-institute-bioscience/QuaTradis extra: skip-lints: @@ -66,5 +66,5 @@ extra: - sbastkowski - maplesond - thanhleviet - doi: - - 10.1093/bioinformatics/btw022 + identifiers: + - doi:10.1093/bioinformatics/btw022 diff --git a/recipes/querynator/meta.yaml b/recipes/querynator/meta.yaml index d6936b6ac72d9..c8abd1a63d7bb 100644 --- a/recipes/querynator/meta.yaml +++ b/recipes/querynator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "querynator" %} -{% set version = "0.5.4" %} +{% set version = "0.5.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 803aff3939b21ce35f92a1d39bd2c4db2f9a8cc1f96a409e939ef3bbeb1fbaf2 + sha256: 32536a2b03b8e7590f01dc7edea5af486a0ffc04126a7370dd1e10e2045357b1 build: number: 0 diff --git a/recipes/quota_anchor/build.sh b/recipes/quota_anchor/build.sh new file mode 100644 index 0000000000000..71922513c1169 --- /dev/null +++ b/recipes/quota_anchor/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +$PYTHON -m pip install --no-deps --ignore-installed . -vv +echo "[software] +gffread = ${PREFIX}/bin/gffread +AnchorWave = ${PREFIX}/bin/anchorwave +diamond = ${PREFIX}/bin/diamond +blastp = ${PREFIX}/bin/blastp +makeblastdb = ${PREFIX}/bin/makeblastdb +muscle = ${PREFIX}/bin/muscle +mafft = ${PREFIX}/bin/mafft +yn00 = ${PREFIX}/bin/yn00 +pal2nal = ${PREFIX}/bin/pal2nal.pl " > ${SP_DIR}/quota_anchor/config_file/software_path.ini diff --git a/recipes/quota_anchor/meta.yaml b/recipes/quota_anchor/meta.yaml new file mode 100644 index 0000000000000..bd563736d46b1 --- /dev/null +++ b/recipes/quota_anchor/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "quota_anchor" %} +{% set version = "0.0.1a0" %} +{% set sha256 = "01d8520825fee67f8c73803d3bbe7855291592c064cd2d5712d02e104a71a8fa" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/baoxingsong/quota_Anchor/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - gffread + - biopython + - blast + - diamond + - AnchorWave + - muscle + - mafft + - matplotlib-base + - pal2nal + - paml + - plotnine + - seaborn + - pandas + - numpy + + +test: + commands: + - 'quota_Anchor 2>&1 | grep "usage: quota_Anchor"' + +about: + home: https://github.com/baoxingsong/quota_Anchor + license: MIT + summary: 'Strand and WGD aware syntenic gene identification' + description: "Strand and WGD aware syntenic gene identification for comparative genomics" + dev_url: https://github.com/baoxingsong/quota_Anchor diff --git a/recipes/r-anndata/build.sh b/recipes/r-anndata/build.sh deleted file mode 100644 index bec411402e62f..0000000000000 --- a/recipes/r-anndata/build.sh +++ /dev/null @@ -1 +0,0 @@ -$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/r-anndata/meta.yaml b/recipes/r-anndata/meta.yaml index ce8403f580d3d..0d2095fcfb869 100644 --- a/recipes/r-anndata/meta.yaml +++ b/recipes/r-anndata/meta.yaml @@ -1,20 +1,22 @@ -{% set version = "0.7.5.4" %} +{% set version = "0.7.5.6" %} package: name: r-anndata version: {{ version }} source: - url: - - https://github.com/dynverse/anndata/archive/refs/tags/{{ version }}.tar.gz - sha256: 35561748978b82739eb75b64e0532919b122eccebf8cc765c964e549884a56cd + url: https://github.com/dynverse/anndata/archive/refs/tags/{{ version }}.tar.gz + sha256: 1a4dc28c5a99a1d816d0b6cf7eabc6388a61af03b53b38297cfce304ae6c8bcb build: - number: 2 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + script: ${R} CMD INSTALL --build . ${R_ARGS} + run_exports: + - {{ pin_subpackage('r-anndata', max_pin="x.x") }} requirements: host: @@ -41,6 +43,7 @@ about: summary: "A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format." license_family: MIT license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT' + dev_url: https://github.com/dynverse/anndata extra: recipe-maintainers: diff --git a/recipes/r-buencolors/build.sh b/recipes/r-buencolors/build.sh new file mode 100644 index 0000000000000..b8d2635525637 --- /dev/null +++ b/recipes/r-buencolors/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash +export DISABLE_AUTOBREW=1 +${R} CMD INSTALL --build . ${R_ARGS} diff --git a/recipes/r-buencolors/meta.yaml b/recipes/r-buencolors/meta.yaml new file mode 100644 index 0000000000000..51fca6e5f9c0a --- /dev/null +++ b/recipes/r-buencolors/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "0.5.6" %} +{% set github = "https://github.com/caleblareau/BuenColors" %} +{% set commit = "f1bc8e640d129ef319a0db49b169a64b00026e00" %} + +package: + name: r-buencolors + version: "{{ version }}" + +source: + url: "{{ github }}/archive/{{ commit }}.zip" + sha256: 6caa14acafd81c9619d795e5dd56ef9fa7a37280d35fe9afe9b4bd9ff3cd776f + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage("r-buencolors", max_pin="x.x") }} + +requirements: + host: + - r-base + - r-ggplot2 + - r-mass + run: + - r-base + - r-ggplot2 + - r-mass + +test: + commands: + - $R -e "library(BuenColors)" + +about: + home: {{ github }} + dev_url: {{ github }} + license: MIT + license_family: MIT + license_file: + - {{ environ["PREFIX"] }}/lib/R/share/licenses/MIT + - LICENSE + summary: R utility package for color mapping and plot aesthetics. + +extra: + recipe-maintainers: + - mfansler diff --git a/recipes/r-cobrar/meta.yaml b/recipes/r-cobrar/meta.yaml new file mode 100644 index 0000000000000..1b8dd50554991 --- /dev/null +++ b/recipes/r-cobrar/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "cobrar" %} +{% set version = '0.1.0' %} +{% set github = "https://github.com/Waschina/cobrar" %} +{% set sha256 = '8b8d7f7604fd93130f999a41ee30ce94c16f998520dfd73d6842d34ff96270a6' %} + +package: + name: r-{{ name }} + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ github }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + script: R CMD INSTALL --build . + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage("r-cobrar", max_pin="x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - make + host: + - glpk >=4.65 + - libsbml >=5.18.0 + - r-base + - r-rcpp + - r-rcpparmadillo + - r-matrix + run: + - glpk >=4.65 + - libsbml >=5.18.0 + - r-base + - r-rcpp + - r-rcpparmadillo + - r-matrix + +test: + commands: + - $R -e "library('cobrar')" + +about: + home: https://github.com/Waschina/cobrar + license: GPL-3.0-or-later + summary: COnstraint-based Reconstruction and Analysis (COBRA) of metabolic networks in R + license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + doc_url: https://waschina.github.io/cobrar/ + dev_url: https://github.com/Waschina/cobrar + +extra: + recipe-maintainers: + - Waschina + diff --git a/recipes/r-diffcorr/meta.yaml b/recipes/r-diffcorr/meta.yaml index 75a7764de28b5..71a4ef28bc8e3 100644 --- a/recipes/r-diffcorr/meta.yaml +++ b/recipes/r-diffcorr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.4.3' %} +{% set version = '0.4.4' %} package: name: r-diffcorr @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/DiffCorr_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/DiffCorr/DiffCorr_{{ version }}.tar.gz - sha256: b0d811cbd78eb69484fb184522cc358d9ad56235b85ee56bef22fc3c1d2df3f3 + sha256: c729fe399aceaf3afb975777ff3483e5d557d9b55b33fe5803bdb8949ff33b17 build: number: 0 diff --git a/recipes/r-facets/meta.yaml b/recipes/r-facets/meta.yaml index 6cd13c2138670..4bbd9aa678bdd 100644 --- a/recipes/r-facets/meta.yaml +++ b/recipes/r-facets/meta.yaml @@ -7,7 +7,9 @@ source: sha256: aa671d4fc66e10ce2fe4c8b2cbac4946da8a1564627240ea916db6cd8ec2a6c5 build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("r-facets", max_pin="x") }} rpaths: - lib/R/lib/ - lib/ @@ -35,5 +37,7 @@ about: license_family: GPL3 extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:facets diff --git a/recipes/r-grain/meta.yaml b/recipes/r-grain/meta.yaml index 18c6cd5efde07..b7779e3c6a07e 100644 --- a/recipes/r-grain/meta.yaml +++ b/recipes/r-grain/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.4.1' %} +{% set version = '1.4.2' %} package: name: r-grain @@ -8,10 +8,10 @@ source: url: - {{ cran_mirror }}/src/contrib/gRain_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/gRain/gRain_{{ version }}.tar.gz - sha256: d9f926aa876270ab4ae156a70703ec8ccd384cc6a7bfe5de4d1de3ef9e056485 + sha256: 487d5287e1d8b473e8dd96317744ffc77366a4a9f3056376f0bb766898acce74 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -57,3 +57,7 @@ about: license_family: GPL3 license_file: - {{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2 + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/r-mams/meta.yaml b/recipes/r-mams/meta.yaml new file mode 100644 index 0000000000000..673fe63a605e3 --- /dev/null +++ b/recipes/r-mams/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.1" %} +{% set sha256 = "90b4658c20f8420d3e158522d5e94ada026ff8bc9a71f644f6bd5c78c9539bfd" %} + +package: + name: r-mams + version: '{{ version }}' + +source: + url: https://github.com/single-cell-mams/rmams/archive/refs/tags/{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + script: ${R} CMD INSTALL --build . ${R_ARGS} + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage("r-mams", max_pin="x") }} + +requirements: + host: + - r-base + - r-seurat + - r-jsonlite + - r-rmdformats + - r-r.methodss3 + - r-anndata + - bioconductor-scran + - bioconductor-scater + - bioconductor-singlecellexperiment + - bioconductor-dropletutils + - bioconductor-annotationdbi + - bioconductor-org.hs.eg.db + run: + - r-base + - r-seurat + - r-jsonlite + - r-rmdformats + - r-r.methodss3 + - r-anndata + - bioconductor-scran + - bioconductor-scater + - bioconductor-singlecellexperiment + - bioconductor-dropletutils + - bioconductor-annotationdbi + - bioconductor-org.hs.eg.db + +test: + commands: + - $R -e "library('rmams')" + +about: + home: "https://github.com/single-cell-mams/rmams" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "R package for Matrix and Analysis Metadata Standards." + dev_url: "https://github.com/single-cell-mams/rmams" + doc_url: "https://single-cell-mams.github.io/rmams" + +extra: + recipe-maintainers: + - pmb59 + - irzamsarfraz diff --git a/recipes/r-mfassignr/meta.yaml b/recipes/r-mfassignr/meta.yaml index c2d1902a1d541..421e7b81ce8ea 100644 --- a/recipes/r-mfassignr/meta.yaml +++ b/recipes/r-mfassignr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mfassignr" %} -{% set version = "1.0.3" %} +{% set version = "1.1.1" %} {% set github = "https://github.com/RECETOX" %} package: @@ -8,7 +8,7 @@ package: source: url: "{{ github }}/MFAssignR/archive/refs/tags/v{{ version }}.tar.gz" - sha256: facb0d53f39d25f7c8ea6a04d87d218a4bf3e72c4b0257f1c028f40f99962a22 + sha256: 11d0c871871e52010978df0273221f95ccd21e950585e19a63d8b40ea23aebcb build: number: 0 @@ -27,12 +27,14 @@ requirements: - r-tidyr >=0.8.1 - r-ggplot2 >=3.0.0 - r-colorRamps >=2.3 + - r-gtools >=3.9.5 run: - r-base >=3.4.1 - r-dplyr >=0.7.6 - r-tidyr >=0.8.1 - r-ggplot2 >=3.0.0 - r-colorRamps >=2.3 + - r-gtools >=3.9.5 test: commands: diff --git a/recipes/r-mspbwt/LICENSE b/recipes/r-mspbwt/LICENSE new file mode 100644 index 0000000000000..94a9ed024d385 --- /dev/null +++ b/recipes/r-mspbwt/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/r-mspbwt/build.sh b/recipes/r-mspbwt/build.sh new file mode 100644 index 0000000000000..461b46a617216 --- /dev/null +++ b/recipes/r-mspbwt/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +export LC_ALL=C.UTF-8 +export LANG=C.UTF-8 + + +$R CMD INSTALL --build --install-tests mspbwt + diff --git a/recipes/r-mspbwt/meta.yaml b/recipes/r-mspbwt/meta.yaml new file mode 100644 index 0000000000000..c4e12068526ed --- /dev/null +++ b/recipes/r-mspbwt/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "0.1.0" %} +{% set sha256 = "384330b4deb7b8f1f83ec705c48a099f7ef890beb14a6dd97e117beb4ae92888" %} + +package: + name: r-mspbwt + version: '{{ version }}' + +source: + - url: https://github.com/rwdavies/mspbwt/archive/refs/tags/{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + number: 1 + run_exports: + - {{ pin_subpackage('r-mspbwt', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - r-base + - r-rcpp <=1.0.12 + - r-data.table >=1.11.8 + - r-rrbgen >=0.0.6 + - r-stitch >=1.7.0 + run: + - r-base + - r-rcpp <=1.0.12 + - r-data.table >=1.11.8 + - r-rrbgen >=0.0.6 + - r-stitch >=1.7.0 + +test: + commands: + - $R -e "library('mspbwt');" + +about: + home: https://github.com/rwdavies/mspbwt + license: GPL-3.0-only + license_family: GPL3 + license_file: LICENSE + summary: Multi Symbol Positional Burrows Wheeler Transform + doc_url: https://github.com/rwdavies/mspbwt + dev_url: https://github.com/rwdavies/mspbwt + +extra: + additional-platforms: + - linux-aarch64 + recipe-maintainers: + - Zilong-Li + - rwdavies diff --git a/recipes/r-mutsigextractor/meta.yaml b/recipes/r-mutsigextractor/meta.yaml index 43ca06abbf2c8..f37f235e466e4 100644 --- a/recipes/r-mutsigextractor/meta.yaml +++ b/recipes/r-mutsigextractor/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.28" %} -{% set sha256 = "395d89050444f87babf22e3341d4898e3b0d283462ffb1f161da3b8bdc975aee" %} +{% set version = "1.29" %} +{% set sha256 = "7edea78713d59166c8a03c374288e3f72ddcb9b69b0ce06def7c76f27ce49f45" %} package: name: r-mutsigextractor diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml index bbfbdc7933bbf..999f9600bc26a 100644 --- a/recipes/r-oncopharmadb/meta.yaml +++ b/recipes/r-oncopharmadb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-oncopharmadb" %} -{% set version = "1.5.1" %} +{% set version = "1.7.0" %} {% set github = "https://github.com/sigven/oncoPharmaDB" %} package: @@ -8,7 +8,7 @@ package: source: url: https://github.com/sigven/pharmOncoX/archive/refs/tags/{{ version }}.tar.gz - sha256: 7765b9122063aeacd96db0c536141ab2e23a116a84e313b7264d707a09c92316 + sha256: 001e9b133028b00df90fa7081ad315fcb28be671ac7477cf6b689f0e0ca539fb build: number: 0 diff --git a/recipes/r-quilt/build.sh b/recipes/r-quilt/build.sh index b0bb175fa394d..b40cab9ea78ae 100644 --- a/recipes/r-quilt/build.sh +++ b/recipes/r-quilt/build.sh @@ -1,10 +1,17 @@ #!/bin/bash +set -xe + +mkdir -p $PREFIX/bin + export LC_ALL=C.UTF-8 export LANG=C.UTF-8 -cp $SRC_DIR/QUILT.R $PREFIX/bin/ -cd $SRC_DIR/QUILT - -$R CMD INSTALL --build --install-tests . +cp -rf $SRC_DIR/QUILT.R $PREFIX/bin/ +cp -rf $SRC_DIR/QUILT_prepare_reference.R $PREFIX/bin/ +cp -rf $SRC_DIR/QUILT_HLA_prepare_reference.R $PREFIX/bin/ +cp -rf $SRC_DIR/QUILT2.R $PREFIX/bin/ +cp -rf $SRC_DIR/QUILT2_prepare_reference.R $PREFIX/bin/ +cd $SRC_DIR/QUILT +${R} CMD INSTALL --build --install-tests . ${R_ARGS} diff --git a/recipes/r-quilt/meta.yaml b/recipes/r-quilt/meta.yaml index 75db7688a7028..b18e2ef0e20cd 100644 --- a/recipes/r-quilt/meta.yaml +++ b/recipes/r-quilt/meta.yaml @@ -1,8 +1,9 @@ -{% set version = "1.0.5" %} -{% set sha256 = "88f46a0c0f54260b8df9f150b0cf9bdedba6f9408bb7da36318055f2a9036266" %} +{% set name = "r-quilt" %} +{% set version = "2.0.0" %} +{% set sha256 = "723c52371fd8c495a54165b168db70d8c4ce001cd4dc902e63db0240318e8a6e" %} package: - name: r-quilt + name: '{{ name }}' version: '{{ version }}' source: @@ -10,9 +11,9 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 2 run_exports: - - {{ pin_subpackage('r-quilt', max_pin="1") }} + - {{ pin_subpackage('r-quilt', max_pin="x") }} requirements: build: @@ -20,48 +21,37 @@ requirements: - {{ compiler('cxx') }} host: - r-base - - r-rcpp >=0.12.18 - - r-rcpparmadillo >=0.8.600.0.0 - - r-data.table >=1.11.8 + - r-rcpp <=1.0.12 + - r-rcppeigen - r-rrbgen >=0.0.6 - - r-stitch >=1.6.6 - - xz - - gmp - - mpfr - - mpc >=1.1.0 - - libblas - - zlib + - r-stitch >=1.7.0 + - r-mspbwt >=0.1.0 run: - r-base - - r-rcpp >=0.12.18 - - r-rcpparmadillo >=0.8.600.0.0 - - r-data.table >=1.11.8 + - r-rcpp <=1.0.12 + - r-rcppeigen - r-rrbgen >=0.0.6 - - r-stitch >=1.6.6 - - r-optparse - - xz - - gmp - - mpfr - - mpc >=1.1.0 - - r-testthat >=2.0.0 - - htslib >=1.4 - - samtools >=1.4 - - rsync - - zlib + - r-stitch >=1.7.0 + - r-mspbwt >=0.1.0 + - r-optparse test: commands: - $R -e "library('QUILT'); testthat::test_package('QUILT', stop_on_failure = TRUE, stop_on_warning = TRUE, filter = 'acceptance-one', reporter = 'summary')" - 'QUILT.R --help' + about: home: https://github.com/rwdavies/quilt - license: GPL-3.0-only + license: "GPL-3.0-only" license_family: GPL3 license_file: LICENSE - summary: Read aware low coverage whole genome sequence imputation from a reference panel + summary: "Rapid and accurate genotype imputation from low coverage short read, long read, and cell free DNA sequence." doc_url: https://github.com/rwdavies/quilt dev_url: https://github.com/rwdavies/quilt extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: + - Zilong-Li - rwdavies diff --git a/recipes/r-recetox-aplcms/meta.yaml b/recipes/r-recetox-aplcms/meta.yaml index 01bb61a31fb8b..f47239d4c8f56 100644 --- a/recipes/r-recetox-aplcms/meta.yaml +++ b/recipes/r-recetox-aplcms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recetox-aplcms" %} -{% set version = "0.13.2" %} +{% set version = "0.13.3" %} {% set github = "https://github.com/RECETOX/recetox-aplcms" %} package: @@ -8,7 +8,7 @@ package: source: url: "https://github.com/RECETOX/recetox-aplcms/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 070e1dc9df4e3bff0e55d1332ee0a738ed368a03dbd485a37b14120408be08b2 + sha256: 3b37e51e959cba7cab6691f66dd2bb8279c4112fc5155576e0efef4ded2ad10b build: number: 0 diff --git a/recipes/r-signac/build.sh b/recipes/r-signac/build.sh index fa2264035f2b0..d1df318472b53 100644 --- a/recipes/r-signac/build.sh +++ b/recipes/r-signac/build.sh @@ -6,7 +6,7 @@ if [[ ${target_platform} =~ linux.* ]] || [[ ${target_platform} == win-32 ]] || export DISABLE_AUTOBREW=1 mv DESCRIPTION DESCRIPTION.old grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION - ${R} CMD INSTALL --build . + ${R} CMD INSTALL --build . ${R_ARGS} else mkdir -p "${PREFIX}"/lib/R/library/Signac mv ./* "${PREFIX}"/lib/R/library/Signac diff --git a/recipes/r-signac/meta.yaml b/recipes/r-signac/meta.yaml index ed619910d09f3..6bc0eb3d6e0cb 100644 --- a/recipes/r-signac/meta.yaml +++ b/recipes/r-signac/meta.yaml @@ -1,14 +1,15 @@ -{% set version = '1.13.0' %} +{% set name = "r-signac" %} +{% set version = '1.14.0' %} package: - name: r-signac + name: {{ name }} version: {{ version|replace("-", "_") }} source: url: - {{ cran_mirror }}/src/contrib/Signac_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/Signac/Signac_{{ version }}.tar.gz - sha256: d9b4103c6437391834b2d9e2aab8829f186b6e09d070dfe2a66cc12583241b2a + sha256: e0aad9e2c27c148fdd376081c2de1e3db46b1835eac83ef41fe562e08363c59e build: number: 0 @@ -34,7 +35,7 @@ requirements: - r-rcpproll - bioconductor-rsamtools - bioconductor-s4vectors - - r-seuratobject >=4.0.0 + - r-seuratobject >=5.0.2 - r-data.table - r-dplyr >=1.0.0 - r-fastmatch @@ -61,7 +62,7 @@ requirements: - r-rcpproll - bioconductor-rsamtools - bioconductor-s4vectors - - r-seuratobject >=4.0.0 + - r-seuratobject >=5.0.2 - r-data.table - r-dplyr >=1.0.0 - r-fastmatch @@ -83,7 +84,7 @@ test: - $R -e "library('Signac')" about: - home: https://github.com/timoast/signac, https://satijalab.org/signac + home: "https://github.com/timoast/signac" license: MIT summary: 'A framework for the analysis and exploration of single-cell chromatin data. The ''Signac'' package contains functions for quantifying single-cell chromatin data, computing @@ -93,3 +94,5 @@ about: license_file: - {{ environ["PREFIX"] }}/lib/R/share/licenses/MIT - LICENSE + doc_url: "https://satijalab.org/signac" + dev_url: "https://github.com/timoast/signac" diff --git a/recipes/r-sigqc/meta.yaml b/recipes/r-sigqc/meta.yaml index 282817c329e6d..1b32c8487d739 100644 --- a/recipes/r-sigqc/meta.yaml +++ b/recipes/r-sigqc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.23' %} +{% set version = '0.1.24' %} package: name: r-sigqc @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/sigQC_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/sigQC/sigQC_{{ version }}.tar.gz - sha256: a883ad4b9d0fe3605d73d575030e45e6a89ad1a895bf78303e041808a889ec3a + sha256: a27a567d2c13aaf110b86f4fd6b15cc8949d5bd28fe0e44b92a65b163544e27c build: noarch: generic - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-sigqc', max_pin="x.x") }} requirements: host: diff --git a/recipes/r-stitch/build.sh b/recipes/r-stitch/build.sh index 56a790ad9541b..3a36f7dff68f8 100644 --- a/recipes/r-stitch/build.sh +++ b/recipes/r-stitch/build.sh @@ -2,12 +2,11 @@ set -xe +export LC_ALL=C.UTF-8 +export LANG=C.UTF-8 + mkdir -p $PREFIX/bin -cp STITCH.R $PREFIX/bin - -# patch a Git submodule -pushd src/SeqLib/ -patch -p1 < ${RECIPE_DIR}/seqlib-aarch64.patch -popd - -$R CMD INSTALL --build --install-tests . +cp -rf STITCH.R $PREFIX/bin + +cd $SRC_DIR/STITCH +${R} CMD INSTALL --build --install-tests . ${R_ARGS} diff --git a/recipes/r-stitch/meta.yaml b/recipes/r-stitch/meta.yaml index 34537d7679da9..7cea5b5efce68 100644 --- a/recipes/r-stitch/meta.yaml +++ b/recipes/r-stitch/meta.yaml @@ -1,22 +1,19 @@ -{% set version = "1.6.11" %} -{% set sha256_package = "eb6a8e121eb9689597da9ec5a105ba5392e458ab30510fe26b260b81a6d9fdb0" %} -{% set sha256_script = "0c61d79cf519e5c5ae33807725577da3d1599bcc89413c3a6bce3fb7c99090c7" %} +{% set version = "1.7.1" %} +{% set sha256 = "e4ff3eb406dd5bb52d3311cfe59b7b8508b14df874d5a5f6bd970abd02de3428" %} package: name: r-stitch version: '{{ version }}' source: - - url: https://github.com/rwdavies/stitch/releases/download/{{ version }}/STITCH_{{ version }}.tar.gz - sha256: '{{ sha256_package }}' - - url: https://raw.githubusercontent.com/rwdavies/STITCH/{{ version }}/STITCH.R - sha256: '{{ sha256_script }}' + - url: https://github.com/rwdavies/stitch/archive/refs/tags/{{ version }}.tar.gz + sha256: '{{ sha256 }}' build: number: 0 run_exports: - {{ pin_subpackage('r-stitch', max_pin="x") }} - + requirements: build: - {{ compiler('c') }} @@ -25,10 +22,10 @@ requirements: - automake - pkg-config - make - - libcxx <17 # [osx] + - libcxx >=16 # [osx] host: - r-base - - r-rcpp >=0.12.18 + - r-rcpp <=1.0.12 - r-rcpparmadillo >=0.8.600.0.0 - r-data.table >=1.11.8 - r-rrbgen >=0.0.6 @@ -38,7 +35,7 @@ requirements: - mpc >=1.1.0 - libblas - zlib - - libcxx <17 # [osx] + - libcxx >=16 # [osx] run: - r-base - r-rcpp >=0.12.18 @@ -46,15 +43,10 @@ requirements: - r-data.table >=1.11.8 - r-rrbgen >=0.0.6 - r-optparse - - xz - - gmp - - mpfr - - mpc >=1.1.0 - r-testthat >=2.0.0 - htslib >=1.4 - samtools >=1.4 - rsync - - zlib test: commands: @@ -66,7 +58,7 @@ about: license: GPL-3.0-only license_family: GPL3 license_file: LICENSE - summary: STITCH - Sequencing To Imputation Through Constructing Haplotypes + summary: "STITCH - Sequencing To Imputation Through Constructing Haplotypes." doc_url: https://github.com/rwdavies/stitch dev_url: https://github.com/rwdavies/stitch @@ -74,4 +66,5 @@ extra: additional-platforms: - linux-aarch64 recipe-maintainers: + - Zilong-Li - rwdavies diff --git a/recipes/r-wgcna/meta.yaml b/recipes/r-wgcna/meta.yaml index 04f5371fe99aa..36f76edf48f76 100644 --- a/recipes/r-wgcna/meta.yaml +++ b/recipes/r-wgcna/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.71' %} +{% set version = '1.73' %} package: name: r-wgcna @@ -8,10 +8,10 @@ source: url: - {{ cran_mirror }}/src/contrib/WGCNA_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/WGCNA/WGCNA_{{ version }}.tar.gz - sha256: 21f5349e888ea76241912600ee5c35a0d2fd50180568b9b08b2b597f099bf708 + sha256: e8a0a367a93190dd9f738578a82d31856e004b9de46d2775e4ed0f44a95063ce build: - number: 5 + number: 0 run_exports: - {{ pin_subpackage("r-wgcna", max_pin="x") }} rpaths: diff --git a/recipes/rapidnj/build.sh b/recipes/rapidnj/build.sh index 9ff3b44dfe4df..8381fefdb8c22 100755 --- a/recipes/rapidnj/build.sh +++ b/recipes/rapidnj/build.sh @@ -1,5 +1,7 @@ #!/bin/sh -make CC="${CXX}" LINK="${CXX}" SWITCHES="${CPPFLAGS} ${CXXFLAGS} -std=c++14 ${LDFLAGS}" +set -xe + +make -j ${CPU_COUNT} CC="${CXX}" LINK="${CXX}" SWITCHES="${CPPFLAGS} ${CXXFLAGS} -std=c++14 ${LDFLAGS}" install -d "${PREFIX}/bin" install bin/rapidnj "${PREFIX}/bin/" diff --git a/recipes/rapidnj/meta.yaml b/recipes/rapidnj/meta.yaml index 150a9f9f9673a..885e496afe478 100644 --- a/recipes/rapidnj/meta.yaml +++ b/recipes/rapidnj/meta.yaml @@ -7,9 +7,13 @@ package: source: url: https://github.com/johnlees/rapidnj/archive/v{{ version }}.tar.gz sha256: 7b81dc84cb1d4ac6e24d15e18ae50460b496bc3476a0bc0935553dff085480dd + patches: + - rapidnj-aarch64.patch # [aarch64 or arm64] build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage('rapidnj', max_pin="x") }} requirements: build: @@ -23,14 +27,18 @@ test: about: home: http://birc.au.dk/software/rapidnj/ - license: GPL-2 + license: GPL-2-only license_family: GPL license_file: LICENSE summary: RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations. + dev_url: https://github.com/johnlees/rapidnj extra: - identifiers: - - doi:10.1007/978-3-540-87361-7_10 + additional-platforms: + - linux-aarch64 + - osx-arm64 + identifiers: + - doi:10.1007/978-3-540-87361-7_10 diff --git a/recipes/rapidnj/rapidnj-aarch64.patch b/recipes/rapidnj/rapidnj-aarch64.patch new file mode 100644 index 0000000000000..9f33d3de82e07 --- /dev/null +++ b/recipes/rapidnj/rapidnj-aarch64.patch @@ -0,0 +1,9485 @@ +diff --git c/Makefile i/Makefile +index d8087e2..fc63986 100644 +--- c/Makefile ++++ i/Makefile +@@ -14,7 +14,7 @@ INCLUDES= -Isrc/distanceCalculation -Isrc/ -Ilib/includes + else + CC = g++ + LINK = g++ +-OPTIMIZATION_LEVEL=-O3 -msse2 ++OPTIMIZATION_LEVEL=-O3 + DEBUG= -Wall #-g #-pg + OBJECTFLAG =-o + COMPILEFLAG =-c +diff --git c/src/distanceCalculation/bitDistanceProtein.cpp i/src/distanceCalculation/bitDistanceProtein.cpp +index 8a53811..d21fa7f 100755 +--- c/src/distanceCalculation/bitDistanceProtein.cpp ++++ i/src/distanceCalculation/bitDistanceProtein.cpp +@@ -1,5 +1,10 @@ + #include "bitDistanceProtein.hpp" ++ ++#ifdef __ARM_NEON ++#include "sse2neon.h" ++#else + #include ++#endif + + v4ui bitDistanceProtein::mask1of8 = _mm_set_epi32(0x01010101,0x01010101,0x01010101,0x01010101); + v4ui bitDistanceProtein::mask8 = _mm_set_epi32(0x00ff00ff,0x00ff00ff,0x00ff00ff,0x00ff00ff); +diff --git c/src/sse2neon.h i/src/sse2neon.h +new file mode 100644 +index 0000000..50f5646 +--- /dev/null ++++ i/src/sse2neon.h +@@ -0,0 +1,9429 @@ ++#ifndef SSE2NEON_H ++#define SSE2NEON_H ++ ++/* ++ * sse2neon is freely redistributable under the MIT License. ++ * ++ * Copyright (c) 2015-2024 SSE2NEON Contributors. ++ * ++ * Permission is hereby granted, free of charge, to any person obtaining a copy ++ * of this software and associated documentation files (the "Software"), to deal ++ * in the Software without restriction, including without limitation the rights ++ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell ++ * copies of the Software, and to permit persons to whom the Software is ++ * furnished to do so, subject to the following conditions: ++ * ++ * The above copyright notice and this permission notice shall be included in ++ * all copies or substantial portions of the Software. ++ * ++ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR ++ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, ++ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE ++ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER ++ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, ++ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE ++ * SOFTWARE. ++ */ ++ ++// This header file provides a simple API translation layer ++// between SSE intrinsics to their corresponding Arm/Aarch64 NEON versions ++// ++// Contributors to this work are: ++// John W. Ratcliff ++// Brandon Rowlett ++// Ken Fast ++// Eric van Beurden ++// Alexander Potylitsin ++// Hasindu Gamaarachchi ++// Jim Huang ++// Mark Cheng ++// Malcolm James MacLeod ++// Devin Hussey (easyaspi314) ++// Sebastian Pop ++// Developer Ecosystem Engineering ++// Danila Kutenin ++// François Turban (JishinMaster) ++// Pei-Hsuan Hung ++// Yang-Hao Yuan ++// Syoyo Fujita ++// Brecht Van Lommel ++// Jonathan Hue ++// Cuda Chen ++// Aymen Qader ++// Anthony Roberts ++ ++/* Tunable configurations */ ++ ++/* Enable precise implementation of math operations ++ * This would slow down the computation a bit, but gives consistent result with ++ * x86 SSE. (e.g. would solve a hole or NaN pixel in the rendering result) ++ */ ++/* _mm_min|max_ps|ss|pd|sd */ ++#ifndef SSE2NEON_PRECISE_MINMAX ++#define SSE2NEON_PRECISE_MINMAX (0) ++#endif ++/* _mm_rcp_ps */ ++#ifndef SSE2NEON_PRECISE_DIV ++#define SSE2NEON_PRECISE_DIV (0) ++#endif ++/* _mm_sqrt_ps and _mm_rsqrt_ps */ ++#ifndef SSE2NEON_PRECISE_SQRT ++#define SSE2NEON_PRECISE_SQRT (0) ++#endif ++/* _mm_dp_pd */ ++#ifndef SSE2NEON_PRECISE_DP ++#define SSE2NEON_PRECISE_DP (0) ++#endif ++ ++/* Enable inclusion of windows.h on MSVC platforms ++ * This makes _mm_clflush functional on windows, as there is no builtin. ++ */ ++#ifndef SSE2NEON_INCLUDE_WINDOWS_H ++#define SSE2NEON_INCLUDE_WINDOWS_H (0) ++#endif ++ ++/* compiler specific definitions */ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma push_macro("FORCE_INLINE") ++#pragma push_macro("ALIGN_STRUCT") ++#define FORCE_INLINE static inline __attribute__((always_inline)) ++#define ALIGN_STRUCT(x) __attribute__((aligned(x))) ++#define _sse2neon_likely(x) __builtin_expect(!!(x), 1) ++#define _sse2neon_unlikely(x) __builtin_expect(!!(x), 0) ++#elif defined(_MSC_VER) ++#if _MSVC_TRADITIONAL ++#error Using the traditional MSVC preprocessor is not supported! Use /Zc:preprocessor instead. ++#endif ++#ifndef FORCE_INLINE ++#define FORCE_INLINE static inline ++#endif ++#ifndef ALIGN_STRUCT ++#define ALIGN_STRUCT(x) __declspec(align(x)) ++#endif ++#define _sse2neon_likely(x) (x) ++#define _sse2neon_unlikely(x) (x) ++#else ++#pragma message("Macro name collisions may happen with unsupported compilers.") ++#endif ++ ++ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma push_macro("FORCE_INLINE_OPTNONE") ++#define FORCE_INLINE_OPTNONE static inline __attribute__((optimize("O0"))) ++#elif defined(__clang__) ++#pragma push_macro("FORCE_INLINE_OPTNONE") ++#define FORCE_INLINE_OPTNONE static inline __attribute__((optnone)) ++#else ++#define FORCE_INLINE_OPTNONE FORCE_INLINE ++#endif ++ ++#if !defined(__clang__) && defined(__GNUC__) && __GNUC__ < 10 ++#warning "GCC versions earlier than 10 are not supported." ++#endif ++ ++/* C language does not allow initializing a variable with a function call. */ ++#ifdef __cplusplus ++#define _sse2neon_const static const ++#else ++#define _sse2neon_const const ++#endif ++ ++#include ++#include ++#include ++ ++FORCE_INLINE double sse2neon_recast_u64_f64(uint64_t u64) ++{ ++ double f64; ++ memcpy(&f64, &u64, sizeof(uint64_t)); ++ return f64; ++} ++FORCE_INLINE int64_t sse2neon_recast_f64_s64(double f64) ++{ ++ int64_t i64; ++ memcpy(&i64, &f64, sizeof(uint64_t)); ++ return i64; ++} ++ ++#if defined(_WIN32) ++/* Definitions for _mm_{malloc,free} are provided by ++ * from both MinGW-w64 and MSVC. ++ */ ++#define SSE2NEON_ALLOC_DEFINED ++#endif ++ ++/* If using MSVC */ ++#ifdef _MSC_VER ++#include ++#if SSE2NEON_INCLUDE_WINDOWS_H ++#include ++#include ++#endif ++ ++#if !defined(__cplusplus) ++#error SSE2NEON only supports C++ compilation with this compiler ++#endif ++ ++#ifdef SSE2NEON_ALLOC_DEFINED ++#include ++#endif ++ ++#if (defined(_M_AMD64) || defined(__x86_64__)) || \ ++ (defined(_M_ARM64) || defined(__arm64__)) ++#define SSE2NEON_HAS_BITSCAN64 ++#endif ++#endif ++ ++#if defined(__GNUC__) || defined(__clang__) ++#define _sse2neon_define0(type, s, body) \ ++ __extension__({ \ ++ type _a = (s); \ ++ body \ ++ }) ++#define _sse2neon_define1(type, s, body) \ ++ __extension__({ \ ++ type _a = (s); \ ++ body \ ++ }) ++#define _sse2neon_define2(type, a, b, body) \ ++ __extension__({ \ ++ type _a = (a), _b = (b); \ ++ body \ ++ }) ++#define _sse2neon_return(ret) (ret) ++#else ++#define _sse2neon_define0(type, a, body) [=](type _a) { body }(a) ++#define _sse2neon_define1(type, a, body) [](type _a) { body }(a) ++#define _sse2neon_define2(type, a, b, body) \ ++ [](type _a, type _b) { body }((a), (b)) ++#define _sse2neon_return(ret) return ret ++#endif ++ ++#define _sse2neon_init(...) \ ++ { \ ++ __VA_ARGS__ \ ++ } ++ ++/* Compiler barrier */ ++#if defined(_MSC_VER) && !defined(__clang__) ++#define SSE2NEON_BARRIER() _ReadWriteBarrier() ++#else ++#define SSE2NEON_BARRIER() \ ++ do { \ ++ __asm__ __volatile__("" ::: "memory"); \ ++ (void) 0; \ ++ } while (0) ++#endif ++ ++/* Memory barriers ++ * __atomic_thread_fence does not include a compiler barrier; instead, ++ * the barrier is part of __atomic_load/__atomic_store's "volatile-like" ++ * semantics. ++ */ ++#if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 201112L) ++#include ++#endif ++ ++FORCE_INLINE void _sse2neon_smp_mb(void) ++{ ++ SSE2NEON_BARRIER(); ++#if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 201112L) && \ ++ !defined(__STDC_NO_ATOMICS__) ++ atomic_thread_fence(memory_order_seq_cst); ++#elif defined(__GNUC__) || defined(__clang__) ++ __atomic_thread_fence(__ATOMIC_SEQ_CST); ++#else /* MSVC */ ++ __dmb(_ARM64_BARRIER_ISH); ++#endif ++} ++ ++/* Architecture-specific build options */ ++/* FIXME: #pragma GCC push_options is only available on GCC */ ++#if defined(__GNUC__) ++#if defined(__arm__) && __ARM_ARCH == 7 ++/* According to ARM C Language Extensions Architecture specification, ++ * __ARM_NEON is defined to a value indicating the Advanced SIMD (NEON) ++ * architecture supported. ++ */ ++#if !defined(__ARM_NEON) || !defined(__ARM_NEON__) ++#error "You must enable NEON instructions (e.g. -mfpu=neon) to use SSE2NEON." ++#endif ++#if !defined(__clang__) ++#pragma GCC push_options ++#pragma GCC target("fpu=neon") ++#endif ++#elif defined(__aarch64__) || defined(_M_ARM64) ++#if !defined(__clang__) && !defined(_MSC_VER) ++#pragma GCC push_options ++#pragma GCC target("+simd") ++#endif ++#elif __ARM_ARCH == 8 ++#if !defined(__ARM_NEON) || !defined(__ARM_NEON__) ++#error \ ++ "You must enable NEON instructions (e.g. -mfpu=neon-fp-armv8) to use SSE2NEON." ++#endif ++#if !defined(__clang__) && !defined(_MSC_VER) ++#pragma GCC push_options ++#endif ++#else ++#error \ ++ "Unsupported target. Must be either ARMv7-A+NEON or ARMv8-A \ ++(you could try setting target explicitly with -march or -mcpu)" ++#endif ++#endif ++ ++#include ++#if (!defined(__aarch64__) && !defined(_M_ARM64)) && (__ARM_ARCH == 8) ++#if defined __has_include && __has_include() ++#include ++#endif ++#endif ++ ++/* Apple Silicon cache lines are double of what is commonly used by Intel, AMD ++ * and other Arm microarchitectures use. ++ * From sysctl -a on Apple M1: ++ * hw.cachelinesize: 128 ++ */ ++#if defined(__APPLE__) && (defined(__aarch64__) || defined(__arm64__)) ++#define SSE2NEON_CACHELINE_SIZE 128 ++#else ++#define SSE2NEON_CACHELINE_SIZE 64 ++#endif ++ ++/* Rounding functions require either Aarch64 instructions or libm fallback */ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++#include ++#endif ++ ++/* On ARMv7, some registers, such as PMUSERENR and PMCCNTR, are read-only ++ * or even not accessible in user mode. ++ * To write or access to these registers in user mode, ++ * we have to perform syscall instead. ++ */ ++#if (!defined(__aarch64__) && !defined(_M_ARM64)) ++#include ++#endif ++ ++/* "__has_builtin" can be used to query support for built-in functions ++ * provided by gcc/clang and other compilers that support it. ++ */ ++#ifndef __has_builtin /* GCC prior to 10 or non-clang compilers */ ++/* Compatibility with gcc <= 9 */ ++#if defined(__GNUC__) && (__GNUC__ <= 9) ++#define __has_builtin(x) HAS##x ++#define HAS__builtin_popcount 1 ++#define HAS__builtin_popcountll 1 ++ ++// __builtin_shuffle introduced in GCC 4.7.0 ++#if (__GNUC__ >= 5) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)) ++#define HAS__builtin_shuffle 1 ++#else ++#define HAS__builtin_shuffle 0 ++#endif ++ ++#define HAS__builtin_shufflevector 0 ++#define HAS__builtin_nontemporal_store 0 ++#else ++#define __has_builtin(x) 0 ++#endif ++#endif ++ ++/** ++ * MACRO for shuffle parameter for _mm_shuffle_ps(). ++ * Argument fp3 is a digit[0123] that represents the fp from argument "b" ++ * of mm_shuffle_ps that will be placed in fp3 of result. fp2 is the same ++ * for fp2 in result. fp1 is a digit[0123] that represents the fp from ++ * argument "a" of mm_shuffle_ps that will be places in fp1 of result. ++ * fp0 is the same for fp0 of result. ++ */ ++#define _MM_SHUFFLE(fp3, fp2, fp1, fp0) \ ++ (((fp3) << 6) | ((fp2) << 4) | ((fp1) << 2) | ((fp0))) ++ ++#if __has_builtin(__builtin_shufflevector) ++#define _sse2neon_shuffle(type, a, b, ...) \ ++ __builtin_shufflevector(a, b, __VA_ARGS__) ++#elif __has_builtin(__builtin_shuffle) ++#define _sse2neon_shuffle(type, a, b, ...) \ ++ __extension__({ \ ++ type tmp = {__VA_ARGS__}; \ ++ __builtin_shuffle(a, b, tmp); \ ++ }) ++#endif ++ ++#ifdef _sse2neon_shuffle ++#define vshuffle_s16(a, b, ...) _sse2neon_shuffle(int16x4_t, a, b, __VA_ARGS__) ++#define vshuffleq_s16(a, b, ...) _sse2neon_shuffle(int16x8_t, a, b, __VA_ARGS__) ++#define vshuffle_s32(a, b, ...) _sse2neon_shuffle(int32x2_t, a, b, __VA_ARGS__) ++#define vshuffleq_s32(a, b, ...) _sse2neon_shuffle(int32x4_t, a, b, __VA_ARGS__) ++#define vshuffle_s64(a, b, ...) _sse2neon_shuffle(int64x1_t, a, b, __VA_ARGS__) ++#define vshuffleq_s64(a, b, ...) _sse2neon_shuffle(int64x2_t, a, b, __VA_ARGS__) ++#endif ++ ++/* Rounding mode macros. */ ++#define _MM_FROUND_TO_NEAREST_INT 0x00 ++#define _MM_FROUND_TO_NEG_INF 0x01 ++#define _MM_FROUND_TO_POS_INF 0x02 ++#define _MM_FROUND_TO_ZERO 0x03 ++#define _MM_FROUND_CUR_DIRECTION 0x04 ++#define _MM_FROUND_NO_EXC 0x08 ++#define _MM_FROUND_RAISE_EXC 0x00 ++#define _MM_FROUND_NINT (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_FLOOR (_MM_FROUND_TO_NEG_INF | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_CEIL (_MM_FROUND_TO_POS_INF | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_TRUNC (_MM_FROUND_TO_ZERO | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_RINT (_MM_FROUND_CUR_DIRECTION | _MM_FROUND_RAISE_EXC) ++#define _MM_FROUND_NEARBYINT (_MM_FROUND_CUR_DIRECTION | _MM_FROUND_NO_EXC) ++#define _MM_ROUND_NEAREST 0x0000 ++#define _MM_ROUND_DOWN 0x2000 ++#define _MM_ROUND_UP 0x4000 ++#define _MM_ROUND_TOWARD_ZERO 0x6000 ++/* Flush zero mode macros. */ ++#define _MM_FLUSH_ZERO_MASK 0x8000 ++#define _MM_FLUSH_ZERO_ON 0x8000 ++#define _MM_FLUSH_ZERO_OFF 0x0000 ++/* Denormals are zeros mode macros. */ ++#define _MM_DENORMALS_ZERO_MASK 0x0040 ++#define _MM_DENORMALS_ZERO_ON 0x0040 ++#define _MM_DENORMALS_ZERO_OFF 0x0000 ++ ++/* indicate immediate constant argument in a given range */ ++#define __constrange(a, b) const ++ ++/* A few intrinsics accept traditional data types like ints or floats, but ++ * most operate on data types that are specific to SSE. ++ * If a vector type ends in d, it contains doubles, and if it does not have ++ * a suffix, it contains floats. An integer vector type can contain any type ++ * of integer, from chars to shorts to unsigned long longs. ++ */ ++typedef int64x1_t __m64; ++typedef float32x4_t __m128; /* 128-bit vector containing 4 floats */ ++// On ARM 32-bit architecture, the float64x2_t is not supported. ++// The data type __m128d should be represented in a different way for related ++// intrinsic conversion. ++#if defined(__aarch64__) || defined(_M_ARM64) ++typedef float64x2_t __m128d; /* 128-bit vector containing 2 doubles */ ++#else ++typedef float32x4_t __m128d; ++#endif ++typedef int64x2_t __m128i; /* 128-bit vector containing integers */ ++ ++// Some intrinsics operate on unaligned data types. ++typedef int16_t ALIGN_STRUCT(1) unaligned_int16_t; ++typedef int32_t ALIGN_STRUCT(1) unaligned_int32_t; ++typedef int64_t ALIGN_STRUCT(1) unaligned_int64_t; ++ ++// __int64 is defined in the Intrinsics Guide which maps to different datatype ++// in different data model ++#if !(defined(_WIN32) || defined(_WIN64) || defined(__int64)) ++#if (defined(__x86_64__) || defined(__i386__)) ++#define __int64 long long ++#else ++#define __int64 int64_t ++#endif ++#endif ++ ++/* type-safe casting between types */ ++ ++#define vreinterpretq_m128_f16(x) vreinterpretq_f32_f16(x) ++#define vreinterpretq_m128_f32(x) (x) ++#define vreinterpretq_m128_f64(x) vreinterpretq_f32_f64(x) ++ ++#define vreinterpretq_m128_u8(x) vreinterpretq_f32_u8(x) ++#define vreinterpretq_m128_u16(x) vreinterpretq_f32_u16(x) ++#define vreinterpretq_m128_u32(x) vreinterpretq_f32_u32(x) ++#define vreinterpretq_m128_u64(x) vreinterpretq_f32_u64(x) ++ ++#define vreinterpretq_m128_s8(x) vreinterpretq_f32_s8(x) ++#define vreinterpretq_m128_s16(x) vreinterpretq_f32_s16(x) ++#define vreinterpretq_m128_s32(x) vreinterpretq_f32_s32(x) ++#define vreinterpretq_m128_s64(x) vreinterpretq_f32_s64(x) ++ ++#define vreinterpretq_f16_m128(x) vreinterpretq_f16_f32(x) ++#define vreinterpretq_f32_m128(x) (x) ++#define vreinterpretq_f64_m128(x) vreinterpretq_f64_f32(x) ++ ++#define vreinterpretq_u8_m128(x) vreinterpretq_u8_f32(x) ++#define vreinterpretq_u16_m128(x) vreinterpretq_u16_f32(x) ++#define vreinterpretq_u32_m128(x) vreinterpretq_u32_f32(x) ++#define vreinterpretq_u64_m128(x) vreinterpretq_u64_f32(x) ++ ++#define vreinterpretq_s8_m128(x) vreinterpretq_s8_f32(x) ++#define vreinterpretq_s16_m128(x) vreinterpretq_s16_f32(x) ++#define vreinterpretq_s32_m128(x) vreinterpretq_s32_f32(x) ++#define vreinterpretq_s64_m128(x) vreinterpretq_s64_f32(x) ++ ++#define vreinterpretq_m128i_s8(x) vreinterpretq_s64_s8(x) ++#define vreinterpretq_m128i_s16(x) vreinterpretq_s64_s16(x) ++#define vreinterpretq_m128i_s32(x) vreinterpretq_s64_s32(x) ++#define vreinterpretq_m128i_s64(x) (x) ++ ++#define vreinterpretq_m128i_u8(x) vreinterpretq_s64_u8(x) ++#define vreinterpretq_m128i_u16(x) vreinterpretq_s64_u16(x) ++#define vreinterpretq_m128i_u32(x) vreinterpretq_s64_u32(x) ++#define vreinterpretq_m128i_u64(x) vreinterpretq_s64_u64(x) ++ ++#define vreinterpretq_f32_m128i(x) vreinterpretq_f32_s64(x) ++#define vreinterpretq_f64_m128i(x) vreinterpretq_f64_s64(x) ++ ++#define vreinterpretq_s8_m128i(x) vreinterpretq_s8_s64(x) ++#define vreinterpretq_s16_m128i(x) vreinterpretq_s16_s64(x) ++#define vreinterpretq_s32_m128i(x) vreinterpretq_s32_s64(x) ++#define vreinterpretq_s64_m128i(x) (x) ++ ++#define vreinterpretq_u8_m128i(x) vreinterpretq_u8_s64(x) ++#define vreinterpretq_u16_m128i(x) vreinterpretq_u16_s64(x) ++#define vreinterpretq_u32_m128i(x) vreinterpretq_u32_s64(x) ++#define vreinterpretq_u64_m128i(x) vreinterpretq_u64_s64(x) ++ ++#define vreinterpret_m64_s8(x) vreinterpret_s64_s8(x) ++#define vreinterpret_m64_s16(x) vreinterpret_s64_s16(x) ++#define vreinterpret_m64_s32(x) vreinterpret_s64_s32(x) ++#define vreinterpret_m64_s64(x) (x) ++ ++#define vreinterpret_m64_u8(x) vreinterpret_s64_u8(x) ++#define vreinterpret_m64_u16(x) vreinterpret_s64_u16(x) ++#define vreinterpret_m64_u32(x) vreinterpret_s64_u32(x) ++#define vreinterpret_m64_u64(x) vreinterpret_s64_u64(x) ++ ++#define vreinterpret_m64_f16(x) vreinterpret_s64_f16(x) ++#define vreinterpret_m64_f32(x) vreinterpret_s64_f32(x) ++#define vreinterpret_m64_f64(x) vreinterpret_s64_f64(x) ++ ++#define vreinterpret_u8_m64(x) vreinterpret_u8_s64(x) ++#define vreinterpret_u16_m64(x) vreinterpret_u16_s64(x) ++#define vreinterpret_u32_m64(x) vreinterpret_u32_s64(x) ++#define vreinterpret_u64_m64(x) vreinterpret_u64_s64(x) ++ ++#define vreinterpret_s8_m64(x) vreinterpret_s8_s64(x) ++#define vreinterpret_s16_m64(x) vreinterpret_s16_s64(x) ++#define vreinterpret_s32_m64(x) vreinterpret_s32_s64(x) ++#define vreinterpret_s64_m64(x) (x) ++ ++#define vreinterpret_f32_m64(x) vreinterpret_f32_s64(x) ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#define vreinterpretq_m128d_s32(x) vreinterpretq_f64_s32(x) ++#define vreinterpretq_m128d_s64(x) vreinterpretq_f64_s64(x) ++ ++#define vreinterpretq_m128d_u64(x) vreinterpretq_f64_u64(x) ++ ++#define vreinterpretq_m128d_f32(x) vreinterpretq_f64_f32(x) ++#define vreinterpretq_m128d_f64(x) (x) ++ ++#define vreinterpretq_s64_m128d(x) vreinterpretq_s64_f64(x) ++ ++#define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f64(x) ++#define vreinterpretq_u64_m128d(x) vreinterpretq_u64_f64(x) ++ ++#define vreinterpretq_f64_m128d(x) (x) ++#define vreinterpretq_f32_m128d(x) vreinterpretq_f32_f64(x) ++#else ++#define vreinterpretq_m128d_s32(x) vreinterpretq_f32_s32(x) ++#define vreinterpretq_m128d_s64(x) vreinterpretq_f32_s64(x) ++ ++#define vreinterpretq_m128d_u32(x) vreinterpretq_f32_u32(x) ++#define vreinterpretq_m128d_u64(x) vreinterpretq_f32_u64(x) ++ ++#define vreinterpretq_m128d_f32(x) (x) ++ ++#define vreinterpretq_s64_m128d(x) vreinterpretq_s64_f32(x) ++ ++#define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f32(x) ++#define vreinterpretq_u64_m128d(x) vreinterpretq_u64_f32(x) ++ ++#define vreinterpretq_f32_m128d(x) (x) ++#endif ++ ++// A struct is defined in this header file called 'SIMDVec' which can be used ++// by applications which attempt to access the contents of an __m128 struct ++// directly. It is important to note that accessing the __m128 struct directly ++// is bad coding practice by Microsoft: @see: ++// https://learn.microsoft.com/en-us/cpp/cpp/m128 ++// ++// However, some legacy source code may try to access the contents of an __m128 ++// struct directly so the developer can use the SIMDVec as an alias for it. Any ++// casting must be done manually by the developer, as you cannot cast or ++// otherwise alias the base NEON data type for intrinsic operations. ++// ++// union intended to allow direct access to an __m128 variable using the names ++// that the MSVC compiler provides. This union should really only be used when ++// trying to access the members of the vector as integer values. GCC/clang ++// allow native access to the float members through a simple array access ++// operator (in C since 4.6, in C++ since 4.8). ++// ++// Ideally direct accesses to SIMD vectors should not be used since it can cause ++// a performance hit. If it really is needed however, the original __m128 ++// variable can be aliased with a pointer to this union and used to access ++// individual components. The use of this union should be hidden behind a macro ++// that is used throughout the codebase to access the members instead of always ++// declaring this type of variable. ++typedef union ALIGN_STRUCT(16) SIMDVec { ++ float m128_f32[4]; // as floats - DON'T USE. Added for convenience. ++ int8_t m128_i8[16]; // as signed 8-bit integers. ++ int16_t m128_i16[8]; // as signed 16-bit integers. ++ int32_t m128_i32[4]; // as signed 32-bit integers. ++ int64_t m128_i64[2]; // as signed 64-bit integers. ++ uint8_t m128_u8[16]; // as unsigned 8-bit integers. ++ uint16_t m128_u16[8]; // as unsigned 16-bit integers. ++ uint32_t m128_u32[4]; // as unsigned 32-bit integers. ++ uint64_t m128_u64[2]; // as unsigned 64-bit integers. ++} SIMDVec; ++ ++// casting using SIMDVec ++#define vreinterpretq_nth_u64_m128i(x, n) (((SIMDVec *) &x)->m128_u64[n]) ++#define vreinterpretq_nth_u32_m128i(x, n) (((SIMDVec *) &x)->m128_u32[n]) ++#define vreinterpretq_nth_u8_m128i(x, n) (((SIMDVec *) &x)->m128_u8[n]) ++ ++/* SSE macros */ ++#define _MM_GET_FLUSH_ZERO_MODE _sse2neon_mm_get_flush_zero_mode ++#define _MM_SET_FLUSH_ZERO_MODE _sse2neon_mm_set_flush_zero_mode ++#define _MM_GET_DENORMALS_ZERO_MODE _sse2neon_mm_get_denormals_zero_mode ++#define _MM_SET_DENORMALS_ZERO_MODE _sse2neon_mm_set_denormals_zero_mode ++ ++// Function declaration ++// SSE ++FORCE_INLINE unsigned int _MM_GET_ROUNDING_MODE(void); ++FORCE_INLINE __m128 _mm_move_ss(__m128, __m128); ++FORCE_INLINE __m128 _mm_or_ps(__m128, __m128); ++FORCE_INLINE __m128 _mm_set_ps1(float); ++FORCE_INLINE __m128 _mm_setzero_ps(void); ++// SSE2 ++FORCE_INLINE __m128i _mm_and_si128(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_castps_si128(__m128); ++FORCE_INLINE __m128i _mm_cmpeq_epi32(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_cvtps_epi32(__m128); ++FORCE_INLINE __m128d _mm_move_sd(__m128d, __m128d); ++FORCE_INLINE __m128i _mm_or_si128(__m128i, __m128i); ++FORCE_INLINE __m128i _mm_set_epi32(int, int, int, int); ++FORCE_INLINE __m128i _mm_set_epi64x(int64_t, int64_t); ++FORCE_INLINE __m128d _mm_set_pd(double, double); ++FORCE_INLINE __m128i _mm_set1_epi32(int); ++FORCE_INLINE __m128i _mm_setzero_si128(void); ++// SSE4.1 ++FORCE_INLINE __m128d _mm_ceil_pd(__m128d); ++FORCE_INLINE __m128 _mm_ceil_ps(__m128); ++FORCE_INLINE __m128d _mm_floor_pd(__m128d); ++FORCE_INLINE __m128 _mm_floor_ps(__m128); ++FORCE_INLINE_OPTNONE __m128d _mm_round_pd(__m128d, int); ++FORCE_INLINE_OPTNONE __m128 _mm_round_ps(__m128, int); ++// SSE4.2 ++FORCE_INLINE uint32_t _mm_crc32_u8(uint32_t, uint8_t); ++ ++/* Backwards compatibility for compilers with lack of specific type support */ ++ ++// Older gcc does not define vld1q_u8_x4 type ++#if defined(__GNUC__) && !defined(__clang__) && \ ++ ((__GNUC__ <= 13 && defined(__arm__)) || \ ++ (__GNUC__ == 10 && __GNUC_MINOR__ < 3 && defined(__aarch64__)) || \ ++ (__GNUC__ <= 9 && defined(__aarch64__))) ++FORCE_INLINE uint8x16x4_t _sse2neon_vld1q_u8_x4(const uint8_t *p) ++{ ++ uint8x16x4_t ret; ++ ret.val[0] = vld1q_u8(p + 0); ++ ret.val[1] = vld1q_u8(p + 16); ++ ret.val[2] = vld1q_u8(p + 32); ++ ret.val[3] = vld1q_u8(p + 48); ++ return ret; ++} ++#else ++// Wraps vld1q_u8_x4 ++FORCE_INLINE uint8x16x4_t _sse2neon_vld1q_u8_x4(const uint8_t *p) ++{ ++ return vld1q_u8_x4(p); ++} ++#endif ++ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++/* emulate vaddv u8 variant */ ++FORCE_INLINE uint8_t _sse2neon_vaddv_u8(uint8x8_t v8) ++{ ++ const uint64x1_t v1 = vpaddl_u32(vpaddl_u16(vpaddl_u8(v8))); ++ return vget_lane_u8(vreinterpret_u8_u64(v1), 0); ++} ++#else ++// Wraps vaddv_u8 ++FORCE_INLINE uint8_t _sse2neon_vaddv_u8(uint8x8_t v8) ++{ ++ return vaddv_u8(v8); ++} ++#endif ++ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++/* emulate vaddvq u8 variant */ ++FORCE_INLINE uint8_t _sse2neon_vaddvq_u8(uint8x16_t a) ++{ ++ uint8x8_t tmp = vpadd_u8(vget_low_u8(a), vget_high_u8(a)); ++ uint8_t res = 0; ++ for (int i = 0; i < 8; ++i) ++ res += tmp[i]; ++ return res; ++} ++#else ++// Wraps vaddvq_u8 ++FORCE_INLINE uint8_t _sse2neon_vaddvq_u8(uint8x16_t a) ++{ ++ return vaddvq_u8(a); ++} ++#endif ++ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++/* emulate vaddvq u16 variant */ ++FORCE_INLINE uint16_t _sse2neon_vaddvq_u16(uint16x8_t a) ++{ ++ uint32x4_t m = vpaddlq_u16(a); ++ uint64x2_t n = vpaddlq_u32(m); ++ uint64x1_t o = vget_low_u64(n) + vget_high_u64(n); ++ ++ return vget_lane_u32((uint32x2_t) o, 0); ++} ++#else ++// Wraps vaddvq_u16 ++FORCE_INLINE uint16_t _sse2neon_vaddvq_u16(uint16x8_t a) ++{ ++ return vaddvq_u16(a); ++} ++#endif ++ ++/* Function Naming Conventions ++ * The naming convention of SSE intrinsics is straightforward. A generic SSE ++ * intrinsic function is given as follows: ++ * _mm__ ++ * ++ * The parts of this format are given as follows: ++ * 1. describes the operation performed by the intrinsic ++ * 2. identifies the data type of the function's primary arguments ++ * ++ * This last part, , is a little complicated. It identifies the ++ * content of the input values, and can be set to any of the following values: ++ * + ps - vectors contain floats (ps stands for packed single-precision) ++ * + pd - vectors contain doubles (pd stands for packed double-precision) ++ * + epi8/epi16/epi32/epi64 - vectors contain 8-bit/16-bit/32-bit/64-bit ++ * signed integers ++ * + epu8/epu16/epu32/epu64 - vectors contain 8-bit/16-bit/32-bit/64-bit ++ * unsigned integers ++ * + si128 - unspecified 128-bit vector or 256-bit vector ++ * + m128/m128i/m128d - identifies input vector types when they are different ++ * than the type of the returned vector ++ * ++ * For example, _mm_setzero_ps. The _mm implies that the function returns ++ * a 128-bit vector. The _ps at the end implies that the argument vectors ++ * contain floats. ++ * ++ * A complete example: Byte Shuffle - pshufb (_mm_shuffle_epi8) ++ * // Set packed 16-bit integers. 128 bits, 8 short, per 16 bits ++ * __m128i v_in = _mm_setr_epi16(1, 2, 3, 4, 5, 6, 7, 8); ++ * // Set packed 8-bit integers ++ * // 128 bits, 16 chars, per 8 bits ++ * __m128i v_perm = _mm_setr_epi8(1, 0, 2, 3, 8, 9, 10, 11, ++ * 4, 5, 12, 13, 6, 7, 14, 15); ++ * // Shuffle packed 8-bit integers ++ * __m128i v_out = _mm_shuffle_epi8(v_in, v_perm); // pshufb ++ */ ++ ++/* Constants for use with _mm_prefetch. */ ++enum _mm_hint { ++ _MM_HINT_NTA = 0, /* load data to L1 and L2 cache, mark it as NTA */ ++ _MM_HINT_T0 = 1, /* load data to L1 and L2 cache */ ++ _MM_HINT_T1 = 2, /* load data to L2 cache only */ ++ _MM_HINT_T2 = 3, /* load data to L2 cache only, mark it as NTA */ ++}; ++ ++// The bit field mapping to the FPCR(floating-point control register) ++typedef struct { ++ uint16_t res0; ++ uint8_t res1 : 6; ++ uint8_t bit22 : 1; ++ uint8_t bit23 : 1; ++ uint8_t bit24 : 1; ++ uint8_t res2 : 7; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint32_t res3; ++#endif ++} fpcr_bitfield; ++ ++// Takes the upper 64 bits of a and places it in the low end of the result ++// Takes the lower 64 bits of b and places it into the high end of the result. ++FORCE_INLINE __m128 _mm_shuffle_ps_1032(__m128 a, __m128 b) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a32, b10)); ++} ++ ++// takes the lower two 32-bit values from a and swaps them and places in high ++// end of result takes the higher two 32 bit values from b and swaps them and ++// places in low end of result. ++FORCE_INLINE __m128 _mm_shuffle_ps_2301(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b23 = vrev64_f32(vget_high_f32(vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b23)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0321(__m128 a, __m128 b) ++{ ++ float32x2_t a21 = vget_high_f32( ++ vextq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 3)); ++ float32x2_t b03 = vget_low_f32( ++ vextq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b), 3)); ++ return vreinterpretq_m128_f32(vcombine_f32(a21, b03)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2103(__m128 a, __m128 b) ++{ ++ float32x2_t a03 = vget_low_f32( ++ vextq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 3)); ++ float32x2_t b21 = vget_high_f32( ++ vextq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b), 3)); ++ return vreinterpretq_m128_f32(vcombine_f32(a03, b21)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1010(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b10)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1001(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b10)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0101(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b01)); ++} ++ ++// keeps the low 64 bits of b in the low and puts the high 64 bits of a in the ++// high ++FORCE_INLINE __m128 _mm_shuffle_ps_3210(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b32)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0011(__m128 a, __m128 b) ++{ ++ float32x2_t a11 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(a)), 1); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a11, b00)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0022(__m128 a, __m128 b) ++{ ++ float32x2_t a22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a22, b00)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2200(__m128 a, __m128 b) ++{ ++ float32x2_t a00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t b22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a00, b22)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_3202(__m128 a, __m128 b) ++{ ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ float32x2_t a22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t a02 = vset_lane_f32(a0, a22, 1); /* TODO: use vzip ?*/ ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a02, b32)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1133(__m128 a, __m128 b) ++{ ++ float32x2_t a33 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 1); ++ float32x2_t b11 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a33, b11)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2010(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32_t b2 = vgetq_lane_f32(vreinterpretq_f32_m128(b), 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b20)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2001(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32_t b2 = vgetq_lane_f32(b, 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b20)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2032(__m128 a, __m128 b) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32_t b2 = vgetq_lane_f32(b, 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a32, b20)); ++} ++ ++// For MSVC, we check only if it is ARM64, as every single ARM64 processor ++// supported by WoA has crypto extensions. If this changes in the future, ++// this can be verified via the runtime-only method of: ++// IsProcessorFeaturePresent(PF_ARM_V8_CRYPTO_INSTRUCTIONS_AVAILABLE) ++#if (defined(_M_ARM64) && !defined(__clang__)) || \ ++ (defined(__ARM_FEATURE_CRYPTO) && \ ++ (defined(__aarch64__) || __has_builtin(__builtin_arm_crypto_vmullp64))) ++// Wraps vmull_p64 ++FORCE_INLINE uint64x2_t _sse2neon_vmull_p64(uint64x1_t _a, uint64x1_t _b) ++{ ++ poly64_t a = vget_lane_p64(vreinterpret_p64_u64(_a), 0); ++ poly64_t b = vget_lane_p64(vreinterpret_p64_u64(_b), 0); ++#if defined(_MSC_VER) && !defined(__clang__) ++ __n64 a1 = {a}, b1 = {b}; ++ return vreinterpretq_u64_p128(vmull_p64(a1, b1)); ++#else ++ return vreinterpretq_u64_p128(vmull_p64(a, b)); ++#endif ++} ++#else // ARMv7 polyfill ++// ARMv7/some A64 lacks vmull_p64, but it has vmull_p8. ++// ++// vmull_p8 calculates 8 8-bit->16-bit polynomial multiplies, but we need a ++// 64-bit->128-bit polynomial multiply. ++// ++// It needs some work and is somewhat slow, but it is still faster than all ++// known scalar methods. ++// ++// Algorithm adapted to C from ++// https://www.workofard.com/2017/07/ghash-for-low-end-cores/, which is adapted ++// from "Fast Software Polynomial Multiplication on ARM Processors Using the ++// NEON Engine" by Danilo Camara, Conrado Gouvea, Julio Lopez and Ricardo Dahab ++// (https://hal.inria.fr/hal-01506572) ++static uint64x2_t _sse2neon_vmull_p64(uint64x1_t _a, uint64x1_t _b) ++{ ++ poly8x8_t a = vreinterpret_p8_u64(_a); ++ poly8x8_t b = vreinterpret_p8_u64(_b); ++ ++ // Masks ++ uint8x16_t k48_32 = vcombine_u8(vcreate_u8(0x0000ffffffffffff), ++ vcreate_u8(0x00000000ffffffff)); ++ uint8x16_t k16_00 = vcombine_u8(vcreate_u8(0x000000000000ffff), ++ vcreate_u8(0x0000000000000000)); ++ ++ // Do the multiplies, rotating with vext to get all combinations ++ uint8x16_t d = vreinterpretq_u8_p16(vmull_p8(a, b)); // D = A0 * B0 ++ uint8x16_t e = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 1))); // E = A0 * B1 ++ uint8x16_t f = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 1), b)); // F = A1 * B0 ++ uint8x16_t g = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 2))); // G = A0 * B2 ++ uint8x16_t h = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 2), b)); // H = A2 * B0 ++ uint8x16_t i = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 3))); // I = A0 * B3 ++ uint8x16_t j = ++ vreinterpretq_u8_p16(vmull_p8(vext_p8(a, a, 3), b)); // J = A3 * B0 ++ uint8x16_t k = ++ vreinterpretq_u8_p16(vmull_p8(a, vext_p8(b, b, 4))); // L = A0 * B4 ++ ++ // Add cross products ++ uint8x16_t l = veorq_u8(e, f); // L = E + F ++ uint8x16_t m = veorq_u8(g, h); // M = G + H ++ uint8x16_t n = veorq_u8(i, j); // N = I + J ++ ++ // Interleave. Using vzip1 and vzip2 prevents Clang from emitting TBL ++ // instructions. ++#if defined(__aarch64__) ++ uint8x16_t lm_p0 = vreinterpretq_u8_u64( ++ vzip1q_u64(vreinterpretq_u64_u8(l), vreinterpretq_u64_u8(m))); ++ uint8x16_t lm_p1 = vreinterpretq_u8_u64( ++ vzip2q_u64(vreinterpretq_u64_u8(l), vreinterpretq_u64_u8(m))); ++ uint8x16_t nk_p0 = vreinterpretq_u8_u64( ++ vzip1q_u64(vreinterpretq_u64_u8(n), vreinterpretq_u64_u8(k))); ++ uint8x16_t nk_p1 = vreinterpretq_u8_u64( ++ vzip2q_u64(vreinterpretq_u64_u8(n), vreinterpretq_u64_u8(k))); ++#else ++ uint8x16_t lm_p0 = vcombine_u8(vget_low_u8(l), vget_low_u8(m)); ++ uint8x16_t lm_p1 = vcombine_u8(vget_high_u8(l), vget_high_u8(m)); ++ uint8x16_t nk_p0 = vcombine_u8(vget_low_u8(n), vget_low_u8(k)); ++ uint8x16_t nk_p1 = vcombine_u8(vget_high_u8(n), vget_high_u8(k)); ++#endif ++ // t0 = (L) (P0 + P1) << 8 ++ // t1 = (M) (P2 + P3) << 16 ++ uint8x16_t t0t1_tmp = veorq_u8(lm_p0, lm_p1); ++ uint8x16_t t0t1_h = vandq_u8(lm_p1, k48_32); ++ uint8x16_t t0t1_l = veorq_u8(t0t1_tmp, t0t1_h); ++ ++ // t2 = (N) (P4 + P5) << 24 ++ // t3 = (K) (P6 + P7) << 32 ++ uint8x16_t t2t3_tmp = veorq_u8(nk_p0, nk_p1); ++ uint8x16_t t2t3_h = vandq_u8(nk_p1, k16_00); ++ uint8x16_t t2t3_l = veorq_u8(t2t3_tmp, t2t3_h); ++ ++ // De-interleave ++#if defined(__aarch64__) ++ uint8x16_t t0 = vreinterpretq_u8_u64( ++ vuzp1q_u64(vreinterpretq_u64_u8(t0t1_l), vreinterpretq_u64_u8(t0t1_h))); ++ uint8x16_t t1 = vreinterpretq_u8_u64( ++ vuzp2q_u64(vreinterpretq_u64_u8(t0t1_l), vreinterpretq_u64_u8(t0t1_h))); ++ uint8x16_t t2 = vreinterpretq_u8_u64( ++ vuzp1q_u64(vreinterpretq_u64_u8(t2t3_l), vreinterpretq_u64_u8(t2t3_h))); ++ uint8x16_t t3 = vreinterpretq_u8_u64( ++ vuzp2q_u64(vreinterpretq_u64_u8(t2t3_l), vreinterpretq_u64_u8(t2t3_h))); ++#else ++ uint8x16_t t1 = vcombine_u8(vget_high_u8(t0t1_l), vget_high_u8(t0t1_h)); ++ uint8x16_t t0 = vcombine_u8(vget_low_u8(t0t1_l), vget_low_u8(t0t1_h)); ++ uint8x16_t t3 = vcombine_u8(vget_high_u8(t2t3_l), vget_high_u8(t2t3_h)); ++ uint8x16_t t2 = vcombine_u8(vget_low_u8(t2t3_l), vget_low_u8(t2t3_h)); ++#endif ++ // Shift the cross products ++ uint8x16_t t0_shift = vextq_u8(t0, t0, 15); // t0 << 8 ++ uint8x16_t t1_shift = vextq_u8(t1, t1, 14); // t1 << 16 ++ uint8x16_t t2_shift = vextq_u8(t2, t2, 13); // t2 << 24 ++ uint8x16_t t3_shift = vextq_u8(t3, t3, 12); // t3 << 32 ++ ++ // Accumulate the products ++ uint8x16_t cross1 = veorq_u8(t0_shift, t1_shift); ++ uint8x16_t cross2 = veorq_u8(t2_shift, t3_shift); ++ uint8x16_t mix = veorq_u8(d, cross1); ++ uint8x16_t r = veorq_u8(mix, cross2); ++ return vreinterpretq_u64_u8(r); ++} ++#endif // ARMv7 polyfill ++ ++// C equivalent: ++// __m128i _mm_shuffle_epi32_default(__m128i a, ++// __constrange(0, 255) int imm) { ++// __m128i ret; ++// ret[0] = a[imm & 0x3]; ret[1] = a[(imm >> 2) & 0x3]; ++// ret[2] = a[(imm >> 4) & 0x03]; ret[3] = a[(imm >> 6) & 0x03]; ++// return ret; ++// } ++#define _mm_shuffle_epi32_default(a, imm) \ ++ vreinterpretq_m128i_s32(vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 6) & 0x3), \ ++ vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 4) & 0x3), \ ++ vsetq_lane_s32(vgetq_lane_s32(vreinterpretq_s32_m128i(a), \ ++ ((imm) >> 2) & 0x3), \ ++ vmovq_n_s32(vgetq_lane_s32( \ ++ vreinterpretq_s32_m128i(a), (imm) & (0x3))), \ ++ 1), \ ++ 2), \ ++ 3)) ++ ++// Takes the upper 64 bits of a and places it in the low end of the result ++// Takes the lower 64 bits of a and places it into the high end of the result. ++FORCE_INLINE __m128i _mm_shuffle_epi_1032(__m128i a) ++{ ++ int32x2_t a32 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a32, a10)); ++} ++ ++// takes the lower two 32-bit values from a and swaps them and places in low end ++// of result takes the higher two 32 bit values from a and swaps them and places ++// in high end of result. ++FORCE_INLINE __m128i _mm_shuffle_epi_2301(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ int32x2_t a23 = vrev64_s32(vget_high_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a23)); ++} ++ ++// rotates the least significant 32 bits into the most significant 32 bits, and ++// shifts the rest down ++FORCE_INLINE __m128i _mm_shuffle_epi_0321(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vextq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(a), 1)); ++} ++ ++// rotates the most significant 32 bits into the least significant 32 bits, and ++// shifts the rest up ++FORCE_INLINE __m128i _mm_shuffle_epi_2103(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vextq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(a), 3)); ++} ++ ++// gets the lower 64 bits of a, and places it in the upper 64 bits ++// gets the lower 64 bits of a and places it in the lower 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_1010(__m128i a) ++{ ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a10, a10)); ++} ++ ++// gets the lower 64 bits of a, swaps the 0 and 1 elements, and places it in the ++// lower 64 bits gets the lower 64 bits of a, and places it in the upper 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_1001(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a10)); ++} ++ ++// gets the lower 64 bits of a, swaps the 0 and 1 elements and places it in the ++// upper 64 bits gets the lower 64 bits of a, swaps the 0 and 1 elements, and ++// places it in the lower 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_0101(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a01)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_2211(__m128i a) ++{ ++ int32x2_t a11 = vdup_lane_s32(vget_low_s32(vreinterpretq_s32_m128i(a)), 1); ++ int32x2_t a22 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 0); ++ return vreinterpretq_m128i_s32(vcombine_s32(a11, a22)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_0122(__m128i a) ++{ ++ int32x2_t a22 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 0); ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a22, a01)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_3332(__m128i a) ++{ ++ int32x2_t a32 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t a33 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 1); ++ return vreinterpretq_m128i_s32(vcombine_s32(a32, a33)); ++} ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#define _mm_shuffle_epi32_splat(a, imm) \ ++ vreinterpretq_m128i_s32(vdupq_laneq_s32(vreinterpretq_s32_m128i(a), (imm))) ++#else ++#define _mm_shuffle_epi32_splat(a, imm) \ ++ vreinterpretq_m128i_s32( \ ++ vdupq_n_s32(vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm)))) ++#endif ++ ++// NEON does not support a general purpose permute intrinsic. ++// Shuffle single-precision (32-bit) floating-point elements in a using the ++// control in imm8, and store the results in dst. ++// ++// C equivalent: ++// __m128 _mm_shuffle_ps_default(__m128 a, __m128 b, ++// __constrange(0, 255) int imm) { ++// __m128 ret; ++// ret[0] = a[imm & 0x3]; ret[1] = a[(imm >> 2) & 0x3]; ++// ret[2] = b[(imm >> 4) & 0x03]; ret[3] = b[(imm >> 6) & 0x03]; ++// return ret; ++// } ++// ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_ps ++#define _mm_shuffle_ps_default(a, b, imm) \ ++ vreinterpretq_m128_f32(vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(b), ((imm) >> 6) & 0x3), \ ++ vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(b), ((imm) >> 4) & 0x3), \ ++ vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(a), ((imm) >> 2) & 0x3), \ ++ vmovq_n_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(a), (imm) & (0x3))), \ ++ 1), \ ++ 2), \ ++ 3)) ++ ++// Shuffle 16-bit integers in the low 64 bits of a using the control in imm8. ++// Store the results in the low 64 bits of dst, with the high 64 bits being ++// copied from a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shufflelo_epi16 ++#define _mm_shufflelo_epi16_function(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, int16x8_t ret = vreinterpretq_s16_m128i(_a); \ ++ int16x4_t lowBits = vget_low_s16(ret); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, (imm) & (0x3)), ret, 0); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 2) & 0x3), ret, \ ++ 1); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 4) & 0x3), ret, \ ++ 2); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 6) & 0x3), ret, \ ++ 3); \ ++ _sse2neon_return(vreinterpretq_m128i_s16(ret));) ++ ++// Shuffle 16-bit integers in the high 64 bits of a using the control in imm8. ++// Store the results in the high 64 bits of dst, with the low 64 bits being ++// copied from a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shufflehi_epi16 ++#define _mm_shufflehi_epi16_function(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, int16x8_t ret = vreinterpretq_s16_m128i(_a); \ ++ int16x4_t highBits = vget_high_s16(ret); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, (imm) & (0x3)), ret, 4); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 2) & 0x3), ret, \ ++ 5); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 4) & 0x3), ret, \ ++ 6); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 6) & 0x3), ret, \ ++ 7); \ ++ _sse2neon_return(vreinterpretq_m128i_s16(ret));) ++ ++/* MMX */ ++ ++//_mm_empty is a no-op on arm ++FORCE_INLINE void _mm_empty(void) {} ++ ++/* SSE */ ++ ++// Add packed single-precision (32-bit) floating-point elements in a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_ps ++FORCE_INLINE __m128 _mm_add_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vaddq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Add the lower single-precision (32-bit) floating-point element in a and b, ++// store the result in the lower element of dst, and copy the upper 3 packed ++// elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_ss ++FORCE_INLINE __m128 _mm_add_ss(__m128 a, __m128 b) ++{ ++ float32_t b0 = vgetq_lane_f32(vreinterpretq_f32_m128(b), 0); ++ float32x4_t value = vsetq_lane_f32(b0, vdupq_n_f32(0), 0); ++ // the upper values in the result must be the remnants of . ++ return vreinterpretq_m128_f32(vaddq_f32(a, value)); ++} ++ ++// Compute the bitwise AND of packed single-precision (32-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_and_ps ++FORCE_INLINE __m128 _mm_and_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vandq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Compute the bitwise NOT of packed single-precision (32-bit) floating-point ++// elements in a and then AND with b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_andnot_ps ++FORCE_INLINE __m128 _mm_andnot_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vbicq_s32(vreinterpretq_s32_m128(b), ++ vreinterpretq_s32_m128(a))); // *NOTE* argument swap ++} ++ ++// Average packed unsigned 16-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_avg_pu16 ++FORCE_INLINE __m64 _mm_avg_pu16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u16( ++ vrhadd_u16(vreinterpret_u16_m64(a), vreinterpret_u16_m64(b))); ++} ++ ++// Average packed unsigned 8-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_avg_pu8 ++FORCE_INLINE __m64 _mm_avg_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vrhadd_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for equality, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_ps ++FORCE_INLINE __m128 _mm_cmpeq_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for equality, store the result in the lower element of dst, and copy the ++// upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_ss ++FORCE_INLINE __m128 _mm_cmpeq_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpeq_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for greater-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpge_ps ++FORCE_INLINE __m128 _mm_cmpge_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for greater-than-or-equal, store the result in the lower element of dst, ++// and copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpge_ss ++FORCE_INLINE __m128 _mm_cmpge_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpge_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for greater-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_ps ++FORCE_INLINE __m128 _mm_cmpgt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for greater-than, store the result in the lower element of dst, and copy ++// the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_ss ++FORCE_INLINE __m128 _mm_cmpgt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpgt_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for less-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmple_ps ++FORCE_INLINE __m128 _mm_cmple_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for less-than-or-equal, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmple_ss ++FORCE_INLINE __m128 _mm_cmple_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmple_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for less-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_ps ++FORCE_INLINE __m128 _mm_cmplt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for less-than, store the result in the lower element of dst, and copy the ++// upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_ss ++FORCE_INLINE __m128 _mm_cmplt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmplt_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpneq_ps ++FORCE_INLINE __m128 _mm_cmpneq_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-equal, store the result in the lower element of dst, and copy the ++// upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpneq_ss ++FORCE_INLINE __m128 _mm_cmpneq_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpneq_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-greater-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnge_ps ++FORCE_INLINE __m128 _mm_cmpnge_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-greater-than-or-equal, store the result in the lower element of ++// dst, and copy the upper 3 packed elements from a to the upper elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnge_ss ++FORCE_INLINE __m128 _mm_cmpnge_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnge_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-greater-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpngt_ps ++FORCE_INLINE __m128 _mm_cmpngt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-greater-than, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpngt_ss ++FORCE_INLINE __m128 _mm_cmpngt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpngt_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-less-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnle_ps ++FORCE_INLINE __m128 _mm_cmpnle_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-less-than-or-equal, store the result in the lower element of dst, ++// and copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnle_ss ++FORCE_INLINE __m128 _mm_cmpnle_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnle_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// for not-less-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnlt_ps ++FORCE_INLINE __m128 _mm_cmpnlt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b for not-less-than, store the result in the lower element of dst, and copy ++// the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnlt_ss ++FORCE_INLINE __m128 _mm_cmpnlt_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpnlt_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// to see if neither is NaN, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpord_ps ++// ++// See also: ++// http://stackoverflow.com/questions/8627331/what-does-ordered-unordered-comparison-mean ++// http://stackoverflow.com/questions/29349621/neon-isnanval-intrinsics ++FORCE_INLINE __m128 _mm_cmpord_ps(__m128 a, __m128 b) ++{ ++ // Note: NEON does not have ordered compare builtin ++ // Need to compare a eq a and b eq b to check for NaN ++ // Do AND of results to get final ++ uint32x4_t ceqaa = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t ceqbb = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_u32(vandq_u32(ceqaa, ceqbb)); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b to see if neither is NaN, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpord_ss ++FORCE_INLINE __m128 _mm_cmpord_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpord_ps(a, b)); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b ++// to see if either is NaN, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpunord_ps ++FORCE_INLINE __m128 _mm_cmpunord_ps(__m128 a, __m128 b) ++{ ++ uint32x4_t f32a = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t f32b = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_u32(vmvnq_u32(vandq_u32(f32a, f32b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b to see if either is NaN, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpunord_ss ++FORCE_INLINE __m128 _mm_cmpunord_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_cmpunord_ps(a, b)); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for equality, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comieq_ss ++FORCE_INLINE int _mm_comieq_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_eq_b = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_eq_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for greater-than-or-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comige_ss ++FORCE_INLINE int _mm_comige_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_ge_b = ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_ge_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for greater-than, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comigt_ss ++FORCE_INLINE int _mm_comigt_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_gt_b = ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_gt_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for less-than-or-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comile_ss ++FORCE_INLINE int _mm_comile_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_le_b = ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_le_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for less-than, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comilt_ss ++FORCE_INLINE int _mm_comilt_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_lt_b = ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return vgetq_lane_u32(a_lt_b, 0) & 0x1; ++} ++ ++// Compare the lower single-precision (32-bit) floating-point element in a and b ++// for not-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comineq_ss ++FORCE_INLINE int _mm_comineq_ss(__m128 a, __m128 b) ++{ ++ return !_mm_comieq_ss(a, b); ++} ++ ++// Convert packed signed 32-bit integers in b to packed single-precision ++// (32-bit) floating-point elements, store the results in the lower 2 elements ++// of dst, and copy the upper 2 packed elements from a to the upper elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvt_pi2ps ++FORCE_INLINE __m128 _mm_cvt_pi2ps(__m128 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vcvt_f32_s32(vreinterpret_s32_m64(b)), ++ vget_high_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvt_ps2pi ++FORCE_INLINE __m64 _mm_cvt_ps2pi(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpret_m64_s32( ++ vget_low_s32(vcvtnq_s32_f32(vrndiq_f32(vreinterpretq_f32_m128(a))))); ++#else ++ return vreinterpret_m64_s32(vcvt_s32_f32(vget_low_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION))))); ++#endif ++} ++ ++// Convert the signed 32-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvt_si2ss ++FORCE_INLINE __m128 _mm_cvt_si2ss(__m128 a, int b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32((float) b, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvt_ss2si ++FORCE_INLINE int _mm_cvt_ss2si(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vgetq_lane_s32(vcvtnq_s32_f32(vrndiq_f32(vreinterpretq_f32_m128(a))), ++ 0); ++#else ++ float32_t data = vgetq_lane_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION)), 0); ++ return (int32_t) data; ++#endif ++} ++ ++// Convert packed 16-bit integers in a to packed single-precision (32-bit) ++// floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi16_ps ++FORCE_INLINE __m128 _mm_cvtpi16_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_s32(vmovl_s16(vreinterpret_s16_m64(a)))); ++} ++ ++// Convert packed 32-bit integers in b to packed single-precision (32-bit) ++// floating-point elements, store the results in the lower 2 elements of dst, ++// and copy the upper 2 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi32_ps ++FORCE_INLINE __m128 _mm_cvtpi32_ps(__m128 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vcvt_f32_s32(vreinterpret_s32_m64(b)), ++ vget_high_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert packed signed 32-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, store the results in the lower 2 elements ++// of dst, then convert the packed signed 32-bit integers in b to ++// single-precision (32-bit) floating-point element, and store the results in ++// the upper 2 elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi32x2_ps ++FORCE_INLINE __m128 _mm_cvtpi32x2_ps(__m64 a, __m64 b) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32( ++ vcombine_s32(vreinterpret_s32_m64(a), vreinterpret_s32_m64(b)))); ++} ++ ++// Convert the lower packed 8-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi8_ps ++FORCE_INLINE __m128 _mm_cvtpi8_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32( ++ vmovl_s16(vget_low_s16(vmovl_s8(vreinterpret_s8_m64(a)))))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 16-bit integers, and store the results in dst. Note: this intrinsic ++// will generate 0x7FFF, rather than 0x8000, for input values between 0x7FFF and ++// 0x7FFFFFFF. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_pi16 ++FORCE_INLINE __m64 _mm_cvtps_pi16(__m128 a) ++{ ++ return vreinterpret_m64_s16( ++ vqmovn_s32(vreinterpretq_s32_m128i(_mm_cvtps_epi32(a)))); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_pi32 ++#define _mm_cvtps_pi32(a) _mm_cvt_ps2pi(a) ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 8-bit integers, and store the results in lower 4 elements of dst. ++// Note: this intrinsic will generate 0x7F, rather than 0x80, for input values ++// between 0x7F and 0x7FFFFFFF. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_pi8 ++FORCE_INLINE __m64 _mm_cvtps_pi8(__m128 a) ++{ ++ return vreinterpret_m64_s8(vqmovn_s16( ++ vcombine_s16(vreinterpret_s16_m64(_mm_cvtps_pi16(a)), vdup_n_s16(0)))); ++} ++ ++// Convert packed unsigned 16-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpu16_ps ++FORCE_INLINE __m128 _mm_cvtpu16_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_u32(vmovl_u16(vreinterpret_u16_m64(a)))); ++} ++ ++// Convert the lower packed unsigned 8-bit integers in a to packed ++// single-precision (32-bit) floating-point elements, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpu8_ps ++FORCE_INLINE __m128 _mm_cvtpu8_ps(__m64 a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_u32( ++ vmovl_u16(vget_low_u16(vmovl_u8(vreinterpret_u8_m64(a)))))); ++} ++ ++// Convert the signed 32-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi32_ss ++#define _mm_cvtsi32_ss(a, b) _mm_cvt_si2ss(a, b) ++ ++// Convert the signed 64-bit integer b to a single-precision (32-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64_ss ++FORCE_INLINE __m128 _mm_cvtsi64_ss(__m128 a, int64_t b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32((float) b, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Copy the lower single-precision (32-bit) floating-point element of a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtss_f32 ++FORCE_INLINE float _mm_cvtss_f32(__m128 a) ++{ ++ return vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtss_si32 ++#define _mm_cvtss_si32(a) _mm_cvt_ss2si(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtss_si64 ++FORCE_INLINE int64_t _mm_cvtss_si64(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return (int64_t) vgetq_lane_f32(vrndiq_f32(vreinterpretq_f32_m128(a)), 0); ++#else ++ float32_t data = vgetq_lane_f32( ++ vreinterpretq_f32_m128(_mm_round_ps(a, _MM_FROUND_CUR_DIRECTION)), 0); ++ return (int64_t) data; ++#endif ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtt_ps2pi ++FORCE_INLINE __m64 _mm_cvtt_ps2pi(__m128 a) ++{ ++ return vreinterpret_m64_s32( ++ vget_low_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a)))); ++} ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtt_ss2si ++FORCE_INLINE int _mm_cvtt_ss2si(__m128 a) ++{ ++ return vgetq_lane_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a)), 0); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttps_pi32 ++#define _mm_cvttps_pi32(a) _mm_cvtt_ps2pi(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttss_si32 ++#define _mm_cvttss_si32(a) _mm_cvtt_ss2si(a) ++ ++// Convert the lower single-precision (32-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttss_si64 ++FORCE_INLINE int64_t _mm_cvttss_si64(__m128 a) ++{ ++ return (int64_t) vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++} ++ ++// Divide packed single-precision (32-bit) floating-point elements in a by ++// packed elements in b, and store the results in dst. ++// Due to ARMv7-A NEON's lack of a precise division intrinsic, we implement ++// division by multiplying a by b's reciprocal before using the Newton-Raphson ++// method to approximate the results. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_div_ps ++FORCE_INLINE __m128 _mm_div_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vdivq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x4_t recip = vrecpeq_f32(vreinterpretq_f32_m128(b)); ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(b))); ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vmulq_f32(vreinterpretq_f32_m128(a), recip)); ++#endif ++} ++ ++// Divide the lower single-precision (32-bit) floating-point element in a by the ++// lower single-precision (32-bit) floating-point element in b, store the result ++// in the lower element of dst, and copy the upper 3 packed elements from a to ++// the upper elements of dst. ++// Warning: ARMv7-A does not produce the same result compared to Intel and not ++// IEEE-compliant. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_div_ss ++FORCE_INLINE __m128 _mm_div_ss(__m128 a, __m128 b) ++{ ++ float32_t value = ++ vgetq_lane_f32(vreinterpretq_f32_m128(_mm_div_ps(a, b)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Extract a 16-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_pi16 ++#define _mm_extract_pi16(a, imm) \ ++ (int32_t) vget_lane_u16(vreinterpret_u16_m64(a), (imm)) ++ ++// Free aligned memory that was allocated with _mm_malloc. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_free ++#if !defined(SSE2NEON_ALLOC_DEFINED) ++FORCE_INLINE void _mm_free(void *addr) ++{ ++ free(addr); ++} ++#endif ++ ++FORCE_INLINE uint64_t _sse2neon_get_fpcr(void) ++{ ++ uint64_t value; ++#if defined(_MSC_VER) && !defined(__clang__) ++ value = _ReadStatusReg(ARM64_FPCR); ++#else ++ __asm__ __volatile__("mrs %0, FPCR" : "=r"(value)); /* read */ ++#endif ++ return value; ++} ++ ++FORCE_INLINE void _sse2neon_set_fpcr(uint64_t value) ++{ ++#if defined(_MSC_VER) && !defined(__clang__) ++ _WriteStatusReg(ARM64_FPCR, value); ++#else ++ __asm__ __volatile__("msr FPCR, %0" ::"r"(value)); /* write */ ++#endif ++} ++ ++// Macro: Get the flush zero bits from the MXCSR control and status register. ++// The flush zero may contain any of the following flags: _MM_FLUSH_ZERO_ON or ++// _MM_FLUSH_ZERO_OFF ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_MM_GET_FLUSH_ZERO_MODE ++FORCE_INLINE unsigned int _sse2neon_mm_get_flush_zero_mode(void) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ return r.field.bit24 ? _MM_FLUSH_ZERO_ON : _MM_FLUSH_ZERO_OFF; ++} ++ ++// Macro: Get the rounding mode bits from the MXCSR control and status register. ++// The rounding mode may contain any of the following flags: _MM_ROUND_NEAREST, ++// _MM_ROUND_DOWN, _MM_ROUND_UP, _MM_ROUND_TOWARD_ZERO ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_MM_GET_ROUNDING_MODE ++FORCE_INLINE unsigned int _MM_GET_ROUNDING_MODE(void) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ if (r.field.bit22) { ++ return r.field.bit23 ? _MM_ROUND_TOWARD_ZERO : _MM_ROUND_UP; ++ } else { ++ return r.field.bit23 ? _MM_ROUND_DOWN : _MM_ROUND_NEAREST; ++ } ++} ++ ++// Copy a to dst, and insert the 16-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_pi16 ++#define _mm_insert_pi16(a, b, imm) \ ++ vreinterpret_m64_s16(vset_lane_s16((b), vreinterpret_s16_m64(a), (imm))) ++ ++// Load 128-bits (composed of 4 packed single-precision (32-bit) floating-point ++// elements) from memory into dst. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_ps ++FORCE_INLINE __m128 _mm_load_ps(const float *p) ++{ ++ return vreinterpretq_m128_f32(vld1q_f32(p)); ++} ++ ++// Load a single-precision (32-bit) floating-point element from memory into all ++// elements of dst. ++// ++// dst[31:0] := MEM[mem_addr+31:mem_addr] ++// dst[63:32] := MEM[mem_addr+31:mem_addr] ++// dst[95:64] := MEM[mem_addr+31:mem_addr] ++// dst[127:96] := MEM[mem_addr+31:mem_addr] ++// ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_ps1 ++#define _mm_load_ps1 _mm_load1_ps ++ ++// Load a single-precision (32-bit) floating-point element from memory into the ++// lower of dst, and zero the upper 3 elements. mem_addr does not need to be ++// aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_ss ++FORCE_INLINE __m128 _mm_load_ss(const float *p) ++{ ++ return vreinterpretq_m128_f32(vsetq_lane_f32(*p, vdupq_n_f32(0), 0)); ++} ++ ++// Load a single-precision (32-bit) floating-point element from memory into all ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load1_ps ++FORCE_INLINE __m128 _mm_load1_ps(const float *p) ++{ ++ return vreinterpretq_m128_f32(vld1q_dup_f32(p)); ++} ++ ++// Load 2 single-precision (32-bit) floating-point elements from memory into the ++// upper 2 elements of dst, and copy the lower 2 elements from a to dst. ++// mem_addr does not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadh_pi ++FORCE_INLINE __m128 _mm_loadh_pi(__m128 a, __m64 const *p) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vget_low_f32(a), vld1_f32((const float32_t *) p))); ++} ++ ++// Load 2 single-precision (32-bit) floating-point elements from memory into the ++// lower 2 elements of dst, and copy the upper 2 elements from a to dst. ++// mem_addr does not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadl_pi ++FORCE_INLINE __m128 _mm_loadl_pi(__m128 a, __m64 const *p) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vld1_f32((const float32_t *) p), vget_high_f32(a))); ++} ++ ++// Load 4 single-precision (32-bit) floating-point elements from memory into dst ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadr_ps ++FORCE_INLINE __m128 _mm_loadr_ps(const float *p) ++{ ++ float32x4_t v = vrev64q_f32(vld1q_f32(p)); ++ return vreinterpretq_m128_f32(vextq_f32(v, v, 2)); ++} ++ ++// Load 128-bits (composed of 4 packed single-precision (32-bit) floating-point ++// elements) from memory into dst. mem_addr does not need to be aligned on any ++// particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_ps ++FORCE_INLINE __m128 _mm_loadu_ps(const float *p) ++{ ++ // for neon, alignment doesn't matter, so _mm_load_ps and _mm_loadu_ps are ++ // equivalent for neon ++ return vreinterpretq_m128_f32(vld1q_f32(p)); ++} ++ ++// Load unaligned 16-bit integer from memory into the first element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_si16 ++FORCE_INLINE __m128i _mm_loadu_si16(const void *p) ++{ ++ return vreinterpretq_m128i_s16( ++ vsetq_lane_s16(*(const unaligned_int16_t *) p, vdupq_n_s16(0), 0)); ++} ++ ++// Load unaligned 64-bit integer from memory into the first element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_si64 ++FORCE_INLINE __m128i _mm_loadu_si64(const void *p) ++{ ++ return vreinterpretq_m128i_s64( ++ vsetq_lane_s64(*(const unaligned_int64_t *) p, vdupq_n_s64(0), 0)); ++} ++ ++// Allocate size bytes of memory, aligned to the alignment specified in align, ++// and return a pointer to the allocated memory. _mm_free should be used to free ++// memory that is allocated with _mm_malloc. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_malloc ++#if !defined(SSE2NEON_ALLOC_DEFINED) ++FORCE_INLINE void *_mm_malloc(size_t size, size_t align) ++{ ++ void *ptr; ++ if (align == 1) ++ return malloc(size); ++ if (align == 2 || (sizeof(void *) == 8 && align == 4)) ++ align = sizeof(void *); ++ if (!posix_memalign(&ptr, align, size)) ++ return ptr; ++ return NULL; ++} ++#endif ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_maskmove_si64 ++FORCE_INLINE void _mm_maskmove_si64(__m64 a, __m64 mask, char *mem_addr) ++{ ++ int8x8_t shr_mask = vshr_n_s8(vreinterpret_s8_m64(mask), 7); ++ __m128 b = _mm_load_ps((const float *) mem_addr); ++ int8x8_t masked = ++ vbsl_s8(vreinterpret_u8_s8(shr_mask), vreinterpret_s8_m64(a), ++ vreinterpret_s8_u64(vget_low_u64(vreinterpretq_u64_m128(b)))); ++ vst1_s8((int8_t *) mem_addr, masked); ++} ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_maskmovq ++#define _m_maskmovq(a, mask, mem_addr) _mm_maskmove_si64(a, mask, mem_addr) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_pi16 ++FORCE_INLINE __m64 _mm_max_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vmax_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b, ++// and store packed maximum values in dst. dst does not follow the IEEE Standard ++// for Floating-Point Arithmetic (IEEE 754) maximum value when inputs are NaN or ++// signed-zero values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_ps ++FORCE_INLINE __m128 _mm_max_ps(__m128 a, __m128 b) ++{ ++#if SSE2NEON_PRECISE_MINMAX ++ float32x4_t _a = vreinterpretq_f32_m128(a); ++ float32x4_t _b = vreinterpretq_f32_m128(b); ++ return vreinterpretq_m128_f32(vbslq_f32(vcgtq_f32(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128_f32( ++ vmaxq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#endif ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_pu8 ++FORCE_INLINE __m64 _mm_max_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vmax_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b, store the maximum value in the lower element of dst, and copy the upper 3 ++// packed elements from a to the upper element of dst. dst does not follow the ++// IEEE Standard for Floating-Point Arithmetic (IEEE 754) maximum value when ++// inputs are NaN or signed-zero values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_ss ++FORCE_INLINE __m128 _mm_max_ss(__m128 a, __m128 b) ++{ ++ float32_t value = vgetq_lane_f32(_mm_max_ps(a, b), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Compare packed signed 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_pi16 ++FORCE_INLINE __m64 _mm_min_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vmin_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Compare packed single-precision (32-bit) floating-point elements in a and b, ++// and store packed minimum values in dst. dst does not follow the IEEE Standard ++// for Floating-Point Arithmetic (IEEE 754) minimum value when inputs are NaN or ++// signed-zero values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_ps ++FORCE_INLINE __m128 _mm_min_ps(__m128 a, __m128 b) ++{ ++#if SSE2NEON_PRECISE_MINMAX ++ float32x4_t _a = vreinterpretq_f32_m128(a); ++ float32x4_t _b = vreinterpretq_f32_m128(b); ++ return vreinterpretq_m128_f32(vbslq_f32(vcltq_f32(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128_f32( ++ vminq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#endif ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_pu8 ++FORCE_INLINE __m64 _mm_min_pu8(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u8( ++ vmin_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))); ++} ++ ++// Compare the lower single-precision (32-bit) floating-point elements in a and ++// b, store the minimum value in the lower element of dst, and copy the upper 3 ++// packed elements from a to the upper element of dst. dst does not follow the ++// IEEE Standard for Floating-Point Arithmetic (IEEE 754) minimum value when ++// inputs are NaN or signed-zero values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_ss ++FORCE_INLINE __m128 _mm_min_ss(__m128 a, __m128 b) ++{ ++ float32_t value = vgetq_lane_f32(_mm_min_ps(a, b), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Move the lower single-precision (32-bit) floating-point element from b to the ++// lower element of dst, and copy the upper 3 packed elements from a to the ++// upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_move_ss ++FORCE_INLINE __m128 _mm_move_ss(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(vgetq_lane_f32(vreinterpretq_f32_m128(b), 0), ++ vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Move the upper 2 single-precision (32-bit) floating-point elements from b to ++// the lower 2 elements of dst, and copy the upper 2 elements from a to the ++// upper 2 elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movehl_ps ++FORCE_INLINE __m128 _mm_movehl_ps(__m128 a, __m128 b) ++{ ++#if defined(aarch64__) ++ return vreinterpretq_m128_u64( ++ vzip2q_u64(vreinterpretq_u64_m128(b), vreinterpretq_u64_m128(a))); ++#else ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(b32, a32)); ++#endif ++} ++ ++// Move the lower 2 single-precision (32-bit) floating-point elements from b to ++// the upper 2 elements of dst, and copy the lower 2 elements from a to the ++// lower 2 elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movelh_ps ++FORCE_INLINE __m128 _mm_movelh_ps(__m128 __A, __m128 __B) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(__A)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(__B)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b10)); ++} ++ ++// Create mask from the most significant bit of each 8-bit element in a, and ++// store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movemask_pi8 ++FORCE_INLINE int _mm_movemask_pi8(__m64 a) ++{ ++ uint8x8_t input = vreinterpret_u8_m64(a); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ static const int8_t shift[8] = {0, 1, 2, 3, 4, 5, 6, 7}; ++ uint8x8_t tmp = vshr_n_u8(input, 7); ++ return vaddv_u8(vshl_u8(tmp, vld1_s8(shift))); ++#else ++ // Refer the implementation of `_mm_movemask_epi8` ++ uint16x4_t high_bits = vreinterpret_u16_u8(vshr_n_u8(input, 7)); ++ uint32x2_t paired16 = ++ vreinterpret_u32_u16(vsra_n_u16(high_bits, high_bits, 7)); ++ uint8x8_t paired32 = ++ vreinterpret_u8_u32(vsra_n_u32(paired16, paired16, 14)); ++ return vget_lane_u8(paired32, 0) | ((int) vget_lane_u8(paired32, 4) << 4); ++#endif ++} ++ ++// Set each bit of mask dst based on the most significant bit of the ++// corresponding packed single-precision (32-bit) floating-point element in a. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movemask_ps ++FORCE_INLINE int _mm_movemask_ps(__m128 a) ++{ ++ uint32x4_t input = vreinterpretq_u32_m128(a); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ static const int32_t shift[4] = {0, 1, 2, 3}; ++ uint32x4_t tmp = vshrq_n_u32(input, 31); ++ return vaddvq_u32(vshlq_u32(tmp, vld1q_s32(shift))); ++#else ++ // Uses the exact same method as _mm_movemask_epi8, see that for details. ++ // Shift out everything but the sign bits with a 32-bit unsigned shift ++ // right. ++ uint64x2_t high_bits = vreinterpretq_u64_u32(vshrq_n_u32(input, 31)); ++ // Merge the two pairs together with a 64-bit unsigned shift right + add. ++ uint8x16_t paired = ++ vreinterpretq_u8_u64(vsraq_n_u64(high_bits, high_bits, 31)); ++ // Extract the result. ++ return vgetq_lane_u8(paired, 0) | (vgetq_lane_u8(paired, 8) << 2); ++#endif ++} ++ ++// Multiply packed single-precision (32-bit) floating-point elements in a and b, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_ps ++FORCE_INLINE_OPTNONE __m128 _mm_mul_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vmulq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Multiply the lower single-precision (32-bit) floating-point element in a and ++// b, store the result in the lower element of dst, and copy the upper 3 packed ++// elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_ss ++FORCE_INLINE __m128 _mm_mul_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_mul_ps(a, b)); ++} ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhi_pu16 ++FORCE_INLINE __m64 _mm_mulhi_pu16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u16(vshrn_n_u32( ++ vmull_u16(vreinterpret_u16_m64(a), vreinterpret_u16_m64(b)), 16)); ++} ++ ++// Compute the bitwise OR of packed single-precision (32-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_or_ps ++FORCE_INLINE __m128 _mm_or_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vorrq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Average packed unsigned 8-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pavgb ++#define _m_pavgb(a, b) _mm_avg_pu8(a, b) ++ ++// Average packed unsigned 16-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pavgw ++#define _m_pavgw(a, b) _mm_avg_pu16(a, b) ++ ++// Extract a 16-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pextrw ++#define _m_pextrw(a, imm) _mm_extract_pi16(a, imm) ++ ++// Copy a to dst, and insert the 16-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=m_pinsrw ++#define _m_pinsrw(a, i, imm) _mm_insert_pi16(a, i, imm) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pmaxsw ++#define _m_pmaxsw(a, b) _mm_max_pi16(a, b) ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pmaxub ++#define _m_pmaxub(a, b) _mm_max_pu8(a, b) ++ ++// Compare packed signed 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pminsw ++#define _m_pminsw(a, b) _mm_min_pi16(a, b) ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pminub ++#define _m_pminub(a, b) _mm_min_pu8(a, b) ++ ++// Create mask from the most significant bit of each 8-bit element in a, and ++// store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pmovmskb ++#define _m_pmovmskb(a) _mm_movemask_pi8(a) ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pmulhuw ++#define _m_pmulhuw(a, b) _mm_mulhi_pu16(a, b) ++ ++// Fetch the line of data from memory that contains address p to a location in ++// the cache hierarchy specified by the locality hint i. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_prefetch ++FORCE_INLINE void _mm_prefetch(char const *p, int i) ++{ ++ (void) i; ++#if defined(_MSC_VER) && !defined(__clang__) ++ switch (i) { ++ case _MM_HINT_NTA: ++ __prefetch2(p, 1); ++ break; ++ case _MM_HINT_T0: ++ __prefetch2(p, 0); ++ break; ++ case _MM_HINT_T1: ++ __prefetch2(p, 2); ++ break; ++ case _MM_HINT_T2: ++ __prefetch2(p, 4); ++ break; ++ } ++#else ++ switch (i) { ++ case _MM_HINT_NTA: ++ __builtin_prefetch(p, 0, 0); ++ break; ++ case _MM_HINT_T0: ++ __builtin_prefetch(p, 0, 3); ++ break; ++ case _MM_HINT_T1: ++ __builtin_prefetch(p, 0, 2); ++ break; ++ case _MM_HINT_T2: ++ __builtin_prefetch(p, 0, 1); ++ break; ++ } ++#endif ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce four ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=m_psadbw ++#define _m_psadbw(a, b) _mm_sad_pu8(a, b) ++ ++// Shuffle 16-bit integers in a using the control in imm8, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_m_pshufw ++#define _m_pshufw(a, imm) _mm_shuffle_pi16(a, imm) ++ ++// Compute the approximate reciprocal of packed single-precision (32-bit) ++// floating-point elements in a, and store the results in dst. The maximum ++// relative error for this approximation is less than 1.5*2^-12. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_rcp_ps ++FORCE_INLINE __m128 _mm_rcp_ps(__m128 in) ++{ ++ float32x4_t recip = vrecpeq_f32(vreinterpretq_f32_m128(in)); ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(in))); ++#if SSE2NEON_PRECISE_DIV ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(in))); ++#endif ++ return vreinterpretq_m128_f32(recip); ++} ++ ++// Compute the approximate reciprocal of the lower single-precision (32-bit) ++// floating-point element in a, store the result in the lower element of dst, ++// and copy the upper 3 packed elements from a to the upper elements of dst. The ++// maximum relative error for this approximation is less than 1.5*2^-12. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_rcp_ss ++FORCE_INLINE __m128 _mm_rcp_ss(__m128 a) ++{ ++ return _mm_move_ss(a, _mm_rcp_ps(a)); ++} ++ ++// Compute the approximate reciprocal square root of packed single-precision ++// (32-bit) floating-point elements in a, and store the results in dst. The ++// maximum relative error for this approximation is less than 1.5*2^-12. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_rsqrt_ps ++FORCE_INLINE __m128 _mm_rsqrt_ps(__m128 in) ++{ ++ float32x4_t out = vrsqrteq_f32(vreinterpretq_f32_m128(in)); ++ ++ // Generate masks for detecting whether input has any 0.0f/-0.0f ++ // (which becomes positive/negative infinity by IEEE-754 arithmetic rules). ++ const uint32x4_t pos_inf = vdupq_n_u32(0x7F800000); ++ const uint32x4_t neg_inf = vdupq_n_u32(0xFF800000); ++ const uint32x4_t has_pos_zero = ++ vceqq_u32(pos_inf, vreinterpretq_u32_f32(out)); ++ const uint32x4_t has_neg_zero = ++ vceqq_u32(neg_inf, vreinterpretq_u32_f32(out)); ++ ++ out = vmulq_f32( ++ out, vrsqrtsq_f32(vmulq_f32(vreinterpretq_f32_m128(in), out), out)); ++#if SSE2NEON_PRECISE_SQRT ++ // Additional Netwon-Raphson iteration for accuracy ++ out = vmulq_f32( ++ out, vrsqrtsq_f32(vmulq_f32(vreinterpretq_f32_m128(in), out), out)); ++#endif ++ ++ // Set output vector element to infinity/negative-infinity if ++ // the corresponding input vector element is 0.0f/-0.0f. ++ out = vbslq_f32(has_pos_zero, (float32x4_t) pos_inf, out); ++ out = vbslq_f32(has_neg_zero, (float32x4_t) neg_inf, out); ++ ++ return vreinterpretq_m128_f32(out); ++} ++ ++// Compute the approximate reciprocal square root of the lower single-precision ++// (32-bit) floating-point element in a, store the result in the lower element ++// of dst, and copy the upper 3 packed elements from a to the upper elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_rsqrt_ss ++FORCE_INLINE __m128 _mm_rsqrt_ss(__m128 in) ++{ ++ return vsetq_lane_f32(vgetq_lane_f32(_mm_rsqrt_ps(in), 0), in, 0); ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce four ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sad_pu8 ++FORCE_INLINE __m64 _mm_sad_pu8(__m64 a, __m64 b) ++{ ++ uint64x1_t t = vpaddl_u32(vpaddl_u16( ++ vpaddl_u8(vabd_u8(vreinterpret_u8_m64(a), vreinterpret_u8_m64(b))))); ++ return vreinterpret_m64_u16( ++ vset_lane_u16((int) vget_lane_u64(t, 0), vdup_n_u16(0), 0)); ++} ++ ++// Macro: Set the flush zero bits of the MXCSR control and status register to ++// the value in unsigned 32-bit integer a. The flush zero may contain any of the ++// following flags: _MM_FLUSH_ZERO_ON or _MM_FLUSH_ZERO_OFF ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_MM_SET_FLUSH_ZERO_MODE ++FORCE_INLINE void _sse2neon_mm_set_flush_zero_mode(unsigned int flag) ++{ ++ // AArch32 Advanced SIMD arithmetic always uses the Flush-to-zero setting, ++ // regardless of the value of the FZ bit. ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ r.field.bit24 = (flag & _MM_FLUSH_ZERO_MASK) == _MM_FLUSH_ZERO_ON; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ _sse2neon_set_fpcr(r.value); ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Set packed single-precision (32-bit) floating-point elements in dst with the ++// supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_ps ++FORCE_INLINE __m128 _mm_set_ps(float w, float z, float y, float x) ++{ ++ float ALIGN_STRUCT(16) data[4] = {x, y, z, w}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Broadcast single-precision (32-bit) floating-point value a to all elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_ps1 ++FORCE_INLINE __m128 _mm_set_ps1(float _w) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(_w)); ++} ++ ++// Macro: Set the rounding mode bits of the MXCSR control and status register to ++// the value in unsigned 32-bit integer a. The rounding mode may contain any of ++// the following flags: _MM_ROUND_NEAREST, _MM_ROUND_DOWN, _MM_ROUND_UP, ++// _MM_ROUND_TOWARD_ZERO ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_MM_SET_ROUNDING_MODE ++FORCE_INLINE_OPTNONE void _MM_SET_ROUNDING_MODE(int rounding) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ switch (rounding) { ++ case _MM_ROUND_TOWARD_ZERO: ++ r.field.bit22 = 1; ++ r.field.bit23 = 1; ++ break; ++ case _MM_ROUND_DOWN: ++ r.field.bit22 = 0; ++ r.field.bit23 = 1; ++ break; ++ case _MM_ROUND_UP: ++ r.field.bit22 = 1; ++ r.field.bit23 = 0; ++ break; ++ default: //_MM_ROUND_NEAREST ++ r.field.bit22 = 0; ++ r.field.bit23 = 0; ++ } ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ _sse2neon_set_fpcr(r.value); ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Copy single-precision (32-bit) floating-point element a to the lower element ++// of dst, and zero the upper 3 elements. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_ss ++FORCE_INLINE __m128 _mm_set_ss(float a) ++{ ++ return vreinterpretq_m128_f32(vsetq_lane_f32(a, vdupq_n_f32(0), 0)); ++} ++ ++// Broadcast single-precision (32-bit) floating-point value a to all elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_ps ++FORCE_INLINE __m128 _mm_set1_ps(float _w) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(_w)); ++} ++ ++// Set the MXCSR control and status register with the value in unsigned 32-bit ++// integer a. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setcsr ++// FIXME: _mm_setcsr() implementation supports changing the rounding mode only. ++FORCE_INLINE void _mm_setcsr(unsigned int a) ++{ ++ _MM_SET_ROUNDING_MODE(a); ++} ++ ++// Get the unsigned 32-bit value of the MXCSR control and status register. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_getcsr ++// FIXME: _mm_getcsr() implementation supports reading the rounding mode only. ++FORCE_INLINE unsigned int _mm_getcsr(void) ++{ ++ return _MM_GET_ROUNDING_MODE(); ++} ++ ++// Set packed single-precision (32-bit) floating-point elements in dst with the ++// supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_ps ++FORCE_INLINE __m128 _mm_setr_ps(float w, float z, float y, float x) ++{ ++ float ALIGN_STRUCT(16) data[4] = {w, z, y, x}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Return vector of type __m128 with all elements set to zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setzero_ps ++FORCE_INLINE __m128 _mm_setzero_ps(void) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(0)); ++} ++ ++// Shuffle 16-bit integers in a using the control in imm8, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_pi16 ++#ifdef _sse2neon_shuffle ++#define _mm_shuffle_pi16(a, imm) \ ++ vreinterpret_m64_s16(vshuffle_s16( \ ++ vreinterpret_s16_m64(a), vreinterpret_s16_m64(a), (imm & 0x3), \ ++ ((imm >> 2) & 0x3), ((imm >> 4) & 0x3), ((imm >> 6) & 0x3))) ++#else ++#define _mm_shuffle_pi16(a, imm) \ ++ _sse2neon_define1( \ ++ __m64, a, int16x4_t ret; \ ++ ret = vmov_n_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(_a), (imm) & (0x3))); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(_a), ((imm) >> 2) & 0x3), ret, \ ++ 1); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(_a), ((imm) >> 4) & 0x3), ret, \ ++ 2); \ ++ ret = vset_lane_s16( \ ++ vget_lane_s16(vreinterpret_s16_m64(_a), ((imm) >> 6) & 0x3), ret, \ ++ 3); \ ++ _sse2neon_return(vreinterpret_m64_s16(ret));) ++#endif ++ ++// Perform a serializing operation on all store-to-memory instructions that were ++// issued prior to this instruction. Guarantees that every store instruction ++// that precedes, in program order, is globally visible before any store ++// instruction which follows the fence in program order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sfence ++FORCE_INLINE void _mm_sfence(void) ++{ ++ _sse2neon_smp_mb(); ++} ++ ++// Perform a serializing operation on all load-from-memory and store-to-memory ++// instructions that were issued prior to this instruction. Guarantees that ++// every memory access that precedes, in program order, the memory fence ++// instruction is globally visible before any memory instruction which follows ++// the fence in program order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mfence ++FORCE_INLINE void _mm_mfence(void) ++{ ++ _sse2neon_smp_mb(); ++} ++ ++// Perform a serializing operation on all load-from-memory instructions that ++// were issued prior to this instruction. Guarantees that every load instruction ++// that precedes, in program order, is globally visible before any load ++// instruction which follows the fence in program order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_lfence ++FORCE_INLINE void _mm_lfence(void) ++{ ++ _sse2neon_smp_mb(); ++} ++ ++// FORCE_INLINE __m128 _mm_shuffle_ps(__m128 a, __m128 b, __constrange(0,255) ++// int imm) ++#ifdef _sse2neon_shuffle ++#define _mm_shuffle_ps(a, b, imm) \ ++ __extension__({ \ ++ float32x4_t _input1 = vreinterpretq_f32_m128(a); \ ++ float32x4_t _input2 = vreinterpretq_f32_m128(b); \ ++ float32x4_t _shuf = \ ++ vshuffleq_s32(_input1, _input2, (imm) & (0x3), ((imm) >> 2) & 0x3, \ ++ (((imm) >> 4) & 0x3) + 4, (((imm) >> 6) & 0x3) + 4); \ ++ vreinterpretq_m128_f32(_shuf); \ ++ }) ++#else // generic ++#define _mm_shuffle_ps(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m128, a, b, __m128 ret; switch (imm) { \ ++ case _MM_SHUFFLE(1, 0, 3, 2): \ ++ ret = _mm_shuffle_ps_1032(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 3, 0, 1): \ ++ ret = _mm_shuffle_ps_2301(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(0, 3, 2, 1): \ ++ ret = _mm_shuffle_ps_0321(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 1, 0, 3): \ ++ ret = _mm_shuffle_ps_2103(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 1, 0): \ ++ ret = _mm_movelh_ps(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 0, 1): \ ++ ret = _mm_shuffle_ps_1001(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 0, 1): \ ++ ret = _mm_shuffle_ps_0101(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 1, 0): \ ++ ret = _mm_shuffle_ps_3210(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 1, 1): \ ++ ret = _mm_shuffle_ps_0011(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 2, 2): \ ++ ret = _mm_shuffle_ps_0022(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 0, 0): \ ++ ret = _mm_shuffle_ps_2200(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 0, 2): \ ++ ret = _mm_shuffle_ps_3202(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 3, 2): \ ++ ret = _mm_movehl_ps(_b, _a); \ ++ break; \ ++ case _MM_SHUFFLE(1, 1, 3, 3): \ ++ ret = _mm_shuffle_ps_1133(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 1, 0): \ ++ ret = _mm_shuffle_ps_2010(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 0, 1): \ ++ ret = _mm_shuffle_ps_2001(_a, _b); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 3, 2): \ ++ ret = _mm_shuffle_ps_2032(_a, _b); \ ++ break; \ ++ default: \ ++ ret = _mm_shuffle_ps_default(_a, _b, (imm)); \ ++ break; \ ++ } _sse2neon_return(ret);) ++#endif ++ ++// Compute the square root of packed single-precision (32-bit) floating-point ++// elements in a, and store the results in dst. ++// Due to ARMv7-A NEON's lack of a precise square root intrinsic, we implement ++// square root by multiplying input in with its reciprocal square root before ++// using the Newton-Raphson method to approximate the results. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sqrt_ps ++FORCE_INLINE __m128 _mm_sqrt_ps(__m128 in) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) && !SSE2NEON_PRECISE_SQRT ++ return vreinterpretq_m128_f32(vsqrtq_f32(vreinterpretq_f32_m128(in))); ++#else ++ float32x4_t recip = vrsqrteq_f32(vreinterpretq_f32_m128(in)); ++ ++ // Test for vrsqrteq_f32(0) -> positive infinity case. ++ // Change to zero, so that s * 1/sqrt(s) result is zero too. ++ const uint32x4_t pos_inf = vdupq_n_u32(0x7F800000); ++ const uint32x4_t div_by_zero = ++ vceqq_u32(pos_inf, vreinterpretq_u32_f32(recip)); ++ recip = vreinterpretq_f32_u32( ++ vandq_u32(vmvnq_u32(div_by_zero), vreinterpretq_u32_f32(recip))); ++ ++ recip = vmulq_f32( ++ vrsqrtsq_f32(vmulq_f32(recip, recip), vreinterpretq_f32_m128(in)), ++ recip); ++ // Additional Netwon-Raphson iteration for accuracy ++ recip = vmulq_f32( ++ vrsqrtsq_f32(vmulq_f32(recip, recip), vreinterpretq_f32_m128(in)), ++ recip); ++ ++ // sqrt(s) = s * 1/sqrt(s) ++ return vreinterpretq_m128_f32(vmulq_f32(vreinterpretq_f32_m128(in), recip)); ++#endif ++} ++ ++// Compute the square root of the lower single-precision (32-bit) floating-point ++// element in a, store the result in the lower element of dst, and copy the ++// upper 3 packed elements from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sqrt_ss ++FORCE_INLINE __m128 _mm_sqrt_ss(__m128 in) ++{ ++ float32_t value = ++ vgetq_lane_f32(vreinterpretq_f32_m128(_mm_sqrt_ps(in)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(in), 0)); ++} ++ ++// Store 128-bits (composed of 4 packed single-precision (32-bit) floating-point ++// elements) from a into memory. mem_addr must be aligned on a 16-byte boundary ++// or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_ps ++FORCE_INLINE void _mm_store_ps(float *p, __m128 a) ++{ ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++} ++ ++// Store the lower single-precision (32-bit) floating-point element from a into ++// 4 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_ps1 ++FORCE_INLINE void _mm_store_ps1(float *p, __m128 a) ++{ ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ vst1q_f32(p, vdupq_n_f32(a0)); ++} ++ ++// Store the lower single-precision (32-bit) floating-point element from a into ++// memory. mem_addr does not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_ss ++FORCE_INLINE void _mm_store_ss(float *p, __m128 a) ++{ ++ vst1q_lane_f32(p, vreinterpretq_f32_m128(a), 0); ++} ++ ++// Store the lower single-precision (32-bit) floating-point element from a into ++// 4 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store1_ps ++#define _mm_store1_ps _mm_store_ps1 ++ ++// Store the upper 2 single-precision (32-bit) floating-point elements from a ++// into memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeh_pi ++FORCE_INLINE void _mm_storeh_pi(__m64 *p, __m128 a) ++{ ++ *p = vreinterpret_m64_f32(vget_high_f32(a)); ++} ++ ++// Store the lower 2 single-precision (32-bit) floating-point elements from a ++// into memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storel_pi ++FORCE_INLINE void _mm_storel_pi(__m64 *p, __m128 a) ++{ ++ *p = vreinterpret_m64_f32(vget_low_f32(a)); ++} ++ ++// Store 4 single-precision (32-bit) floating-point elements from a into memory ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storer_ps ++FORCE_INLINE void _mm_storer_ps(float *p, __m128 a) ++{ ++ float32x4_t tmp = vrev64q_f32(vreinterpretq_f32_m128(a)); ++ float32x4_t rev = vextq_f32(tmp, tmp, 2); ++ vst1q_f32(p, rev); ++} ++ ++// Store 128-bits (composed of 4 packed single-precision (32-bit) floating-point ++// elements) from a into memory. mem_addr does not need to be aligned on any ++// particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_ps ++FORCE_INLINE void _mm_storeu_ps(float *p, __m128 a) ++{ ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++} ++ ++// Stores 16-bits of integer data a at the address p. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_si16 ++FORCE_INLINE void _mm_storeu_si16(void *p, __m128i a) ++{ ++ vst1q_lane_s16((int16_t *) p, vreinterpretq_s16_m128i(a), 0); ++} ++ ++// Stores 64-bits of integer data a at the address p. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_si64 ++FORCE_INLINE void _mm_storeu_si64(void *p, __m128i a) ++{ ++ vst1q_lane_s64((int64_t *) p, vreinterpretq_s64_m128i(a), 0); ++} ++ ++// Store 64-bits of integer data from a into memory using a non-temporal memory ++// hint. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_pi ++FORCE_INLINE void _mm_stream_pi(__m64 *p, __m64 a) ++{ ++ vst1_s64((int64_t *) p, vreinterpret_s64_m64(a)); ++} ++ ++// Store 128-bits (composed of 4 packed single-precision (32-bit) floating- ++// point elements) from a into memory using a non-temporal memory hint. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_ps ++FORCE_INLINE void _mm_stream_ps(float *p, __m128 a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, (float32x4_t *) p); ++#else ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++#endif ++} ++ ++// Subtract packed single-precision (32-bit) floating-point elements in b from ++// packed single-precision (32-bit) floating-point elements in a, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_ps ++FORCE_INLINE __m128 _mm_sub_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vsubq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Subtract the lower single-precision (32-bit) floating-point element in b from ++// the lower single-precision (32-bit) floating-point element in a, store the ++// result in the lower element of dst, and copy the upper 3 packed elements from ++// a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_ss ++FORCE_INLINE __m128 _mm_sub_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_sub_ps(a, b)); ++} ++ ++// Macro: Transpose the 4x4 matrix formed by the 4 rows of single-precision ++// (32-bit) floating-point elements in row0, row1, row2, and row3, and store the ++// transposed matrix in these vectors (row0 now contains column 0, etc.). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=MM_TRANSPOSE4_PS ++#define _MM_TRANSPOSE4_PS(row0, row1, row2, row3) \ ++ do { \ ++ float32x4x2_t ROW01 = vtrnq_f32(row0, row1); \ ++ float32x4x2_t ROW23 = vtrnq_f32(row2, row3); \ ++ row0 = vcombine_f32(vget_low_f32(ROW01.val[0]), \ ++ vget_low_f32(ROW23.val[0])); \ ++ row1 = vcombine_f32(vget_low_f32(ROW01.val[1]), \ ++ vget_low_f32(ROW23.val[1])); \ ++ row2 = vcombine_f32(vget_high_f32(ROW01.val[0]), \ ++ vget_high_f32(ROW23.val[0])); \ ++ row3 = vcombine_f32(vget_high_f32(ROW01.val[1]), \ ++ vget_high_f32(ROW23.val[1])); \ ++ } while (0) ++ ++// according to the documentation, these intrinsics behave the same as the ++// non-'u' versions. We'll just alias them here. ++#define _mm_ucomieq_ss _mm_comieq_ss ++#define _mm_ucomige_ss _mm_comige_ss ++#define _mm_ucomigt_ss _mm_comigt_ss ++#define _mm_ucomile_ss _mm_comile_ss ++#define _mm_ucomilt_ss _mm_comilt_ss ++#define _mm_ucomineq_ss _mm_comineq_ss ++ ++// Return vector of type __m128i with undefined elements. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_undefined_si128 ++FORCE_INLINE __m128i _mm_undefined_si128(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128i a; ++#if defined(_MSC_VER) ++ a = _mm_setzero_si128(); ++#endif ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Return vector of type __m128 with undefined elements. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_undefined_ps ++FORCE_INLINE __m128 _mm_undefined_ps(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128 a; ++#if defined(_MSC_VER) ++ a = _mm_setzero_ps(); ++#endif ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Unpack and interleave single-precision (32-bit) floating-point elements from ++// the high half a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_ps ++FORCE_INLINE __m128 _mm_unpackhi_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vzip2q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a1 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b1 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ float32x2x2_t result = vzip_f32(a1, b1); ++ return vreinterpretq_m128_f32(vcombine_f32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave single-precision (32-bit) floating-point elements from ++// the low half of a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_ps ++FORCE_INLINE __m128 _mm_unpacklo_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vzip1q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a1 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b1 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ float32x2x2_t result = vzip_f32(a1, b1); ++ return vreinterpretq_m128_f32(vcombine_f32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Compute the bitwise XOR of packed single-precision (32-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_xor_ps ++FORCE_INLINE __m128 _mm_xor_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ veorq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++/* SSE2 */ ++ ++// Add packed 16-bit integers in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_epi16 ++FORCE_INLINE __m128i _mm_add_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vaddq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Add packed 32-bit integers in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_epi32 ++FORCE_INLINE __m128i _mm_add_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vaddq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Add packed 64-bit integers in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_epi64 ++FORCE_INLINE __m128i _mm_add_epi64(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s64( ++ vaddq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++} ++ ++// Add packed 8-bit integers in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_epi8 ++FORCE_INLINE __m128i _mm_add_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vaddq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Add packed double-precision (64-bit) floating-point elements in a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_pd ++FORCE_INLINE __m128d _mm_add_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vaddq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ double c[2]; ++ c[0] = a0 + b0; ++ c[1] = a1 + b1; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Add the lower double-precision (64-bit) floating-point element in a and b, ++// store the result in the lower element of dst, and copy the upper element from ++// a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_sd ++FORCE_INLINE __m128d _mm_add_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_add_pd(a, b)); ++#else ++ double a0, a1, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double c[2]; ++ c[0] = a0 + b0; ++ c[1] = a1; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Add 64-bit integers a and b, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_add_si64 ++FORCE_INLINE __m64 _mm_add_si64(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s64( ++ vadd_s64(vreinterpret_s64_m64(a), vreinterpret_s64_m64(b))); ++} ++ ++// Add packed signed 16-bit integers in a and b using saturation, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_adds_epi16 ++FORCE_INLINE __m128i _mm_adds_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vqaddq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Add packed signed 8-bit integers in a and b using saturation, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_adds_epi8 ++FORCE_INLINE __m128i _mm_adds_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vqaddq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Add packed unsigned 16-bit integers in a and b using saturation, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_adds_epu16 ++FORCE_INLINE __m128i _mm_adds_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vqaddq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Add packed unsigned 8-bit integers in a and b using saturation, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_adds_epu8 ++FORCE_INLINE __m128i _mm_adds_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vqaddq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compute the bitwise AND of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_and_pd ++FORCE_INLINE __m128d _mm_and_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ vandq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_and_si128 ++FORCE_INLINE __m128i _mm_and_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vandq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compute the bitwise NOT of packed double-precision (64-bit) floating-point ++// elements in a and then AND with b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_andnot_pd ++FORCE_INLINE __m128d _mm_andnot_pd(__m128d a, __m128d b) ++{ ++ // *NOTE* argument swap ++ return vreinterpretq_m128d_s64( ++ vbicq_s64(vreinterpretq_s64_m128d(b), vreinterpretq_s64_m128d(a))); ++} ++ ++// Compute the bitwise NOT of 128 bits (representing integer data) in a and then ++// AND with b, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_andnot_si128 ++FORCE_INLINE __m128i _mm_andnot_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vbicq_s32(vreinterpretq_s32_m128i(b), ++ vreinterpretq_s32_m128i(a))); // *NOTE* argument swap ++} ++ ++// Average packed unsigned 16-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_avg_epu16 ++FORCE_INLINE __m128i _mm_avg_epu16(__m128i a, __m128i b) ++{ ++ return (__m128i) vrhaddq_u16(vreinterpretq_u16_m128i(a), ++ vreinterpretq_u16_m128i(b)); ++} ++ ++// Average packed unsigned 8-bit integers in a and b, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_avg_epu8 ++FORCE_INLINE __m128i _mm_avg_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vrhaddq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Shift a left by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_bslli_si128 ++#define _mm_bslli_si128(a, imm) _mm_slli_si128(a, imm) ++ ++// Shift a right by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_bsrli_si128 ++#define _mm_bsrli_si128(a, imm) _mm_srli_si128(a, imm) ++ ++// Cast vector of type __m128d to type __m128. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castpd_ps ++FORCE_INLINE __m128 _mm_castpd_ps(__m128d a) ++{ ++ return vreinterpretq_m128_s64(vreinterpretq_s64_m128d(a)); ++} ++ ++// Cast vector of type __m128d to type __m128i. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castpd_si128 ++FORCE_INLINE __m128i _mm_castpd_si128(__m128d a) ++{ ++ return vreinterpretq_m128i_s64(vreinterpretq_s64_m128d(a)); ++} ++ ++// Cast vector of type __m128 to type __m128d. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castps_pd ++FORCE_INLINE __m128d _mm_castps_pd(__m128 a) ++{ ++ return vreinterpretq_m128d_s32(vreinterpretq_s32_m128(a)); ++} ++ ++// Cast vector of type __m128 to type __m128i. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castps_si128 ++FORCE_INLINE __m128i _mm_castps_si128(__m128 a) ++{ ++ return vreinterpretq_m128i_s32(vreinterpretq_s32_m128(a)); ++} ++ ++// Cast vector of type __m128i to type __m128d. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castsi128_pd ++FORCE_INLINE __m128d _mm_castsi128_pd(__m128i a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vreinterpretq_f64_m128i(a)); ++#else ++ return vreinterpretq_m128d_f32(vreinterpretq_f32_m128i(a)); ++#endif ++} ++ ++// Cast vector of type __m128i to type __m128. This intrinsic is only used for ++// compilation and does not generate any instructions, thus it has zero latency. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_castsi128_ps ++FORCE_INLINE __m128 _mm_castsi128_ps(__m128i a) ++{ ++ return vreinterpretq_m128_s32(vreinterpretq_s32_m128i(a)); ++} ++ ++// Invalidate and flush the cache line that contains p from all levels of the ++// cache hierarchy. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_clflush ++#if defined(__APPLE__) ++#include ++#endif ++FORCE_INLINE void _mm_clflush(void const *p) ++{ ++ (void) p; ++ ++ /* sys_icache_invalidate is supported since macOS 10.5. ++ * However, it does not work on non-jailbroken iOS devices, although the ++ * compilation is successful. ++ */ ++#if defined(__APPLE__) ++ sys_icache_invalidate((void *) (uintptr_t) p, SSE2NEON_CACHELINE_SIZE); ++#elif defined(__GNUC__) || defined(__clang__) ++ uintptr_t ptr = (uintptr_t) p; ++ __builtin___clear_cache((char *) ptr, ++ (char *) ptr + SSE2NEON_CACHELINE_SIZE); ++#elif (_MSC_VER) && SSE2NEON_INCLUDE_WINDOWS_H ++ FlushInstructionCache(GetCurrentProcess(), p, SSE2NEON_CACHELINE_SIZE); ++#endif ++} ++ ++// Compare packed 16-bit integers in a and b for equality, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_epi16 ++FORCE_INLINE __m128i _mm_cmpeq_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vceqq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed 32-bit integers in a and b for equality, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_epi32 ++FORCE_INLINE __m128i _mm_cmpeq_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vceqq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed 8-bit integers in a and b for equality, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_epi8 ++FORCE_INLINE __m128i _mm_cmpeq_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vceqq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for equality, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_pd ++FORCE_INLINE __m128d _mm_cmpeq_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128d_u32(vandq_u32(cmp, swapped)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for equality, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpeq_sd ++FORCE_INLINE __m128d _mm_cmpeq_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpeq_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for greater-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpge_pd ++FORCE_INLINE __m128d _mm_cmpge_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vcgeq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = a0 >= b0 ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1 >= b1 ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for greater-than-or-equal, store the result in the lower element of dst, ++// and copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpge_sd ++FORCE_INLINE __m128d _mm_cmpge_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmpge_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ uint64_t a1 = vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ uint64_t d[2]; ++ d[0] = a0 >= b0 ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed signed 16-bit integers in a and b for greater-than, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_epi16 ++FORCE_INLINE __m128i _mm_cmpgt_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcgtq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed signed 32-bit integers in a and b for greater-than, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_epi32 ++FORCE_INLINE __m128i _mm_cmpgt_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vcgtq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b for greater-than, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_epi8 ++FORCE_INLINE __m128i _mm_cmpgt_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcgtq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for greater-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_pd ++FORCE_INLINE __m128d _mm_cmpgt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vcgtq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = a0 > b0 ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1 > b1 ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for greater-than, store the result in the lower element of dst, and copy ++// the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpgt_sd ++FORCE_INLINE __m128d _mm_cmpgt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmpgt_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ uint64_t a1 = vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ uint64_t d[2]; ++ d[0] = a0 > b0 ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for less-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmple_pd ++FORCE_INLINE __m128d _mm_cmple_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vcleq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = a0 <= b0 ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1 <= b1 ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for less-than-or-equal, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmple_sd ++FORCE_INLINE __m128d _mm_cmple_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmple_pd(a, b)); ++#else ++ // expand "_mm_cmpge_pd()" to reduce unnecessary operations ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ uint64_t a1 = vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ uint64_t d[2]; ++ d[0] = a0 <= b0 ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed signed 16-bit integers in a and b for less-than, and store the ++// results in dst. Note: This intrinsic emits the pcmpgtw instruction with the ++// order of the operands switched. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_epi16 ++FORCE_INLINE __m128i _mm_cmplt_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcltq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed signed 32-bit integers in a and b for less-than, and store the ++// results in dst. Note: This intrinsic emits the pcmpgtd instruction with the ++// order of the operands switched. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_epi32 ++FORCE_INLINE __m128i _mm_cmplt_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vcltq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b for less-than, and store the ++// results in dst. Note: This intrinsic emits the pcmpgtb instruction with the ++// order of the operands switched. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_epi8 ++FORCE_INLINE __m128i _mm_cmplt_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcltq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for less-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_pd ++FORCE_INLINE __m128d _mm_cmplt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64( ++ vcltq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = a0 < b0 ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1 < b1 ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for less-than, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmplt_sd ++FORCE_INLINE __m128d _mm_cmplt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmplt_pd(a, b)); ++#else ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ uint64_t a1 = vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ uint64_t d[2]; ++ d[0] = a0 < b0 ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpneq_pd ++FORCE_INLINE __m128d _mm_cmpneq_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_s32(vmvnq_s32(vreinterpretq_s32_u64( ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))))); ++#else ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128d_u32(vmvnq_u32(vandq_u32(cmp, swapped))); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-equal, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpneq_sd ++FORCE_INLINE __m128d _mm_cmpneq_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpneq_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-greater-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnge_pd ++FORCE_INLINE __m128d _mm_cmpnge_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcgeq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = !(a0 >= b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = !(a1 >= b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-greater-than-or-equal, store the result in the lower element of ++// dst, and copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnge_sd ++FORCE_INLINE __m128d _mm_cmpnge_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnge_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-greater-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_cmpngt_pd ++FORCE_INLINE __m128d _mm_cmpngt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcgtq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = !(a0 > b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = !(a1 > b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-greater-than, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpngt_sd ++FORCE_INLINE __m128d _mm_cmpngt_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpngt_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-less-than-or-equal, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnle_pd ++FORCE_INLINE __m128d _mm_cmpnle_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcleq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = !(a0 <= b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = !(a1 <= b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-less-than-or-equal, store the result in the lower element of dst, ++// and copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnle_sd ++FORCE_INLINE __m128d _mm_cmpnle_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnle_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// for not-less-than, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnlt_pd ++FORCE_INLINE __m128d _mm_cmpnlt_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_u64(veorq_u64( ++ vcltq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)), ++ vdupq_n_u64(UINT64_MAX))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = !(a0 < b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = !(a1 < b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b for not-less-than, store the result in the lower element of dst, and copy ++// the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpnlt_sd ++FORCE_INLINE __m128d _mm_cmpnlt_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_cmpnlt_pd(a, b)); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// to see if neither is NaN, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpord_pd ++FORCE_INLINE __m128d _mm_cmpord_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ // Excluding NaNs, any two floating point numbers can be compared. ++ uint64x2_t not_nan_a = ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(a)); ++ uint64x2_t not_nan_b = ++ vceqq_f64(vreinterpretq_f64_m128d(b), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_u64(vandq_u64(not_nan_a, not_nan_b)); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = (a0 == a0 && b0 == b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = (a1 == a1 && b1 == b1) ? ~UINT64_C(0) : UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b to see if neither is NaN, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpord_sd ++FORCE_INLINE __m128d _mm_cmpord_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmpord_pd(a, b)); ++#else ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ uint64_t a1 = vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ uint64_t d[2]; ++ d[0] = (a0 == a0 && b0 == b0) ? ~UINT64_C(0) : UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b ++// to see if either is NaN, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpunord_pd ++FORCE_INLINE __m128d _mm_cmpunord_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ // Two NaNs are not equal in comparison operation. ++ uint64x2_t not_nan_a = ++ vceqq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(a)); ++ uint64x2_t not_nan_b = ++ vceqq_f64(vreinterpretq_f64_m128d(b), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_s32( ++ vmvnq_s32(vreinterpretq_s32_u64(vandq_u64(not_nan_a, not_nan_b)))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ uint64_t d[2]; ++ d[0] = (a0 == a0 && b0 == b0) ? UINT64_C(0) : ~UINT64_C(0); ++ d[1] = (a1 == a1 && b1 == b1) ? UINT64_C(0) : ~UINT64_C(0); ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b to see if either is NaN, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpunord_sd ++FORCE_INLINE __m128d _mm_cmpunord_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_cmpunord_pd(a, b)); ++#else ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ uint64_t a1 = vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ uint64_t d[2]; ++ d[0] = (a0 == a0 && b0 == b0) ? UINT64_C(0) : ~UINT64_C(0); ++ d[1] = a1; ++ ++ return vreinterpretq_m128d_u64(vld1q_u64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for greater-than-or-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comige_sd ++FORCE_INLINE int _mm_comige_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vcgeq_f64(a, b), 0) & 0x1; ++#else ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ return a0 >= b0; ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for greater-than, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comigt_sd ++FORCE_INLINE int _mm_comigt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vcgtq_f64(a, b), 0) & 0x1; ++#else ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ ++ return a0 > b0; ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for less-than-or-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comile_sd ++FORCE_INLINE int _mm_comile_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vcleq_f64(a, b), 0) & 0x1; ++#else ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ ++ return a0 <= b0; ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for less-than, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comilt_sd ++FORCE_INLINE int _mm_comilt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vcltq_f64(a, b), 0) & 0x1; ++#else ++ double a0, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ ++ return a0 < b0; ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for equality, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comieq_sd ++FORCE_INLINE int _mm_comieq_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_u64(vceqq_f64(a, b), 0) & 0x1; ++#else ++ uint32x4_t a_not_nan = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(a)); ++ uint32x4_t b_not_nan = ++ vceqq_u32(vreinterpretq_u32_m128d(b), vreinterpretq_u32_m128d(b)); ++ uint32x4_t a_and_b_not_nan = vandq_u32(a_not_nan, b_not_nan); ++ uint32x4_t a_eq_b = ++ vceqq_u32(vreinterpretq_u32_m128d(a), vreinterpretq_u32_m128d(b)); ++ uint64x2_t and_results = vandq_u64(vreinterpretq_u64_u32(a_and_b_not_nan), ++ vreinterpretq_u64_u32(a_eq_b)); ++ return vgetq_lane_u64(and_results, 0) & 0x1; ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point element in a and b ++// for not-equal, and return the boolean result (0 or 1). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_comineq_sd ++FORCE_INLINE int _mm_comineq_sd(__m128d a, __m128d b) ++{ ++ return !_mm_comieq_sd(a, b); ++} ++ ++// Convert packed signed 32-bit integers in a to packed double-precision ++// (64-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi32_pd ++FORCE_INLINE __m128d _mm_cvtepi32_pd(__m128i a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcvtq_f64_s64(vmovl_s32(vget_low_s32(vreinterpretq_s32_m128i(a))))); ++#else ++ double a0 = (double) vgetq_lane_s32(vreinterpretq_s32_m128i(a), 0); ++ double a1 = (double) vgetq_lane_s32(vreinterpretq_s32_m128i(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Convert packed signed 32-bit integers in a to packed single-precision ++// (32-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi32_ps ++FORCE_INLINE __m128 _mm_cvtepi32_ps(__m128i a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32(vreinterpretq_s32_m128i(a))); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpd_epi32 ++FORCE_INLINE_OPTNONE __m128i _mm_cvtpd_epi32(__m128d a) ++{ ++// vrnd32xq_f64 not supported on clang ++#if defined(__ARM_FEATURE_FRINT) && !defined(__clang__) ++ float64x2_t rounded = vrnd32xq_f64(vreinterpretq_f64_m128d(a)); ++ int64x2_t integers = vcvtq_s64_f64(rounded); ++ return vreinterpretq_m128i_s32( ++ vcombine_s32(vmovn_s64(integers), vdup_n_s32(0))); ++#else ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double d0, d1; ++ d0 = sse2neon_recast_u64_f64( ++ vgetq_lane_u64(vreinterpretq_u64_m128d(rnd), 0)); ++ d1 = sse2neon_recast_u64_f64( ++ vgetq_lane_u64(vreinterpretq_u64_m128d(rnd), 1)); ++ return _mm_set_epi32(0, 0, (int32_t) d1, (int32_t) d0); ++#endif ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpd_pi32 ++FORCE_INLINE_OPTNONE __m64 _mm_cvtpd_pi32(__m128d a) ++{ ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double d0, d1; ++ d0 = sse2neon_recast_u64_f64( ++ vgetq_lane_u64(vreinterpretq_u64_m128d(rnd), 0)); ++ d1 = sse2neon_recast_u64_f64( ++ vgetq_lane_u64(vreinterpretq_u64_m128d(rnd), 1)); ++ int32_t ALIGN_STRUCT(16) data[2] = {(int32_t) d0, (int32_t) d1}; ++ return vreinterpret_m64_s32(vld1_s32(data)); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed single-precision (32-bit) floating-point elements, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpd_ps ++FORCE_INLINE __m128 _mm_cvtpd_ps(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float32x2_t tmp = vcvt_f32_f64(vreinterpretq_f64_m128d(a)); ++ return vreinterpretq_m128_f32(vcombine_f32(tmp, vdup_n_f32(0))); ++#else ++ double a0, a1; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ return _mm_set_ps(0, 0, (float) a1, (float) a0); ++#endif ++} ++ ++// Convert packed signed 32-bit integers in a to packed double-precision ++// (64-bit) floating-point elements, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtpi32_pd ++FORCE_INLINE __m128d _mm_cvtpi32_pd(__m64 a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcvtq_f64_s64(vmovl_s32(vreinterpret_s32_m64(a)))); ++#else ++ double a0 = (double) vget_lane_s32(vreinterpret_s32_m64(a), 0); ++ double a1 = (double) vget_lane_s32(vreinterpret_s32_m64(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_epi32 ++// *NOTE*. The default rounding mode on SSE is 'round to even', which ARMv7-A ++// does not support! It is supported on ARMv8-A however. ++FORCE_INLINE __m128i _mm_cvtps_epi32(__m128 a) ++{ ++#if defined(__ARM_FEATURE_FRINT) ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(vrnd32xq_f32(a))); ++#elif (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ switch (_MM_GET_ROUNDING_MODE()) { ++ case _MM_ROUND_NEAREST: ++ return vreinterpretq_m128i_s32(vcvtnq_s32_f32(a)); ++ case _MM_ROUND_DOWN: ++ return vreinterpretq_m128i_s32(vcvtmq_s32_f32(a)); ++ case _MM_ROUND_UP: ++ return vreinterpretq_m128i_s32(vcvtpq_s32_f32(a)); ++ default: // _MM_ROUND_TOWARD_ZERO ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(a)); ++ } ++#else ++ float *f = (float *) &a; ++ switch (_MM_GET_ROUNDING_MODE()) { ++ case _MM_ROUND_NEAREST: { ++ uint32x4_t signmask = vdupq_n_u32(0x80000000); ++ float32x4_t half = vbslq_f32(signmask, vreinterpretq_f32_m128(a), ++ vdupq_n_f32(0.5f)); /* +/- 0.5 */ ++ int32x4_t r_normal = vcvtq_s32_f32(vaddq_f32( ++ vreinterpretq_f32_m128(a), half)); /* round to integer: [a + 0.5]*/ ++ int32x4_t r_trunc = vcvtq_s32_f32( ++ vreinterpretq_f32_m128(a)); /* truncate to integer: [a] */ ++ int32x4_t plusone = vreinterpretq_s32_u32(vshrq_n_u32( ++ vreinterpretq_u32_s32(vnegq_s32(r_trunc)), 31)); /* 1 or 0 */ ++ int32x4_t r_even = vbicq_s32(vaddq_s32(r_trunc, plusone), ++ vdupq_n_s32(1)); /* ([a] + {0,1}) & ~1 */ ++ float32x4_t delta = vsubq_f32( ++ vreinterpretq_f32_m128(a), ++ vcvtq_f32_s32(r_trunc)); /* compute delta: delta = (a - [a]) */ ++ uint32x4_t is_delta_half = ++ vceqq_f32(delta, half); /* delta == +/- 0.5 */ ++ return vreinterpretq_m128i_s32( ++ vbslq_s32(is_delta_half, r_even, r_normal)); ++ } ++ case _MM_ROUND_DOWN: ++ return _mm_set_epi32(floorf(f[3]), floorf(f[2]), floorf(f[1]), ++ floorf(f[0])); ++ case _MM_ROUND_UP: ++ return _mm_set_epi32(ceilf(f[3]), ceilf(f[2]), ceilf(f[1]), ++ ceilf(f[0])); ++ default: // _MM_ROUND_TOWARD_ZERO ++ return _mm_set_epi32((int32_t) f[3], (int32_t) f[2], (int32_t) f[1], ++ (int32_t) f[0]); ++ } ++#endif ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed double-precision (64-bit) floating-point elements, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtps_pd ++FORCE_INLINE __m128d _mm_cvtps_pd(__m128 a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcvt_f64_f32(vget_low_f32(vreinterpretq_f32_m128(a)))); ++#else ++ double a0 = (double) vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ double a1 = (double) vgetq_lane_f32(vreinterpretq_f32_m128(a), 1); ++ return _mm_set_pd(a1, a0); ++#endif ++} ++ ++// Copy the lower double-precision (64-bit) floating-point element of a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_f64 ++FORCE_INLINE double _mm_cvtsd_f64(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return (double) vgetq_lane_f64(vreinterpretq_f64_m128d(a), 0); ++#else ++ double _a = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ return _a; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 32-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_si32 ++FORCE_INLINE int32_t _mm_cvtsd_si32(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return (int32_t) vgetq_lane_f64(vrndiq_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double ret = sse2neon_recast_u64_f64( ++ vgetq_lane_u64(vreinterpretq_u64_m128d(rnd), 0)); ++ return (int32_t) ret; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_si64 ++FORCE_INLINE int64_t _mm_cvtsd_si64(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return (int64_t) vgetq_lane_f64(vrndiq_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ __m128d rnd = _mm_round_pd(a, _MM_FROUND_CUR_DIRECTION); ++ double ret = sse2neon_recast_u64_f64( ++ vgetq_lane_u64(vreinterpretq_u64_m128d(rnd), 0)); ++ return (int64_t) ret; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_si64x ++#define _mm_cvtsd_si64x _mm_cvtsd_si64 ++ ++// Convert the lower double-precision (64-bit) floating-point element in b to a ++// single-precision (32-bit) floating-point element, store the result in the ++// lower element of dst, and copy the upper 3 packed elements from a to the ++// upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsd_ss ++FORCE_INLINE __m128 _mm_cvtsd_ss(__m128 a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32(vsetq_lane_f32( ++ vget_lane_f32(vcvt_f32_f64(vreinterpretq_f64_m128d(b)), 0), ++ vreinterpretq_f32_m128(a), 0)); ++#else ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32((float) b0, vreinterpretq_f32_m128(a), 0)); ++#endif ++} ++ ++// Copy the lower 32-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi128_si32 ++FORCE_INLINE int _mm_cvtsi128_si32(__m128i a) ++{ ++ return vgetq_lane_s32(vreinterpretq_s32_m128i(a), 0); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi128_si64 ++FORCE_INLINE int64_t _mm_cvtsi128_si64(__m128i a) ++{ ++ return vgetq_lane_s64(vreinterpretq_s64_m128i(a), 0); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi128_si64x ++#define _mm_cvtsi128_si64x(a) _mm_cvtsi128_si64(a) ++ ++// Convert the signed 32-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi32_sd ++FORCE_INLINE __m128d _mm_cvtsi32_sd(__m128d a, int32_t b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64((double) b, vreinterpretq_f64_m128d(a), 0)); ++#else ++ int64_t _b = sse2neon_recast_f64_s64((double) b); ++ return vreinterpretq_m128d_s64( ++ vsetq_lane_s64(_b, vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi128_si64x ++#define _mm_cvtsi128_si64x(a) _mm_cvtsi128_si64(a) ++ ++// Copy 32-bit integer a to the lower elements of dst, and zero the upper ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi32_si128 ++FORCE_INLINE __m128i _mm_cvtsi32_si128(int a) ++{ ++ return vreinterpretq_m128i_s32(vsetq_lane_s32(a, vdupq_n_s32(0), 0)); ++} ++ ++// Convert the signed 64-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64_sd ++FORCE_INLINE __m128d _mm_cvtsi64_sd(__m128d a, int64_t b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64((double) b, vreinterpretq_f64_m128d(a), 0)); ++#else ++ int64_t _b = sse2neon_recast_f64_s64((double) b); ++ return vreinterpretq_m128d_s64( ++ vsetq_lane_s64(_b, vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Copy 64-bit integer a to the lower element of dst, and zero the upper ++// element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64_si128 ++FORCE_INLINE __m128i _mm_cvtsi64_si128(int64_t a) ++{ ++ return vreinterpretq_m128i_s64(vsetq_lane_s64(a, vdupq_n_s64(0), 0)); ++} ++ ++// Copy 64-bit integer a to the lower element of dst, and zero the upper ++// element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64x_si128 ++#define _mm_cvtsi64x_si128(a) _mm_cvtsi64_si128(a) ++ ++// Convert the signed 64-bit integer b to a double-precision (64-bit) ++// floating-point element, store the result in the lower element of dst, and ++// copy the upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtsi64x_sd ++#define _mm_cvtsi64x_sd(a, b) _mm_cvtsi64_sd(a, b) ++ ++// Convert the lower single-precision (32-bit) floating-point element in b to a ++// double-precision (64-bit) floating-point element, store the result in the ++// lower element of dst, and copy the upper element from a to the upper element ++// of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtss_sd ++FORCE_INLINE __m128d _mm_cvtss_sd(__m128d a, __m128 b) ++{ ++ double d = (double) vgetq_lane_f32(vreinterpretq_f32_m128(b), 0); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64(d, vreinterpretq_f64_m128d(a), 0)); ++#else ++ return vreinterpretq_m128d_s64(vsetq_lane_s64( ++ sse2neon_recast_f64_s64(d), vreinterpretq_s64_m128d(a), 0)); ++#endif ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttpd_epi32 ++FORCE_INLINE __m128i _mm_cvttpd_epi32(__m128d a) ++{ ++ double a0, a1; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ return _mm_set_epi32(0, 0, (int32_t) a1, (int32_t) a0); ++} ++ ++// Convert packed double-precision (64-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttpd_pi32 ++FORCE_INLINE_OPTNONE __m64 _mm_cvttpd_pi32(__m128d a) ++{ ++ double a0, a1; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ int32_t ALIGN_STRUCT(16) data[2] = {(int32_t) a0, (int32_t) a1}; ++ return vreinterpret_m64_s32(vld1_s32(data)); ++} ++ ++// Convert packed single-precision (32-bit) floating-point elements in a to ++// packed 32-bit integers with truncation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttps_epi32 ++FORCE_INLINE __m128i _mm_cvttps_epi32(__m128 a) ++{ ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a))); ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 32-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttsd_si32 ++FORCE_INLINE int32_t _mm_cvttsd_si32(__m128d a) ++{ ++ double _a = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ return (int32_t) _a; ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttsd_si64 ++FORCE_INLINE int64_t _mm_cvttsd_si64(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vgetq_lane_s64(vcvtq_s64_f64(vreinterpretq_f64_m128d(a)), 0); ++#else ++ double _a = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ return (int64_t) _a; ++#endif ++} ++ ++// Convert the lower double-precision (64-bit) floating-point element in a to a ++// 64-bit integer with truncation, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvttsd_si64x ++#define _mm_cvttsd_si64x(a) _mm_cvttsd_si64(a) ++ ++// Divide packed double-precision (64-bit) floating-point elements in a by ++// packed elements in b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_div_pd ++FORCE_INLINE __m128d _mm_div_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vdivq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ double c[2]; ++ c[0] = a0 / b0; ++ c[1] = a1 / b1; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Divide the lower double-precision (64-bit) floating-point element in a by the ++// lower double-precision (64-bit) floating-point element in b, store the result ++// in the lower element of dst, and copy the upper element from a to the upper ++// element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_div_sd ++FORCE_INLINE __m128d _mm_div_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x2_t tmp = ++ vdivq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b)); ++ return vreinterpretq_m128d_f64( ++ vsetq_lane_f64(vgetq_lane_f64(vreinterpretq_f64_m128d(a), 1), tmp, 1)); ++#else ++ return _mm_move_sd(a, _mm_div_pd(a, b)); ++#endif ++} ++ ++// Extract a 16-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi16 ++// FORCE_INLINE int _mm_extract_epi16(__m128i a, __constrange(0,8) int imm) ++#define _mm_extract_epi16(a, imm) \ ++ vgetq_lane_u16(vreinterpretq_u16_m128i(a), (imm)) ++ ++// Copy a to dst, and insert the 16-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_epi16 ++// FORCE_INLINE __m128i _mm_insert_epi16(__m128i a, int b, ++// __constrange(0,8) int imm) ++#define _mm_insert_epi16(a, b, imm) \ ++ vreinterpretq_m128i_s16( \ ++ vsetq_lane_s16((b), vreinterpretq_s16_m128i(a), (imm))) ++ ++// Load 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from memory into dst. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_pd ++FORCE_INLINE __m128d _mm_load_pd(const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vld1q_f64(p)); ++#else ++ const float *fp = (const float *) p; ++ float ALIGN_STRUCT(16) data[4] = {fp[0], fp[1], fp[2], fp[3]}; ++ return vreinterpretq_m128d_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_pd1 ++#define _mm_load_pd1 _mm_load1_pd ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// lower of dst, and zero the upper element. mem_addr does not need to be ++// aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_sd ++FORCE_INLINE __m128d _mm_load_sd(const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vsetq_lane_f64(*p, vdupq_n_f64(0), 0)); ++#else ++ const float *fp = (const float *) p; ++ float ALIGN_STRUCT(16) data[4] = {fp[0], fp[1], 0, 0}; ++ return vreinterpretq_m128d_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Load 128-bits of integer data from memory into dst. mem_addr must be aligned ++// on a 16-byte boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load_si128 ++FORCE_INLINE __m128i _mm_load_si128(const __m128i *p) ++{ ++ return vreinterpretq_m128i_s32(vld1q_s32((const int32_t *) p)); ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_load1_pd ++FORCE_INLINE __m128d _mm_load1_pd(const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vld1q_dup_f64(p)); ++#else ++ return vreinterpretq_m128d_s64(vdupq_n_s64(*(const int64_t *) p)); ++#endif ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// upper element of dst, and copy the lower element from a to dst. mem_addr does ++// not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadh_pd ++FORCE_INLINE __m128d _mm_loadh_pd(__m128d a, const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcombine_f64(vget_low_f64(vreinterpretq_f64_m128d(a)), vld1_f64(p))); ++#else ++ return vreinterpretq_m128d_f32(vcombine_f32( ++ vget_low_f32(vreinterpretq_f32_m128d(a)), vld1_f32((const float *) p))); ++#endif ++} ++ ++// Load 64-bit integer from memory into the first element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadl_epi64 ++FORCE_INLINE __m128i _mm_loadl_epi64(__m128i const *p) ++{ ++ /* Load the lower 64 bits of the value pointed to by p into the ++ * lower 64 bits of the result, zeroing the upper 64 bits of the result. ++ */ ++ return vreinterpretq_m128i_s32( ++ vcombine_s32(vld1_s32((int32_t const *) p), vcreate_s32(0))); ++} ++ ++// Load a double-precision (64-bit) floating-point element from memory into the ++// lower element of dst, and copy the upper element from a to dst. mem_addr does ++// not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadl_pd ++FORCE_INLINE __m128d _mm_loadl_pd(__m128d a, const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vcombine_f64(vld1_f64(p), vget_high_f64(vreinterpretq_f64_m128d(a)))); ++#else ++ return vreinterpretq_m128d_f32( ++ vcombine_f32(vld1_f32((const float *) p), ++ vget_high_f32(vreinterpretq_f32_m128d(a)))); ++#endif ++} ++ ++// Load 2 double-precision (64-bit) floating-point elements from memory into dst ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadr_pd ++FORCE_INLINE __m128d _mm_loadr_pd(const double *p) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x2_t v = vld1q_f64(p); ++ return vreinterpretq_m128d_f64(vextq_f64(v, v, 1)); ++#else ++ int64x2_t v = vld1q_s64((const int64_t *) p); ++ return vreinterpretq_m128d_s64(vextq_s64(v, v, 1)); ++#endif ++} ++ ++// Loads two double-precision from unaligned memory, floating-point values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_pd ++FORCE_INLINE __m128d _mm_loadu_pd(const double *p) ++{ ++ return _mm_load_pd(p); ++} ++ ++// Load 128-bits of integer data from memory into dst. mem_addr does not need to ++// be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_si128 ++FORCE_INLINE __m128i _mm_loadu_si128(const __m128i *p) ++{ ++ return vreinterpretq_m128i_s32(vld1q_s32((const unaligned_int32_t *) p)); ++} ++ ++// Load unaligned 32-bit integer from memory into the first element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loadu_si32 ++FORCE_INLINE __m128i _mm_loadu_si32(const void *p) ++{ ++ return vreinterpretq_m128i_s32( ++ vsetq_lane_s32(*(const unaligned_int32_t *) p, vdupq_n_s32(0), 0)); ++} ++ ++// Multiply packed signed 16-bit integers in a and b, producing intermediate ++// signed 32-bit integers. Horizontally add adjacent pairs of intermediate ++// 32-bit integers, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_madd_epi16 ++FORCE_INLINE __m128i _mm_madd_epi16(__m128i a, __m128i b) ++{ ++ int32x4_t low = vmull_s16(vget_low_s16(vreinterpretq_s16_m128i(a)), ++ vget_low_s16(vreinterpretq_s16_m128i(b))); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int32x4_t high = ++ vmull_high_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b)); ++ ++ return vreinterpretq_m128i_s32(vpaddq_s32(low, high)); ++#else ++ int32x4_t high = vmull_s16(vget_high_s16(vreinterpretq_s16_m128i(a)), ++ vget_high_s16(vreinterpretq_s16_m128i(b))); ++ ++ int32x2_t low_sum = vpadd_s32(vget_low_s32(low), vget_high_s32(low)); ++ int32x2_t high_sum = vpadd_s32(vget_low_s32(high), vget_high_s32(high)); ++ ++ return vreinterpretq_m128i_s32(vcombine_s32(low_sum, high_sum)); ++#endif ++} ++ ++// Conditionally store 8-bit integer elements from a into memory using mask ++// (elements are not stored when the highest bit is not set in the corresponding ++// element) and a non-temporal memory hint. mem_addr does not need to be aligned ++// on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_maskmoveu_si128 ++FORCE_INLINE void _mm_maskmoveu_si128(__m128i a, __m128i mask, char *mem_addr) ++{ ++ int8x16_t shr_mask = vshrq_n_s8(vreinterpretq_s8_m128i(mask), 7); ++ __m128 b = _mm_load_ps((const float *) mem_addr); ++ int8x16_t masked = ++ vbslq_s8(vreinterpretq_u8_s8(shr_mask), vreinterpretq_s8_m128i(a), ++ vreinterpretq_s8_m128(b)); ++ vst1q_s8((int8_t *) mem_addr, masked); ++} ++ ++// Compare packed signed 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epi16 ++FORCE_INLINE __m128i _mm_max_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vmaxq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epu8 ++FORCE_INLINE __m128i _mm_max_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vmaxq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b, ++// and store packed maximum values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_pd ++FORCE_INLINE __m128d _mm_max_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#if SSE2NEON_PRECISE_MINMAX ++ float64x2_t _a = vreinterpretq_f64_m128d(a); ++ float64x2_t _b = vreinterpretq_f64_m128d(b); ++ return vreinterpretq_m128d_f64(vbslq_f64(vcgtq_f64(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128d_f64( ++ vmaxq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#endif ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ int64_t d[2]; ++ d[0] = a0 > b0 ? sse2neon_recast_f64_s64(a0) : sse2neon_recast_f64_s64(b0); ++ d[1] = a1 > b1 ? sse2neon_recast_f64_s64(a1) : sse2neon_recast_f64_s64(b1); ++ ++ return vreinterpretq_m128d_s64(vld1q_s64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b, store the maximum value in the lower element of dst, and copy the upper ++// element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_sd ++FORCE_INLINE __m128d _mm_max_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_max_pd(a, b)); ++#else ++ double a0, a1, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double c[2] = {a0 > b0 ? a0 : b0, a1}; ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) c)); ++#endif ++} ++ ++// Compare packed signed 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epi16 ++FORCE_INLINE __m128i _mm_min_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vminq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed unsigned 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epu8 ++FORCE_INLINE __m128i _mm_min_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vminq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Compare packed double-precision (64-bit) floating-point elements in a and b, ++// and store packed minimum values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_pd ++FORCE_INLINE __m128d _mm_min_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#if SSE2NEON_PRECISE_MINMAX ++ float64x2_t _a = vreinterpretq_f64_m128d(a); ++ float64x2_t _b = vreinterpretq_f64_m128d(b); ++ return vreinterpretq_m128d_f64(vbslq_f64(vcltq_f64(_a, _b), _a, _b)); ++#else ++ return vreinterpretq_m128d_f64( ++ vminq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#endif ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ int64_t d[2]; ++ d[0] = a0 < b0 ? sse2neon_recast_f64_s64(a0) : sse2neon_recast_f64_s64(b0); ++ d[1] = a1 < b1 ? sse2neon_recast_f64_s64(a1) : sse2neon_recast_f64_s64(b1); ++ return vreinterpretq_m128d_s64(vld1q_s64(d)); ++#endif ++} ++ ++// Compare the lower double-precision (64-bit) floating-point elements in a and ++// b, store the minimum value in the lower element of dst, and copy the upper ++// element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_sd ++FORCE_INLINE __m128d _mm_min_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_min_pd(a, b)); ++#else ++ double a0, a1, b0; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ b0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double c[2] = {a0 < b0 ? a0 : b0, a1}; ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) c)); ++#endif ++} ++ ++// Copy the lower 64-bit integer in a to the lower element of dst, and zero the ++// upper element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_move_epi64 ++FORCE_INLINE __m128i _mm_move_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_s64( ++ vsetq_lane_s64(0, vreinterpretq_s64_m128i(a), 1)); ++} ++ ++// Move the lower double-precision (64-bit) floating-point element from b to the ++// lower element of dst, and copy the upper element from a to the upper element ++// of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_move_sd ++FORCE_INLINE __m128d _mm_move_sd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_f32( ++ vcombine_f32(vget_low_f32(vreinterpretq_f32_m128d(b)), ++ vget_high_f32(vreinterpretq_f32_m128d(a)))); ++} ++ ++// Create mask from the most significant bit of each 8-bit element in a, and ++// store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movemask_epi8 ++FORCE_INLINE int _mm_movemask_epi8(__m128i a) ++{ ++ // Use increasingly wide shifts+adds to collect the sign bits ++ // together. ++ // Since the widening shifts would be rather confusing to follow in little ++ // endian, everything will be illustrated in big endian order instead. This ++ // has a different result - the bits would actually be reversed on a big ++ // endian machine. ++ ++ // Starting input (only half the elements are shown): ++ // 89 ff 1d c0 00 10 99 33 ++ uint8x16_t input = vreinterpretq_u8_m128i(a); ++ ++ // Shift out everything but the sign bits with an unsigned shift right. ++ // ++ // Bytes of the vector:: ++ // 89 ff 1d c0 00 10 99 33 ++ // \ \ \ \ \ \ \ \ high_bits = (uint16x4_t)(input >> 7) ++ // | | | | | | | | ++ // 01 01 00 01 00 00 01 00 ++ // ++ // Bits of first important lane(s): ++ // 10001001 (89) ++ // \______ ++ // | ++ // 00000001 (01) ++ uint16x8_t high_bits = vreinterpretq_u16_u8(vshrq_n_u8(input, 7)); ++ ++ // Merge the even lanes together with a 16-bit unsigned shift right + add. ++ // 'xx' represents garbage data which will be ignored in the final result. ++ // In the important bytes, the add functions like a binary OR. ++ // ++ // 01 01 00 01 00 00 01 00 ++ // \_ | \_ | \_ | \_ | paired16 = (uint32x4_t)(input + (input >> 7)) ++ // \| \| \| \| ++ // xx 03 xx 01 xx 00 xx 02 ++ // ++ // 00000001 00000001 (01 01) ++ // \_______ | ++ // \| ++ // xxxxxxxx xxxxxx11 (xx 03) ++ uint32x4_t paired16 = ++ vreinterpretq_u32_u16(vsraq_n_u16(high_bits, high_bits, 7)); ++ ++ // Repeat with a wider 32-bit shift + add. ++ // xx 03 xx 01 xx 00 xx 02 ++ // \____ | \____ | paired32 = (uint64x1_t)(paired16 + (paired16 >> ++ // 14)) ++ // \| \| ++ // xx xx xx 0d xx xx xx 02 ++ // ++ // 00000011 00000001 (03 01) ++ // \\_____ || ++ // '----.\|| ++ // xxxxxxxx xxxx1101 (xx 0d) ++ uint64x2_t paired32 = ++ vreinterpretq_u64_u32(vsraq_n_u32(paired16, paired16, 14)); ++ ++ // Last, an even wider 64-bit shift + add to get our result in the low 8 bit ++ // lanes. xx xx xx 0d xx xx xx 02 ++ // \_________ | paired64 = (uint8x8_t)(paired32 + (paired32 >> ++ // 28)) ++ // \| ++ // xx xx xx xx xx xx xx d2 ++ // ++ // 00001101 00000010 (0d 02) ++ // \ \___ | | ++ // '---. \| | ++ // xxxxxxxx 11010010 (xx d2) ++ uint8x16_t paired64 = ++ vreinterpretq_u8_u64(vsraq_n_u64(paired32, paired32, 28)); ++ ++ // Extract the low 8 bits from each 64-bit lane with 2 8-bit extracts. ++ // xx xx xx xx xx xx xx d2 ++ // || return paired64[0] ++ // d2 ++ // Note: Little endian would return the correct value 4b (01001011) instead. ++ return vgetq_lane_u8(paired64, 0) | ((int) vgetq_lane_u8(paired64, 8) << 8); ++} ++ ++// Set each bit of mask dst based on the most significant bit of the ++// corresponding packed double-precision (64-bit) floating-point element in a. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movemask_pd ++FORCE_INLINE int _mm_movemask_pd(__m128d a) ++{ ++ uint64x2_t input = vreinterpretq_u64_m128d(a); ++ uint64x2_t high_bits = vshrq_n_u64(input, 63); ++ return (int) (vgetq_lane_u64(high_bits, 0) | ++ (vgetq_lane_u64(high_bits, 1) << 1)); ++} ++ ++// Copy the lower 64-bit integer in a to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movepi64_pi64 ++FORCE_INLINE __m64 _mm_movepi64_pi64(__m128i a) ++{ ++ return vreinterpret_m64_s64(vget_low_s64(vreinterpretq_s64_m128i(a))); ++} ++ ++// Copy the 64-bit integer a to the lower element of dst, and zero the upper ++// element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movpi64_epi64 ++FORCE_INLINE __m128i _mm_movpi64_epi64(__m64 a) ++{ ++ return vreinterpretq_m128i_s64( ++ vcombine_s64(vreinterpret_s64_m64(a), vdup_n_s64(0))); ++} ++ ++// Multiply the low unsigned 32-bit integers from each packed 64-bit element in ++// a and b, and store the unsigned 64-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_epu32 ++FORCE_INLINE __m128i _mm_mul_epu32(__m128i a, __m128i b) ++{ ++ // vmull_u32 upcasts instead of masking, so we downcast. ++ uint32x2_t a_lo = vmovn_u64(vreinterpretq_u64_m128i(a)); ++ uint32x2_t b_lo = vmovn_u64(vreinterpretq_u64_m128i(b)); ++ return vreinterpretq_m128i_u64(vmull_u32(a_lo, b_lo)); ++} ++ ++// Multiply packed double-precision (64-bit) floating-point elements in a and b, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_pd ++FORCE_INLINE __m128d _mm_mul_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vmulq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ double c[2]; ++ c[0] = a0 * b0; ++ c[1] = a1 * b1; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Multiply the lower double-precision (64-bit) floating-point element in a and ++// b, store the result in the lower element of dst, and copy the upper element ++// from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_mul_sd ++FORCE_INLINE __m128d _mm_mul_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_mul_pd(a, b)); ++} ++ ++// Multiply the low unsigned 32-bit integers from a and b, and store the ++// unsigned 64-bit result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_su32 ++FORCE_INLINE __m64 _mm_mul_su32(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_u64(vget_low_u64( ++ vmull_u32(vreinterpret_u32_m64(a), vreinterpret_u32_m64(b)))); ++} ++ ++// Multiply the packed signed 16-bit integers in a and b, producing intermediate ++// 32-bit integers, and store the high 16 bits of the intermediate integers in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhi_epi16 ++FORCE_INLINE __m128i _mm_mulhi_epi16(__m128i a, __m128i b) ++{ ++ /* FIXME: issue with large values because of result saturation */ ++ // int16x8_t ret = vqdmulhq_s16(vreinterpretq_s16_m128i(a), ++ // vreinterpretq_s16_m128i(b)); /* =2*a*b */ return ++ // vreinterpretq_m128i_s16(vshrq_n_s16(ret, 1)); ++ int16x4_t a3210 = vget_low_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b3210 = vget_low_s16(vreinterpretq_s16_m128i(b)); ++ int32x4_t ab3210 = vmull_s16(a3210, b3210); /* 3333222211110000 */ ++ int16x4_t a7654 = vget_high_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b7654 = vget_high_s16(vreinterpretq_s16_m128i(b)); ++ int32x4_t ab7654 = vmull_s16(a7654, b7654); /* 7777666655554444 */ ++ uint16x8x2_t r = ++ vuzpq_u16(vreinterpretq_u16_s32(ab3210), vreinterpretq_u16_s32(ab7654)); ++ return vreinterpretq_m128i_u16(r.val[1]); ++} ++ ++// Multiply the packed unsigned 16-bit integers in a and b, producing ++// intermediate 32-bit integers, and store the high 16 bits of the intermediate ++// integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhi_epu16 ++FORCE_INLINE __m128i _mm_mulhi_epu16(__m128i a, __m128i b) ++{ ++ uint16x4_t a3210 = vget_low_u16(vreinterpretq_u16_m128i(a)); ++ uint16x4_t b3210 = vget_low_u16(vreinterpretq_u16_m128i(b)); ++ uint32x4_t ab3210 = vmull_u16(a3210, b3210); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint32x4_t ab7654 = ++ vmull_high_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b)); ++ uint16x8_t r = vuzp2q_u16(vreinterpretq_u16_u32(ab3210), ++ vreinterpretq_u16_u32(ab7654)); ++ return vreinterpretq_m128i_u16(r); ++#else ++ uint16x4_t a7654 = vget_high_u16(vreinterpretq_u16_m128i(a)); ++ uint16x4_t b7654 = vget_high_u16(vreinterpretq_u16_m128i(b)); ++ uint32x4_t ab7654 = vmull_u16(a7654, b7654); ++ uint16x8x2_t r = ++ vuzpq_u16(vreinterpretq_u16_u32(ab3210), vreinterpretq_u16_u32(ab7654)); ++ return vreinterpretq_m128i_u16(r.val[1]); ++#endif ++} ++ ++// Multiply the packed 16-bit integers in a and b, producing intermediate 32-bit ++// integers, and store the low 16 bits of the intermediate integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mullo_epi16 ++FORCE_INLINE __m128i _mm_mullo_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vmulq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compute the bitwise OR of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_or_pd ++FORCE_INLINE __m128d _mm_or_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ vorrq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Compute the bitwise OR of 128 bits (representing integer data) in a and b, ++// and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_or_si128 ++FORCE_INLINE __m128i _mm_or_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vorrq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Convert packed signed 16-bit integers from a and b to packed 8-bit integers ++// using signed saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_packs_epi16 ++FORCE_INLINE __m128i _mm_packs_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vcombine_s8(vqmovn_s16(vreinterpretq_s16_m128i(a)), ++ vqmovn_s16(vreinterpretq_s16_m128i(b)))); ++} ++ ++// Convert packed signed 32-bit integers from a and b to packed 16-bit integers ++// using signed saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_packs_epi32 ++FORCE_INLINE __m128i _mm_packs_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vqmovn_s32(vreinterpretq_s32_m128i(a)), ++ vqmovn_s32(vreinterpretq_s32_m128i(b)))); ++} ++ ++// Convert packed signed 16-bit integers from a and b to packed 8-bit integers ++// using unsigned saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_packus_epi16 ++FORCE_INLINE __m128i _mm_packus_epi16(const __m128i a, const __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcombine_u8(vqmovun_s16(vreinterpretq_s16_m128i(a)), ++ vqmovun_s16(vreinterpretq_s16_m128i(b)))); ++} ++ ++// Pause the processor. This is typically used in spin-wait loops and depending ++// on the x86 processor typical values are in the 40-100 cycle range. The ++// 'yield' instruction isn't a good fit because it's effectively a nop on most ++// Arm cores. Experience with several databases has shown has shown an 'isb' is ++// a reasonable approximation. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_pause ++FORCE_INLINE void _mm_pause(void) ++{ ++#if defined(_MSC_VER) && !defined(__clang__) ++ __isb(_ARM64_BARRIER_SY); ++#else ++ __asm__ __volatile__("isb\n"); ++#endif ++} ++ ++// Compute the absolute differences of packed unsigned 8-bit integers in a and ++// b, then horizontally sum each consecutive 8 differences to produce two ++// unsigned 16-bit integers, and pack these unsigned 16-bit integers in the low ++// 16 bits of 64-bit elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sad_epu8 ++FORCE_INLINE __m128i _mm_sad_epu8(__m128i a, __m128i b) ++{ ++ uint16x8_t t = vpaddlq_u8(vabdq_u8((uint8x16_t) a, (uint8x16_t) b)); ++ return vreinterpretq_m128i_u64(vpaddlq_u32(vpaddlq_u16(t))); ++} ++ ++// Set packed 16-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi16 ++FORCE_INLINE __m128i _mm_set_epi16(short i7, ++ short i6, ++ short i5, ++ short i4, ++ short i3, ++ short i2, ++ short i1, ++ short i0) ++{ ++ int16_t ALIGN_STRUCT(16) data[8] = {i0, i1, i2, i3, i4, i5, i6, i7}; ++ return vreinterpretq_m128i_s16(vld1q_s16(data)); ++} ++ ++// Set packed 32-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi32 ++FORCE_INLINE __m128i _mm_set_epi32(int i3, int i2, int i1, int i0) ++{ ++ int32_t ALIGN_STRUCT(16) data[4] = {i0, i1, i2, i3}; ++ return vreinterpretq_m128i_s32(vld1q_s32(data)); ++} ++ ++// Set packed 64-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi64 ++FORCE_INLINE __m128i _mm_set_epi64(__m64 i1, __m64 i2) ++{ ++ return _mm_set_epi64x(vget_lane_s64(i1, 0), vget_lane_s64(i2, 0)); ++} ++ ++// Set packed 64-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi64x ++FORCE_INLINE __m128i _mm_set_epi64x(int64_t i1, int64_t i2) ++{ ++ return vreinterpretq_m128i_s64( ++ vcombine_s64(vcreate_s64(i2), vcreate_s64(i1))); ++} ++ ++// Set packed 8-bit integers in dst with the supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_epi8 ++FORCE_INLINE __m128i _mm_set_epi8(signed char b15, ++ signed char b14, ++ signed char b13, ++ signed char b12, ++ signed char b11, ++ signed char b10, ++ signed char b9, ++ signed char b8, ++ signed char b7, ++ signed char b6, ++ signed char b5, ++ signed char b4, ++ signed char b3, ++ signed char b2, ++ signed char b1, ++ signed char b0) ++{ ++ int8_t ALIGN_STRUCT(16) ++ data[16] = {(int8_t) b0, (int8_t) b1, (int8_t) b2, (int8_t) b3, ++ (int8_t) b4, (int8_t) b5, (int8_t) b6, (int8_t) b7, ++ (int8_t) b8, (int8_t) b9, (int8_t) b10, (int8_t) b11, ++ (int8_t) b12, (int8_t) b13, (int8_t) b14, (int8_t) b15}; ++ return (__m128i) vld1q_s8(data); ++} ++ ++// Set packed double-precision (64-bit) floating-point elements in dst with the ++// supplied values. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_pd ++FORCE_INLINE __m128d _mm_set_pd(double e1, double e0) ++{ ++ double ALIGN_STRUCT(16) data[2] = {e0, e1}; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vld1q_f64((float64_t *) data)); ++#else ++ return vreinterpretq_m128d_f32(vld1q_f32((float32_t *) data)); ++#endif ++} ++ ++// Broadcast double-precision (64-bit) floating-point value a to all elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_pd1 ++#define _mm_set_pd1 _mm_set1_pd ++ ++// Copy double-precision (64-bit) floating-point element a to the lower element ++// of dst, and zero the upper element. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set_sd ++FORCE_INLINE __m128d _mm_set_sd(double a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vsetq_lane_f64(a, vdupq_n_f64(0), 0)); ++#else ++ return _mm_set_pd(0, a); ++#endif ++} ++ ++// Broadcast 16-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi16 ++FORCE_INLINE __m128i _mm_set1_epi16(short w) ++{ ++ return vreinterpretq_m128i_s16(vdupq_n_s16(w)); ++} ++ ++// Broadcast 32-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi32 ++FORCE_INLINE __m128i _mm_set1_epi32(int _i) ++{ ++ return vreinterpretq_m128i_s32(vdupq_n_s32(_i)); ++} ++ ++// Broadcast 64-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi64 ++FORCE_INLINE __m128i _mm_set1_epi64(__m64 _i) ++{ ++ return vreinterpretq_m128i_s64(vdupq_lane_s64(_i, 0)); ++} ++ ++// Broadcast 64-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi64x ++FORCE_INLINE __m128i _mm_set1_epi64x(int64_t _i) ++{ ++ return vreinterpretq_m128i_s64(vdupq_n_s64(_i)); ++} ++ ++// Broadcast 8-bit integer a to all elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_epi8 ++FORCE_INLINE __m128i _mm_set1_epi8(signed char w) ++{ ++ return vreinterpretq_m128i_s8(vdupq_n_s8(w)); ++} ++ ++// Broadcast double-precision (64-bit) floating-point value a to all elements of ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_set1_pd ++FORCE_INLINE __m128d _mm_set1_pd(double d) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vdupq_n_f64(d)); ++#else ++ int64_t _d = sse2neon_recast_f64_s64(d); ++ return vreinterpretq_m128d_s64(vdupq_n_s64(_d)); ++#endif ++} ++ ++// Set packed 16-bit integers in dst with the supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_epi16 ++FORCE_INLINE __m128i _mm_setr_epi16(short w0, ++ short w1, ++ short w2, ++ short w3, ++ short w4, ++ short w5, ++ short w6, ++ short w7) ++{ ++ int16_t ALIGN_STRUCT(16) data[8] = {w0, w1, w2, w3, w4, w5, w6, w7}; ++ return vreinterpretq_m128i_s16(vld1q_s16((int16_t *) data)); ++} ++ ++// Set packed 32-bit integers in dst with the supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_epi32 ++FORCE_INLINE __m128i _mm_setr_epi32(int i3, int i2, int i1, int i0) ++{ ++ int32_t ALIGN_STRUCT(16) data[4] = {i3, i2, i1, i0}; ++ return vreinterpretq_m128i_s32(vld1q_s32(data)); ++} ++ ++// Set packed 64-bit integers in dst with the supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_epi64 ++FORCE_INLINE __m128i _mm_setr_epi64(__m64 e1, __m64 e0) ++{ ++ return vreinterpretq_m128i_s64(vcombine_s64(e1, e0)); ++} ++ ++// Set packed 8-bit integers in dst with the supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_epi8 ++FORCE_INLINE __m128i _mm_setr_epi8(signed char b0, ++ signed char b1, ++ signed char b2, ++ signed char b3, ++ signed char b4, ++ signed char b5, ++ signed char b6, ++ signed char b7, ++ signed char b8, ++ signed char b9, ++ signed char b10, ++ signed char b11, ++ signed char b12, ++ signed char b13, ++ signed char b14, ++ signed char b15) ++{ ++ int8_t ALIGN_STRUCT(16) ++ data[16] = {(int8_t) b0, (int8_t) b1, (int8_t) b2, (int8_t) b3, ++ (int8_t) b4, (int8_t) b5, (int8_t) b6, (int8_t) b7, ++ (int8_t) b8, (int8_t) b9, (int8_t) b10, (int8_t) b11, ++ (int8_t) b12, (int8_t) b13, (int8_t) b14, (int8_t) b15}; ++ return (__m128i) vld1q_s8(data); ++} ++ ++// Set packed double-precision (64-bit) floating-point elements in dst with the ++// supplied values in reverse order. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setr_pd ++FORCE_INLINE __m128d _mm_setr_pd(double e1, double e0) ++{ ++ return _mm_set_pd(e0, e1); ++} ++ ++// Return vector of type __m128d with all elements set to zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setzero_pd ++FORCE_INLINE __m128d _mm_setzero_pd(void) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vdupq_n_f64(0)); ++#else ++ return vreinterpretq_m128d_f32(vdupq_n_f32(0)); ++#endif ++} ++ ++// Return vector of type __m128i with all elements set to zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_setzero_si128 ++FORCE_INLINE __m128i _mm_setzero_si128(void) ++{ ++ return vreinterpretq_m128i_s32(vdupq_n_s32(0)); ++} ++ ++// Shuffle 32-bit integers in a using the control in imm8, and store the results ++// in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_epi32 ++// FORCE_INLINE __m128i _mm_shuffle_epi32(__m128i a, ++// __constrange(0,255) int imm) ++#if defined(_sse2neon_shuffle) ++#define _mm_shuffle_epi32(a, imm) \ ++ __extension__({ \ ++ int32x4_t _input = vreinterpretq_s32_m128i(a); \ ++ int32x4_t _shuf = \ ++ vshuffleq_s32(_input, _input, (imm) & (0x3), ((imm) >> 2) & 0x3, \ ++ ((imm) >> 4) & 0x3, ((imm) >> 6) & 0x3); \ ++ vreinterpretq_m128i_s32(_shuf); \ ++ }) ++#else // generic ++#define _mm_shuffle_epi32(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, __m128i ret; switch (imm) { \ ++ case _MM_SHUFFLE(1, 0, 3, 2): \ ++ ret = _mm_shuffle_epi_1032(_a); \ ++ break; \ ++ case _MM_SHUFFLE(2, 3, 0, 1): \ ++ ret = _mm_shuffle_epi_2301(_a); \ ++ break; \ ++ case _MM_SHUFFLE(0, 3, 2, 1): \ ++ ret = _mm_shuffle_epi_0321(_a); \ ++ break; \ ++ case _MM_SHUFFLE(2, 1, 0, 3): \ ++ ret = _mm_shuffle_epi_2103(_a); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 1, 0): \ ++ ret = _mm_shuffle_epi_1010(_a); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 0, 1): \ ++ ret = _mm_shuffle_epi_1001(_a); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 0, 1): \ ++ ret = _mm_shuffle_epi_0101(_a); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 1, 1): \ ++ ret = _mm_shuffle_epi_2211(_a); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 2, 2): \ ++ ret = _mm_shuffle_epi_0122(_a); \ ++ break; \ ++ case _MM_SHUFFLE(3, 3, 3, 2): \ ++ ret = _mm_shuffle_epi_3332(_a); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 0, 0): \ ++ ret = _mm_shuffle_epi32_splat(_a, 0); \ ++ break; \ ++ case _MM_SHUFFLE(1, 1, 1, 1): \ ++ ret = _mm_shuffle_epi32_splat(_a, 1); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 2, 2): \ ++ ret = _mm_shuffle_epi32_splat(_a, 2); \ ++ break; \ ++ case _MM_SHUFFLE(3, 3, 3, 3): \ ++ ret = _mm_shuffle_epi32_splat(_a, 3); \ ++ break; \ ++ default: \ ++ ret = _mm_shuffle_epi32_default(_a, (imm)); \ ++ break; \ ++ } _sse2neon_return(ret);) ++#endif ++ ++// Shuffle double-precision (64-bit) floating-point elements using the control ++// in imm8, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_pd ++#ifdef _sse2neon_shuffle ++#define _mm_shuffle_pd(a, b, imm8) \ ++ vreinterpretq_m128d_s64( \ ++ vshuffleq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b), \ ++ imm8 & 0x1, ((imm8 & 0x2) >> 1) + 2)) ++#else ++#define _mm_shuffle_pd(a, b, imm8) \ ++ _mm_castsi128_pd(_mm_set_epi64x( \ ++ vgetq_lane_s64(vreinterpretq_s64_m128d(b), (imm8 & 0x2) >> 1), \ ++ vgetq_lane_s64(vreinterpretq_s64_m128d(a), imm8 & 0x1))) ++#endif ++ ++// FORCE_INLINE __m128i _mm_shufflehi_epi16(__m128i a, ++// __constrange(0,255) int imm) ++#if defined(_sse2neon_shuffle) ++#define _mm_shufflehi_epi16(a, imm) \ ++ __extension__({ \ ++ int16x8_t _input = vreinterpretq_s16_m128i(a); \ ++ int16x8_t _shuf = \ ++ vshuffleq_s16(_input, _input, 0, 1, 2, 3, ((imm) & (0x3)) + 4, \ ++ (((imm) >> 2) & 0x3) + 4, (((imm) >> 4) & 0x3) + 4, \ ++ (((imm) >> 6) & 0x3) + 4); \ ++ vreinterpretq_m128i_s16(_shuf); \ ++ }) ++#else // generic ++#define _mm_shufflehi_epi16(a, imm) _mm_shufflehi_epi16_function((a), (imm)) ++#endif ++ ++// FORCE_INLINE __m128i _mm_shufflelo_epi16(__m128i a, ++// __constrange(0,255) int imm) ++#if defined(_sse2neon_shuffle) ++#define _mm_shufflelo_epi16(a, imm) \ ++ __extension__({ \ ++ int16x8_t _input = vreinterpretq_s16_m128i(a); \ ++ int16x8_t _shuf = vshuffleq_s16( \ ++ _input, _input, ((imm) & (0x3)), (((imm) >> 2) & 0x3), \ ++ (((imm) >> 4) & 0x3), (((imm) >> 6) & 0x3), 4, 5, 6, 7); \ ++ vreinterpretq_m128i_s16(_shuf); \ ++ }) ++#else // generic ++#define _mm_shufflelo_epi16(a, imm) _mm_shufflelo_epi16_function((a), (imm)) ++#endif ++ ++// Shift packed 16-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sll_epi16 ++FORCE_INLINE __m128i _mm_sll_epi16(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_setzero_si128(); ++ ++ int16x8_t vc = vdupq_n_s16((int16_t) c); ++ return vreinterpretq_m128i_s16(vshlq_s16(vreinterpretq_s16_m128i(a), vc)); ++} ++ ++// Shift packed 32-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sll_epi32 ++FORCE_INLINE __m128i _mm_sll_epi32(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_setzero_si128(); ++ ++ int32x4_t vc = vdupq_n_s32((int32_t) c); ++ return vreinterpretq_m128i_s32(vshlq_s32(vreinterpretq_s32_m128i(a), vc)); ++} ++ ++// Shift packed 64-bit integers in a left by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sll_epi64 ++FORCE_INLINE __m128i _mm_sll_epi64(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~63)) ++ return _mm_setzero_si128(); ++ ++ int64x2_t vc = vdupq_n_s64((int64_t) c); ++ return vreinterpretq_m128i_s64(vshlq_s64(vreinterpretq_s64_m128i(a), vc)); ++} ++ ++// Shift packed 16-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_slli_epi16 ++FORCE_INLINE __m128i _mm_slli_epi16(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~15)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s16( ++ vshlq_s16(vreinterpretq_s16_m128i(a), vdupq_n_s16(imm))); ++} ++ ++// Shift packed 32-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_slli_epi32 ++FORCE_INLINE __m128i _mm_slli_epi32(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~31)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s32( ++ vshlq_s32(vreinterpretq_s32_m128i(a), vdupq_n_s32(imm))); ++} ++ ++// Shift packed 64-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_slli_epi64 ++FORCE_INLINE __m128i _mm_slli_epi64(__m128i a, int imm) ++{ ++ if (_sse2neon_unlikely(imm & ~63)) ++ return _mm_setzero_si128(); ++ return vreinterpretq_m128i_s64( ++ vshlq_s64(vreinterpretq_s64_m128i(a), vdupq_n_s64(imm))); ++} ++ ++// Shift a left by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_slli_si128 ++#define _mm_slli_si128(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, int8x16_t ret; \ ++ if (_sse2neon_unlikely(imm == 0)) ret = vreinterpretq_s8_m128i(_a); \ ++ else if (_sse2neon_unlikely((imm) & ~15)) ret = vdupq_n_s8(0); \ ++ else ret = vextq_s8(vdupq_n_s8(0), vreinterpretq_s8_m128i(_a), \ ++ ((imm <= 0 || imm > 15) ? 0 : (16 - imm))); \ ++ _sse2neon_return(vreinterpretq_m128i_s8(ret));) ++ ++// Compute the square root of packed double-precision (64-bit) floating-point ++// elements in a, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sqrt_pd ++FORCE_INLINE __m128d _mm_sqrt_pd(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vsqrtq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double a0, a1; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double _a0 = sqrt(a0); ++ double _a1 = sqrt(a1); ++ return _mm_set_pd(_a1, _a0); ++#endif ++} ++ ++// Compute the square root of the lower double-precision (64-bit) floating-point ++// element in b, store the result in the lower element of dst, and copy the ++// upper element from a to the upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sqrt_sd ++FORCE_INLINE __m128d _mm_sqrt_sd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return _mm_move_sd(a, _mm_sqrt_pd(b)); ++#else ++ double _a, _b; ++ _a = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ _b = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ return _mm_set_pd(_a, sqrt(_b)); ++#endif ++} ++ ++// Shift packed 16-bit integers in a right by count while shifting in sign bits, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sra_epi16 ++FORCE_INLINE __m128i _mm_sra_epi16(__m128i a, __m128i count) ++{ ++ int64_t c = vgetq_lane_s64(count, 0); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_cmplt_epi16(a, _mm_setzero_si128()); ++ return vreinterpretq_m128i_s16( ++ vshlq_s16((int16x8_t) a, vdupq_n_s16((int) -c))); ++} ++ ++// Shift packed 32-bit integers in a right by count while shifting in sign bits, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sra_epi32 ++FORCE_INLINE __m128i _mm_sra_epi32(__m128i a, __m128i count) ++{ ++ int64_t c = vgetq_lane_s64(count, 0); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_cmplt_epi32(a, _mm_setzero_si128()); ++ return vreinterpretq_m128i_s32( ++ vshlq_s32((int32x4_t) a, vdupq_n_s32((int) -c))); ++} ++ ++// Shift packed 16-bit integers in a right by imm8 while shifting in sign ++// bits, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srai_epi16 ++FORCE_INLINE __m128i _mm_srai_epi16(__m128i a, int imm) ++{ ++ const int count = (imm & ~15) ? 15 : imm; ++ return (__m128i) vshlq_s16((int16x8_t) a, vdupq_n_s16(-count)); ++} ++ ++// Shift packed 32-bit integers in a right by imm8 while shifting in sign bits, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srai_epi32 ++// FORCE_INLINE __m128i _mm_srai_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_srai_epi32(a, imm) \ ++ _sse2neon_define0( \ ++ __m128i, a, __m128i ret; if (_sse2neon_unlikely((imm) == 0)) { \ ++ ret = _a; \ ++ } else if (_sse2neon_likely(0 < (imm) && (imm) < 32)) { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshlq_s32(vreinterpretq_s32_m128i(_a), vdupq_n_s32(-(imm)))); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshrq_n_s32(vreinterpretq_s32_m128i(_a), 31)); \ ++ } _sse2neon_return(ret);) ++ ++// Shift packed 16-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srl_epi16 ++FORCE_INLINE __m128i _mm_srl_epi16(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~15)) ++ return _mm_setzero_si128(); ++ ++ int16x8_t vc = vdupq_n_s16(-(int16_t) c); ++ return vreinterpretq_m128i_u16(vshlq_u16(vreinterpretq_u16_m128i(a), vc)); ++} ++ ++// Shift packed 32-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srl_epi32 ++FORCE_INLINE __m128i _mm_srl_epi32(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~31)) ++ return _mm_setzero_si128(); ++ ++ int32x4_t vc = vdupq_n_s32(-(int32_t) c); ++ return vreinterpretq_m128i_u32(vshlq_u32(vreinterpretq_u32_m128i(a), vc)); ++} ++ ++// Shift packed 64-bit integers in a right by count while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srl_epi64 ++FORCE_INLINE __m128i _mm_srl_epi64(__m128i a, __m128i count) ++{ ++ uint64_t c = vreinterpretq_nth_u64_m128i(count, 0); ++ if (_sse2neon_unlikely(c & ~63)) ++ return _mm_setzero_si128(); ++ ++ int64x2_t vc = vdupq_n_s64(-(int64_t) c); ++ return vreinterpretq_m128i_u64(vshlq_u64(vreinterpretq_u64_m128i(a), vc)); ++} ++ ++// Shift packed 16-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srli_epi16 ++#define _mm_srli_epi16(a, imm) \ ++ _sse2neon_define0( \ ++ __m128i, a, __m128i ret; if (_sse2neon_unlikely((imm) & ~15)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u16( \ ++ vshlq_u16(vreinterpretq_u16_m128i(_a), vdupq_n_s16(-(imm)))); \ ++ } _sse2neon_return(ret);) ++ ++// Shift packed 32-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srli_epi32 ++// FORCE_INLINE __m128i _mm_srli_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_srli_epi32(a, imm) \ ++ _sse2neon_define0( \ ++ __m128i, a, __m128i ret; if (_sse2neon_unlikely((imm) & ~31)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u32( \ ++ vshlq_u32(vreinterpretq_u32_m128i(_a), vdupq_n_s32(-(imm)))); \ ++ } _sse2neon_return(ret);) ++ ++// Shift packed 64-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srli_epi64 ++#define _mm_srli_epi64(a, imm) \ ++ _sse2neon_define0( \ ++ __m128i, a, __m128i ret; if (_sse2neon_unlikely((imm) & ~63)) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u64( \ ++ vshlq_u64(vreinterpretq_u64_m128i(_a), vdupq_n_s64(-(imm)))); \ ++ } _sse2neon_return(ret);) ++ ++// Shift a right by imm8 bytes while shifting in zeros, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_srli_si128 ++#define _mm_srli_si128(a, imm) \ ++ _sse2neon_define1( \ ++ __m128i, a, int8x16_t ret; \ ++ if (_sse2neon_unlikely((imm) & ~15)) ret = vdupq_n_s8(0); \ ++ else ret = vextq_s8(vreinterpretq_s8_m128i(_a), vdupq_n_s8(0), \ ++ (imm > 15 ? 0 : imm)); \ ++ _sse2neon_return(vreinterpretq_m128i_s8(ret));) ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory. mem_addr must be aligned on a 16-byte boundary ++// or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_pd ++FORCE_INLINE void _mm_store_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ vst1q_f64((float64_t *) mem_addr, vreinterpretq_f64_m128d(a)); ++#else ++ vst1q_f32((float32_t *) mem_addr, vreinterpretq_f32_m128d(a)); ++#endif ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// 2 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_pd1 ++FORCE_INLINE void _mm_store_pd1(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x1_t a_low = vget_low_f64(vreinterpretq_f64_m128d(a)); ++ vst1q_f64((float64_t *) mem_addr, ++ vreinterpretq_f64_m128d(vcombine_f64(a_low, a_low))); ++#else ++ float32x2_t a_low = vget_low_f32(vreinterpretq_f32_m128d(a)); ++ vst1q_f32((float32_t *) mem_addr, ++ vreinterpretq_f32_m128d(vcombine_f32(a_low, a_low))); ++#endif ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// memory. mem_addr does not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_store_sd ++FORCE_INLINE void _mm_store_sd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ vst1_f64((float64_t *) mem_addr, vget_low_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_u64((uint64_t *) mem_addr, vget_low_u64(vreinterpretq_u64_m128d(a))); ++#endif ++} ++ ++// Store 128-bits of integer data from a into memory. mem_addr must be aligned ++// on a 16-byte boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_store_si128 ++FORCE_INLINE void _mm_store_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, vreinterpretq_s32_m128i(a)); ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// 2 contiguous elements in memory. mem_addr must be aligned on a 16-byte ++// boundary or a general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#expand=9,526,5601&text=_mm_store1_pd ++#define _mm_store1_pd _mm_store_pd1 ++ ++// Store the upper double-precision (64-bit) floating-point element from a into ++// memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeh_pd ++FORCE_INLINE void _mm_storeh_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ vst1_f64((float64_t *) mem_addr, vget_high_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_f32((float32_t *) mem_addr, vget_high_f32(vreinterpretq_f32_m128d(a))); ++#endif ++} ++ ++// Store 64-bit integer from the first element of a into memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storel_epi64 ++FORCE_INLINE void _mm_storel_epi64(__m128i *a, __m128i b) ++{ ++ vst1_u64((uint64_t *) a, vget_low_u64(vreinterpretq_u64_m128i(b))); ++} ++ ++// Store the lower double-precision (64-bit) floating-point element from a into ++// memory. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storel_pd ++FORCE_INLINE void _mm_storel_pd(double *mem_addr, __m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ vst1_f64((float64_t *) mem_addr, vget_low_f64(vreinterpretq_f64_m128d(a))); ++#else ++ vst1_f32((float32_t *) mem_addr, vget_low_f32(vreinterpretq_f32_m128d(a))); ++#endif ++} ++ ++// Store 2 double-precision (64-bit) floating-point elements from a into memory ++// in reverse order. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storer_pd ++FORCE_INLINE void _mm_storer_pd(double *mem_addr, __m128d a) ++{ ++ float32x4_t f = vreinterpretq_f32_m128d(a); ++ _mm_store_pd(mem_addr, vreinterpretq_m128d_f32(vextq_f32(f, f, 2))); ++} ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory. mem_addr does not need to be aligned on any ++// particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_pd ++FORCE_INLINE void _mm_storeu_pd(double *mem_addr, __m128d a) ++{ ++ _mm_store_pd(mem_addr, a); ++} ++ ++// Store 128-bits of integer data from a into memory. mem_addr does not need to ++// be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_si128 ++FORCE_INLINE void _mm_storeu_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, vreinterpretq_s32_m128i(a)); ++} ++ ++// Store 32-bit integer from the first element of a into memory. mem_addr does ++// not need to be aligned on any particular boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_storeu_si32 ++FORCE_INLINE void _mm_storeu_si32(void *p, __m128i a) ++{ ++ vst1q_lane_s32((int32_t *) p, vreinterpretq_s32_m128i(a), 0); ++} ++ ++// Store 128-bits (composed of 2 packed double-precision (64-bit) floating-point ++// elements) from a into memory using a non-temporal memory hint. mem_addr must ++// be aligned on a 16-byte boundary or a general-protection exception may be ++// generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_pd ++FORCE_INLINE void _mm_stream_pd(double *p, __m128d a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, (__m128d *) p); ++#elif defined(__aarch64__) || defined(_M_ARM64) ++ vst1q_f64(p, vreinterpretq_f64_m128d(a)); ++#else ++ vst1q_s64((int64_t *) p, vreinterpretq_s64_m128d(a)); ++#endif ++} ++ ++// Store 128-bits of integer data from a into memory using a non-temporal memory ++// hint. mem_addr must be aligned on a 16-byte boundary or a general-protection ++// exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_si128 ++FORCE_INLINE void _mm_stream_si128(__m128i *p, __m128i a) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ __builtin_nontemporal_store(a, p); ++#else ++ vst1q_s64((int64_t *) p, vreinterpretq_s64_m128i(a)); ++#endif ++} ++ ++// Store 32-bit integer a into memory using a non-temporal hint to minimize ++// cache pollution. If the cache line containing address mem_addr is already in ++// the cache, the cache will be updated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_si32 ++FORCE_INLINE void _mm_stream_si32(int *p, int a) ++{ ++ vst1q_lane_s32((int32_t *) p, vdupq_n_s32(a), 0); ++} ++ ++// Store 64-bit integer a into memory using a non-temporal hint to minimize ++// cache pollution. If the cache line containing address mem_addr is already in ++// the cache, the cache will be updated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_si64 ++FORCE_INLINE void _mm_stream_si64(__int64 *p, __int64 a) ++{ ++ vst1_s64((int64_t *) p, vdup_n_s64((int64_t) a)); ++} ++ ++// Subtract packed 16-bit integers in b from packed 16-bit integers in a, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_epi16 ++FORCE_INLINE __m128i _mm_sub_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vsubq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Subtract packed 32-bit integers in b from packed 32-bit integers in a, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_epi32 ++FORCE_INLINE __m128i _mm_sub_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vsubq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Subtract packed 64-bit integers in b from packed 64-bit integers in a, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_epi64 ++FORCE_INLINE __m128i _mm_sub_epi64(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s64( ++ vsubq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++} ++ ++// Subtract packed 8-bit integers in b from packed 8-bit integers in a, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_epi8 ++FORCE_INLINE __m128i _mm_sub_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vsubq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Subtract packed double-precision (64-bit) floating-point elements in b from ++// packed double-precision (64-bit) floating-point elements in a, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_sub_pd ++FORCE_INLINE __m128d _mm_sub_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vsubq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ double c[2]; ++ c[0] = a0 - b0; ++ c[1] = a1 - b1; ++ return vld1q_f32((float32_t *) c); ++#endif ++} ++ ++// Subtract the lower double-precision (64-bit) floating-point element in b from ++// the lower double-precision (64-bit) floating-point element in a, store the ++// result in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_sd ++FORCE_INLINE __m128d _mm_sub_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_sub_pd(a, b)); ++} ++ ++// Subtract 64-bit integer b from 64-bit integer a, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sub_si64 ++FORCE_INLINE __m64 _mm_sub_si64(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s64( ++ vsub_s64(vreinterpret_s64_m64(a), vreinterpret_s64_m64(b))); ++} ++ ++// Subtract packed signed 16-bit integers in b from packed 16-bit integers in a ++// using saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_subs_epi16 ++FORCE_INLINE __m128i _mm_subs_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vqsubq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Subtract packed signed 8-bit integers in b from packed 8-bit integers in a ++// using saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_subs_epi8 ++FORCE_INLINE __m128i _mm_subs_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vqsubq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Subtract packed unsigned 16-bit integers in b from packed unsigned 16-bit ++// integers in a using saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_subs_epu16 ++FORCE_INLINE __m128i _mm_subs_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vqsubq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Subtract packed unsigned 8-bit integers in b from packed unsigned 8-bit ++// integers in a using saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_subs_epu8 ++FORCE_INLINE __m128i _mm_subs_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vqsubq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++#define _mm_ucomieq_sd _mm_comieq_sd ++#define _mm_ucomige_sd _mm_comige_sd ++#define _mm_ucomigt_sd _mm_comigt_sd ++#define _mm_ucomile_sd _mm_comile_sd ++#define _mm_ucomilt_sd _mm_comilt_sd ++#define _mm_ucomineq_sd _mm_comineq_sd ++ ++// Return vector of type __m128d with undefined elements. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_undefined_pd ++FORCE_INLINE __m128d _mm_undefined_pd(void) ++{ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wuninitialized" ++#endif ++ __m128d a; ++#if defined(_MSC_VER) && !defined(__clang__) ++ a = _mm_setzero_pd(); ++#endif ++ return a; ++#if defined(__GNUC__) || defined(__clang__) ++#pragma GCC diagnostic pop ++#endif ++} ++ ++// Unpack and interleave 16-bit integers from the high half of a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_epi16 ++FORCE_INLINE __m128i _mm_unpackhi_epi16(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16( ++ vzip2q_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++#else ++ int16x4_t a1 = vget_high_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b1 = vget_high_s16(vreinterpretq_s16_m128i(b)); ++ int16x4x2_t result = vzip_s16(a1, b1); ++ return vreinterpretq_m128i_s16(vcombine_s16(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave 32-bit integers from the high half of a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_epi32 ++FORCE_INLINE __m128i _mm_unpackhi_epi32(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s32( ++ vzip2q_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++#else ++ int32x2_t a1 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t b1 = vget_high_s32(vreinterpretq_s32_m128i(b)); ++ int32x2x2_t result = vzip_s32(a1, b1); ++ return vreinterpretq_m128i_s32(vcombine_s32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave 64-bit integers from the high half of a and b, and ++// store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_epi64 ++FORCE_INLINE __m128i _mm_unpackhi_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s64( ++ vzip2q_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++#else ++ int64x1_t a_h = vget_high_s64(vreinterpretq_s64_m128i(a)); ++ int64x1_t b_h = vget_high_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vcombine_s64(a_h, b_h)); ++#endif ++} ++ ++// Unpack and interleave 8-bit integers from the high half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_epi8 ++FORCE_INLINE __m128i _mm_unpackhi_epi8(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s8( ++ vzip2q_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++#else ++ int8x8_t a1 = ++ vreinterpret_s8_s16(vget_high_s16(vreinterpretq_s16_m128i(a))); ++ int8x8_t b1 = ++ vreinterpret_s8_s16(vget_high_s16(vreinterpretq_s16_m128i(b))); ++ int8x8x2_t result = vzip_s8(a1, b1); ++ return vreinterpretq_m128i_s8(vcombine_s8(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave double-precision (64-bit) floating-point elements from ++// the high half of a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpackhi_pd ++FORCE_INLINE __m128d _mm_unpackhi_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vzip2q_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ return vreinterpretq_m128d_s64( ++ vcombine_s64(vget_high_s64(vreinterpretq_s64_m128d(a)), ++ vget_high_s64(vreinterpretq_s64_m128d(b)))); ++#endif ++} ++ ++// Unpack and interleave 16-bit integers from the low half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_epi16 ++FORCE_INLINE __m128i _mm_unpacklo_epi16(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16( ++ vzip1q_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++#else ++ int16x4_t a1 = vget_low_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b1 = vget_low_s16(vreinterpretq_s16_m128i(b)); ++ int16x4x2_t result = vzip_s16(a1, b1); ++ return vreinterpretq_m128i_s16(vcombine_s16(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave 32-bit integers from the low half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_epi32 ++FORCE_INLINE __m128i _mm_unpacklo_epi32(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s32( ++ vzip1q_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++#else ++ int32x2_t a1 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t b1 = vget_low_s32(vreinterpretq_s32_m128i(b)); ++ int32x2x2_t result = vzip_s32(a1, b1); ++ return vreinterpretq_m128i_s32(vcombine_s32(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave 64-bit integers from the low half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_epi64 ++FORCE_INLINE __m128i _mm_unpacklo_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s64( ++ vzip1q_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++#else ++ int64x1_t a_l = vget_low_s64(vreinterpretq_s64_m128i(a)); ++ int64x1_t b_l = vget_low_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vcombine_s64(a_l, b_l)); ++#endif ++} ++ ++// Unpack and interleave 8-bit integers from the low half of a and b, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_epi8 ++FORCE_INLINE __m128i _mm_unpacklo_epi8(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s8( ++ vzip1q_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++#else ++ int8x8_t a1 = vreinterpret_s8_s16(vget_low_s16(vreinterpretq_s16_m128i(a))); ++ int8x8_t b1 = vreinterpret_s8_s16(vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int8x8x2_t result = vzip_s8(a1, b1); ++ return vreinterpretq_m128i_s8(vcombine_s8(result.val[0], result.val[1])); ++#endif ++} ++ ++// Unpack and interleave double-precision (64-bit) floating-point elements from ++// the low half of a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_unpacklo_pd ++FORCE_INLINE __m128d _mm_unpacklo_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vzip1q_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ return vreinterpretq_m128d_s64( ++ vcombine_s64(vget_low_s64(vreinterpretq_s64_m128d(a)), ++ vget_low_s64(vreinterpretq_s64_m128d(b)))); ++#endif ++} ++ ++// Compute the bitwise XOR of packed double-precision (64-bit) floating-point ++// elements in a and b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_xor_pd ++FORCE_INLINE __m128d _mm_xor_pd(__m128d a, __m128d b) ++{ ++ return vreinterpretq_m128d_s64( ++ veorq_s64(vreinterpretq_s64_m128d(a), vreinterpretq_s64_m128d(b))); ++} ++ ++// Compute the bitwise XOR of 128 bits (representing integer data) in a and b, ++// and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_xor_si128 ++FORCE_INLINE __m128i _mm_xor_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ veorq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++/* SSE3 */ ++ ++// Alternatively add and subtract packed double-precision (64-bit) ++// floating-point elements in a to/from packed elements in b, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_addsub_pd ++FORCE_INLINE __m128d _mm_addsub_pd(__m128d a, __m128d b) ++{ ++ _sse2neon_const __m128d mask = _mm_set_pd(1.0f, -1.0f); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vfmaq_f64(vreinterpretq_f64_m128d(a), ++ vreinterpretq_f64_m128d(b), ++ vreinterpretq_f64_m128d(mask))); ++#else ++ return _mm_add_pd(_mm_mul_pd(b, mask), a); ++#endif ++} ++ ++// Alternatively add and subtract packed single-precision (32-bit) ++// floating-point elements in a to/from packed elements in b, and store the ++// results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=addsub_ps ++FORCE_INLINE __m128 _mm_addsub_ps(__m128 a, __m128 b) ++{ ++ _sse2neon_const __m128 mask = _mm_setr_ps(-1.0f, 1.0f, -1.0f, 1.0f); ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_FMA) /* VFPv4+ */ ++ return vreinterpretq_m128_f32(vfmaq_f32(vreinterpretq_f32_m128(a), ++ vreinterpretq_f32_m128(mask), ++ vreinterpretq_f32_m128(b))); ++#else ++ return _mm_add_ps(_mm_mul_ps(b, mask), a); ++#endif ++} ++ ++// Horizontally add adjacent pairs of double-precision (64-bit) floating-point ++// elements in a and b, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_pd ++FORCE_INLINE __m128d _mm_hadd_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vpaddq_f64(vreinterpretq_f64_m128d(a), vreinterpretq_f64_m128d(b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ double c[] = {a0 + a1, b0 + b1}; ++ return vreinterpretq_m128d_u64(vld1q_u64((uint64_t *) c)); ++#endif ++} ++ ++// Horizontally add adjacent pairs of single-precision (32-bit) floating-point ++// elements in a and b, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_ps ++FORCE_INLINE __m128 _mm_hadd_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vpaddq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++#else ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vpadd_f32(a10, a32), vpadd_f32(b10, b32))); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of double-precision (64-bit) ++// floating-point elements in a and b, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_pd ++FORCE_INLINE __m128d _mm_hsub_pd(__m128d a, __m128d b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x2_t _a = vreinterpretq_f64_m128d(a); ++ float64x2_t _b = vreinterpretq_f64_m128d(b); ++ return vreinterpretq_m128d_f64( ++ vsubq_f64(vuzp1q_f64(_a, _b), vuzp2q_f64(_a, _b))); ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ double c[] = {a0 - a1, b0 - b1}; ++ return vreinterpretq_m128d_u64(vld1q_u64((uint64_t *) c)); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of single-precision (32-bit) ++// floating-point elements in a and b, and pack the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_ps ++FORCE_INLINE __m128 _mm_hsub_ps(__m128 _a, __m128 _b) ++{ ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vsubq_f32(vuzp1q_f32(a, b), vuzp2q_f32(a, b))); ++#else ++ float32x4x2_t c = vuzpq_f32(a, b); ++ return vreinterpretq_m128_f32(vsubq_f32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Load 128-bits of integer data from unaligned memory into dst. This intrinsic ++// may perform better than _mm_loadu_si128 when the data crosses a cache line ++// boundary. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_lddqu_si128 ++#define _mm_lddqu_si128 _mm_loadu_si128 ++ ++// Load a double-precision (64-bit) floating-point element from memory into both ++// elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_loaddup_pd ++#define _mm_loaddup_pd _mm_load1_pd ++ ++// Duplicate the low double-precision (64-bit) floating-point element from a, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movedup_pd ++FORCE_INLINE __m128d _mm_movedup_pd(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64( ++ vdupq_laneq_f64(vreinterpretq_f64_m128d(a), 0)); ++#else ++ return vreinterpretq_m128d_u64( ++ vdupq_n_u64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0))); ++#endif ++} ++ ++// Duplicate odd-indexed single-precision (32-bit) floating-point elements ++// from a, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_movehdup_ps ++FORCE_INLINE __m128 _mm_movehdup_ps(__m128 a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vtrn2q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a))); ++#elif defined(_sse2neon_shuffle) ++ return vreinterpretq_m128_f32(vshuffleq_s32( ++ vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 1, 1, 3, 3)); ++#else ++ float32_t a1 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 1); ++ float32_t a3 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 3); ++ float ALIGN_STRUCT(16) data[4] = {a1, a1, a3, a3}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++#endif ++} ++ ++// Duplicate even-indexed single-precision (32-bit) floating-point elements ++// from a, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_moveldup_ps ++FORCE_INLINE __m128 _mm_moveldup_ps(__m128 a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128_f32( ++ vtrn1q_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a))); ++#elif defined(_sse2neon_shuffle) ++ return vreinterpretq_m128_f32(vshuffleq_s32( ++ vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 0, 0, 2, 2)); ++#else ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ float32_t a2 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 2); ++ float ALIGN_STRUCT(16) data[4] = {a0, a0, a2, a2}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++#endif ++} ++ ++/* SSSE3 */ ++ ++// Compute the absolute value of packed signed 16-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_epi16 ++FORCE_INLINE __m128i _mm_abs_epi16(__m128i a) ++{ ++ return vreinterpretq_m128i_s16(vabsq_s16(vreinterpretq_s16_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 32-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_epi32 ++FORCE_INLINE __m128i _mm_abs_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_s32(vabsq_s32(vreinterpretq_s32_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 8-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_epi8 ++FORCE_INLINE __m128i _mm_abs_epi8(__m128i a) ++{ ++ return vreinterpretq_m128i_s8(vabsq_s8(vreinterpretq_s8_m128i(a))); ++} ++ ++// Compute the absolute value of packed signed 16-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_pi16 ++FORCE_INLINE __m64 _mm_abs_pi16(__m64 a) ++{ ++ return vreinterpret_m64_s16(vabs_s16(vreinterpret_s16_m64(a))); ++} ++ ++// Compute the absolute value of packed signed 32-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_pi32 ++FORCE_INLINE __m64 _mm_abs_pi32(__m64 a) ++{ ++ return vreinterpret_m64_s32(vabs_s32(vreinterpret_s32_m64(a))); ++} ++ ++// Compute the absolute value of packed signed 8-bit integers in a, and store ++// the unsigned results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_abs_pi8 ++FORCE_INLINE __m64 _mm_abs_pi8(__m64 a) ++{ ++ return vreinterpret_m64_s8(vabs_s8(vreinterpret_s8_m64(a))); ++} ++ ++// Concatenate 16-byte blocks in a and b into a 32-byte temporary result, shift ++// the result right by imm8 bytes, and store the low 16 bytes in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_alignr_epi8 ++#if defined(__GNUC__) && !defined(__clang__) ++#define _mm_alignr_epi8(a, b, imm) \ ++ __extension__({ \ ++ uint8x16_t _a = vreinterpretq_u8_m128i(a); \ ++ uint8x16_t _b = vreinterpretq_u8_m128i(b); \ ++ __m128i ret; \ ++ if (_sse2neon_unlikely((imm) & ~31)) \ ++ ret = vreinterpretq_m128i_u8(vdupq_n_u8(0)); \ ++ else if (imm >= 16) \ ++ ret = _mm_srli_si128(a, imm >= 16 ? imm - 16 : 0); \ ++ else \ ++ ret = \ ++ vreinterpretq_m128i_u8(vextq_u8(_b, _a, imm < 16 ? imm : 0)); \ ++ ret; \ ++ }) ++ ++#else ++#define _mm_alignr_epi8(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m128i, a, b, uint8x16_t __a = vreinterpretq_u8_m128i(_a); \ ++ uint8x16_t __b = vreinterpretq_u8_m128i(_b); __m128i ret; \ ++ if (_sse2neon_unlikely((imm) & ~31)) ret = \ ++ vreinterpretq_m128i_u8(vdupq_n_u8(0)); \ ++ else if (imm >= 16) ret = \ ++ _mm_srli_si128(_a, imm >= 16 ? imm - 16 : 0); \ ++ else ret = \ ++ vreinterpretq_m128i_u8(vextq_u8(__b, __a, imm < 16 ? imm : 0)); \ ++ _sse2neon_return(ret);) ++ ++#endif ++ ++// Concatenate 8-byte blocks in a and b into a 16-byte temporary result, shift ++// the result right by imm8 bytes, and store the low 8 bytes in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_alignr_pi8 ++#define _mm_alignr_pi8(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m64, a, b, __m64 ret; if (_sse2neon_unlikely((imm) >= 16)) { \ ++ ret = vreinterpret_m64_s8(vdup_n_s8(0)); \ ++ } else { \ ++ uint8x8_t tmp_low; \ ++ uint8x8_t tmp_high; \ ++ if ((imm) >= 8) { \ ++ const int idx = (imm) -8; \ ++ tmp_low = vreinterpret_u8_m64(_a); \ ++ tmp_high = vdup_n_u8(0); \ ++ ret = vreinterpret_m64_u8(vext_u8(tmp_low, tmp_high, idx)); \ ++ } else { \ ++ const int idx = (imm); \ ++ tmp_low = vreinterpret_u8_m64(_b); \ ++ tmp_high = vreinterpret_u8_m64(_a); \ ++ ret = vreinterpret_m64_u8(vext_u8(tmp_low, tmp_high, idx)); \ ++ } \ ++ } _sse2neon_return(ret);) ++ ++// Horizontally add adjacent pairs of 16-bit integers in a and b, and pack the ++// signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_epi16 ++FORCE_INLINE __m128i _mm_hadd_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16(vpaddq_s16(a, b)); ++#else ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vpadd_s16(vget_low_s16(a), vget_high_s16(a)), ++ vpadd_s16(vget_low_s16(b), vget_high_s16(b)))); ++#endif ++} ++ ++// Horizontally add adjacent pairs of 32-bit integers in a and b, and pack the ++// signed 32-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_epi32 ++FORCE_INLINE __m128i _mm_hadd_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s32(vpaddq_s32(a, b)); ++#else ++ return vreinterpretq_m128i_s32( ++ vcombine_s32(vpadd_s32(vget_low_s32(a), vget_high_s32(a)), ++ vpadd_s32(vget_low_s32(b), vget_high_s32(b)))); ++#endif ++} ++ ++// Horizontally add adjacent pairs of 16-bit integers in a and b, and pack the ++// signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_pi16 ++FORCE_INLINE __m64 _mm_hadd_pi16(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s16( ++ vpadd_s16(vreinterpret_s16_m64(a), vreinterpret_s16_m64(b))); ++} ++ ++// Horizontally add adjacent pairs of 32-bit integers in a and b, and pack the ++// signed 32-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadd_pi32 ++FORCE_INLINE __m64 _mm_hadd_pi32(__m64 a, __m64 b) ++{ ++ return vreinterpret_m64_s32( ++ vpadd_s32(vreinterpret_s32_m64(a), vreinterpret_s32_m64(b))); ++} ++ ++// Horizontally add adjacent pairs of signed 16-bit integers in a and b using ++// saturation, and pack the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadds_epi16 ++FORCE_INLINE __m128i _mm_hadds_epi16(__m128i _a, __m128i _b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ return vreinterpretq_s64_s16( ++ vqaddq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++ // Interleave using vshrn/vmovn ++ // [a0|a2|a4|a6|b0|b2|b4|b6] ++ // [a1|a3|a5|a7|b1|b3|b5|b7] ++ int16x8_t ab0246 = vcombine_s16(vmovn_s32(a), vmovn_s32(b)); ++ int16x8_t ab1357 = vcombine_s16(vshrn_n_s32(a, 16), vshrn_n_s32(b, 16)); ++ // Saturated add ++ return vreinterpretq_m128i_s16(vqaddq_s16(ab0246, ab1357)); ++#endif ++} ++ ++// Horizontally add adjacent pairs of signed 16-bit integers in a and b using ++// saturation, and pack the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hadds_pi16 ++FORCE_INLINE __m64 _mm_hadds_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpret_s64_s16(vqadd_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t res = vuzp_s16(a, b); ++ return vreinterpret_s64_s16(vqadd_s16(res.val[0], res.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 16-bit integers in a and b, and pack ++// the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_epi16 ++FORCE_INLINE __m128i _mm_hsub_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16( ++ vsubq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int16x8x2_t c = vuzpq_s16(a, b); ++ return vreinterpretq_m128i_s16(vsubq_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 32-bit integers in a and b, and pack ++// the signed 32-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_epi32 ++FORCE_INLINE __m128i _mm_hsub_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s32( ++ vsubq_s32(vuzp1q_s32(a, b), vuzp2q_s32(a, b))); ++#else ++ int32x4x2_t c = vuzpq_s32(a, b); ++ return vreinterpretq_m128i_s32(vsubq_s32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 16-bit integers in a and b, and pack ++// the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsub_pi16 ++FORCE_INLINE __m64 _mm_hsub_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpret_m64_s16(vsub_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t c = vuzp_s16(a, b); ++ return vreinterpret_m64_s16(vsub_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of 32-bit integers in a and b, and pack ++// the signed 32-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_hsub_pi32 ++FORCE_INLINE __m64 _mm_hsub_pi32(__m64 _a, __m64 _b) ++{ ++ int32x2_t a = vreinterpret_s32_m64(_a); ++ int32x2_t b = vreinterpret_s32_m64(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpret_m64_s32(vsub_s32(vuzp1_s32(a, b), vuzp2_s32(a, b))); ++#else ++ int32x2x2_t c = vuzp_s32(a, b); ++ return vreinterpret_m64_s32(vsub_s32(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of signed 16-bit integers in a and b ++// using saturation, and pack the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsubs_epi16 ++FORCE_INLINE __m128i _mm_hsubs_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s16( ++ vqsubq_s16(vuzp1q_s16(a, b), vuzp2q_s16(a, b))); ++#else ++ int16x8x2_t c = vuzpq_s16(a, b); ++ return vreinterpretq_m128i_s16(vqsubq_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Horizontally subtract adjacent pairs of signed 16-bit integers in a and b ++// using saturation, and pack the signed 16-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_hsubs_pi16 ++FORCE_INLINE __m64 _mm_hsubs_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpret_m64_s16(vqsub_s16(vuzp1_s16(a, b), vuzp2_s16(a, b))); ++#else ++ int16x4x2_t c = vuzp_s16(a, b); ++ return vreinterpret_m64_s16(vqsub_s16(c.val[0], c.val[1])); ++#endif ++} ++ ++// Vertically multiply each unsigned 8-bit integer from a with the corresponding ++// signed 8-bit integer from b, producing intermediate signed 16-bit integers. ++// Horizontally add adjacent pairs of intermediate signed 16-bit integers, ++// and pack the saturated results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_maddubs_epi16 ++FORCE_INLINE __m128i _mm_maddubs_epi16(__m128i _a, __m128i _b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint8x16_t a = vreinterpretq_u8_m128i(_a); ++ int8x16_t b = vreinterpretq_s8_m128i(_b); ++ int16x8_t tl = vmulq_s16(vreinterpretq_s16_u16(vmovl_u8(vget_low_u8(a))), ++ vmovl_s8(vget_low_s8(b))); ++ int16x8_t th = vmulq_s16(vreinterpretq_s16_u16(vmovl_u8(vget_high_u8(a))), ++ vmovl_s8(vget_high_s8(b))); ++ return vreinterpretq_m128i_s16( ++ vqaddq_s16(vuzp1q_s16(tl, th), vuzp2q_s16(tl, th))); ++#else ++ // This would be much simpler if x86 would choose to zero extend OR sign ++ // extend, not both. This could probably be optimized better. ++ uint16x8_t a = vreinterpretq_u16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ ++ // Zero extend a ++ int16x8_t a_odd = vreinterpretq_s16_u16(vshrq_n_u16(a, 8)); ++ int16x8_t a_even = vreinterpretq_s16_u16(vbicq_u16(a, vdupq_n_u16(0xff00))); ++ ++ // Sign extend by shifting left then shifting right. ++ int16x8_t b_even = vshrq_n_s16(vshlq_n_s16(b, 8), 8); ++ int16x8_t b_odd = vshrq_n_s16(b, 8); ++ ++ // multiply ++ int16x8_t prod1 = vmulq_s16(a_even, b_even); ++ int16x8_t prod2 = vmulq_s16(a_odd, b_odd); ++ ++ // saturated add ++ return vreinterpretq_m128i_s16(vqaddq_s16(prod1, prod2)); ++#endif ++} ++ ++// Vertically multiply each unsigned 8-bit integer from a with the corresponding ++// signed 8-bit integer from b, producing intermediate signed 16-bit integers. ++// Horizontally add adjacent pairs of intermediate signed 16-bit integers, and ++// pack the saturated results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_maddubs_pi16 ++FORCE_INLINE __m64 _mm_maddubs_pi16(__m64 _a, __m64 _b) ++{ ++ uint16x4_t a = vreinterpret_u16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++ ++ // Zero extend a ++ int16x4_t a_odd = vreinterpret_s16_u16(vshr_n_u16(a, 8)); ++ int16x4_t a_even = vreinterpret_s16_u16(vand_u16(a, vdup_n_u16(0xff))); ++ ++ // Sign extend by shifting left then shifting right. ++ int16x4_t b_even = vshr_n_s16(vshl_n_s16(b, 8), 8); ++ int16x4_t b_odd = vshr_n_s16(b, 8); ++ ++ // multiply ++ int16x4_t prod1 = vmul_s16(a_even, b_even); ++ int16x4_t prod2 = vmul_s16(a_odd, b_odd); ++ ++ // saturated add ++ return vreinterpret_m64_s16(vqadd_s16(prod1, prod2)); ++} ++ ++// Multiply packed signed 16-bit integers in a and b, producing intermediate ++// signed 32-bit integers. Shift right by 15 bits while rounding up, and store ++// the packed 16-bit integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhrs_epi16 ++FORCE_INLINE __m128i _mm_mulhrs_epi16(__m128i a, __m128i b) ++{ ++ // Has issues due to saturation ++ // return vreinterpretq_m128i_s16(vqrdmulhq_s16(a, b)); ++ ++ // Multiply ++ int32x4_t mul_lo = vmull_s16(vget_low_s16(vreinterpretq_s16_m128i(a)), ++ vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int32x4_t mul_hi = vmull_s16(vget_high_s16(vreinterpretq_s16_m128i(a)), ++ vget_high_s16(vreinterpretq_s16_m128i(b))); ++ ++ // Rounding narrowing shift right ++ // narrow = (int16_t)((mul + 16384) >> 15); ++ int16x4_t narrow_lo = vrshrn_n_s32(mul_lo, 15); ++ int16x4_t narrow_hi = vrshrn_n_s32(mul_hi, 15); ++ ++ // Join together ++ return vreinterpretq_m128i_s16(vcombine_s16(narrow_lo, narrow_hi)); ++} ++ ++// Multiply packed signed 16-bit integers in a and b, producing intermediate ++// signed 32-bit integers. Truncate each intermediate integer to the 18 most ++// significant bits, round by adding 1, and store bits [16:1] to dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mulhrs_pi16 ++FORCE_INLINE __m64 _mm_mulhrs_pi16(__m64 a, __m64 b) ++{ ++ int32x4_t mul_extend = ++ vmull_s16((vreinterpret_s16_m64(a)), (vreinterpret_s16_m64(b))); ++ ++ // Rounding narrowing shift right ++ return vreinterpret_m64_s16(vrshrn_n_s32(mul_extend, 15)); ++} ++ ++// Shuffle packed 8-bit integers in a according to shuffle control mask in the ++// corresponding 8-bit element of b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_epi8 ++FORCE_INLINE __m128i _mm_shuffle_epi8(__m128i a, __m128i b) ++{ ++ int8x16_t tbl = vreinterpretq_s8_m128i(a); // input a ++ uint8x16_t idx = vreinterpretq_u8_m128i(b); // input b ++ uint8x16_t idx_masked = ++ vandq_u8(idx, vdupq_n_u8(0x8F)); // avoid using meaningless bits ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_s8(vqtbl1q_s8(tbl, idx_masked)); ++#elif defined(__GNUC__) ++ int8x16_t ret; ++ // %e and %f represent the even and odd D registers ++ // respectively. ++ __asm__ __volatile__( ++ "vtbl.8 %e[ret], {%e[tbl], %f[tbl]}, %e[idx]\n" ++ "vtbl.8 %f[ret], {%e[tbl], %f[tbl]}, %f[idx]\n" ++ : [ret] "=&w"(ret) ++ : [tbl] "w"(tbl), [idx] "w"(idx_masked)); ++ return vreinterpretq_m128i_s8(ret); ++#else ++ // use this line if testing on aarch64 ++ int8x8x2_t a_split = {vget_low_s8(tbl), vget_high_s8(tbl)}; ++ return vreinterpretq_m128i_s8( ++ vcombine_s8(vtbl2_s8(a_split, vget_low_u8(idx_masked)), ++ vtbl2_s8(a_split, vget_high_u8(idx_masked)))); ++#endif ++} ++ ++// Shuffle packed 8-bit integers in a according to shuffle control mask in the ++// corresponding 8-bit element of b, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_shuffle_pi8 ++FORCE_INLINE __m64 _mm_shuffle_pi8(__m64 a, __m64 b) ++{ ++ const int8x8_t controlMask = ++ vand_s8(vreinterpret_s8_m64(b), vdup_n_s8((int8_t) (0x1 << 7 | 0x07))); ++ int8x8_t res = vtbl1_s8(vreinterpret_s8_m64(a), controlMask); ++ return vreinterpret_m64_s8(res); ++} ++ ++// Negate packed 16-bit integers in a when the corresponding signed ++// 16-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_epi16 ++FORCE_INLINE __m128i _mm_sign_epi16(__m128i _a, __m128i _b) ++{ ++ int16x8_t a = vreinterpretq_s16_m128i(_a); ++ int16x8_t b = vreinterpretq_s16_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFF : 0 ++ uint16x8_t ltMask = vreinterpretq_u16_s16(vshrq_n_s16(b, 15)); ++ // (b == 0) ? 0xFFFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int16x8_t zeroMask = vreinterpretq_s16_u16(vceqzq_s16(b)); ++#else ++ int16x8_t zeroMask = vreinterpretq_s16_u16(vceqq_s16(b, vdupq_n_s16(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s16(a) equals to negative ++ // 'a') based on ltMask ++ int16x8_t masked = vbslq_s16(ltMask, vnegq_s16(a), a); ++ // res = masked & (~zeroMask) ++ int16x8_t res = vbicq_s16(masked, zeroMask); ++ return vreinterpretq_m128i_s16(res); ++} ++ ++// Negate packed 32-bit integers in a when the corresponding signed ++// 32-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_epi32 ++FORCE_INLINE __m128i _mm_sign_epi32(__m128i _a, __m128i _b) ++{ ++ int32x4_t a = vreinterpretq_s32_m128i(_a); ++ int32x4_t b = vreinterpretq_s32_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFFFFFF : 0 ++ uint32x4_t ltMask = vreinterpretq_u32_s32(vshrq_n_s32(b, 31)); ++ ++ // (b == 0) ? 0xFFFFFFFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int32x4_t zeroMask = vreinterpretq_s32_u32(vceqzq_s32(b)); ++#else ++ int32x4_t zeroMask = vreinterpretq_s32_u32(vceqq_s32(b, vdupq_n_s32(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s32(a) equals to negative ++ // 'a') based on ltMask ++ int32x4_t masked = vbslq_s32(ltMask, vnegq_s32(a), a); ++ // res = masked & (~zeroMask) ++ int32x4_t res = vbicq_s32(masked, zeroMask); ++ return vreinterpretq_m128i_s32(res); ++} ++ ++// Negate packed 8-bit integers in a when the corresponding signed ++// 8-bit integer in b is negative, and store the results in dst. ++// Element in dst are zeroed out when the corresponding element ++// in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_epi8 ++FORCE_INLINE __m128i _mm_sign_epi8(__m128i _a, __m128i _b) ++{ ++ int8x16_t a = vreinterpretq_s8_m128i(_a); ++ int8x16_t b = vreinterpretq_s8_m128i(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFF : 0 ++ uint8x16_t ltMask = vreinterpretq_u8_s8(vshrq_n_s8(b, 7)); ++ ++ // (b == 0) ? 0xFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int8x16_t zeroMask = vreinterpretq_s8_u8(vceqzq_s8(b)); ++#else ++ int8x16_t zeroMask = vreinterpretq_s8_u8(vceqq_s8(b, vdupq_n_s8(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vnegq_s8(a) return negative 'a') ++ // based on ltMask ++ int8x16_t masked = vbslq_s8(ltMask, vnegq_s8(a), a); ++ // res = masked & (~zeroMask) ++ int8x16_t res = vbicq_s8(masked, zeroMask); ++ ++ return vreinterpretq_m128i_s8(res); ++} ++ ++// Negate packed 16-bit integers in a when the corresponding signed 16-bit ++// integer in b is negative, and store the results in dst. Element in dst are ++// zeroed out when the corresponding element in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_pi16 ++FORCE_INLINE __m64 _mm_sign_pi16(__m64 _a, __m64 _b) ++{ ++ int16x4_t a = vreinterpret_s16_m64(_a); ++ int16x4_t b = vreinterpret_s16_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFF : 0 ++ uint16x4_t ltMask = vreinterpret_u16_s16(vshr_n_s16(b, 15)); ++ ++ // (b == 0) ? 0xFFFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int16x4_t zeroMask = vreinterpret_s16_u16(vceqz_s16(b)); ++#else ++ int16x4_t zeroMask = vreinterpret_s16_u16(vceq_s16(b, vdup_n_s16(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s16(a) return negative 'a') ++ // based on ltMask ++ int16x4_t masked = vbsl_s16(ltMask, vneg_s16(a), a); ++ // res = masked & (~zeroMask) ++ int16x4_t res = vbic_s16(masked, zeroMask); ++ ++ return vreinterpret_m64_s16(res); ++} ++ ++// Negate packed 32-bit integers in a when the corresponding signed 32-bit ++// integer in b is negative, and store the results in dst. Element in dst are ++// zeroed out when the corresponding element in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_pi32 ++FORCE_INLINE __m64 _mm_sign_pi32(__m64 _a, __m64 _b) ++{ ++ int32x2_t a = vreinterpret_s32_m64(_a); ++ int32x2_t b = vreinterpret_s32_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFFFFFFFF : 0 ++ uint32x2_t ltMask = vreinterpret_u32_s32(vshr_n_s32(b, 31)); ++ ++ // (b == 0) ? 0xFFFFFFFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int32x2_t zeroMask = vreinterpret_s32_u32(vceqz_s32(b)); ++#else ++ int32x2_t zeroMask = vreinterpret_s32_u32(vceq_s32(b, vdup_n_s32(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s32(a) return negative 'a') ++ // based on ltMask ++ int32x2_t masked = vbsl_s32(ltMask, vneg_s32(a), a); ++ // res = masked & (~zeroMask) ++ int32x2_t res = vbic_s32(masked, zeroMask); ++ ++ return vreinterpret_m64_s32(res); ++} ++ ++// Negate packed 8-bit integers in a when the corresponding signed 8-bit integer ++// in b is negative, and store the results in dst. Element in dst are zeroed out ++// when the corresponding element in b is zero. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_sign_pi8 ++FORCE_INLINE __m64 _mm_sign_pi8(__m64 _a, __m64 _b) ++{ ++ int8x8_t a = vreinterpret_s8_m64(_a); ++ int8x8_t b = vreinterpret_s8_m64(_b); ++ ++ // signed shift right: faster than vclt ++ // (b < 0) ? 0xFF : 0 ++ uint8x8_t ltMask = vreinterpret_u8_s8(vshr_n_s8(b, 7)); ++ ++ // (b == 0) ? 0xFF : 0 ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int8x8_t zeroMask = vreinterpret_s8_u8(vceqz_s8(b)); ++#else ++ int8x8_t zeroMask = vreinterpret_s8_u8(vceq_s8(b, vdup_n_s8(0))); ++#endif ++ ++ // bitwise select either a or negative 'a' (vneg_s8(a) return negative 'a') ++ // based on ltMask ++ int8x8_t masked = vbsl_s8(ltMask, vneg_s8(a), a); ++ // res = masked & (~zeroMask) ++ int8x8_t res = vbic_s8(masked, zeroMask); ++ ++ return vreinterpret_m64_s8(res); ++} ++ ++/* SSE4.1 */ ++ ++// Blend packed 16-bit integers from a and b using control mask imm8, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blend_epi16 ++// FORCE_INLINE __m128i _mm_blend_epi16(__m128i a, __m128i b, ++// __constrange(0,255) int imm) ++#define _mm_blend_epi16(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m128i, a, b, \ ++ const uint16_t _mask[8] = \ ++ _sse2neon_init(((imm) & (1 << 0)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 1)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 2)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 3)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 4)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 5)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 6)) ? (uint16_t) -1 : 0x0, \ ++ ((imm) & (1 << 7)) ? (uint16_t) -1 : 0x0); \ ++ uint16x8_t _mask_vec = vld1q_u16(_mask); \ ++ uint16x8_t __a = vreinterpretq_u16_m128i(_a); \ ++ uint16x8_t __b = vreinterpretq_u16_m128i(_b); _sse2neon_return( \ ++ vreinterpretq_m128i_u16(vbslq_u16(_mask_vec, __b, __a)));) ++ ++// Blend packed double-precision (64-bit) floating-point elements from a and b ++// using control mask imm8, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blend_pd ++#define _mm_blend_pd(a, b, imm) \ ++ _sse2neon_define2( \ ++ __m128d, a, b, \ ++ const uint64_t _mask[2] = \ ++ _sse2neon_init(((imm) & (1 << 0)) ? ~UINT64_C(0) : UINT64_C(0), \ ++ ((imm) & (1 << 1)) ? ~UINT64_C(0) : UINT64_C(0)); \ ++ uint64x2_t _mask_vec = vld1q_u64(_mask); \ ++ uint64x2_t __a = vreinterpretq_u64_m128d(_a); \ ++ uint64x2_t __b = vreinterpretq_u64_m128d(_b); _sse2neon_return( \ ++ vreinterpretq_m128d_u64(vbslq_u64(_mask_vec, __b, __a)));) ++ ++// Blend packed single-precision (32-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blend_ps ++FORCE_INLINE __m128 _mm_blend_ps(__m128 _a, __m128 _b, const char imm8) ++{ ++ const uint32_t ALIGN_STRUCT(16) ++ data[4] = {((imm8) & (1 << 0)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 1)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 2)) ? UINT32_MAX : 0, ++ ((imm8) & (1 << 3)) ? UINT32_MAX : 0}; ++ uint32x4_t mask = vld1q_u32(data); ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++ return vreinterpretq_m128_f32(vbslq_f32(mask, b, a)); ++} ++ ++// Blend packed 8-bit integers from a and b using mask, and store the results in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blendv_epi8 ++FORCE_INLINE __m128i _mm_blendv_epi8(__m128i _a, __m128i _b, __m128i _mask) ++{ ++ // Use a signed shift right to create a mask with the sign bit ++ uint8x16_t mask = ++ vreinterpretq_u8_s8(vshrq_n_s8(vreinterpretq_s8_m128i(_mask), 7)); ++ uint8x16_t a = vreinterpretq_u8_m128i(_a); ++ uint8x16_t b = vreinterpretq_u8_m128i(_b); ++ return vreinterpretq_m128i_u8(vbslq_u8(mask, b, a)); ++} ++ ++// Blend packed double-precision (64-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blendv_pd ++FORCE_INLINE __m128d _mm_blendv_pd(__m128d _a, __m128d _b, __m128d _mask) ++{ ++ uint64x2_t mask = ++ vreinterpretq_u64_s64(vshrq_n_s64(vreinterpretq_s64_m128d(_mask), 63)); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ float64x2_t a = vreinterpretq_f64_m128d(_a); ++ float64x2_t b = vreinterpretq_f64_m128d(_b); ++ return vreinterpretq_m128d_f64(vbslq_f64(mask, b, a)); ++#else ++ uint64x2_t a = vreinterpretq_u64_m128d(_a); ++ uint64x2_t b = vreinterpretq_u64_m128d(_b); ++ return vreinterpretq_m128d_u64(vbslq_u64(mask, b, a)); ++#endif ++} ++ ++// Blend packed single-precision (32-bit) floating-point elements from a and b ++// using mask, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_blendv_ps ++FORCE_INLINE __m128 _mm_blendv_ps(__m128 _a, __m128 _b, __m128 _mask) ++{ ++ // Use a signed shift right to create a mask with the sign bit ++ uint32x4_t mask = ++ vreinterpretq_u32_s32(vshrq_n_s32(vreinterpretq_s32_m128(_mask), 31)); ++ float32x4_t a = vreinterpretq_f32_m128(_a); ++ float32x4_t b = vreinterpretq_f32_m128(_b); ++ return vreinterpretq_m128_f32(vbslq_f32(mask, b, a)); ++} ++ ++// Round the packed double-precision (64-bit) floating-point elements in a up ++// to an integer value, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_ceil_pd ++FORCE_INLINE __m128d _mm_ceil_pd(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vrndpq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double a0, a1; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ return _mm_set_pd(ceil(a1), ceil(a0)); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a up to ++// an integer value, and store the results as packed single-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_ceil_ps ++FORCE_INLINE __m128 _mm_ceil_ps(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpretq_m128_f32(vrndpq_f32(vreinterpretq_f32_m128(a))); ++#else ++ float *f = (float *) &a; ++ return _mm_set_ps(ceilf(f[3]), ceilf(f[2]), ceilf(f[1]), ceilf(f[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b up to ++// an integer value, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_ceil_sd ++FORCE_INLINE __m128d _mm_ceil_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_ceil_pd(b)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b up to ++// an integer value, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_ceil_ss ++FORCE_INLINE __m128 _mm_ceil_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_ceil_ps(b)); ++} ++ ++// Compare packed 64-bit integers in a and b for equality, and store the results ++// in dst ++FORCE_INLINE __m128i _mm_cmpeq_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_u64( ++ vceqq_u64(vreinterpretq_u64_m128i(a), vreinterpretq_u64_m128i(b))); ++#else ++ // ARMv7 lacks vceqq_u64 ++ // (a == b) -> (a_lo == b_lo) && (a_hi == b_hi) ++ uint32x4_t cmp = ++ vceqq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b)); ++ uint32x4_t swapped = vrev64q_u32(cmp); ++ return vreinterpretq_m128i_u32(vandq_u32(cmp, swapped)); ++#endif ++} ++ ++// Sign extend packed 16-bit integers in a to packed 32-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi16_epi32 ++FORCE_INLINE __m128i _mm_cvtepi16_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vmovl_s16(vget_low_s16(vreinterpretq_s16_m128i(a)))); ++} ++ ++// Sign extend packed 16-bit integers in a to packed 64-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi16_epi64 ++FORCE_INLINE __m128i _mm_cvtepi16_epi64(__m128i a) ++{ ++ int16x8_t s16x8 = vreinterpretq_s16_m128i(a); /* xxxx xxxx xxxx 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000x 000x 000B 000A */ ++ int64x2_t s64x2 = vmovl_s32(vget_low_s32(s32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_s64(s64x2); ++} ++ ++// Sign extend packed 32-bit integers in a to packed 64-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi32_epi64 ++FORCE_INLINE __m128i _mm_cvtepi32_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_s64( ++ vmovl_s32(vget_low_s32(vreinterpretq_s32_m128i(a)))); ++} ++ ++// Sign extend packed 8-bit integers in a to packed 16-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi8_epi16 ++FORCE_INLINE __m128i _mm_cvtepi8_epi16(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ return vreinterpretq_m128i_s16(s16x8); ++} ++ ++// Sign extend packed 8-bit integers in a to packed 32-bit integers, and store ++// the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi8_epi32 ++FORCE_INLINE __m128i _mm_cvtepi8_epi32(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000D 000C 000B 000A */ ++ return vreinterpretq_m128i_s32(s32x4); ++} ++ ++// Sign extend packed 8-bit integers in the low 8 bytes of a to packed 64-bit ++// integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepi8_epi64 ++FORCE_INLINE __m128i _mm_cvtepi8_epi64(__m128i a) ++{ ++ int8x16_t s8x16 = vreinterpretq_s8_m128i(a); /* xxxx xxxx xxxx xxBA */ ++ int16x8_t s16x8 = vmovl_s8(vget_low_s8(s8x16)); /* 0x0x 0x0x 0x0x 0B0A */ ++ int32x4_t s32x4 = vmovl_s16(vget_low_s16(s16x8)); /* 000x 000x 000B 000A */ ++ int64x2_t s64x2 = vmovl_s32(vget_low_s32(s32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_s64(s64x2); ++} ++ ++// Zero extend packed unsigned 16-bit integers in a to packed 32-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu16_epi32 ++FORCE_INLINE __m128i _mm_cvtepu16_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_u32( ++ vmovl_u16(vget_low_u16(vreinterpretq_u16_m128i(a)))); ++} ++ ++// Zero extend packed unsigned 16-bit integers in a to packed 64-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu16_epi64 ++FORCE_INLINE __m128i _mm_cvtepu16_epi64(__m128i a) ++{ ++ uint16x8_t u16x8 = vreinterpretq_u16_m128i(a); /* xxxx xxxx xxxx 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000x 000x 000B 000A */ ++ uint64x2_t u64x2 = vmovl_u32(vget_low_u32(u32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_u64(u64x2); ++} ++ ++// Zero extend packed unsigned 32-bit integers in a to packed 64-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu32_epi64 ++FORCE_INLINE __m128i _mm_cvtepu32_epi64(__m128i a) ++{ ++ return vreinterpretq_m128i_u64( ++ vmovl_u32(vget_low_u32(vreinterpretq_u32_m128i(a)))); ++} ++ ++// Zero extend packed unsigned 8-bit integers in a to packed 16-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu8_epi16 ++FORCE_INLINE __m128i _mm_cvtepu8_epi16(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx HGFE DCBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0H0G 0F0E 0D0C 0B0A */ ++ return vreinterpretq_m128i_u16(u16x8); ++} ++ ++// Zero extend packed unsigned 8-bit integers in a to packed 32-bit integers, ++// and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu8_epi32 ++FORCE_INLINE __m128i _mm_cvtepu8_epi32(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx xxxx DCBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000D 000C 000B 000A */ ++ return vreinterpretq_m128i_u32(u32x4); ++} ++ ++// Zero extend packed unsigned 8-bit integers in the low 8 bytes of a to packed ++// 64-bit integers, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cvtepu8_epi64 ++FORCE_INLINE __m128i _mm_cvtepu8_epi64(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_m128i(a); /* xxxx xxxx xxxx xxBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0x0x 0x0x 0x0x 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000x 000x 000B 000A */ ++ uint64x2_t u64x2 = vmovl_u32(vget_low_u32(u32x4)); /* 0000 000B 0000 000A */ ++ return vreinterpretq_m128i_u64(u64x2); ++} ++ ++// Conditionally multiply the packed double-precision (64-bit) floating-point ++// elements in a and b using the high 4 bits in imm8, sum the four products, and ++// conditionally store the sum in dst using the low 4 bits of imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_dp_pd ++FORCE_INLINE __m128d _mm_dp_pd(__m128d a, __m128d b, const int imm) ++{ ++ // Generate mask value from constant immediate bit value ++ const int64_t bit0Mask = imm & 0x01 ? UINT64_MAX : 0; ++ const int64_t bit1Mask = imm & 0x02 ? UINT64_MAX : 0; ++#if !SSE2NEON_PRECISE_DP ++ const int64_t bit4Mask = imm & 0x10 ? UINT64_MAX : 0; ++ const int64_t bit5Mask = imm & 0x20 ? UINT64_MAX : 0; ++#endif ++ // Conditional multiplication ++#if !SSE2NEON_PRECISE_DP ++ __m128d mul = _mm_mul_pd(a, b); ++ const __m128d mulMask = ++ _mm_castsi128_pd(_mm_set_epi64x(bit5Mask, bit4Mask)); ++ __m128d tmp = _mm_and_pd(mul, mulMask); ++#else ++#if defined(__aarch64__) || defined(_M_ARM64) ++ double d0 = (imm & 0x10) ? vgetq_lane_f64(vreinterpretq_f64_m128d(a), 0) * ++ vgetq_lane_f64(vreinterpretq_f64_m128d(b), 0) ++ : 0; ++ double d1 = (imm & 0x20) ? vgetq_lane_f64(vreinterpretq_f64_m128d(a), 1) * ++ vgetq_lane_f64(vreinterpretq_f64_m128d(b), 1) ++ : 0; ++#else ++ double a0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ double a1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ double b0 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 0)); ++ double b1 = ++ sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(b), 1)); ++ double d0 = (imm & 0x10) ? a0 * b0 : 0; ++ double d1 = (imm & 0x20) ? a1 * b1 : 0; ++#endif ++ __m128d tmp = _mm_set_pd(d1, d0); ++#endif ++ // Sum the products ++#if defined(__aarch64__) || defined(_M_ARM64) ++ double sum = vpaddd_f64(vreinterpretq_f64_m128d(tmp)); ++#else ++ double _tmp0 = sse2neon_recast_u64_f64( ++ vgetq_lane_u64(vreinterpretq_u64_m128d(tmp), 0)); ++ double _tmp1 = sse2neon_recast_u64_f64( ++ vgetq_lane_u64(vreinterpretq_u64_m128d(tmp), 1)); ++ double sum = _tmp0 + _tmp1; ++#endif ++ // Conditionally store the sum ++ const __m128d sumMask = ++ _mm_castsi128_pd(_mm_set_epi64x(bit1Mask, bit0Mask)); ++ __m128d res = _mm_and_pd(_mm_set_pd1(sum), sumMask); ++ return res; ++} ++ ++// Conditionally multiply the packed single-precision (32-bit) floating-point ++// elements in a and b using the high 4 bits in imm8, sum the four products, ++// and conditionally store the sum in dst using the low 4 bits of imm. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_dp_ps ++FORCE_INLINE __m128 _mm_dp_ps(__m128 a, __m128 b, const int imm) ++{ ++ float32x4_t elementwise_prod = _mm_mul_ps(a, b); ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ /* shortcuts */ ++ if (imm == 0xFF) { ++ return _mm_set1_ps(vaddvq_f32(elementwise_prod)); ++ } ++ ++ if ((imm & 0x0F) == 0x0F) { ++ if (!(imm & (1 << 4))) ++ elementwise_prod = vsetq_lane_f32(0.0f, elementwise_prod, 0); ++ if (!(imm & (1 << 5))) ++ elementwise_prod = vsetq_lane_f32(0.0f, elementwise_prod, 1); ++ if (!(imm & (1 << 6))) ++ elementwise_prod = vsetq_lane_f32(0.0f, elementwise_prod, 2); ++ if (!(imm & (1 << 7))) ++ elementwise_prod = vsetq_lane_f32(0.0f, elementwise_prod, 3); ++ ++ return _mm_set1_ps(vaddvq_f32(elementwise_prod)); ++ } ++#endif ++ ++ float s = 0.0f; ++ ++ if (imm & (1 << 4)) ++ s += vgetq_lane_f32(elementwise_prod, 0); ++ if (imm & (1 << 5)) ++ s += vgetq_lane_f32(elementwise_prod, 1); ++ if (imm & (1 << 6)) ++ s += vgetq_lane_f32(elementwise_prod, 2); ++ if (imm & (1 << 7)) ++ s += vgetq_lane_f32(elementwise_prod, 3); ++ ++ const float32_t res[4] = { ++ (imm & 0x1) ? s : 0.0f, ++ (imm & 0x2) ? s : 0.0f, ++ (imm & 0x4) ? s : 0.0f, ++ (imm & 0x8) ? s : 0.0f, ++ }; ++ return vreinterpretq_m128_f32(vld1q_f32(res)); ++} ++ ++// Extract a 32-bit integer from a, selected with imm8, and store the result in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi32 ++// FORCE_INLINE int _mm_extract_epi32(__m128i a, __constrange(0,4) int imm) ++#define _mm_extract_epi32(a, imm) \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm)) ++ ++// Extract a 64-bit integer from a, selected with imm8, and store the result in ++// dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi64 ++// FORCE_INLINE __int64 _mm_extract_epi64(__m128i a, __constrange(0,2) int imm) ++#define _mm_extract_epi64(a, imm) \ ++ vgetq_lane_s64(vreinterpretq_s64_m128i(a), (imm)) ++ ++// Extract an 8-bit integer from a, selected with imm8, and store the result in ++// the lower element of dst. FORCE_INLINE int _mm_extract_epi8(__m128i a, ++// __constrange(0,16) int imm) ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi8 ++#define _mm_extract_epi8(a, imm) vgetq_lane_u8(vreinterpretq_u8_m128i(a), (imm)) ++ ++// Extracts the selected single-precision (32-bit) floating-point from a. ++// FORCE_INLINE int _mm_extract_ps(__m128 a, __constrange(0,4) int imm) ++#define _mm_extract_ps(a, imm) vgetq_lane_s32(vreinterpretq_s32_m128(a), (imm)) ++ ++// Round the packed double-precision (64-bit) floating-point elements in a down ++// to an integer value, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_floor_pd ++FORCE_INLINE __m128d _mm_floor_pd(__m128d a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128d_f64(vrndmq_f64(vreinterpretq_f64_m128d(a))); ++#else ++ double a0, a1; ++ a0 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 0)); ++ a1 = sse2neon_recast_u64_f64(vgetq_lane_u64(vreinterpretq_u64_m128d(a), 1)); ++ return _mm_set_pd(floor(a1), floor(a0)); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a down ++// to an integer value, and store the results as packed single-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_floor_ps ++FORCE_INLINE __m128 _mm_floor_ps(__m128 a) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ return vreinterpretq_m128_f32(vrndmq_f32(vreinterpretq_f32_m128(a))); ++#else ++ float *f = (float *) &a; ++ return _mm_set_ps(floorf(f[3]), floorf(f[2]), floorf(f[1]), floorf(f[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b down to ++// an integer value, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_floor_sd ++FORCE_INLINE __m128d _mm_floor_sd(__m128d a, __m128d b) ++{ ++ return _mm_move_sd(a, _mm_floor_pd(b)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b down to ++// an integer value, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_floor_ss ++FORCE_INLINE __m128 _mm_floor_ss(__m128 a, __m128 b) ++{ ++ return _mm_move_ss(a, _mm_floor_ps(b)); ++} ++ ++// Copy a to dst, and insert the 32-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_epi32 ++// FORCE_INLINE __m128i _mm_insert_epi32(__m128i a, int b, ++// __constrange(0,4) int imm) ++#define _mm_insert_epi32(a, b, imm) \ ++ vreinterpretq_m128i_s32( \ ++ vsetq_lane_s32((b), vreinterpretq_s32_m128i(a), (imm))) ++ ++// Copy a to dst, and insert the 64-bit integer i into dst at the location ++// specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_epi64 ++// FORCE_INLINE __m128i _mm_insert_epi64(__m128i a, __int64 b, ++// __constrange(0,2) int imm) ++#define _mm_insert_epi64(a, b, imm) \ ++ vreinterpretq_m128i_s64( \ ++ vsetq_lane_s64((b), vreinterpretq_s64_m128i(a), (imm))) ++ ++// Copy a to dst, and insert the lower 8-bit integer from i into dst at the ++// location specified by imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_insert_epi8 ++// FORCE_INLINE __m128i _mm_insert_epi8(__m128i a, int b, ++// __constrange(0,16) int imm) ++#define _mm_insert_epi8(a, b, imm) \ ++ vreinterpretq_m128i_s8(vsetq_lane_s8((b), vreinterpretq_s8_m128i(a), (imm))) ++ ++// Copy a to tmp, then insert a single-precision (32-bit) floating-point ++// element from b into tmp using the control in imm8. Store tmp to dst using ++// the mask in imm8 (elements are zeroed out when the corresponding bit is set). ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=insert_ps ++#define _mm_insert_ps(a, b, imm8) \ ++ _sse2neon_define2( \ ++ __m128, a, b, \ ++ float32x4_t tmp1 = \ ++ vsetq_lane_f32(vgetq_lane_f32(_b, (imm8 >> 6) & 0x3), \ ++ vreinterpretq_f32_m128(_a), 0); \ ++ float32x4_t tmp2 = \ ++ vsetq_lane_f32(vgetq_lane_f32(tmp1, 0), \ ++ vreinterpretq_f32_m128(_a), ((imm8 >> 4) & 0x3)); \ ++ const uint32_t data[4] = \ ++ _sse2neon_init(((imm8) & (1 << 0)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 1)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 2)) ? UINT32_MAX : 0, \ ++ ((imm8) & (1 << 3)) ? UINT32_MAX : 0); \ ++ uint32x4_t mask = vld1q_u32(data); \ ++ float32x4_t all_zeros = vdupq_n_f32(0); \ ++ \ ++ _sse2neon_return(vreinterpretq_m128_f32( \ ++ vbslq_f32(mask, all_zeros, vreinterpretq_f32_m128(tmp2))));) ++ ++// Compare packed signed 32-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epi32 ++FORCE_INLINE __m128i _mm_max_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vmaxq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epi8 ++FORCE_INLINE __m128i _mm_max_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vmaxq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed unsigned 16-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epu16 ++FORCE_INLINE __m128i _mm_max_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vmaxq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Compare packed unsigned 32-bit integers in a and b, and store packed maximum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epu32 ++FORCE_INLINE __m128i _mm_max_epu32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vmaxq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b))); ++} ++ ++// Compare packed signed 32-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epi32 ++FORCE_INLINE __m128i _mm_min_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vminq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compare packed signed 8-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epi8 ++FORCE_INLINE __m128i _mm_min_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vminq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compare packed unsigned 16-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_min_epu16 ++FORCE_INLINE __m128i _mm_min_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vminq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Compare packed unsigned 32-bit integers in a and b, and store packed minimum ++// values in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_max_epu32 ++FORCE_INLINE __m128i _mm_min_epu32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vminq_u32(vreinterpretq_u32_m128i(a), vreinterpretq_u32_m128i(b))); ++} ++ ++// Horizontally compute the minimum amongst the packed unsigned 16-bit integers ++// in a, store the minimum and index in dst, and zero the remaining bits in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_minpos_epu16 ++FORCE_INLINE __m128i _mm_minpos_epu16(__m128i a) ++{ ++ __m128i dst; ++ uint16_t min, idx = 0; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ // Find the minimum value ++ min = vminvq_u16(vreinterpretq_u16_m128i(a)); ++ ++ // Get the index of the minimum value ++ static const uint16_t idxv[] = {0, 1, 2, 3, 4, 5, 6, 7}; ++ uint16x8_t minv = vdupq_n_u16(min); ++ uint16x8_t cmeq = vceqq_u16(minv, vreinterpretq_u16_m128i(a)); ++ idx = vminvq_u16(vornq_u16(vld1q_u16(idxv), cmeq)); ++#else ++ // Find the minimum value ++ __m64 tmp; ++ tmp = vreinterpret_m64_u16( ++ vmin_u16(vget_low_u16(vreinterpretq_u16_m128i(a)), ++ vget_high_u16(vreinterpretq_u16_m128i(a)))); ++ tmp = vreinterpret_m64_u16( ++ vpmin_u16(vreinterpret_u16_m64(tmp), vreinterpret_u16_m64(tmp))); ++ tmp = vreinterpret_m64_u16( ++ vpmin_u16(vreinterpret_u16_m64(tmp), vreinterpret_u16_m64(tmp))); ++ min = vget_lane_u16(vreinterpret_u16_m64(tmp), 0); ++ // Get the index of the minimum value ++ int i; ++ for (i = 0; i < 8; i++) { ++ if (min == vgetq_lane_u16(vreinterpretq_u16_m128i(a), 0)) { ++ idx = (uint16_t) i; ++ break; ++ } ++ a = _mm_srli_si128(a, 2); ++ } ++#endif ++ // Generate result ++ dst = _mm_setzero_si128(); ++ dst = vreinterpretq_m128i_u16( ++ vsetq_lane_u16(min, vreinterpretq_u16_m128i(dst), 0)); ++ dst = vreinterpretq_m128i_u16( ++ vsetq_lane_u16(idx, vreinterpretq_u16_m128i(dst), 1)); ++ return dst; ++} ++ ++// Compute the sum of absolute differences (SADs) of quadruplets of unsigned ++// 8-bit integers in a compared to those in b, and store the 16-bit results in ++// dst. Eight SADs are performed using one quadruplet from b and eight ++// quadruplets from a. One quadruplet is selected from b starting at on the ++// offset specified in imm8. Eight quadruplets are formed from sequential 8-bit ++// integers selected from a starting at the offset specified in imm8. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mpsadbw_epu8 ++FORCE_INLINE __m128i _mm_mpsadbw_epu8(__m128i a, __m128i b, const int imm) ++{ ++ uint8x16_t _a, _b; ++ ++ switch (imm & 0x4) { ++ case 0: ++ // do nothing ++ _a = vreinterpretq_u8_m128i(a); ++ break; ++ case 4: ++ _a = vreinterpretq_u8_u32(vextq_u32(vreinterpretq_u32_m128i(a), ++ vreinterpretq_u32_m128i(a), 1)); ++ break; ++ default: ++#if defined(__GNUC__) || defined(__clang__) ++ __builtin_unreachable(); ++#elif defined(_MSC_VER) ++ __assume(0); ++#endif ++ break; ++ } ++ ++ switch (imm & 0x3) { ++ case 0: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 0))); ++ break; ++ case 1: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 1))); ++ break; ++ case 2: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 2))); ++ break; ++ case 3: ++ _b = vreinterpretq_u8_u32( ++ vdupq_n_u32(vgetq_lane_u32(vreinterpretq_u32_m128i(b), 3))); ++ break; ++ default: ++#if defined(__GNUC__) || defined(__clang__) ++ __builtin_unreachable(); ++#elif defined(_MSC_VER) ++ __assume(0); ++#endif ++ break; ++ } ++ ++ int16x8_t c04, c15, c26, c37; ++ uint8x8_t low_b = vget_low_u8(_b); ++ c04 = vreinterpretq_s16_u16(vabdl_u8(vget_low_u8(_a), low_b)); ++ uint8x16_t _a_1 = vextq_u8(_a, _a, 1); ++ c15 = vreinterpretq_s16_u16(vabdl_u8(vget_low_u8(_a_1), low_b)); ++ uint8x16_t _a_2 = vextq_u8(_a, _a, 2); ++ c26 = vreinterpretq_s16_u16(vabdl_u8(vget_low_u8(_a_2), low_b)); ++ uint8x16_t _a_3 = vextq_u8(_a, _a, 3); ++ c37 = vreinterpretq_s16_u16(vabdl_u8(vget_low_u8(_a_3), low_b)); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ // |0|4|2|6| ++ c04 = vpaddq_s16(c04, c26); ++ // |1|5|3|7| ++ c15 = vpaddq_s16(c15, c37); ++ ++ int32x4_t trn1_c = ++ vtrn1q_s32(vreinterpretq_s32_s16(c04), vreinterpretq_s32_s16(c15)); ++ int32x4_t trn2_c = ++ vtrn2q_s32(vreinterpretq_s32_s16(c04), vreinterpretq_s32_s16(c15)); ++ return vreinterpretq_m128i_s16(vpaddq_s16(vreinterpretq_s16_s32(trn1_c), ++ vreinterpretq_s16_s32(trn2_c))); ++#else ++ int16x4_t c01, c23, c45, c67; ++ c01 = vpadd_s16(vget_low_s16(c04), vget_low_s16(c15)); ++ c23 = vpadd_s16(vget_low_s16(c26), vget_low_s16(c37)); ++ c45 = vpadd_s16(vget_high_s16(c04), vget_high_s16(c15)); ++ c67 = vpadd_s16(vget_high_s16(c26), vget_high_s16(c37)); ++ ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vpadd_s16(c01, c23), vpadd_s16(c45, c67))); ++#endif ++} ++ ++// Multiply the low signed 32-bit integers from each packed 64-bit element in ++// a and b, and store the signed 64-bit results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mul_epi32 ++FORCE_INLINE __m128i _mm_mul_epi32(__m128i a, __m128i b) ++{ ++ // vmull_s32 upcasts instead of masking, so we downcast. ++ int32x2_t a_lo = vmovn_s64(vreinterpretq_s64_m128i(a)); ++ int32x2_t b_lo = vmovn_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vmull_s32(a_lo, b_lo)); ++} ++ ++// Multiply the packed 32-bit integers in a and b, producing intermediate 64-bit ++// integers, and store the low 32 bits of the intermediate integers in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_mullo_epi32 ++FORCE_INLINE __m128i _mm_mullo_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vmulq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Convert packed signed 32-bit integers from a and b to packed 16-bit integers ++// using unsigned saturation, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_packus_epi32 ++FORCE_INLINE __m128i _mm_packus_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcombine_u16(vqmovun_s32(vreinterpretq_s32_m128i(a)), ++ vqmovun_s32(vreinterpretq_s32_m128i(b)))); ++} ++ ++// Round the packed double-precision (64-bit) floating-point elements in a using ++// the rounding parameter, and store the results as packed double-precision ++// floating-point elements in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_round_pd ++FORCE_INLINE_OPTNONE __m128d _mm_round_pd(__m128d a, int rounding) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ switch (rounding) { ++ case (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128d_f64(vrndnq_f64(vreinterpretq_f64_m128d(a))); ++ case (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC): ++ return _mm_floor_pd(a); ++ case (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC): ++ return _mm_ceil_pd(a); ++ case (_MM_FROUND_TO_ZERO | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128d_f64(vrndq_f64(vreinterpretq_f64_m128d(a))); ++ default: //_MM_FROUND_CUR_DIRECTION ++ return vreinterpretq_m128d_f64(vrndiq_f64(vreinterpretq_f64_m128d(a))); ++ } ++#else ++ double *v_double = (double *) &a; ++ ++ if (rounding == (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_NEAREST)) { ++ double res[2], tmp; ++ for (int i = 0; i < 2; i++) { ++ tmp = (v_double[i] < 0) ? -v_double[i] : v_double[i]; ++ double roundDown = floor(tmp); // Round down value ++ double roundUp = ceil(tmp); // Round up value ++ double diffDown = tmp - roundDown; ++ double diffUp = roundUp - tmp; ++ if (diffDown < diffUp) { ++ /* If it's closer to the round down value, then use it */ ++ res[i] = roundDown; ++ } else if (diffDown > diffUp) { ++ /* If it's closer to the round up value, then use it */ ++ res[i] = roundUp; ++ } else { ++ /* If it's equidistant between round up and round down value, ++ * pick the one which is an even number */ ++ double half = roundDown / 2; ++ if (half != floor(half)) { ++ /* If the round down value is odd, return the round up value ++ */ ++ res[i] = roundUp; ++ } else { ++ /* If the round up value is odd, return the round down value ++ */ ++ res[i] = roundDown; ++ } ++ } ++ res[i] = (v_double[i] < 0) ? -res[i] : res[i]; ++ } ++ return _mm_set_pd(res[1], res[0]); ++ } else if (rounding == (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_DOWN)) { ++ return _mm_floor_pd(a); ++ } else if (rounding == (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_UP)) { ++ return _mm_ceil_pd(a); ++ } ++ return _mm_set_pd(v_double[1] > 0 ? floor(v_double[1]) : ceil(v_double[1]), ++ v_double[0] > 0 ? floor(v_double[0]) : ceil(v_double[0])); ++#endif ++} ++ ++// Round the packed single-precision (32-bit) floating-point elements in a using ++// the rounding parameter, and store the results as packed single-precision ++// floating-point elements in dst. ++// software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_round_ps ++FORCE_INLINE_OPTNONE __m128 _mm_round_ps(__m128 a, int rounding) ++{ ++#if (defined(__aarch64__) || defined(_M_ARM64)) || \ ++ defined(__ARM_FEATURE_DIRECTED_ROUNDING) ++ switch (rounding) { ++ case (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128_f32(vrndnq_f32(vreinterpretq_f32_m128(a))); ++ case (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC): ++ return _mm_floor_ps(a); ++ case (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC): ++ return _mm_ceil_ps(a); ++ case (_MM_FROUND_TO_ZERO | _MM_FROUND_NO_EXC): ++ return vreinterpretq_m128_f32(vrndq_f32(vreinterpretq_f32_m128(a))); ++ default: //_MM_FROUND_CUR_DIRECTION ++ return vreinterpretq_m128_f32(vrndiq_f32(vreinterpretq_f32_m128(a))); ++ } ++#else ++ float *v_float = (float *) &a; ++ ++ if (rounding == (_MM_FROUND_TO_NEAREST_INT | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_NEAREST)) { ++ uint32x4_t signmask = vdupq_n_u32(0x80000000); ++ float32x4_t half = vbslq_f32(signmask, vreinterpretq_f32_m128(a), ++ vdupq_n_f32(0.5f)); /* +/- 0.5 */ ++ int32x4_t r_normal = vcvtq_s32_f32(vaddq_f32( ++ vreinterpretq_f32_m128(a), half)); /* round to integer: [a + 0.5]*/ ++ int32x4_t r_trunc = vcvtq_s32_f32( ++ vreinterpretq_f32_m128(a)); /* truncate to integer: [a] */ ++ int32x4_t plusone = vreinterpretq_s32_u32(vshrq_n_u32( ++ vreinterpretq_u32_s32(vnegq_s32(r_trunc)), 31)); /* 1 or 0 */ ++ int32x4_t r_even = vbicq_s32(vaddq_s32(r_trunc, plusone), ++ vdupq_n_s32(1)); /* ([a] + {0,1}) & ~1 */ ++ float32x4_t delta = vsubq_f32( ++ vreinterpretq_f32_m128(a), ++ vcvtq_f32_s32(r_trunc)); /* compute delta: delta = (a - [a]) */ ++ uint32x4_t is_delta_half = ++ vceqq_f32(delta, half); /* delta == +/- 0.5 */ ++ return vreinterpretq_m128_f32( ++ vcvtq_f32_s32(vbslq_s32(is_delta_half, r_even, r_normal))); ++ } else if (rounding == (_MM_FROUND_TO_NEG_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_DOWN)) { ++ return _mm_floor_ps(a); ++ } else if (rounding == (_MM_FROUND_TO_POS_INF | _MM_FROUND_NO_EXC) || ++ (rounding == _MM_FROUND_CUR_DIRECTION && ++ _MM_GET_ROUNDING_MODE() == _MM_ROUND_UP)) { ++ return _mm_ceil_ps(a); ++ } ++ return _mm_set_ps(v_float[3] > 0 ? floorf(v_float[3]) : ceilf(v_float[3]), ++ v_float[2] > 0 ? floorf(v_float[2]) : ceilf(v_float[2]), ++ v_float[1] > 0 ? floorf(v_float[1]) : ceilf(v_float[1]), ++ v_float[0] > 0 ? floorf(v_float[0]) : ceilf(v_float[0])); ++#endif ++} ++ ++// Round the lower double-precision (64-bit) floating-point element in b using ++// the rounding parameter, store the result as a double-precision floating-point ++// element in the lower element of dst, and copy the upper element from a to the ++// upper element of dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_round_sd ++FORCE_INLINE __m128d _mm_round_sd(__m128d a, __m128d b, int rounding) ++{ ++ return _mm_move_sd(a, _mm_round_pd(b, rounding)); ++} ++ ++// Round the lower single-precision (32-bit) floating-point element in b using ++// the rounding parameter, store the result as a single-precision floating-point ++// element in the lower element of dst, and copy the upper 3 packed elements ++// from a to the upper elements of dst. Rounding is done according to the ++// rounding[3:0] parameter, which can be one of: ++// (_MM_FROUND_TO_NEAREST_INT |_MM_FROUND_NO_EXC) // round to nearest, and ++// suppress exceptions ++// (_MM_FROUND_TO_NEG_INF |_MM_FROUND_NO_EXC) // round down, and ++// suppress exceptions ++// (_MM_FROUND_TO_POS_INF |_MM_FROUND_NO_EXC) // round up, and suppress ++// exceptions ++// (_MM_FROUND_TO_ZERO |_MM_FROUND_NO_EXC) // truncate, and suppress ++// exceptions _MM_FROUND_CUR_DIRECTION // use MXCSR.RC; see ++// _MM_SET_ROUNDING_MODE ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_round_ss ++FORCE_INLINE __m128 _mm_round_ss(__m128 a, __m128 b, int rounding) ++{ ++ return _mm_move_ss(a, _mm_round_ps(b, rounding)); ++} ++ ++// Load 128-bits of integer data from memory into dst using a non-temporal ++// memory hint. mem_addr must be aligned on a 16-byte boundary or a ++// general-protection exception may be generated. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_stream_load_si128 ++FORCE_INLINE __m128i _mm_stream_load_si128(__m128i *p) ++{ ++#if __has_builtin(__builtin_nontemporal_store) ++ return __builtin_nontemporal_load(p); ++#else ++ return vreinterpretq_m128i_s64(vld1q_s64((int64_t *) p)); ++#endif ++} ++ ++// Compute the bitwise NOT of a and then AND with a 128-bit vector containing ++// all 1's, and return 1 if the result is zero, otherwise return 0. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_test_all_ones ++FORCE_INLINE int _mm_test_all_ones(__m128i a) ++{ ++ return (uint64_t) (vgetq_lane_s64(a, 0) & vgetq_lane_s64(a, 1)) == ++ ~(uint64_t) 0; ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and ++// mask, and return 1 if the result is zero, otherwise return 0. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_test_all_zeros ++FORCE_INLINE int _mm_test_all_zeros(__m128i a, __m128i mask) ++{ ++ int64x2_t a_and_mask = ++ vandq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(mask)); ++ return !(vgetq_lane_s64(a_and_mask, 0) | vgetq_lane_s64(a_and_mask, 1)); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and ++// mask, and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute ++// the bitwise NOT of a and then AND with mask, and set CF to 1 if the result is ++// zero, otherwise set CF to 0. Return 1 if both the ZF and CF values are zero, ++// otherwise return 0. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=mm_test_mix_ones_zero ++// Note: Argument names may be wrong in the Intel intrinsics guide. ++FORCE_INLINE int _mm_test_mix_ones_zeros(__m128i a, __m128i mask) ++{ ++ uint64x2_t v = vreinterpretq_u64_m128i(a); ++ uint64x2_t m = vreinterpretq_u64_m128i(mask); ++ ++ // find ones (set-bits) and zeros (clear-bits) under clip mask ++ uint64x2_t ones = vandq_u64(m, v); ++ uint64x2_t zeros = vbicq_u64(m, v); ++ ++ // If both 128-bit variables are populated (non-zero) then return 1. ++ // For comparison purposes, first compact each var down to 32-bits. ++ uint32x2_t reduced = vpmax_u32(vqmovn_u64(ones), vqmovn_u64(zeros)); ++ ++ // if folding minimum is non-zero then both vars must be non-zero ++ return (vget_lane_u32(vpmin_u32(reduced, reduced), 0) != 0); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return the CF value. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_testc_si128 ++FORCE_INLINE int _mm_testc_si128(__m128i a, __m128i b) ++{ ++ int64x2_t s64 = ++ vbicq_s64(vreinterpretq_s64_m128i(b), vreinterpretq_s64_m128i(a)); ++ return !(vgetq_lane_s64(s64, 0) | vgetq_lane_s64(s64, 1)); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return 1 if both the ZF and CF values are zero, ++// otherwise return 0. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_testnzc_si128 ++#define _mm_testnzc_si128(a, b) _mm_test_mix_ones_zeros(a, b) ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and b, ++// and set ZF to 1 if the result is zero, otherwise set ZF to 0. Compute the ++// bitwise NOT of a and then AND with b, and set CF to 1 if the result is zero, ++// otherwise set CF to 0. Return the ZF value. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_testz_si128 ++FORCE_INLINE int _mm_testz_si128(__m128i a, __m128i b) ++{ ++ int64x2_t s64 = ++ vandq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b)); ++ return !(vgetq_lane_s64(s64, 0) | vgetq_lane_s64(s64, 1)); ++} ++ ++/* SSE4.2 */ ++ ++static const uint16_t ALIGN_STRUCT(16) _sse2neon_cmpestr_mask16b[8] = { ++ 0x01, 0x02, 0x04, 0x08, 0x10, 0x20, 0x40, 0x80, ++}; ++static const uint8_t ALIGN_STRUCT(16) _sse2neon_cmpestr_mask8b[16] = { ++ 0x01, 0x02, 0x04, 0x08, 0x10, 0x20, 0x40, 0x80, ++ 0x01, 0x02, 0x04, 0x08, 0x10, 0x20, 0x40, 0x80, ++}; ++ ++/* specify the source data format */ ++#define _SIDD_UBYTE_OPS 0x00 /* unsigned 8-bit characters */ ++#define _SIDD_UWORD_OPS 0x01 /* unsigned 16-bit characters */ ++#define _SIDD_SBYTE_OPS 0x02 /* signed 8-bit characters */ ++#define _SIDD_SWORD_OPS 0x03 /* signed 16-bit characters */ ++ ++/* specify the comparison operation */ ++#define _SIDD_CMP_EQUAL_ANY 0x00 /* compare equal any: strchr */ ++#define _SIDD_CMP_RANGES 0x04 /* compare ranges */ ++#define _SIDD_CMP_EQUAL_EACH 0x08 /* compare equal each: strcmp */ ++#define _SIDD_CMP_EQUAL_ORDERED 0x0C /* compare equal ordered */ ++ ++/* specify the polarity */ ++#define _SIDD_POSITIVE_POLARITY 0x00 ++#define _SIDD_MASKED_POSITIVE_POLARITY 0x20 ++#define _SIDD_NEGATIVE_POLARITY 0x10 /* negate results */ ++#define _SIDD_MASKED_NEGATIVE_POLARITY \ ++ 0x30 /* negate results only before end of string */ ++ ++/* specify the output selection in _mm_cmpXstri */ ++#define _SIDD_LEAST_SIGNIFICANT 0x00 ++#define _SIDD_MOST_SIGNIFICANT 0x40 ++ ++/* specify the output selection in _mm_cmpXstrm */ ++#define _SIDD_BIT_MASK 0x00 ++#define _SIDD_UNIT_MASK 0x40 ++ ++/* Pattern Matching for C macros. ++ * https://github.com/pfultz2/Cloak/wiki/C-Preprocessor-tricks,-tips,-and-idioms ++ */ ++ ++/* catenate */ ++#define SSE2NEON_PRIMITIVE_CAT(a, ...) a##__VA_ARGS__ ++#define SSE2NEON_CAT(a, b) SSE2NEON_PRIMITIVE_CAT(a, b) ++ ++#define SSE2NEON_IIF(c) SSE2NEON_PRIMITIVE_CAT(SSE2NEON_IIF_, c) ++/* run the 2nd parameter */ ++#define SSE2NEON_IIF_0(t, ...) __VA_ARGS__ ++/* run the 1st parameter */ ++#define SSE2NEON_IIF_1(t, ...) t ++ ++#define SSE2NEON_COMPL(b) SSE2NEON_PRIMITIVE_CAT(SSE2NEON_COMPL_, b) ++#define SSE2NEON_COMPL_0 1 ++#define SSE2NEON_COMPL_1 0 ++ ++#define SSE2NEON_DEC(x) SSE2NEON_PRIMITIVE_CAT(SSE2NEON_DEC_, x) ++#define SSE2NEON_DEC_1 0 ++#define SSE2NEON_DEC_2 1 ++#define SSE2NEON_DEC_3 2 ++#define SSE2NEON_DEC_4 3 ++#define SSE2NEON_DEC_5 4 ++#define SSE2NEON_DEC_6 5 ++#define SSE2NEON_DEC_7 6 ++#define SSE2NEON_DEC_8 7 ++#define SSE2NEON_DEC_9 8 ++#define SSE2NEON_DEC_10 9 ++#define SSE2NEON_DEC_11 10 ++#define SSE2NEON_DEC_12 11 ++#define SSE2NEON_DEC_13 12 ++#define SSE2NEON_DEC_14 13 ++#define SSE2NEON_DEC_15 14 ++#define SSE2NEON_DEC_16 15 ++ ++/* detection */ ++#define SSE2NEON_CHECK_N(x, n, ...) n ++#define SSE2NEON_CHECK(...) SSE2NEON_CHECK_N(__VA_ARGS__, 0, ) ++#define SSE2NEON_PROBE(x) x, 1, ++ ++#define SSE2NEON_NOT(x) SSE2NEON_CHECK(SSE2NEON_PRIMITIVE_CAT(SSE2NEON_NOT_, x)) ++#define SSE2NEON_NOT_0 SSE2NEON_PROBE(~) ++ ++#define SSE2NEON_BOOL(x) SSE2NEON_COMPL(SSE2NEON_NOT(x)) ++#define SSE2NEON_IF(c) SSE2NEON_IIF(SSE2NEON_BOOL(c)) ++ ++#define SSE2NEON_EAT(...) ++#define SSE2NEON_EXPAND(...) __VA_ARGS__ ++#define SSE2NEON_WHEN(c) SSE2NEON_IF(c)(SSE2NEON_EXPAND, SSE2NEON_EAT) ++ ++/* recursion */ ++/* deferred expression */ ++#define SSE2NEON_EMPTY() ++#define SSE2NEON_DEFER(id) id SSE2NEON_EMPTY() ++#define SSE2NEON_OBSTRUCT(...) __VA_ARGS__ SSE2NEON_DEFER(SSE2NEON_EMPTY)() ++#define SSE2NEON_EXPAND(...) __VA_ARGS__ ++ ++#define SSE2NEON_EVAL(...) \ ++ SSE2NEON_EVAL1(SSE2NEON_EVAL1(SSE2NEON_EVAL1(__VA_ARGS__))) ++#define SSE2NEON_EVAL1(...) \ ++ SSE2NEON_EVAL2(SSE2NEON_EVAL2(SSE2NEON_EVAL2(__VA_ARGS__))) ++#define SSE2NEON_EVAL2(...) \ ++ SSE2NEON_EVAL3(SSE2NEON_EVAL3(SSE2NEON_EVAL3(__VA_ARGS__))) ++#define SSE2NEON_EVAL3(...) __VA_ARGS__ ++ ++#define SSE2NEON_REPEAT(count, macro, ...) \ ++ SSE2NEON_WHEN(count) \ ++ (SSE2NEON_OBSTRUCT(SSE2NEON_REPEAT_INDIRECT)()( \ ++ SSE2NEON_DEC(count), macro, \ ++ __VA_ARGS__) SSE2NEON_OBSTRUCT(macro)(SSE2NEON_DEC(count), \ ++ __VA_ARGS__)) ++#define SSE2NEON_REPEAT_INDIRECT() SSE2NEON_REPEAT ++ ++#define SSE2NEON_SIZE_OF_byte 8 ++#define SSE2NEON_NUMBER_OF_LANES_byte 16 ++#define SSE2NEON_SIZE_OF_word 16 ++#define SSE2NEON_NUMBER_OF_LANES_word 8 ++ ++#define SSE2NEON_COMPARE_EQUAL_THEN_FILL_LANE(i, type) \ ++ mtx[i] = vreinterpretq_m128i_##type(vceqq_##type( \ ++ vdupq_n_##type(vgetq_lane_##type(vreinterpretq_##type##_m128i(b), i)), \ ++ vreinterpretq_##type##_m128i(a))); ++ ++#define SSE2NEON_FILL_LANE(i, type) \ ++ vec_b[i] = \ ++ vdupq_n_##type(vgetq_lane_##type(vreinterpretq_##type##_m128i(b), i)); ++ ++#define PCMPSTR_RANGES(a, b, mtx, data_type_prefix, type_prefix, size, \ ++ number_of_lanes, byte_or_word) \ ++ do { \ ++ SSE2NEON_CAT( \ ++ data_type_prefix, \ ++ SSE2NEON_CAT(size, \ ++ SSE2NEON_CAT(x, SSE2NEON_CAT(number_of_lanes, _t)))) \ ++ vec_b[number_of_lanes]; \ ++ __m128i mask = SSE2NEON_IIF(byte_or_word)( \ ++ vreinterpretq_m128i_u16(vdupq_n_u16(0xff)), \ ++ vreinterpretq_m128i_u32(vdupq_n_u32(0xffff))); \ ++ SSE2NEON_EVAL(SSE2NEON_REPEAT(number_of_lanes, SSE2NEON_FILL_LANE, \ ++ SSE2NEON_CAT(type_prefix, size))) \ ++ for (int i = 0; i < number_of_lanes; i++) { \ ++ mtx[i] = SSE2NEON_CAT(vreinterpretq_m128i_u, \ ++ size)(SSE2NEON_CAT(vbslq_u, size)( \ ++ SSE2NEON_CAT(vreinterpretq_u, \ ++ SSE2NEON_CAT(size, _m128i))(mask), \ ++ SSE2NEON_CAT(vcgeq_, SSE2NEON_CAT(type_prefix, size))( \ ++ vec_b[i], \ ++ SSE2NEON_CAT( \ ++ vreinterpretq_, \ ++ SSE2NEON_CAT(type_prefix, \ ++ SSE2NEON_CAT(size, _m128i(a))))), \ ++ SSE2NEON_CAT(vcleq_, SSE2NEON_CAT(type_prefix, size))( \ ++ vec_b[i], \ ++ SSE2NEON_CAT( \ ++ vreinterpretq_, \ ++ SSE2NEON_CAT(type_prefix, \ ++ SSE2NEON_CAT(size, _m128i(a))))))); \ ++ } \ ++ } while (0) ++ ++#define PCMPSTR_EQ(a, b, mtx, size, number_of_lanes) \ ++ do { \ ++ SSE2NEON_EVAL(SSE2NEON_REPEAT(number_of_lanes, \ ++ SSE2NEON_COMPARE_EQUAL_THEN_FILL_LANE, \ ++ SSE2NEON_CAT(u, size))) \ ++ } while (0) ++ ++#define SSE2NEON_CMP_EQUAL_ANY_IMPL(type) \ ++ static int _sse2neon_cmp_##type##_equal_any(__m128i a, int la, __m128i b, \ ++ int lb) \ ++ { \ ++ __m128i mtx[16]; \ ++ PCMPSTR_EQ(a, b, mtx, SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type)); \ ++ return SSE2NEON_CAT( \ ++ _sse2neon_aggregate_equal_any_, \ ++ SSE2NEON_CAT( \ ++ SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(x, SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, \ ++ type))))(la, lb, mtx); \ ++ } ++ ++#define SSE2NEON_CMP_RANGES_IMPL(type, data_type, us, byte_or_word) \ ++ static int _sse2neon_cmp_##us##type##_ranges(__m128i a, int la, __m128i b, \ ++ int lb) \ ++ { \ ++ __m128i mtx[16]; \ ++ PCMPSTR_RANGES( \ ++ a, b, mtx, data_type, us, SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type), byte_or_word); \ ++ return SSE2NEON_CAT( \ ++ _sse2neon_aggregate_ranges_, \ ++ SSE2NEON_CAT( \ ++ SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(x, SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, \ ++ type))))(la, lb, mtx); \ ++ } ++ ++#define SSE2NEON_CMP_EQUAL_ORDERED_IMPL(type) \ ++ static int _sse2neon_cmp_##type##_equal_ordered(__m128i a, int la, \ ++ __m128i b, int lb) \ ++ { \ ++ __m128i mtx[16]; \ ++ PCMPSTR_EQ(a, b, mtx, SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type)); \ ++ return SSE2NEON_CAT( \ ++ _sse2neon_aggregate_equal_ordered_, \ ++ SSE2NEON_CAT( \ ++ SSE2NEON_CAT(SSE2NEON_SIZE_OF_, type), \ ++ SSE2NEON_CAT(x, \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type))))( \ ++ SSE2NEON_CAT(SSE2NEON_NUMBER_OF_LANES_, type), la, lb, mtx); \ ++ } ++ ++static int _sse2neon_aggregate_equal_any_8x16(int la, int lb, __m128i mtx[16]) ++{ ++ int res = 0; ++ int m = (1 << la) - 1; ++ uint8x8_t vec_mask = vld1_u8(_sse2neon_cmpestr_mask8b); ++ uint8x8_t t_lo = vtst_u8(vdup_n_u8(m & 0xff), vec_mask); ++ uint8x8_t t_hi = vtst_u8(vdup_n_u8(m >> 8), vec_mask); ++ uint8x16_t vec = vcombine_u8(t_lo, t_hi); ++ for (int j = 0; j < lb; j++) { ++ mtx[j] = vreinterpretq_m128i_u8( ++ vandq_u8(vec, vreinterpretq_u8_m128i(mtx[j]))); ++ mtx[j] = vreinterpretq_m128i_u8( ++ vshrq_n_u8(vreinterpretq_u8_m128i(mtx[j]), 7)); ++ int tmp = _sse2neon_vaddvq_u8(vreinterpretq_u8_m128i(mtx[j])) ? 1 : 0; ++ res |= (tmp << j); ++ } ++ return res; ++} ++ ++static int _sse2neon_aggregate_equal_any_16x8(int la, int lb, __m128i mtx[16]) ++{ ++ int res = 0; ++ int m = (1 << la) - 1; ++ uint16x8_t vec = ++ vtstq_u16(vdupq_n_u16(m), vld1q_u16(_sse2neon_cmpestr_mask16b)); ++ for (int j = 0; j < lb; j++) { ++ mtx[j] = vreinterpretq_m128i_u16( ++ vandq_u16(vec, vreinterpretq_u16_m128i(mtx[j]))); ++ mtx[j] = vreinterpretq_m128i_u16( ++ vshrq_n_u16(vreinterpretq_u16_m128i(mtx[j]), 15)); ++ int tmp = _sse2neon_vaddvq_u16(vreinterpretq_u16_m128i(mtx[j])) ? 1 : 0; ++ res |= (tmp << j); ++ } ++ return res; ++} ++ ++/* clang-format off */ ++#define SSE2NEON_GENERATE_CMP_EQUAL_ANY(prefix) \ ++ prefix##IMPL(byte) \ ++ prefix##IMPL(word) ++/* clang-format on */ ++ ++SSE2NEON_GENERATE_CMP_EQUAL_ANY(SSE2NEON_CMP_EQUAL_ANY_) ++ ++static int _sse2neon_aggregate_ranges_16x8(int la, int lb, __m128i mtx[16]) ++{ ++ int res = 0; ++ int m = (1 << la) - 1; ++ uint16x8_t vec = ++ vtstq_u16(vdupq_n_u16(m), vld1q_u16(_sse2neon_cmpestr_mask16b)); ++ for (int j = 0; j < lb; j++) { ++ mtx[j] = vreinterpretq_m128i_u16( ++ vandq_u16(vec, vreinterpretq_u16_m128i(mtx[j]))); ++ mtx[j] = vreinterpretq_m128i_u16( ++ vshrq_n_u16(vreinterpretq_u16_m128i(mtx[j]), 15)); ++ __m128i tmp = vreinterpretq_m128i_u32( ++ vshrq_n_u32(vreinterpretq_u32_m128i(mtx[j]), 16)); ++ uint32x4_t vec_res = vandq_u32(vreinterpretq_u32_m128i(mtx[j]), ++ vreinterpretq_u32_m128i(tmp)); ++#if defined(__aarch64__) || defined(_M_ARM64) ++ int t = vaddvq_u32(vec_res) ? 1 : 0; ++#else ++ uint64x2_t sumh = vpaddlq_u32(vec_res); ++ int t = vgetq_lane_u64(sumh, 0) + vgetq_lane_u64(sumh, 1); ++#endif ++ res |= (t << j); ++ } ++ return res; ++} ++ ++static int _sse2neon_aggregate_ranges_8x16(int la, int lb, __m128i mtx[16]) ++{ ++ int res = 0; ++ int m = (1 << la) - 1; ++ uint8x8_t vec_mask = vld1_u8(_sse2neon_cmpestr_mask8b); ++ uint8x8_t t_lo = vtst_u8(vdup_n_u8(m & 0xff), vec_mask); ++ uint8x8_t t_hi = vtst_u8(vdup_n_u8(m >> 8), vec_mask); ++ uint8x16_t vec = vcombine_u8(t_lo, t_hi); ++ for (int j = 0; j < lb; j++) { ++ mtx[j] = vreinterpretq_m128i_u8( ++ vandq_u8(vec, vreinterpretq_u8_m128i(mtx[j]))); ++ mtx[j] = vreinterpretq_m128i_u8( ++ vshrq_n_u8(vreinterpretq_u8_m128i(mtx[j]), 7)); ++ __m128i tmp = vreinterpretq_m128i_u16( ++ vshrq_n_u16(vreinterpretq_u16_m128i(mtx[j]), 8)); ++ uint16x8_t vec_res = vandq_u16(vreinterpretq_u16_m128i(mtx[j]), ++ vreinterpretq_u16_m128i(tmp)); ++ int t = _sse2neon_vaddvq_u16(vec_res) ? 1 : 0; ++ res |= (t << j); ++ } ++ return res; ++} ++ ++#define SSE2NEON_CMP_RANGES_IS_BYTE 1 ++#define SSE2NEON_CMP_RANGES_IS_WORD 0 ++ ++/* clang-format off */ ++#define SSE2NEON_GENERATE_CMP_RANGES(prefix) \ ++ prefix##IMPL(byte, uint, u, prefix##IS_BYTE) \ ++ prefix##IMPL(byte, int, s, prefix##IS_BYTE) \ ++ prefix##IMPL(word, uint, u, prefix##IS_WORD) \ ++ prefix##IMPL(word, int, s, prefix##IS_WORD) ++/* clang-format on */ ++ ++SSE2NEON_GENERATE_CMP_RANGES(SSE2NEON_CMP_RANGES_) ++ ++#undef SSE2NEON_CMP_RANGES_IS_BYTE ++#undef SSE2NEON_CMP_RANGES_IS_WORD ++ ++static int _sse2neon_cmp_byte_equal_each(__m128i a, int la, __m128i b, int lb) ++{ ++ uint8x16_t mtx = ++ vceqq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b)); ++ int m0 = (la < lb) ? 0 : ((1 << la) - (1 << lb)); ++ int m1 = 0x10000 - (1 << la); ++ int tb = 0x10000 - (1 << lb); ++ uint8x8_t vec_mask, vec0_lo, vec0_hi, vec1_lo, vec1_hi; ++ uint8x8_t tmp_lo, tmp_hi, res_lo, res_hi; ++ vec_mask = vld1_u8(_sse2neon_cmpestr_mask8b); ++ vec0_lo = vtst_u8(vdup_n_u8(m0), vec_mask); ++ vec0_hi = vtst_u8(vdup_n_u8(m0 >> 8), vec_mask); ++ vec1_lo = vtst_u8(vdup_n_u8(m1), vec_mask); ++ vec1_hi = vtst_u8(vdup_n_u8(m1 >> 8), vec_mask); ++ tmp_lo = vtst_u8(vdup_n_u8(tb), vec_mask); ++ tmp_hi = vtst_u8(vdup_n_u8(tb >> 8), vec_mask); ++ ++ res_lo = vbsl_u8(vec0_lo, vdup_n_u8(0), vget_low_u8(mtx)); ++ res_hi = vbsl_u8(vec0_hi, vdup_n_u8(0), vget_high_u8(mtx)); ++ res_lo = vbsl_u8(vec1_lo, tmp_lo, res_lo); ++ res_hi = vbsl_u8(vec1_hi, tmp_hi, res_hi); ++ res_lo = vand_u8(res_lo, vec_mask); ++ res_hi = vand_u8(res_hi, vec_mask); ++ ++ int res = _sse2neon_vaddv_u8(res_lo) + (_sse2neon_vaddv_u8(res_hi) << 8); ++ return res; ++} ++ ++static int _sse2neon_cmp_word_equal_each(__m128i a, int la, __m128i b, int lb) ++{ ++ uint16x8_t mtx = ++ vceqq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b)); ++ int m0 = (la < lb) ? 0 : ((1 << la) - (1 << lb)); ++ int m1 = 0x100 - (1 << la); ++ int tb = 0x100 - (1 << lb); ++ uint16x8_t vec_mask = vld1q_u16(_sse2neon_cmpestr_mask16b); ++ uint16x8_t vec0 = vtstq_u16(vdupq_n_u16(m0), vec_mask); ++ uint16x8_t vec1 = vtstq_u16(vdupq_n_u16(m1), vec_mask); ++ uint16x8_t tmp = vtstq_u16(vdupq_n_u16(tb), vec_mask); ++ mtx = vbslq_u16(vec0, vdupq_n_u16(0), mtx); ++ mtx = vbslq_u16(vec1, tmp, mtx); ++ mtx = vandq_u16(mtx, vec_mask); ++ return _sse2neon_vaddvq_u16(mtx); ++} ++ ++#define SSE2NEON_AGGREGATE_EQUAL_ORDER_IS_UBYTE 1 ++#define SSE2NEON_AGGREGATE_EQUAL_ORDER_IS_UWORD 0 ++ ++#define SSE2NEON_AGGREGATE_EQUAL_ORDER_IMPL(size, number_of_lanes, data_type) \ ++ static int _sse2neon_aggregate_equal_ordered_##size##x##number_of_lanes( \ ++ int bound, int la, int lb, __m128i mtx[16]) \ ++ { \ ++ int res = 0; \ ++ int m1 = SSE2NEON_IIF(data_type)(0x10000, 0x100) - (1 << la); \ ++ uint##size##x8_t vec_mask = SSE2NEON_IIF(data_type)( \ ++ vld1_u##size(_sse2neon_cmpestr_mask##size##b), \ ++ vld1q_u##size(_sse2neon_cmpestr_mask##size##b)); \ ++ uint##size##x##number_of_lanes##_t vec1 = SSE2NEON_IIF(data_type)( \ ++ vcombine_u##size(vtst_u##size(vdup_n_u##size(m1), vec_mask), \ ++ vtst_u##size(vdup_n_u##size(m1 >> 8), vec_mask)), \ ++ vtstq_u##size(vdupq_n_u##size(m1), vec_mask)); \ ++ uint##size##x##number_of_lanes##_t vec_minusone = vdupq_n_u##size(-1); \ ++ uint##size##x##number_of_lanes##_t vec_zero = vdupq_n_u##size(0); \ ++ for (int j = 0; j < lb; j++) { \ ++ mtx[j] = vreinterpretq_m128i_u##size(vbslq_u##size( \ ++ vec1, vec_minusone, vreinterpretq_u##size##_m128i(mtx[j]))); \ ++ } \ ++ for (int j = lb; j < bound; j++) { \ ++ mtx[j] = vreinterpretq_m128i_u##size( \ ++ vbslq_u##size(vec1, vec_minusone, vec_zero)); \ ++ } \ ++ unsigned SSE2NEON_IIF(data_type)(char, short) *ptr = \ ++ (unsigned SSE2NEON_IIF(data_type)(char, short) *) mtx; \ ++ for (int i = 0; i < bound; i++) { \ ++ int val = 1; \ ++ for (int j = 0, k = i; j < bound - i && k < bound; j++, k++) \ ++ val &= ptr[k * bound + j]; \ ++ res += val << i; \ ++ } \ ++ return res; \ ++ } ++ ++/* clang-format off */ ++#define SSE2NEON_GENERATE_AGGREGATE_EQUAL_ORDER(prefix) \ ++ prefix##IMPL(8, 16, prefix##IS_UBYTE) \ ++ prefix##IMPL(16, 8, prefix##IS_UWORD) ++/* clang-format on */ ++ ++SSE2NEON_GENERATE_AGGREGATE_EQUAL_ORDER(SSE2NEON_AGGREGATE_EQUAL_ORDER_) ++ ++#undef SSE2NEON_AGGREGATE_EQUAL_ORDER_IS_UBYTE ++#undef SSE2NEON_AGGREGATE_EQUAL_ORDER_IS_UWORD ++ ++/* clang-format off */ ++#define SSE2NEON_GENERATE_CMP_EQUAL_ORDERED(prefix) \ ++ prefix##IMPL(byte) \ ++ prefix##IMPL(word) ++/* clang-format on */ ++ ++SSE2NEON_GENERATE_CMP_EQUAL_ORDERED(SSE2NEON_CMP_EQUAL_ORDERED_) ++ ++#define SSE2NEON_CMPESTR_LIST \ ++ _(CMP_UBYTE_EQUAL_ANY, cmp_byte_equal_any) \ ++ _(CMP_UWORD_EQUAL_ANY, cmp_word_equal_any) \ ++ _(CMP_SBYTE_EQUAL_ANY, cmp_byte_equal_any) \ ++ _(CMP_SWORD_EQUAL_ANY, cmp_word_equal_any) \ ++ _(CMP_UBYTE_RANGES, cmp_ubyte_ranges) \ ++ _(CMP_UWORD_RANGES, cmp_uword_ranges) \ ++ _(CMP_SBYTE_RANGES, cmp_sbyte_ranges) \ ++ _(CMP_SWORD_RANGES, cmp_sword_ranges) \ ++ _(CMP_UBYTE_EQUAL_EACH, cmp_byte_equal_each) \ ++ _(CMP_UWORD_EQUAL_EACH, cmp_word_equal_each) \ ++ _(CMP_SBYTE_EQUAL_EACH, cmp_byte_equal_each) \ ++ _(CMP_SWORD_EQUAL_EACH, cmp_word_equal_each) \ ++ _(CMP_UBYTE_EQUAL_ORDERED, cmp_byte_equal_ordered) \ ++ _(CMP_UWORD_EQUAL_ORDERED, cmp_word_equal_ordered) \ ++ _(CMP_SBYTE_EQUAL_ORDERED, cmp_byte_equal_ordered) \ ++ _(CMP_SWORD_EQUAL_ORDERED, cmp_word_equal_ordered) ++ ++enum { ++#define _(name, func_suffix) name, ++ SSE2NEON_CMPESTR_LIST ++#undef _ ++}; ++typedef int (*cmpestr_func_t)(__m128i a, int la, __m128i b, int lb); ++static cmpestr_func_t _sse2neon_cmpfunc_table[] = { ++#define _(name, func_suffix) _sse2neon_##func_suffix, ++ SSE2NEON_CMPESTR_LIST ++#undef _ ++}; ++ ++FORCE_INLINE int _sse2neon_sido_negative(int res, int lb, int imm8, int bound) ++{ ++ switch (imm8 & 0x30) { ++ case _SIDD_NEGATIVE_POLARITY: ++ res ^= 0xffffffff; ++ break; ++ case _SIDD_MASKED_NEGATIVE_POLARITY: ++ res ^= (1 << lb) - 1; ++ break; ++ default: ++ break; ++ } ++ ++ return res & ((bound == 8) ? 0xFF : 0xFFFF); ++} ++ ++FORCE_INLINE int _sse2neon_clz(unsigned int x) ++{ ++#if defined(_MSC_VER) && !defined(__clang__) ++ unsigned long cnt = 0; ++ if (_BitScanReverse(&cnt, x)) ++ return 31 - cnt; ++ return 32; ++#else ++ return x != 0 ? __builtin_clz(x) : 32; ++#endif ++} ++ ++FORCE_INLINE int _sse2neon_ctz(unsigned int x) ++{ ++#if defined(_MSC_VER) && !defined(__clang__) ++ unsigned long cnt = 0; ++ if (_BitScanForward(&cnt, x)) ++ return cnt; ++ return 32; ++#else ++ return x != 0 ? __builtin_ctz(x) : 32; ++#endif ++} ++ ++FORCE_INLINE int _sse2neon_ctzll(unsigned long long x) ++{ ++#ifdef _MSC_VER ++ unsigned long cnt; ++#if defined(SSE2NEON_HAS_BITSCAN64) ++ if (_BitScanForward64(&cnt, x)) ++ return (int) (cnt); ++#else ++ if (_BitScanForward(&cnt, (unsigned long) (x))) ++ return (int) cnt; ++ if (_BitScanForward(&cnt, (unsigned long) (x >> 32))) ++ return (int) (cnt + 32); ++#endif /* SSE2NEON_HAS_BITSCAN64 */ ++ return 64; ++#else /* assume GNU compatible compilers */ ++ return x != 0 ? __builtin_ctzll(x) : 64; ++#endif ++} ++ ++#define SSE2NEON_MIN(x, y) (x) < (y) ? (x) : (y) ++ ++#define SSE2NEON_CMPSTR_SET_UPPER(var, imm) \ ++ const int var = (imm & 0x01) ? 8 : 16 ++ ++#define SSE2NEON_CMPESTRX_LEN_PAIR(a, b, la, lb) \ ++ int tmp1 = la ^ (la >> 31); \ ++ la = tmp1 - (la >> 31); \ ++ int tmp2 = lb ^ (lb >> 31); \ ++ lb = tmp2 - (lb >> 31); \ ++ la = SSE2NEON_MIN(la, bound); \ ++ lb = SSE2NEON_MIN(lb, bound) ++ ++// Compare all pairs of character in string a and b, ++// then aggregate the result. ++// As the only difference of PCMPESTR* and PCMPISTR* is the way to calculate the ++// length of string, we use SSE2NEON_CMP{I,E}STRX_GET_LEN to get the length of ++// string a and b. ++#define SSE2NEON_COMP_AGG(a, b, la, lb, imm8, IE) \ ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); \ ++ SSE2NEON_##IE##_LEN_PAIR(a, b, la, lb); \ ++ int r2 = (_sse2neon_cmpfunc_table[imm8 & 0x0f])(a, la, b, lb); \ ++ r2 = _sse2neon_sido_negative(r2, lb, imm8, bound) ++ ++#define SSE2NEON_CMPSTR_GENERATE_INDEX(r2, bound, imm8) \ ++ return (r2 == 0) ? bound \ ++ : ((imm8 & 0x40) ? (31 - _sse2neon_clz(r2)) \ ++ : _sse2neon_ctz(r2)) ++ ++#define SSE2NEON_CMPSTR_GENERATE_MASK(dst) \ ++ __m128i dst = vreinterpretq_m128i_u8(vdupq_n_u8(0)); \ ++ if (imm8 & 0x40) { \ ++ if (bound == 8) { \ ++ uint16x8_t tmp = vtstq_u16(vdupq_n_u16(r2), \ ++ vld1q_u16(_sse2neon_cmpestr_mask16b)); \ ++ dst = vreinterpretq_m128i_u16(vbslq_u16( \ ++ tmp, vdupq_n_u16(-1), vreinterpretq_u16_m128i(dst))); \ ++ } else { \ ++ uint8x16_t vec_r2 = \ ++ vcombine_u8(vdup_n_u8(r2), vdup_n_u8(r2 >> 8)); \ ++ uint8x16_t tmp = \ ++ vtstq_u8(vec_r2, vld1q_u8(_sse2neon_cmpestr_mask8b)); \ ++ dst = vreinterpretq_m128i_u8( \ ++ vbslq_u8(tmp, vdupq_n_u8(-1), vreinterpretq_u8_m128i(dst))); \ ++ } \ ++ } else { \ ++ if (bound == 16) { \ ++ dst = vreinterpretq_m128i_u16( \ ++ vsetq_lane_u16(r2 & 0xffff, vreinterpretq_u16_m128i(dst), 0)); \ ++ } else { \ ++ dst = vreinterpretq_m128i_u8( \ ++ vsetq_lane_u8(r2 & 0xff, vreinterpretq_u8_m128i(dst), 0)); \ ++ } \ ++ } \ ++ return dst ++ ++// Compare packed strings in a and b with lengths la and lb using the control ++// in imm8, and returns 1 if b did not contain a null character and the ++// resulting mask was zero, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestra ++FORCE_INLINE int _mm_cmpestra(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ int lb_cpy = lb; ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ return !r2 & (lb_cpy > bound); ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control in ++// imm8, and returns 1 if the resulting mask was non-zero, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestrc ++FORCE_INLINE int _mm_cmpestrc(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ return r2 != 0; ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control ++// in imm8, and store the generated index in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestri ++FORCE_INLINE int _mm_cmpestri(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ SSE2NEON_CMPSTR_GENERATE_INDEX(r2, bound, imm8); ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control ++// in imm8, and store the generated mask in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestrm ++FORCE_INLINE __m128i ++_mm_cmpestrm(__m128i a, int la, __m128i b, int lb, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ SSE2NEON_CMPSTR_GENERATE_MASK(dst); ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control in ++// imm8, and returns bit 0 of the resulting bit mask. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestro ++FORCE_INLINE int _mm_cmpestro(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPESTRX); ++ return r2 & 1; ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control in ++// imm8, and returns 1 if any character in a was null, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestrs ++FORCE_INLINE int _mm_cmpestrs(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ (void) a; ++ (void) b; ++ (void) lb; ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); ++ return la <= (bound - 1); ++} ++ ++// Compare packed strings in a and b with lengths la and lb using the control in ++// imm8, and returns 1 if any character in b was null, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpestrz ++FORCE_INLINE int _mm_cmpestrz(__m128i a, ++ int la, ++ __m128i b, ++ int lb, ++ const int imm8) ++{ ++ (void) a; ++ (void) b; ++ (void) la; ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); ++ return lb <= (bound - 1); ++} ++ ++#define SSE2NEON_CMPISTRX_LENGTH(str, len, imm8) \ ++ do { \ ++ if (imm8 & 0x01) { \ ++ uint16x8_t equal_mask_##str = \ ++ vceqq_u16(vreinterpretq_u16_m128i(str), vdupq_n_u16(0)); \ ++ uint8x8_t res_##str = vshrn_n_u16(equal_mask_##str, 4); \ ++ uint64_t matches_##str = \ ++ vget_lane_u64(vreinterpret_u64_u8(res_##str), 0); \ ++ len = _sse2neon_ctzll(matches_##str) >> 3; \ ++ } else { \ ++ uint16x8_t equal_mask_##str = vreinterpretq_u16_u8( \ ++ vceqq_u8(vreinterpretq_u8_m128i(str), vdupq_n_u8(0))); \ ++ uint8x8_t res_##str = vshrn_n_u16(equal_mask_##str, 4); \ ++ uint64_t matches_##str = \ ++ vget_lane_u64(vreinterpret_u64_u8(res_##str), 0); \ ++ len = _sse2neon_ctzll(matches_##str) >> 2; \ ++ } \ ++ } while (0) ++ ++#define SSE2NEON_CMPISTRX_LEN_PAIR(a, b, la, lb) \ ++ int la, lb; \ ++ do { \ ++ SSE2NEON_CMPISTRX_LENGTH(a, la, imm8); \ ++ SSE2NEON_CMPISTRX_LENGTH(b, lb, imm8); \ ++ } while (0) ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns 1 if b did not contain a null character and the resulting ++// mask was zero, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistra ++FORCE_INLINE int _mm_cmpistra(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ return !r2 & (lb >= bound); ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns 1 if the resulting mask was non-zero, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistrc ++FORCE_INLINE int _mm_cmpistrc(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ return r2 != 0; ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and store the generated index in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistri ++FORCE_INLINE int _mm_cmpistri(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ SSE2NEON_CMPSTR_GENERATE_INDEX(r2, bound, imm8); ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and store the generated mask in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistrm ++FORCE_INLINE __m128i _mm_cmpistrm(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ SSE2NEON_CMPSTR_GENERATE_MASK(dst); ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns bit 0 of the resulting bit mask. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistro ++FORCE_INLINE int _mm_cmpistro(__m128i a, __m128i b, const int imm8) ++{ ++ SSE2NEON_COMP_AGG(a, b, la, lb, imm8, CMPISTRX); ++ return r2 & 1; ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns 1 if any character in a was null, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistrs ++FORCE_INLINE int _mm_cmpistrs(__m128i a, __m128i b, const int imm8) ++{ ++ (void) b; ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); ++ int la; ++ SSE2NEON_CMPISTRX_LENGTH(a, la, imm8); ++ return la <= (bound - 1); ++} ++ ++// Compare packed strings with implicit lengths in a and b using the control in ++// imm8, and returns 1 if any character in b was null, and 0 otherwise. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_cmpistrz ++FORCE_INLINE int _mm_cmpistrz(__m128i a, __m128i b, const int imm8) ++{ ++ (void) a; ++ SSE2NEON_CMPSTR_SET_UPPER(bound, imm8); ++ int lb; ++ SSE2NEON_CMPISTRX_LENGTH(b, lb, imm8); ++ return lb <= (bound - 1); ++} ++ ++// Compares the 2 signed 64-bit integers in a and the 2 signed 64-bit integers ++// in b for greater than. ++FORCE_INLINE __m128i _mm_cmpgt_epi64(__m128i a, __m128i b) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ return vreinterpretq_m128i_u64( ++ vcgtq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++#else ++ return vreinterpretq_m128i_s64(vshrq_n_s64( ++ vqsubq_s64(vreinterpretq_s64_m128i(b), vreinterpretq_s64_m128i(a)), ++ 63)); ++#endif ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 16-bit integer v, and stores the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_crc32_u16 ++FORCE_INLINE uint32_t _mm_crc32_u16(uint32_t crc, uint16_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32ch %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif ((__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32)) || \ ++ (defined(_M_ARM64) && !defined(__clang__)) ++ crc = __crc32ch(crc, v); ++#else ++ crc = _mm_crc32_u8(crc, v & 0xff); ++ crc = _mm_crc32_u8(crc, (v >> 8) & 0xff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 32-bit integer v, and stores the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_crc32_u32 ++FORCE_INLINE uint32_t _mm_crc32_u32(uint32_t crc, uint32_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cw %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif ((__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32)) || \ ++ (defined(_M_ARM64) && !defined(__clang__)) ++ crc = __crc32cw(crc, v); ++#else ++ crc = _mm_crc32_u16(crc, v & 0xffff); ++ crc = _mm_crc32_u16(crc, (v >> 16) & 0xffff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 64-bit integer v, and stores the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_crc32_u64 ++FORCE_INLINE uint64_t _mm_crc32_u64(uint64_t crc, uint64_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cx %w[c], %w[c], %x[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif (defined(_M_ARM64) && !defined(__clang__)) ++ crc = __crc32cd((uint32_t) crc, v); ++#else ++ crc = _mm_crc32_u32((uint32_t) (crc), v & 0xffffffff); ++ crc = _mm_crc32_u32((uint32_t) (crc), (v >> 32) & 0xffffffff); ++#endif ++ return crc; ++} ++ ++// Starting with the initial value in crc, accumulates a CRC32 value for ++// unsigned 8-bit integer v, and stores the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_crc32_u8 ++FORCE_INLINE uint32_t _mm_crc32_u8(uint32_t crc, uint8_t v) ++{ ++#if defined(__aarch64__) && defined(__ARM_FEATURE_CRC32) ++ __asm__ __volatile__("crc32cb %w[c], %w[c], %w[v]\n\t" ++ : [c] "+r"(crc) ++ : [v] "r"(v)); ++#elif ((__ARM_ARCH == 8) && defined(__ARM_FEATURE_CRC32)) || \ ++ (defined(_M_ARM64) && !defined(__clang__)) ++ crc = __crc32cb(crc, v); ++#else ++ crc ^= v; ++#if defined(__ARM_FEATURE_CRYPTO) ++ // Adapted from: https://mary.rs/lab/crc32/ ++ // Barrent reduction ++ uint64x2_t orig = ++ vcombine_u64(vcreate_u64((uint64_t) (crc) << 24), vcreate_u64(0x0)); ++ uint64x2_t tmp = orig; ++ ++ // Polynomial P(x) of CRC32C ++ uint64_t p = 0x105EC76F1; ++ // Barrett Reduction (in bit-reflected form) constant mu_{64} = \lfloor ++ // 2^{64} / P(x) \rfloor = 0x11f91caf6 ++ uint64_t mu = 0x1dea713f1; ++ ++ // Multiply by mu_{64} ++ tmp = _sse2neon_vmull_p64(vget_low_u64(tmp), vcreate_u64(mu)); ++ // Divide by 2^{64} (mask away the unnecessary bits) ++ tmp = ++ vandq_u64(tmp, vcombine_u64(vcreate_u64(0xFFFFFFFF), vcreate_u64(0x0))); ++ // Multiply by P(x) (shifted left by 1 for alignment reasons) ++ tmp = _sse2neon_vmull_p64(vget_low_u64(tmp), vcreate_u64(p)); ++ // Subtract original from result ++ tmp = veorq_u64(tmp, orig); ++ ++ // Extract the 'lower' (in bit-reflected sense) 32 bits ++ crc = vgetq_lane_u32(vreinterpretq_u32_u64(tmp), 1); ++#else // Fall back to the generic table lookup approach ++ // Adapted from: https://create.stephan-brumme.com/crc32/ ++ // Apply half-byte comparison algorithm for the best ratio between ++ // performance and lookup table. ++ ++ // The lookup table just needs to store every 16th entry ++ // of the standard look-up table. ++ static const uint32_t crc32_half_byte_tbl[] = { ++ 0x00000000, 0x105ec76f, 0x20bd8ede, 0x30e349b1, 0x417b1dbc, 0x5125dad3, ++ 0x61c69362, 0x7198540d, 0x82f63b78, 0x92a8fc17, 0xa24bb5a6, 0xb21572c9, ++ 0xc38d26c4, 0xd3d3e1ab, 0xe330a81a, 0xf36e6f75, ++ }; ++ ++ crc = (crc >> 4) ^ crc32_half_byte_tbl[crc & 0x0F]; ++ crc = (crc >> 4) ^ crc32_half_byte_tbl[crc & 0x0F]; ++#endif ++#endif ++ return crc; ++} ++ ++/* AES */ ++ ++#if !defined(__ARM_FEATURE_CRYPTO) && (!defined(_M_ARM64) || defined(__clang__)) ++/* clang-format off */ ++#define SSE2NEON_AES_SBOX(w) \ ++ { \ ++ w(0x63), w(0x7c), w(0x77), w(0x7b), w(0xf2), w(0x6b), w(0x6f), \ ++ w(0xc5), w(0x30), w(0x01), w(0x67), w(0x2b), w(0xfe), w(0xd7), \ ++ w(0xab), w(0x76), w(0xca), w(0x82), w(0xc9), w(0x7d), w(0xfa), \ ++ w(0x59), w(0x47), w(0xf0), w(0xad), w(0xd4), w(0xa2), w(0xaf), \ ++ w(0x9c), w(0xa4), w(0x72), w(0xc0), w(0xb7), w(0xfd), w(0x93), \ ++ w(0x26), w(0x36), w(0x3f), w(0xf7), w(0xcc), w(0x34), w(0xa5), \ ++ w(0xe5), w(0xf1), w(0x71), w(0xd8), w(0x31), w(0x15), w(0x04), \ ++ w(0xc7), w(0x23), w(0xc3), w(0x18), w(0x96), w(0x05), w(0x9a), \ ++ w(0x07), w(0x12), w(0x80), w(0xe2), w(0xeb), w(0x27), w(0xb2), \ ++ w(0x75), w(0x09), w(0x83), w(0x2c), w(0x1a), w(0x1b), w(0x6e), \ ++ w(0x5a), w(0xa0), w(0x52), w(0x3b), w(0xd6), w(0xb3), w(0x29), \ ++ w(0xe3), w(0x2f), w(0x84), w(0x53), w(0xd1), w(0x00), w(0xed), \ ++ w(0x20), w(0xfc), w(0xb1), w(0x5b), w(0x6a), w(0xcb), w(0xbe), \ ++ w(0x39), w(0x4a), w(0x4c), w(0x58), w(0xcf), w(0xd0), w(0xef), \ ++ w(0xaa), w(0xfb), w(0x43), w(0x4d), w(0x33), w(0x85), w(0x45), \ ++ w(0xf9), w(0x02), w(0x7f), w(0x50), w(0x3c), w(0x9f), w(0xa8), \ ++ w(0x51), w(0xa3), w(0x40), w(0x8f), w(0x92), w(0x9d), w(0x38), \ ++ w(0xf5), w(0xbc), w(0xb6), w(0xda), w(0x21), w(0x10), w(0xff), \ ++ w(0xf3), w(0xd2), w(0xcd), w(0x0c), w(0x13), w(0xec), w(0x5f), \ ++ w(0x97), w(0x44), w(0x17), w(0xc4), w(0xa7), w(0x7e), w(0x3d), \ ++ w(0x64), w(0x5d), w(0x19), w(0x73), w(0x60), w(0x81), w(0x4f), \ ++ w(0xdc), w(0x22), w(0x2a), w(0x90), w(0x88), w(0x46), w(0xee), \ ++ w(0xb8), w(0x14), w(0xde), w(0x5e), w(0x0b), w(0xdb), w(0xe0), \ ++ w(0x32), w(0x3a), w(0x0a), w(0x49), w(0x06), w(0x24), w(0x5c), \ ++ w(0xc2), w(0xd3), w(0xac), w(0x62), w(0x91), w(0x95), w(0xe4), \ ++ w(0x79), w(0xe7), w(0xc8), w(0x37), w(0x6d), w(0x8d), w(0xd5), \ ++ w(0x4e), w(0xa9), w(0x6c), w(0x56), w(0xf4), w(0xea), w(0x65), \ ++ w(0x7a), w(0xae), w(0x08), w(0xba), w(0x78), w(0x25), w(0x2e), \ ++ w(0x1c), w(0xa6), w(0xb4), w(0xc6), w(0xe8), w(0xdd), w(0x74), \ ++ w(0x1f), w(0x4b), w(0xbd), w(0x8b), w(0x8a), w(0x70), w(0x3e), \ ++ w(0xb5), w(0x66), w(0x48), w(0x03), w(0xf6), w(0x0e), w(0x61), \ ++ w(0x35), w(0x57), w(0xb9), w(0x86), w(0xc1), w(0x1d), w(0x9e), \ ++ w(0xe1), w(0xf8), w(0x98), w(0x11), w(0x69), w(0xd9), w(0x8e), \ ++ w(0x94), w(0x9b), w(0x1e), w(0x87), w(0xe9), w(0xce), w(0x55), \ ++ w(0x28), w(0xdf), w(0x8c), w(0xa1), w(0x89), w(0x0d), w(0xbf), \ ++ w(0xe6), w(0x42), w(0x68), w(0x41), w(0x99), w(0x2d), w(0x0f), \ ++ w(0xb0), w(0x54), w(0xbb), w(0x16) \ ++ } ++#define SSE2NEON_AES_RSBOX(w) \ ++ { \ ++ w(0x52), w(0x09), w(0x6a), w(0xd5), w(0x30), w(0x36), w(0xa5), \ ++ w(0x38), w(0xbf), w(0x40), w(0xa3), w(0x9e), w(0x81), w(0xf3), \ ++ w(0xd7), w(0xfb), w(0x7c), w(0xe3), w(0x39), w(0x82), w(0x9b), \ ++ w(0x2f), w(0xff), w(0x87), w(0x34), w(0x8e), w(0x43), w(0x44), \ ++ w(0xc4), w(0xde), w(0xe9), w(0xcb), w(0x54), w(0x7b), w(0x94), \ ++ w(0x32), w(0xa6), w(0xc2), w(0x23), w(0x3d), w(0xee), w(0x4c), \ ++ w(0x95), w(0x0b), w(0x42), w(0xfa), w(0xc3), w(0x4e), w(0x08), \ ++ w(0x2e), w(0xa1), w(0x66), w(0x28), w(0xd9), w(0x24), w(0xb2), \ ++ w(0x76), w(0x5b), w(0xa2), w(0x49), w(0x6d), w(0x8b), w(0xd1), \ ++ w(0x25), w(0x72), w(0xf8), w(0xf6), w(0x64), w(0x86), w(0x68), \ ++ w(0x98), w(0x16), w(0xd4), w(0xa4), w(0x5c), w(0xcc), w(0x5d), \ ++ w(0x65), w(0xb6), w(0x92), w(0x6c), w(0x70), w(0x48), w(0x50), \ ++ w(0xfd), w(0xed), w(0xb9), w(0xda), w(0x5e), w(0x15), w(0x46), \ ++ w(0x57), w(0xa7), w(0x8d), w(0x9d), w(0x84), w(0x90), w(0xd8), \ ++ w(0xab), w(0x00), w(0x8c), w(0xbc), w(0xd3), w(0x0a), w(0xf7), \ ++ w(0xe4), w(0x58), w(0x05), w(0xb8), w(0xb3), w(0x45), w(0x06), \ ++ w(0xd0), w(0x2c), w(0x1e), w(0x8f), w(0xca), w(0x3f), w(0x0f), \ ++ w(0x02), w(0xc1), w(0xaf), w(0xbd), w(0x03), w(0x01), w(0x13), \ ++ w(0x8a), w(0x6b), w(0x3a), w(0x91), w(0x11), w(0x41), w(0x4f), \ ++ w(0x67), w(0xdc), w(0xea), w(0x97), w(0xf2), w(0xcf), w(0xce), \ ++ w(0xf0), w(0xb4), w(0xe6), w(0x73), w(0x96), w(0xac), w(0x74), \ ++ w(0x22), w(0xe7), w(0xad), w(0x35), w(0x85), w(0xe2), w(0xf9), \ ++ w(0x37), w(0xe8), w(0x1c), w(0x75), w(0xdf), w(0x6e), w(0x47), \ ++ w(0xf1), w(0x1a), w(0x71), w(0x1d), w(0x29), w(0xc5), w(0x89), \ ++ w(0x6f), w(0xb7), w(0x62), w(0x0e), w(0xaa), w(0x18), w(0xbe), \ ++ w(0x1b), w(0xfc), w(0x56), w(0x3e), w(0x4b), w(0xc6), w(0xd2), \ ++ w(0x79), w(0x20), w(0x9a), w(0xdb), w(0xc0), w(0xfe), w(0x78), \ ++ w(0xcd), w(0x5a), w(0xf4), w(0x1f), w(0xdd), w(0xa8), w(0x33), \ ++ w(0x88), w(0x07), w(0xc7), w(0x31), w(0xb1), w(0x12), w(0x10), \ ++ w(0x59), w(0x27), w(0x80), w(0xec), w(0x5f), w(0x60), w(0x51), \ ++ w(0x7f), w(0xa9), w(0x19), w(0xb5), w(0x4a), w(0x0d), w(0x2d), \ ++ w(0xe5), w(0x7a), w(0x9f), w(0x93), w(0xc9), w(0x9c), w(0xef), \ ++ w(0xa0), w(0xe0), w(0x3b), w(0x4d), w(0xae), w(0x2a), w(0xf5), \ ++ w(0xb0), w(0xc8), w(0xeb), w(0xbb), w(0x3c), w(0x83), w(0x53), \ ++ w(0x99), w(0x61), w(0x17), w(0x2b), w(0x04), w(0x7e), w(0xba), \ ++ w(0x77), w(0xd6), w(0x26), w(0xe1), w(0x69), w(0x14), w(0x63), \ ++ w(0x55), w(0x21), w(0x0c), w(0x7d) \ ++ } ++/* clang-format on */ ++ ++/* X Macro trick. See https://en.wikipedia.org/wiki/X_Macro */ ++#define SSE2NEON_AES_H0(x) (x) ++static const uint8_t _sse2neon_sbox[256] = SSE2NEON_AES_SBOX(SSE2NEON_AES_H0); ++static const uint8_t _sse2neon_rsbox[256] = SSE2NEON_AES_RSBOX(SSE2NEON_AES_H0); ++#undef SSE2NEON_AES_H0 ++ ++/* x_time function and matrix multiply function */ ++#if !defined(__aarch64__) && !defined(_M_ARM64) ++#define SSE2NEON_XT(x) (((x) << 1) ^ ((((x) >> 7) & 1) * 0x1b)) ++#define SSE2NEON_MULTIPLY(x, y) \ ++ (((y & 1) * x) ^ ((y >> 1 & 1) * SSE2NEON_XT(x)) ^ \ ++ ((y >> 2 & 1) * SSE2NEON_XT(SSE2NEON_XT(x))) ^ \ ++ ((y >> 3 & 1) * SSE2NEON_XT(SSE2NEON_XT(SSE2NEON_XT(x)))) ^ \ ++ ((y >> 4 & 1) * SSE2NEON_XT(SSE2NEON_XT(SSE2NEON_XT(SSE2NEON_XT(x)))))) ++#endif ++ ++// In the absence of crypto extensions, implement aesenc using regular NEON ++// intrinsics instead. See: ++// https://www.workofard.com/2017/01/accelerated-aes-for-the-arm64-linux-kernel/ ++// https://www.workofard.com/2017/07/ghash-for-low-end-cores/ and ++// for more information. ++FORCE_INLINE __m128i _mm_aesenc_si128(__m128i a, __m128i RoundKey) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ static const uint8_t shift_rows[] = { ++ 0x0, 0x5, 0xa, 0xf, 0x4, 0x9, 0xe, 0x3, ++ 0x8, 0xd, 0x2, 0x7, 0xc, 0x1, 0x6, 0xb, ++ }; ++ static const uint8_t ror32by8[] = { ++ 0x1, 0x2, 0x3, 0x0, 0x5, 0x6, 0x7, 0x4, ++ 0x9, 0xa, 0xb, 0x8, 0xd, 0xe, 0xf, 0xc, ++ }; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(a); ++ ++ /* shift rows */ ++ w = vqtbl1q_u8(w, vld1q_u8(shift_rows)); ++ ++ /* sub bytes */ ++ // Here, we separate the whole 256-bytes table into 4 64-bytes tables, and ++ // look up each of the table. After each lookup, we load the next table ++ // which locates at the next 64-bytes. In the meantime, the index in the ++ // table would be smaller than it was, so the index parameters of ++ // `vqtbx4q_u8()` need to be added the same constant as the loaded tables. ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_sbox), w); ++ // 'w-0x40' equals to 'vsubq_u8(w, vdupq_n_u8(0x40))' ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0xc0), w - 0xc0); ++ ++ /* mix columns */ ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w ^= (uint8x16_t) vrev32q_u16((uint16x8_t) v); ++ w ^= vqtbl1q_u8(v ^ w, vld1q_u8(ror32by8)); ++ ++ /* add round key */ ++ return vreinterpretq_m128i_u8(w) ^ RoundKey; ++ ++#else /* ARMv7-A implementation for a table-based AES */ ++#define SSE2NEON_AES_B2W(b0, b1, b2, b3) \ ++ (((uint32_t) (b3) << 24) | ((uint32_t) (b2) << 16) | \ ++ ((uint32_t) (b1) << 8) | (uint32_t) (b0)) ++// multiplying 'x' by 2 in GF(2^8) ++#define SSE2NEON_AES_F2(x) ((x << 1) ^ (((x >> 7) & 1) * 0x011b /* WPOLY */)) ++// multiplying 'x' by 3 in GF(2^8) ++#define SSE2NEON_AES_F3(x) (SSE2NEON_AES_F2(x) ^ x) ++#define SSE2NEON_AES_U0(p) \ ++ SSE2NEON_AES_B2W(SSE2NEON_AES_F2(p), p, p, SSE2NEON_AES_F3(p)) ++#define SSE2NEON_AES_U1(p) \ ++ SSE2NEON_AES_B2W(SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p), p, p) ++#define SSE2NEON_AES_U2(p) \ ++ SSE2NEON_AES_B2W(p, SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p), p) ++#define SSE2NEON_AES_U3(p) \ ++ SSE2NEON_AES_B2W(p, p, SSE2NEON_AES_F3(p), SSE2NEON_AES_F2(p)) ++ ++ // this generates a table containing every possible permutation of ++ // shift_rows() and sub_bytes() with mix_columns(). ++ static const uint32_t ALIGN_STRUCT(16) aes_table[4][256] = { ++ SSE2NEON_AES_SBOX(SSE2NEON_AES_U0), ++ SSE2NEON_AES_SBOX(SSE2NEON_AES_U1), ++ SSE2NEON_AES_SBOX(SSE2NEON_AES_U2), ++ SSE2NEON_AES_SBOX(SSE2NEON_AES_U3), ++ }; ++#undef SSE2NEON_AES_B2W ++#undef SSE2NEON_AES_F2 ++#undef SSE2NEON_AES_F3 ++#undef SSE2NEON_AES_U0 ++#undef SSE2NEON_AES_U1 ++#undef SSE2NEON_AES_U2 ++#undef SSE2NEON_AES_U3 ++ ++ uint32_t x0 = _mm_cvtsi128_si32(a); // get a[31:0] ++ uint32_t x1 = ++ _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0x55)); // get a[63:32] ++ uint32_t x2 = ++ _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0xAA)); // get a[95:64] ++ uint32_t x3 = ++ _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0xFF)); // get a[127:96] ++ ++ // finish the modulo addition step in mix_columns() ++ __m128i out = _mm_set_epi32( ++ (aes_table[0][x3 & 0xff] ^ aes_table[1][(x0 >> 8) & 0xff] ^ ++ aes_table[2][(x1 >> 16) & 0xff] ^ aes_table[3][x2 >> 24]), ++ (aes_table[0][x2 & 0xff] ^ aes_table[1][(x3 >> 8) & 0xff] ^ ++ aes_table[2][(x0 >> 16) & 0xff] ^ aes_table[3][x1 >> 24]), ++ (aes_table[0][x1 & 0xff] ^ aes_table[1][(x2 >> 8) & 0xff] ^ ++ aes_table[2][(x3 >> 16) & 0xff] ^ aes_table[3][x0 >> 24]), ++ (aes_table[0][x0 & 0xff] ^ aes_table[1][(x1 >> 8) & 0xff] ^ ++ aes_table[2][(x2 >> 16) & 0xff] ^ aes_table[3][x3 >> 24])); ++ ++ return _mm_xor_si128(out, RoundKey); ++#endif ++} ++ ++// Perform one round of an AES decryption flow on data (state) in a using the ++// round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesdec_si128 ++FORCE_INLINE __m128i _mm_aesdec_si128(__m128i a, __m128i RoundKey) ++{ ++#if defined(__aarch64__) ++ static const uint8_t inv_shift_rows[] = { ++ 0x0, 0xd, 0xa, 0x7, 0x4, 0x1, 0xe, 0xb, ++ 0x8, 0x5, 0x2, 0xf, 0xc, 0x9, 0x6, 0x3, ++ }; ++ static const uint8_t ror32by8[] = { ++ 0x1, 0x2, 0x3, 0x0, 0x5, 0x6, 0x7, 0x4, ++ 0x9, 0xa, 0xb, 0x8, 0xd, 0xe, 0xf, 0xc, ++ }; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(a); ++ ++ // inverse shift rows ++ w = vqtbl1q_u8(w, vld1q_u8(inv_shift_rows)); ++ ++ // inverse sub bytes ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_rsbox), w); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0xc0), w - 0xc0); ++ ++ // inverse mix columns ++ // multiplying 'v' by 4 in GF(2^8) ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w = (w << 1) ^ (uint8x16_t) (((int8x16_t) w >> 7) & 0x1b); ++ v ^= w; ++ v ^= (uint8x16_t) vrev32q_u16((uint16x8_t) w); ++ ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & ++ 0x1b); // multiplying 'v' by 2 in GF(2^8) ++ w ^= (uint8x16_t) vrev32q_u16((uint16x8_t) v); ++ w ^= vqtbl1q_u8(v ^ w, vld1q_u8(ror32by8)); ++ ++ // add round key ++ return vreinterpretq_m128i_u8(w) ^ RoundKey; ++ ++#else /* ARMv7-A NEON implementation */ ++ /* FIXME: optimized for NEON */ ++ uint8_t i, e, f, g, h, v[4][4]; ++ uint8_t *_a = (uint8_t *) &a; ++ for (i = 0; i < 16; ++i) { ++ v[((i / 4) + (i % 4)) % 4][i % 4] = _sse2neon_rsbox[_a[i]]; ++ } ++ ++ // inverse mix columns ++ for (i = 0; i < 4; ++i) { ++ e = v[i][0]; ++ f = v[i][1]; ++ g = v[i][2]; ++ h = v[i][3]; ++ ++ v[i][0] = SSE2NEON_MULTIPLY(e, 0x0e) ^ SSE2NEON_MULTIPLY(f, 0x0b) ^ ++ SSE2NEON_MULTIPLY(g, 0x0d) ^ SSE2NEON_MULTIPLY(h, 0x09); ++ v[i][1] = SSE2NEON_MULTIPLY(e, 0x09) ^ SSE2NEON_MULTIPLY(f, 0x0e) ^ ++ SSE2NEON_MULTIPLY(g, 0x0b) ^ SSE2NEON_MULTIPLY(h, 0x0d); ++ v[i][2] = SSE2NEON_MULTIPLY(e, 0x0d) ^ SSE2NEON_MULTIPLY(f, 0x09) ^ ++ SSE2NEON_MULTIPLY(g, 0x0e) ^ SSE2NEON_MULTIPLY(h, 0x0b); ++ v[i][3] = SSE2NEON_MULTIPLY(e, 0x0b) ^ SSE2NEON_MULTIPLY(f, 0x0d) ^ ++ SSE2NEON_MULTIPLY(g, 0x09) ^ SSE2NEON_MULTIPLY(h, 0x0e); ++ } ++ ++ return vreinterpretq_m128i_u8(vld1q_u8((uint8_t *) v)) ^ RoundKey; ++#endif ++} ++ ++// Perform the last round of an AES encryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesenclast_si128 ++FORCE_INLINE __m128i _mm_aesenclast_si128(__m128i a, __m128i RoundKey) ++{ ++#if defined(__aarch64__) ++ static const uint8_t shift_rows[] = { ++ 0x0, 0x5, 0xa, 0xf, 0x4, 0x9, 0xe, 0x3, ++ 0x8, 0xd, 0x2, 0x7, 0xc, 0x1, 0x6, 0xb, ++ }; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(a); ++ ++ // shift rows ++ w = vqtbl1q_u8(w, vld1q_u8(shift_rows)); ++ ++ // sub bytes ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_sbox), w); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0xc0), w - 0xc0); ++ ++ // add round key ++ return vreinterpretq_m128i_u8(v) ^ RoundKey; ++ ++#else /* ARMv7-A implementation */ ++ uint8_t v[16] = { ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 0)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 5)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 10)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 15)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 4)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 9)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 14)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 3)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 8)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 13)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 2)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 7)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 12)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 1)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 6)], ++ _sse2neon_sbox[vgetq_lane_u8(vreinterpretq_u8_m128i(a), 11)], ++ }; ++ ++ return vreinterpretq_m128i_u8(vld1q_u8(v)) ^ RoundKey; ++#endif ++} ++ ++// Perform the last round of an AES decryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesdeclast_si128 ++FORCE_INLINE __m128i _mm_aesdeclast_si128(__m128i a, __m128i RoundKey) ++{ ++#if defined(__aarch64__) ++ static const uint8_t inv_shift_rows[] = { ++ 0x0, 0xd, 0xa, 0x7, 0x4, 0x1, 0xe, 0xb, ++ 0x8, 0x5, 0x2, 0xf, 0xc, 0x9, 0x6, 0x3, ++ }; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(a); ++ ++ // inverse shift rows ++ w = vqtbl1q_u8(w, vld1q_u8(inv_shift_rows)); ++ ++ // inverse sub bytes ++ v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_rsbox), w); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_rsbox + 0xc0), w - 0xc0); ++ ++ // add round key ++ return vreinterpretq_m128i_u8(v) ^ RoundKey; ++ ++#else /* ARMv7-A NEON implementation */ ++ /* FIXME: optimized for NEON */ ++ uint8_t v[4][4]; ++ uint8_t *_a = (uint8_t *) &a; ++ for (int i = 0; i < 16; ++i) { ++ v[((i / 4) + (i % 4)) % 4][i % 4] = _sse2neon_rsbox[_a[i]]; ++ } ++ ++ return vreinterpretq_m128i_u8(vld1q_u8((uint8_t *) v)) ^ RoundKey; ++#endif ++} ++ ++// Perform the InvMixColumns transformation on a and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesimc_si128 ++FORCE_INLINE __m128i _mm_aesimc_si128(__m128i a) ++{ ++#if defined(__aarch64__) ++ static const uint8_t ror32by8[] = { ++ 0x1, 0x2, 0x3, 0x0, 0x5, 0x6, 0x7, 0x4, ++ 0x9, 0xa, 0xb, 0x8, 0xd, 0xe, 0xf, 0xc, ++ }; ++ uint8x16_t v = vreinterpretq_u8_m128i(a); ++ uint8x16_t w; ++ ++ // multiplying 'v' by 4 in GF(2^8) ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w = (w << 1) ^ (uint8x16_t) (((int8x16_t) w >> 7) & 0x1b); ++ v ^= w; ++ v ^= (uint8x16_t) vrev32q_u16((uint16x8_t) w); ++ ++ // multiplying 'v' by 2 in GF(2^8) ++ w = (v << 1) ^ (uint8x16_t) (((int8x16_t) v >> 7) & 0x1b); ++ w ^= (uint8x16_t) vrev32q_u16((uint16x8_t) v); ++ w ^= vqtbl1q_u8(v ^ w, vld1q_u8(ror32by8)); ++ return vreinterpretq_m128i_u8(w); ++ ++#else /* ARMv7-A NEON implementation */ ++ uint8_t i, e, f, g, h, v[4][4]; ++ vst1q_u8((uint8_t *) v, vreinterpretq_u8_m128i(a)); ++ for (i = 0; i < 4; ++i) { ++ e = v[i][0]; ++ f = v[i][1]; ++ g = v[i][2]; ++ h = v[i][3]; ++ ++ v[i][0] = SSE2NEON_MULTIPLY(e, 0x0e) ^ SSE2NEON_MULTIPLY(f, 0x0b) ^ ++ SSE2NEON_MULTIPLY(g, 0x0d) ^ SSE2NEON_MULTIPLY(h, 0x09); ++ v[i][1] = SSE2NEON_MULTIPLY(e, 0x09) ^ SSE2NEON_MULTIPLY(f, 0x0e) ^ ++ SSE2NEON_MULTIPLY(g, 0x0b) ^ SSE2NEON_MULTIPLY(h, 0x0d); ++ v[i][2] = SSE2NEON_MULTIPLY(e, 0x0d) ^ SSE2NEON_MULTIPLY(f, 0x09) ^ ++ SSE2NEON_MULTIPLY(g, 0x0e) ^ SSE2NEON_MULTIPLY(h, 0x0b); ++ v[i][3] = SSE2NEON_MULTIPLY(e, 0x0b) ^ SSE2NEON_MULTIPLY(f, 0x0d) ^ ++ SSE2NEON_MULTIPLY(g, 0x09) ^ SSE2NEON_MULTIPLY(h, 0x0e); ++ } ++ ++ return vreinterpretq_m128i_u8(vld1q_u8((uint8_t *) v)); ++#endif ++} ++ ++// Assist in expanding the AES cipher key by computing steps towards generating ++// a round key for encryption cipher using data from a and an 8-bit round ++// constant specified in imm8, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aeskeygenassist_si128 ++// ++// Emits the Advanced Encryption Standard (AES) instruction aeskeygenassist. ++// This instruction generates a round key for AES encryption. See ++// https://kazakov.life/2017/11/01/cryptocurrency-mining-on-ios-devices/ ++// for details. ++FORCE_INLINE __m128i _mm_aeskeygenassist_si128(__m128i a, const int rcon) ++{ ++#if defined(__aarch64__) ++ uint8x16_t _a = vreinterpretq_u8_m128i(a); ++ uint8x16_t v = vqtbl4q_u8(_sse2neon_vld1q_u8_x4(_sse2neon_sbox), _a); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x40), _a - 0x40); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0x80), _a - 0x80); ++ v = vqtbx4q_u8(v, _sse2neon_vld1q_u8_x4(_sse2neon_sbox + 0xc0), _a - 0xc0); ++ ++ uint32x4_t v_u32 = vreinterpretq_u32_u8(v); ++ uint32x4_t ror_v = vorrq_u32(vshrq_n_u32(v_u32, 8), vshlq_n_u32(v_u32, 24)); ++ uint32x4_t ror_xor_v = veorq_u32(ror_v, vdupq_n_u32(rcon)); ++ ++ return vreinterpretq_m128i_u32(vtrn2q_u32(v_u32, ror_xor_v)); ++ ++#else /* ARMv7-A NEON implementation */ ++ uint32_t X1 = _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0x55)); ++ uint32_t X3 = _mm_cvtsi128_si32(_mm_shuffle_epi32(a, 0xFF)); ++ for (int i = 0; i < 4; ++i) { ++ ((uint8_t *) &X1)[i] = _sse2neon_sbox[((uint8_t *) &X1)[i]]; ++ ((uint8_t *) &X3)[i] = _sse2neon_sbox[((uint8_t *) &X3)[i]]; ++ } ++ return _mm_set_epi32(((X3 >> 8) | (X3 << 24)) ^ rcon, X3, ++ ((X1 >> 8) | (X1 << 24)) ^ rcon, X1); ++#endif ++} ++#undef SSE2NEON_AES_SBOX ++#undef SSE2NEON_AES_RSBOX ++ ++#if defined(__aarch64__) ++#undef SSE2NEON_XT ++#undef SSE2NEON_MULTIPLY ++#endif ++ ++#else /* __ARM_FEATURE_CRYPTO */ ++// Implements equivalent of 'aesenc' by combining AESE (with an empty key) and ++// AESMC and then manually applying the real key as an xor operation. This ++// unfortunately means an additional xor op; the compiler should be able to ++// optimize this away for repeated calls however. See ++// https://blog.michaelbrase.com/2018/05/08/emulating-x86-aes-intrinsics-on-armv8-a ++// for more details. ++FORCE_INLINE __m128i _mm_aesenc_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8(veorq_u8( ++ vaesmcq_u8(vaeseq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0))), ++ vreinterpretq_u8_m128i(b))); ++} ++ ++// Perform one round of an AES decryption flow on data (state) in a using the ++// round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesdec_si128 ++FORCE_INLINE __m128i _mm_aesdec_si128(__m128i a, __m128i RoundKey) ++{ ++ return vreinterpretq_m128i_u8(veorq_u8( ++ vaesimcq_u8(vaesdq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0))), ++ vreinterpretq_u8_m128i(RoundKey))); ++} ++ ++// Perform the last round of an AES encryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesenclast_si128 ++FORCE_INLINE __m128i _mm_aesenclast_si128(__m128i a, __m128i RoundKey) ++{ ++ return _mm_xor_si128(vreinterpretq_m128i_u8(vaeseq_u8( ++ vreinterpretq_u8_m128i(a), vdupq_n_u8(0))), ++ RoundKey); ++} ++ ++// Perform the last round of an AES decryption flow on data (state) in a using ++// the round key in RoundKey, and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesdeclast_si128 ++FORCE_INLINE __m128i _mm_aesdeclast_si128(__m128i a, __m128i RoundKey) ++{ ++ return vreinterpretq_m128i_u8( ++ veorq_u8(vaesdq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0)), ++ vreinterpretq_u8_m128i(RoundKey))); ++} ++ ++// Perform the InvMixColumns transformation on a and store the result in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aesimc_si128 ++FORCE_INLINE __m128i _mm_aesimc_si128(__m128i a) ++{ ++ return vreinterpretq_m128i_u8(vaesimcq_u8(vreinterpretq_u8_m128i(a))); ++} ++ ++// Assist in expanding the AES cipher key by computing steps towards generating ++// a round key for encryption cipher using data from a and an 8-bit round ++// constant specified in imm8, and store the result in dst." ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_aeskeygenassist_si128 ++FORCE_INLINE __m128i _mm_aeskeygenassist_si128(__m128i a, const int rcon) ++{ ++ // AESE does ShiftRows and SubBytes on A ++ uint8x16_t u8 = vaeseq_u8(vreinterpretq_u8_m128i(a), vdupq_n_u8(0)); ++ ++#if !defined(_MSC_VER) || defined(__clang__) ++ uint8x16_t dest = { ++ // Undo ShiftRows step from AESE and extract X1 and X3 ++ u8[0x4], u8[0x1], u8[0xE], u8[0xB], // SubBytes(X1) ++ u8[0x1], u8[0xE], u8[0xB], u8[0x4], // ROT(SubBytes(X1)) ++ u8[0xC], u8[0x9], u8[0x6], u8[0x3], // SubBytes(X3) ++ u8[0x9], u8[0x6], u8[0x3], u8[0xC], // ROT(SubBytes(X3)) ++ }; ++ uint32x4_t r = {0, (unsigned) rcon, 0, (unsigned) rcon}; ++ return vreinterpretq_m128i_u8(dest) ^ vreinterpretq_m128i_u32(r); ++#else ++ // We have to do this hack because MSVC is strictly adhering to the CPP ++ // standard, in particular C++03 8.5.1 sub-section 15, which states that ++ // unions must be initialized by their first member type. ++ ++ // As per the Windows ARM64 ABI, it is always little endian, so this works ++ __n128 dest{ ++ ((uint64_t) u8.n128_u8[0x4] << 0) | ((uint64_t) u8.n128_u8[0x1] << 8) | ++ ((uint64_t) u8.n128_u8[0xE] << 16) | ++ ((uint64_t) u8.n128_u8[0xB] << 24) | ++ ((uint64_t) u8.n128_u8[0x1] << 32) | ++ ((uint64_t) u8.n128_u8[0xE] << 40) | ++ ((uint64_t) u8.n128_u8[0xB] << 48) | ++ ((uint64_t) u8.n128_u8[0x4] << 56), ++ ((uint64_t) u8.n128_u8[0xC] << 0) | ((uint64_t) u8.n128_u8[0x9] << 8) | ++ ((uint64_t) u8.n128_u8[0x6] << 16) | ++ ((uint64_t) u8.n128_u8[0x3] << 24) | ++ ((uint64_t) u8.n128_u8[0x9] << 32) | ++ ((uint64_t) u8.n128_u8[0x6] << 40) | ++ ((uint64_t) u8.n128_u8[0x3] << 48) | ++ ((uint64_t) u8.n128_u8[0xC] << 56)}; ++ ++ dest.n128_u32[1] = dest.n128_u32[1] ^ rcon; ++ dest.n128_u32[3] = dest.n128_u32[3] ^ rcon; ++ ++ return dest; ++#endif ++} ++#endif ++ ++/* Others */ ++ ++// Perform a carry-less multiplication of two 64-bit integers, selected from a ++// and b according to imm8, and store the results in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_clmulepi64_si128 ++FORCE_INLINE __m128i _mm_clmulepi64_si128(__m128i _a, __m128i _b, const int imm) ++{ ++ uint64x2_t a = vreinterpretq_u64_m128i(_a); ++ uint64x2_t b = vreinterpretq_u64_m128i(_b); ++ switch (imm & 0x11) { ++ case 0x00: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_low_u64(a), vget_low_u64(b))); ++ case 0x01: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_high_u64(a), vget_low_u64(b))); ++ case 0x10: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_low_u64(a), vget_high_u64(b))); ++ case 0x11: ++ return vreinterpretq_m128i_u64( ++ _sse2neon_vmull_p64(vget_high_u64(a), vget_high_u64(b))); ++ default: ++ abort(); ++ } ++} ++ ++FORCE_INLINE unsigned int _sse2neon_mm_get_denormals_zero_mode(void) ++{ ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ return r.field.bit24 ? _MM_DENORMALS_ZERO_ON : _MM_DENORMALS_ZERO_OFF; ++} ++ ++// Count the number of bits set to 1 in unsigned 32-bit integer a, and ++// return that count in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_popcnt_u32 ++FORCE_INLINE int _mm_popcnt_u32(unsigned int a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#if __has_builtin(__builtin_popcount) ++ return __builtin_popcount(a); ++#elif defined(_MSC_VER) ++ return _CountOneBits(a); ++#else ++ return (int) vaddlv_u8(vcnt_u8(vcreate_u8((uint64_t) a))); ++#endif ++#else ++ uint32_t count = 0; ++ uint8x8_t input_val, count8x8_val; ++ uint16x4_t count16x4_val; ++ uint32x2_t count32x2_val; ++ ++ input_val = vld1_u8((uint8_t *) &a); ++ count8x8_val = vcnt_u8(input_val); ++ count16x4_val = vpaddl_u8(count8x8_val); ++ count32x2_val = vpaddl_u16(count16x4_val); ++ ++ vst1_u32(&count, count32x2_val); ++ return count; ++#endif ++} ++ ++// Count the number of bits set to 1 in unsigned 64-bit integer a, and ++// return that count in dst. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_popcnt_u64 ++FORCE_INLINE int64_t _mm_popcnt_u64(uint64_t a) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++#if __has_builtin(__builtin_popcountll) ++ return __builtin_popcountll(a); ++#elif defined(_MSC_VER) ++ return _CountOneBits64(a); ++#else ++ return (int64_t) vaddlv_u8(vcnt_u8(vcreate_u8(a))); ++#endif ++#else ++ uint64_t count = 0; ++ uint8x8_t input_val, count8x8_val; ++ uint16x4_t count16x4_val; ++ uint32x2_t count32x2_val; ++ uint64x1_t count64x1_val; ++ ++ input_val = vld1_u8((uint8_t *) &a); ++ count8x8_val = vcnt_u8(input_val); ++ count16x4_val = vpaddl_u8(count8x8_val); ++ count32x2_val = vpaddl_u16(count16x4_val); ++ count64x1_val = vpaddl_u32(count32x2_val); ++ vst1_u64(&count, count64x1_val); ++ return count; ++#endif ++} ++ ++FORCE_INLINE_OPTNONE void _sse2neon_mm_set_denormals_zero_mode( ++ unsigned int flag) ++{ ++ // AArch32 Advanced SIMD arithmetic always uses the Flush-to-zero setting, ++ // regardless of the value of the FZ bit. ++ union { ++ fpcr_bitfield field; ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t value; ++#else ++ uint32_t value; ++#endif ++ } r; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ r.value = _sse2neon_get_fpcr(); ++#else ++ __asm__ __volatile__("vmrs %0, FPSCR" : "=r"(r.value)); /* read */ ++#endif ++ ++ r.field.bit24 = (flag & _MM_DENORMALS_ZERO_MASK) == _MM_DENORMALS_ZERO_ON; ++ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ _sse2neon_set_fpcr(r.value); ++#else ++ __asm__ __volatile__("vmsr FPSCR, %0" ::"r"(r)); /* write */ ++#endif ++} ++ ++// Return the current 64-bit value of the processor's time-stamp counter. ++// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=rdtsc ++FORCE_INLINE uint64_t _rdtsc(void) ++{ ++#if defined(__aarch64__) || defined(_M_ARM64) ++ uint64_t val; ++ ++ /* According to ARM DDI 0487F.c, from Armv8.0 to Armv8.5 inclusive, the ++ * system counter is at least 56 bits wide; from Armv8.6, the counter ++ * must be 64 bits wide. So the system counter could be less than 64 ++ * bits wide and it is attributed with the flag 'cap_user_time_short' ++ * is true. ++ */ ++#if defined(_MSC_VER) && !defined(__clang__) ++ val = _ReadStatusReg(ARM64_SYSREG(3, 3, 14, 0, 2)); ++#else ++ __asm__ __volatile__("mrs %0, cntvct_el0" : "=r"(val)); ++#endif ++ ++ return val; ++#else ++ uint32_t pmccntr, pmuseren, pmcntenset; ++ // Read the user mode Performance Monitoring Unit (PMU) ++ // User Enable Register (PMUSERENR) access permissions. ++ __asm__ __volatile__("mrc p15, 0, %0, c9, c14, 0" : "=r"(pmuseren)); ++ if (pmuseren & 1) { // Allows reading PMUSERENR for user mode code. ++ __asm__ __volatile__("mrc p15, 0, %0, c9, c12, 1" : "=r"(pmcntenset)); ++ if (pmcntenset & 0x80000000UL) { // Is it counting? ++ __asm__ __volatile__("mrc p15, 0, %0, c9, c13, 0" : "=r"(pmccntr)); ++ // The counter is set up to count every 64th cycle ++ return (uint64_t) (pmccntr) << 6; ++ } ++ } ++ ++ // Fallback to syscall as we can't enable PMUSERENR in user mode. ++ struct timeval tv; ++ gettimeofday(&tv, NULL); ++ return (uint64_t) (tv.tv_sec) * 1000000 + tv.tv_usec; ++#endif ++} ++ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma pop_macro("ALIGN_STRUCT") ++#pragma pop_macro("FORCE_INLINE") ++#pragma pop_macro("FORCE_INLINE_OPTNONE") ++#endif ++ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC pop_options ++#endif ++ ++#endif +diff --git c/src/stdinclude.h i/src/stdinclude.h +index 2b8f6d3..7802321 100644 +--- c/src/stdinclude.h ++++ i/src/stdinclude.h +@@ -6,11 +6,16 @@ + #include + #include + #include +-#include + #include + #include "pthread.h" + #include "ProgressBar.hpp" + ++#ifdef __ARM_NEON ++#include "sse2neon.h" ++#else ++#include ++#endif ++ + #if defined _WIN32 || defined _WIN64 + #else + #include diff --git a/recipes/rapidshapes/meta.yaml b/recipes/rapidshapes/meta.yaml index 33b9844539cdf..4d47e3bf59d6d 100644 --- a/recipes/rapidshapes/meta.yaml +++ b/recipes/rapidshapes/meta.yaml @@ -1,20 +1,21 @@ -{% set version = "2.3.2" %} +{% set fold_grammars_version = "2.3.2" %} +{% set rapidshapes_version = "2.1.0" %} {% set packagename = "rapidshapes" %} {% set sha256 = "d3e6cc8d2ecd31d4764b41fea589b98c637ff227d7ab3dcfe66f2ad3f24dece5" %} package: name: {{ packagename }} - version: 2.1.0 + version: {{ rapidshapes_version }} source: sha256: {{ sha256 }} # the repository "fold-grammars" contains sources for several programs, i.e. pKiss, RNAshapes, ... # thus, the version number does not correspond to the {{ packagename }} version number #url: https://github.com/jlab/fold-grammars/archive/{{ version }}.tar.gz - url: https://github.com/jlab/fold-grammars/archive/refs/tags/{{ version }}.tar.gz + url: https://github.com/jlab/fold-grammars/archive/refs/tags/{{ fold_grammars_version }}.tar.gz build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('rapidshapes', max_pin="x") }} diff --git a/recipes/rasusa/meta.yaml b/recipes/rasusa/meta.yaml index c8d0778f8e87c..33a3a87765c19 100644 --- a/recipes/rasusa/meta.yaml +++ b/recipes/rasusa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.0" %} +{% set version = "2.1.0" %} {% set name = "rasusa" %} package: @@ -7,10 +7,10 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 7921a94cb5c30c194c3d966e7dd80d034a9cf840d853b3fe1725d90d5800e2bd + sha256: 6d6d97f381bea5a4d070ef7bc132224f3c5c97bc366109261182aa9bc5736d69 build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('rasusa', max_pin="x.x") }} diff --git a/recipes/ratatosk/build.sh b/recipes/ratatosk/build.sh index de6321ef19764..b9db46d931856 100644 --- a/recipes/ratatosk/build.sh +++ b/recipes/ratatosk/build.sh @@ -1,27 +1,25 @@ -#!/bin/bash -set -x +#!/bin/bash -ex -export INCLUDE_PATH="${PREFIX}/include" -export LIBRARY_PATH="${PREFIX}/lib" +mkdir -p "${PREFIX}/bin" + +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CXXFLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64" +export CXXFLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64 -I${PREFIX}/include" -if [ `uname` == Darwin ]; then - # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk for -D_LIBCPP_DISABLE_AVAILABILITY - export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" - export CONFIG_ARGS="-DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" - else - export CONFIG_ARGS="-DCMAKE_INSTALL_PREFIX=${PREFIX}" +if [[ `uname` == Darwin ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" + export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" +else + export CONFIG_ARGS="" fi -mkdir -p "${PREFIX}/bin" - cmake -S . -B build \ - "${CONFIG_ARGS}" \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ -DCMAKE_BUILD_TYPE=Release \ - -DCMAKE_C_COMPILER="${CC}" \ -DCMAKE_CXX_COMPILER="${CXX}" \ - -DCMAKE_CXX_FLAGS="${CXXFLAGS}" + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + "${CONFIG_ARGS}" -cmake --build build/ --target install -j "${CPU_COUNT}" +cmake --build build/ --target install -j "${CPU_COUNT}" -v diff --git a/recipes/ratatosk/meta.yaml b/recipes/ratatosk/meta.yaml index bb8c9634d72bd..1a89715c74931 100644 --- a/recipes/ratatosk/meta.yaml +++ b/recipes/ratatosk/meta.yaml @@ -11,13 +11,15 @@ source: sha256: {{ sha256 }} patches: - cmakelists.patch -- url: https://github.com/pmelsted/bifrost/archive/refs/tags/v1.2.1.tar.gz - sha256: fe93080ef3ea71ff009fc206b5c17dd40fbfd18293000621a83d7d947dfedf1a +- url: https://github.com/pmelsted/bifrost/archive/refs/tags/v1.3.5.tar.gz + sha256: e1b2491328b0cc1a32e433a8a9780f05547fa4b8d674b58abdda9ac8809f5341 folder: Bifrost build: - number: 0 + number: 1 skip: True # [osx] + run_exports: + - {{ pin_subpackage('ratatosk', max_pin="x.x") }} requirements: build: @@ -34,12 +36,17 @@ test: - 'Ratatosk index --help' about: - home: https://github.com/DecodeGenetics/Ratatosk - license: BSD-2-Clause + home: "https://github.com/DecodeGenetics/Ratatosk" + license: "BSD-2-Clause" + license_family: BSD license_file: LICENSE - summary: "Hybrid error correction of long reads using colored de Bruijn graphs" + summary: "Hybrid error correction of long reads using colored de Bruijn graphs." + dev_url: "https://github.com/DecodeGenetics/Ratatosk" + doc_url: "https://github.com/DecodeGenetics/Ratatosk/blob/v{{ version }}/README.md" extra: identifiers: - biotools:ratatosk - doi:10.1186/s13059-020-02244-4 + additional-platforms: + - linux-aarch64 diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index 32e29527edb1f..aabaddcf9f40e 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.9" %} -{% set sha256 = "247b9e0cabe5e4bd454653dbc1bfd0337b381b1e8d595bdd6d409b5693a57bda" %} +{% set version = "1.0" %} +{% set sha256 = "04d94acb727cadf096adf7f023e629361fb6340ef47d47de8977a0d6b76f64aa" %} package: name: {{ name|lower }} @@ -36,6 +36,7 @@ requirements: - upsetplot >=0.9 - packaging - scikit-learn + - goatools test: commands: diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index 2efe7685617b8..fd82baed37726 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recentrifuge" %} -{% set version = "1.14.1" %} +{% set version = "1.15.0" %} package: name: {{ name }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: b9ec5f04b256d24fc768818069838b44d576715b8093f2566fe70b129e659401 + sha256: adacf412188433f4bf54477872218d27340475eb4876af710f2d9b7294d05496 requirements: host: diff --git a/recipes/recognizer/meta.yaml b/recipes/recognizer/meta.yaml index efcc7fb27632f..8d3f66805adc2 100644 --- a/recipes/recognizer/meta.yaml +++ b/recipes/recognizer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "recognizer" %} -{% set version = "1.10.1" %} -{% set sha256 = "1d97b521a5b8660e5dd1726c95b885bcdce53654d01a001d8e6522a9c76d81c2" %} +{% set version = "1.11.1" %} +{% set sha256 = "e385fb307fd64892629bcdad35d43d29ab0ea3703d20b0090e78b5cdaa83ea98" %} package: name: {{ name|lower }} diff --git a/recipes/relion/meta.yaml b/recipes/relion/meta.yaml index b790782ac6bbb..dd09e484e2da1 100644 --- a/recipes/relion/meta.yaml +++ b/recipes/relion/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.0.1" %} +{% set version = "4.0.2" %} package: name: relion @@ -6,10 +6,12 @@ package: source: url: https://github.com/3dem/relion/archive/refs/tags/{{ version }}.tar.gz - sha256: 0ebbd94ad922d7f457e3f3b81f5660e2691a845d9a53f0f1c9fbeb4e54cd5c17 + sha256: 7ccc941a6a885bd850efa8867ea908254d8dc260cf72cc24c375bb9f1d56bf91 build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage('relion', max_pin='x') }} requirements: build: diff --git a/recipes/reneo/meta.yaml b/recipes/reneo/meta.yaml index 1e51b31b26f33..1a5aa03f47493 100644 --- a/recipes/reneo/meta.yaml +++ b/recipes/reneo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "reneo" %} -{% set version = "0.4.0" %} +{% set version = "0.5.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: b74cdf3fca658b00c15db2e52e24877aa58fa43ba242323cc4d8f8fb292fbab7 + sha256: dff9242ae7f70050b2d0a52dc48f6a1252ed0346bef2488e79a9fc4954c25804 build: number: 0 diff --git a/recipes/repeatmasker/build.sh b/recipes/repeatmasker/build.sh index f35333fbfed79..a5bd9e199974f 100644 --- a/recipes/repeatmasker/build.sh +++ b/recipes/repeatmasker/build.sh @@ -1,9 +1,9 @@ #!/bin/bash -RM_DIR=${PREFIX}/share/RepeatMasker +RM_DIR="${PREFIX}/share/RepeatMasker" mkdir -p ${PREFIX}/bin mkdir -p ${RM_DIR} -cp -r * ${RM_DIR} +mv * ${RM_DIR} export LANGUAGE=en_US.UTF-8 export LANG=en_US.UTF-8 @@ -11,7 +11,10 @@ export LC_ALL=en_US.UTF-8 # configure cd ${RM_DIR} -perl ./configure -libdir ${RM_DIR}/Libraries -trf_prgm ${PREFIX}/bin/trf -rmblast_dir ${PREFIX}/bin/ -hmmer_dir ${PREFIX}/bin -abblast_dir ${PREFIX}/bin -crossmatch_dir ${PREFIX}/bin -default_search_engine rmblast +perl ./configure -libdir "${RM_DIR}/Libraries" -trf_prgm "${PREFIX}/bin/trf" \ + -rmblast_dir "${PREFIX}/bin" -hmmer_dir "${PREFIX}/bin" \ + -abblast_dir "${PREFIX}/bin" -crossmatch_dir "${PREFIX}/bin" \ + -default_search_engine rmblast # Delete huge Dfam file, will be downloaded by post-link.sh # Do it now only, because configure needs the full version @@ -20,15 +23,28 @@ echo "Placeholder file, should be replaced on Conda package installation." > ${R # ----- add tools within the bin ------ # add RepeatMasker -ln -s ${RM_DIR}/RepeatMasker ${PREFIX}/bin/RepeatMasker +chmod 0755 ${RM_DIR}/RepeatMasker ${RM_DIR}/DupMasker ${RM_DIR}/ProcessRepeats ${RM_DIR}/RepeatProteinMask +ln -sf ${RM_DIR}/RepeatMasker ${PREFIX}/bin/RepeatMasker # add other tools RM_OTHER_PROGRAMS="DupMasker ProcessRepeats RepeatProteinMask" for name in ${RM_OTHER_PROGRAMS} ; do - ln -s ${RM_DIR}/${name} ${PREFIX}/bin/${name} + ln -sf ${RM_DIR}/${name} ${PREFIX}/bin/${name} done # add all utils for name in ${RM_DIR}/util/* ; do - ln -s $name ${PREFIX}/bin/$(basename $name) + ln -sf $name ${PREFIX}/bin/$(basename $name) done + +# Fix perl shebang +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/RepeatMasker +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/DupMasker +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/ProcessRepeats +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/RepeatProteinMask +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/util/*.pl +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/*.pm +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/*.pl + +rm -rf ${RM_DIR}/util/*.bak +rm -rf ${RM_DIR}/*.bak diff --git a/recipes/repeatmasker/meta.yaml b/recipes/repeatmasker/meta.yaml index c837404507fa1..0fdf342d65868 100644 --- a/recipes/repeatmasker/meta.yaml +++ b/recipes/repeatmasker/meta.yaml @@ -1,20 +1,20 @@ {% set name = "repeatmasker" %} -{% set version = "4.1.5" %} -{% set sha256 = "16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f" %} +{% set version = "4.1.7p1" %} +{% set sha256 = "15222b39178f19c116282437190b64c5ba68f62b0f2044b3bbcbda5e02748993" %} package: name: {{ name }} version: {{ version }} source: - url: https://www.repeatmasker.org/RepeatMasker/RepeatMasker-{{ version }}.tar.gz + url: https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.7-p1.tar.gz sha256: {{ sha256 }} build: number: 1 noarch: generic run_exports: - - {{ pin_subpackage('repeatmasker', max_pin='x.x.x') }} + - {{ pin_subpackage('repeatmasker', max_pin='x') }} requirements: host: @@ -27,24 +27,21 @@ requirements: - trf - perl - h5py + - gzip # [osx] - wget test: -# pvanheus - disable file based tests for -# now - they don't work with Dockerized -# containers - 13/1/2017 -# files: -# - rm_input1.fasta -# - sample_repeats.fasta -# - test_md5.txt commands: - RepeatMasker | grep "RepeatMasker - Mask repetitive DNA" > /dev/null about: - home: https://www.repeatmasker.org - license: Open Software License v2.1 - summary: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. + home: "https://www.repeatmasker.org/RepeatMasker" + license: "Open Software License v2.1" + summary: "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences." + dev_url: "https://github.com/Dfam-consortium/RepeatMasker" + doc_url: "https://www.repeatmasker.org/RepeatMasker" extra: identifiers: - - biotools:RepeatMasker + - biotools:repeatmasker + - usegalaxy-eu:repeatmasker_wrapper diff --git a/recipes/repeatmasker/post-link.sh b/recipes/repeatmasker/post-link.sh old mode 100755 new mode 100644 index ac28ed8558b30..0034f2fb10a0f --- a/recipes/repeatmasker/post-link.sh +++ b/recipes/repeatmasker/post-link.sh @@ -1,17 +1,17 @@ #!/bin/bash -if [ -f /.dockerenv ]; then +if [[ -f /.dockerenv ]]; then cat >> "$PREFIX/.messages.txt" < ${PREFIX}/share/RepeatMasker/Libraries/Dfam.h5 -rm Dfam_curatedonly.h5.gz +wget -O Dfam-RepeatMasker.lib.gz https://www.dfam.org/releases/Dfam_3.8/families/Dfam-RepeatMasker.lib.gz +gunzip -c Dfam-RepeatMasker.lib.gz > ${PREFIX}/share/RepeatMasker/Libraries/RepeatMasker.lib +rm -rf Dfam-RepeatMasker.lib.gz EOF else - echo "Downloading Dfam_curatedonly.h5.gz from www.dfam.org" - wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz - gunzip -c Dfam_curatedonly.h5.gz > ${PREFIX}/share/RepeatMasker/Libraries/Dfam.h5 - rm Dfam_curatedonly.h5.gz + echo "Dfam-RepeatMasker.lib.gz from www.dfam.org" + wget -O Dfam-RepeatMasker.lib.gz https://www.dfam.org/releases/Dfam_3.8/families/Dfam-RepeatMasker.lib.gz + gunzip -c Dfam-RepeatMasker.lib.gz > ${PREFIX}/share/RepeatMasker/Libraries/RepeatMasker.lib + rm -rf Dfam-RepeatMasker.lib.gz fi diff --git a/recipes/repeatmasker/rm_input1.fasta b/recipes/repeatmasker/rm_input1.fasta deleted file mode 100644 index db351cab3a5aa..0000000000000 --- a/recipes/repeatmasker/rm_input1.fasta +++ /dev/null @@ -1,30 +0,0 @@ ->scaffold_1 -TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATCCAATATATTC -CTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGACATCCTCAGTGATTGAAGTGA -CAAAAAGTGGAGCGCACGCAGTGGTCATTACCCTCCAATGGTACTTCTAATTAAGGAAAG -ATTTTTTGCATTCACTGAGCAAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGG -GTCCATTAAACAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT -AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGCCCCAAATTGT -CTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATAATTGTGTTTCTCTCTAGATG -TGCGGTGTCCATCAAGACACTGGATGTCACGTGGTCACTCCTGTGAAGAGCGAACTGTGT -GGAACCCGAAGTACTGTGTGGTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGG -TGGTGAGAGCAGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC -TCTCATCTGCTCGTGTGTGTGTGTGTGTGTGTCCTTGTCAATGTCATTACACAATTTATG -TTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACATCTACTTTCTGTCACCTGATA -CCTCATACTTTACACTCTAATCCCTTTTTCCTTTCTAACTGCTGCTGTGTTAAGCTGTCA -TATTAATATACTAAATAATGATAATATTAATTCTAATAATGATAGTGAATGGAGATTCAC -AATGAAGAAACACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT -TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCAAGGCTGAGTC -TGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGGATTATGCTAGTTTGTGTGAG -ATTAGAGGTCCTGTTGTTACGAGCAAATCAGCAGTCAGCAGGGTAATCTAAATTACATTG -TTCTGTCGGCAATATCCTCTCCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCC -CCACAGTAGTGCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT -ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTGTGATTGTTGG -TGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGATCTCCTGGGATTTTCACACAC -GGCATTCTCTAGAGTTTACTCAGAACGGTGTGGAAAGCAAAAAAACATCCCGCGAGCTGC -AATCCTGCGGATGGAAACACCTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGAT -CAATCTGACAGAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA -AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTACAGCAGCAGAT -GAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACATCTCAGACTGCACAGGACACC -AAAACAAAAACACATCCTGTTTTCTACTGGTGGTAGAGTCACAATTTGGCAATAAGATAA -ATCCATGGACCCAACTTGCCTTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATG diff --git a/recipes/repeatmasker/sample_repeats.fasta b/recipes/repeatmasker/sample_repeats.fasta deleted file mode 100644 index 9f096d40313d6..0000000000000 --- a/recipes/repeatmasker/sample_repeats.fasta +++ /dev/null @@ -1,64 +0,0 @@ ->Asian_seabass_ONSAT_SB_Concensus_Lenght_170_bp -CGAAAAATTTAATAATTTAGGGGTCTTGAGCATGGGCGTGGTAAAATGCCCTCGGTAGCG -CCACCTACATTTTTAAACGGAACAGCCCCTCAAGCCCGTTGCGCCTAAAAATCTGAAAAT -CTGCACACATATGTAACATCCCATGACGCACCAAAAAGTCTCTTGGAGCCA ->Asian_seabass_MOSAT_SB_T_34a_satellite_DNA -TTTGTGACATCACTACATAGTTTGTTGAAAACGTAC ->Asian_seabass_MOSAT_SB_T_34b_satellite_DNA -TTTGTGACATCACACATAGTTGTGGGTCAGTAC  ->Sat_38 -AAAAAATGTCATAGTATAGTATGGCGTCAAAAAACATG ->Asian_seabass_Sat_217_Consensus_Length_217_bp -AGTAAACAAGCATTATGGTTGAAACCATAATTTCCTGTCGGGAGAGCCTTTCCCTCTTTT -GTGCACTGTATGCAATCCCAGAGTGTGAATAAGCGCTTTTCCAGCGTTTTGAGGCTTATT -CAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGACAAAGACAAACTAAGAACTCA -GCCACACGGACATGAAAGTTGTTTTACTTACAATATT ->Asian_seabass_Sat_217_Consensus_Length_427_bp -CCAGCGTTTTGAGGCTTATTCAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGAC -AAGACAAACTAAGAACTCAACACACTGACATGAAAGTTTCTATATTTCTATTAAAATAAA -CAAACATTATGGTTGAAACCATAATTTCATTTCGGGAGAGCCTTTCCCTCTTTGTGGCAC -TGTATGTAATCTGAAGTGTGAATAACGCTTTTCCCGCGTTTGAGGCTTATTCAGCTCAGA -ATGGCTTAATACTGCACTATCTGACCAGGACAAGACAAACTAAGAACTCAGCCACACGGA -CATGAAAGTTGTTTACTTTACAATATTAGTAAACAAGCATTATGGTTGAAACCATAATTT -CCTGTCGGGAAGAGCTTCCCTCTTTTTGTGCACTGTATGCAATCCCAGAGTGTGAATAAG -CGCTTTT ->Asian_seabass_Sat_LM_Consensus_Length_453_bp -CCCAACAAAATAGCACTTACTGCTTTCCAAATTCAAGTCTGTGCCTGTGTTAGGGTAATG -TTGGTGATAAATTGATGTACTTAGCTTATCCTGTGAAAATGGTGTAAAATGGCAGTCTCC -ATGTTTGTTGAAGAAACTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAG -AAATCATGAGTGGCTCTTATTGAAGTGATCAGAGTTGGACTCCATTAAGAAAATGGCTTT -CAATGTAGTCAGTTGCTTTGTCACTTAAAACTGCCCCAACAAGTAGCACTTACTGCAATT -TGGTAGTCAAAGTCAATGCTCAAGTTAAGGGTAATAGTAGTGACATAATAGAAAAATCTC -TAAATATATTTGCTGGCAGCTTTAATATACAGAATGAGTGCCATGATGAATTCTTGATAC -AGAACAGGGACTTCCAAAATCAGCCAACACTAA ->Asian_seabass_Sat_LM_Consensus_Length_218_bp -CCCAACAAAATAGCACTTACTGCTTTCCAAATTCAAGTCTGTGCCTGTGTTAGGGTAATG -TTGGTGATAAATTGATGTACTTAGCTTATCCTGTGAAAATGGTGTAAAATGGCAGTCTCC -TGTTTGTTGAAGAAACTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAGA -AATCATGAGTGGCTCTTATTGAAGTGATCAGAGTTGG ->Asian_seabass_Sat_LM Consensus_Length_150_bp -CTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAGAAATCATGAGTGGCTC -TTATTGAAGTGATCAGAGTTGGACTCCATTAAGAAAATGGCTTTCAATGTAGTCAGTTGC -TTTGTCACTTAAAACTGCCCCAACAAGTAGCA ->Asian_seabass_Sat_Unk_Consensus_Length_341_bp -GTTTGGGTAAAAATATTGTCTATTTACGAGCTATCCTCTATATATTTTTGATCTGATTAA -TAAATACCTCTAGCCCACAAACTGTGGTATTTTGCTATGTGGCAGTTCACCCGAAAGTCC -AGTAGCATTTATCGCATTTTCTAAAGATAGTCAGTGCCTGAAAGTTTGAGGCAGATAAAC -AAATTGTTCAAGTAAGAACTATATCTTTCTTATGATTTTACCGCAATCATACAGGTTGTT -TCTTGTGGTCTGCTGGGCATTGTATCCCTTTGTTGTATGGATTTTTCCTTTCTTTAATGA -TCTCCTCCCTGGAGTTTGTAATCCCTGTTTGTAGTGGAATT ->Asian_seabass_Sat_Unk_Consensus_Length_789_bp -CAAAAAAATGGAAAAAAAAAAAGTGGCTCATTTGAAGTGAATCAGAGTTGGGTAACATTG -TCCTTAATTACAGCTATGCTTATATACTTGATCTGATAATAATACTCTAGCCACAATCTG -TGGGTATTCTGCTATTTGCAGTCCACCCAAAGTCATAGCATTTAATCCATTCTAGGAAGA -TACGTCAGTGCTGAGTTGAGCCAATAACACCAAATTGTCATAAGAACTATTATTTTCTTT -ATGATTTTTACGCATCAGTACAGGTGTTTTCTTGTGGTTTCTGCTGCATGTATCCCTGTT -GTAAGTGGATTCTCCTTTGCTTATGATCTCCTCCGCTGCGTTGTATCCTGTTTGTAGTGG -ATTTCCTTGCACTGATTCTGCCCGCTCTTAATACTGAATGAACGCCCTCCCACCAGTAGT -ACTGCCACCTTTGTTTTTTCACAAAGTGTTCAATGGCCTTGATAATGACTTGGTAACTAC -ATCACCACTTTTTTGTACGTAATCAACAGACAATCACCCATTAAATTCATGCGGCCATTA -GGCAGCTTGATGAGCTGGACATTTGACCTCCCCAATGAATCTTTGCTGATGGGAAACTTA -TTGCCACCATAAAGTGAACCAGCATTGCTATGTCCATGCTGTAATTTGAAAACCCAATAC -AAAGAAGCCCTGCATATATACCTCCCAAATTGGCTTCTGAGACCCGGGCGTAATCACTGC -ATGGCCATAGATAAACATTGAAATCTTCTGTTGCAGTCAGTTTGCTTTTTGTCAACTTTA -AAAACTGCC diff --git a/recipes/repeatmasker/test_md5.txt b/recipes/repeatmasker/test_md5.txt deleted file mode 100644 index 889b949ed65b5..0000000000000 --- a/recipes/repeatmasker/test_md5.txt +++ /dev/null @@ -1 +0,0 @@ -4a505faa3613b2000873516c9977d3db rm_input1.fasta.masked diff --git a/recipes/repic/meta.yaml b/recipes/repic/meta.yaml index 9e6b03404fbc2..364d4afc0ca19 100644 --- a/recipes/repic/meta.yaml +++ b/recipes/repic/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.1" %} +{% set version = "1.0.0" %} package: name: repic @@ -6,7 +6,7 @@ package: source: url: https://github.com/ccameron/REPIC/archive/v{{ version }}.zip - sha256: fd77f660bf6e1fe10138c145d2aa67b69fd4ff30f249047ee49460a185407633 + sha256: 27bc27cea61e012742dba0f7c7a3451f0d29633b5eef3d59b194cfae55194ee0 requirements: host: diff --git a/recipes/resfinder/build.sh b/recipes/resfinder/build.sh index 3c65803ffd5ac..db6efb53eddcb 100644 --- a/recipes/resfinder/build.sh +++ b/recipes/resfinder/build.sh @@ -1,6 +1,8 @@ -#!/bin/bash +#!/bin/bash -ex -${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation +mkdir -p ${PREFIX}/bin + +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir # create folder for database download target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION} @@ -8,8 +10,8 @@ mkdir -p ${target}/db/ touch ${target}/db/.empty # copy script to download database -cp ${RECIPE_DIR}/download-db.sh ${PREFIX}/bin -chmod +x ${PREFIX}/bin/download-db.sh +cp -rf ${RECIPE_DIR}/download-db.sh ${PREFIX}/bin +chmod 0755 ${PREFIX}/bin/download-db.sh # set RESFINDER_DB variable on env activation mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d @@ -20,3 +22,6 @@ EOF cat <> ${PREFIX}/etc/conda/deactivate.d/resfinder.sh unset RESFINDER_DB EOF + +chmod 0755 ${SP_DIR}/resfinder/run_resfinder.py +cp -rf ${SP_DIR}/resfinder/run_resfinder.py ${PREFIX}/bin/ diff --git a/recipes/resfinder/meta.yaml b/recipes/resfinder/meta.yaml index 6614f72cec293..b05f847f72c98 100644 --- a/recipes/resfinder/meta.yaml +++ b/recipes/resfinder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "resfinder" %} -{% set version = "4.5.0" %} +{% set version = "4.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/resfinder-{{ version }}.tar.gz - sha256: 7c2ad096c2f5f746607c4433d327f890776aba996f86112dc4527fc3c2bc0ec4 + sha256: ca682ad8760c9cfbb1163235ce5bdb7c018d5b910937ac8f747d605309ce3c40 patches: - python_path.patch @@ -19,12 +19,11 @@ build: requirements: host: - - python >=3.8 + - python >=3.9 - pip - - pdm-pep517 >=0.12.0 + - pdm-backend run: - - python >=3.8 - # Needs cgelib in conda-forge/bioconda + - python >=3.9 - cgelib >=0.7.3 - cgecore ==1.5.6 - tabulate >=0.8.9 @@ -39,14 +38,16 @@ test: imports: - resfinder commands: - - python -m resfinder --help + - "run_resfinder.py --help" about: - home: https://bitbucket.org/genomicepidemiology/resfinder + home: "https://bitbucket.org/genomicepidemiology/resfinder" summary: "ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria." license: Apache-2.0 license_family: APACHE license_file: LICENSE + dev_url: "https://bitbucket.org/genomicepidemiology/resfinder" + doc_url: "https://bitbucket.org/genomicepidemiology/resfinder/src/master/README.md" extra: notes: "ResFinder requires databases that can be downloaded with download-db.sh." diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml index 4cd79689492b0..36d96e8d1b98d 100644 --- a/recipes/resistify/meta.yaml +++ b/recipes/resistify/meta.yaml @@ -1,5 +1,5 @@ {% set name = "resistify" %} -{% set version = "0.2.2" %} +{% set version = "0.3.0" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 2fd3e8e8c45711d1a4a054727053fb284f8034ec921e7f14e7d5b8a16800c326 + sha256: 3a8f4ccedf38fb1a7cdb3522ad6497d054bd72164155bcdc03aa23133b030623 build: noarch: python diff --git a/recipes/rhotermpredict/meta.yaml b/recipes/rhotermpredict/meta.yaml new file mode 100644 index 0000000000000..3a12f2a870cd3 --- /dev/null +++ b/recipes/rhotermpredict/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "rhotermpredict" %} +{% set version = "3.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/rhotermpredict-{{ version }}.tar.gz + sha256: 15a45581595e647e0f9dca31df45a5820144d2d5a5097bb61102bc57134acc36 + +build: + entry_points: + - rhotermpredict = rhotermpredict.algorithm:main + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + number: 0 + run_exports: + - {{ pin_subpackage("rhotermpredict", max_pin="x") }} + +requirements: + host: + - python + - pip + run: + - python + - numpy >=1.15.4 + - biopython >=0.1.0 + +test: + imports: + - rhotermpredict + commands: + - rhotermpredict --help + +about: + home: https://github.com/barricklab/RhoTermPredict + summary: "RhoTermPredict (Barrick Lab Fork)" + license: AGPL-3.0-or-later + license_family: AGPL + license_file: LICENSE + dev_url: https://github.com/barricklab/RhoTermPredict + +extra: + recipe-maintainers: + - croots diff --git a/recipes/rnaalishapes/meta.yaml b/recipes/rnaalishapes/meta.yaml index f9df163582cb8..17ef0ed23173e 100644 --- a/recipes/rnaalishapes/meta.yaml +++ b/recipes/rnaalishapes/meta.yaml @@ -1,19 +1,20 @@ -{% set version = "2.3.1" %} +{% set fold_grammars_version = "2.3.1" %} +{% set rnaalishapes_version = "2.5.0" %} {% set packagename = "rnaalishapes" %} {% set sha256 = "0c5b7d91893d0a23189f4af3602e18f110f030eac49a3658f7acede23596fde0" %} package: name: {{ packagename }} - version: 2.5.0 + version: {{ rnaalishapes_version }} source: sha256: {{ sha256 }} # the repository "fold-grammars" contains sources for several programs, i.e. pKiss, RNAshapes, ... # thus, the version number does not correspond to the {{ packagename }} version number - url: https://github.com/jlab/fold-grammars/archive/{{ version }}.tar.gz + url: https://github.com/jlab/fold-grammars/archive/{{ fold_grammars_version }}.tar.gz build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('rnaalishapes', max_pin="x") }} diff --git a/recipes/roadies/build.sh b/recipes/roadies/build.sh new file mode 100644 index 0000000000000..201708dac381b --- /dev/null +++ b/recipes/roadies/build.sh @@ -0,0 +1,42 @@ +#!/bin/bash + +# Debugging: Print current directory and list its contents +echo "Current directory: $(pwd)" +echo "Contents:" +ls -al + +mkdir -p $PREFIX/ROADIES + +# Download and setup ASTER repository if not already done +if [ ! -d "ASTER-Linux" ]; then + wget -q https://github.com/chaoszhang/ASTER/archive/refs/heads/Linux.zip -O Linux.zip + unzip -q Linux.zip + cd ASTER-Linux + $CXX -D CASTLES -std=gnu++11 -march=native -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro2 + cd .. +fi + +# Build sampling code +if [ ! -d "workflow/scripts/sampling/build" ]; then + cd workflow/scripts/sampling + mkdir -p build + cd build + cmake .. -DCMAKE_INSTALL_PREFIX=$PREFIX + make + cd ../../../.. +fi + +mkdir -p pasta + + +# Debugging: Print current directory and list its contents before copying +echo "Current directory before copying ROADIES: $(pwd)" +echo "Contents before copying ROADIES:" +ls -al + +# Copy the entire ROADIES directory to the PREFIX directory +cp -r . $PREFIX/ROADIES + +# Debugging: Verify the contents of the PREFIX directory +echo "Contents of PREFIX:" +ls -al $PREFIX \ No newline at end of file diff --git a/recipes/roadies/meta.yaml b/recipes/roadies/meta.yaml new file mode 100644 index 0000000000000..731f2471a53d3 --- /dev/null +++ b/recipes/roadies/meta.yaml @@ -0,0 +1,70 @@ +{% set version = "0.1.4" %} + +package: + name: roadies + version: {{ version }} + +source: + url: https://github.com/TurakhiaLab/ROADIES/archive/v{{ version }}.tar.gz + sha256: e3b4b89f247824c4b61e790f094320624bde47e295e2158a9ad83c05dfa83d54 + +build: + number: 0 + run_exports: + - {{ pin_subpackage("roadies", max_pin=None) }} + +requirements: + build: + - {{ compiler('cxx') }} + - cmake + - make + - wget + - unzip + - openjdk >=1.7 + + host: + - python ==3.9 + - pip + - libboost-devel + - zlib + run: + - python ==3.9 + - biopython + - numpy + - libboost-devel + - pip + - matplotlib-base + - seaborn + - ete3 + - pyyaml + - raxml-ng + - snakemake + - pasta >=1.9.0 + - mashtree + - treeswift >=1.1.28 + - fasttree >=2.1.11 + - alive-progress + +test: + commands: + - python $PREFIX/ROADIES/run_roadies.py --help + +about: + home: "https://github.com/TurakhiaLab/ROADIES" + license: MIT + license_family: MIT + license_file: LICENSE + doc_url: "https://turakhia.ucsd.edu/ROADIES/" + summary: "Reference-free Orthology-free Alignment-free DIscordance aware Estimation of Species tree (ROADIES)" + description: | + ROADIES is an end-to-end pipeline designed for phylogenetic tree inference of the species directly from their raw genomic assemblies. ROADIES offers a fully automated, easy-to-use, scalable solution, eliminating any error-prone manual steps and providing unique flexibility in adjusting the tradeoff between accuracy and runtime. + +extra: + recipe-maintainers: + - ang037 + identifiers: + - doi:10.1101/2024.05.27.596098 + edam: + topic: Phylogenetics + operation: Species tree estimation + \ No newline at end of file diff --git a/recipes/ropebwt3/build.sh b/recipes/ropebwt3/build.sh new file mode 100644 index 0000000000000..5937aa9f2776c --- /dev/null +++ b/recipes/ropebwt3/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash -xe + +make -j ${CPU_COUNT} \ + CC="${CC}" \ + CFLAGS="${CFLAGS} -fcommon -g -Wall -Wc++-compat -O3" \ + LIBS="${LDFLAGS} -lz -lpthread -lm -fopenmp" + +mkdir -p "${PREFIX}/bin" +chmod 0755 ropebwt3 +mv ropebwt3 "${PREFIX}/bin/" diff --git a/recipes/ropebwt3/meta.yaml b/recipes/ropebwt3/meta.yaml new file mode 100644 index 0000000000000..8128c0239fb51 --- /dev/null +++ b/recipes/ropebwt3/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "ropebwt3" %} +{% set version = "3.7" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('ropebwt3', max_pin="x") }} + +source: + url: https://github.com/lh3/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 10a8f2974b5117a62bb490c231bd2539826cedea458798acd3273dc7b6baf9b8 + +requirements: + build: + - make + - {{ compiler('c') }} + host: + - zlib + - libgomp # [linux] + - llvm-openmp # [osx] + +test: + commands: + - "ropebwt3 version /dev/null 2>&1" + +about: + home: "https://github.com/lh3/ropebwt3" + license: MIT + license_family: MIT + license_file: "LICENSE.txt" + summary: "Constructs the FM-index of a large DNA sequence set and searches for matches against the FM-index." + dev_url: "https://github.com/lh3/ropebwt3" + doc_url: "https://github.com/lh3/ropebwt3/blob/v{{ version }}/README.md" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/rukki/build.sh b/recipes/rukki/build.sh new file mode 100644 index 0000000000000..b231ffe52e75f --- /dev/null +++ b/recipes/rukki/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash -euo + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root "${PREFIX}" diff --git a/recipes/rukki/meta.yaml b/recipes/rukki/meta.yaml new file mode 100644 index 0000000000000..e4784932e3704 --- /dev/null +++ b/recipes/rukki/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "rukki" %} +{% set version = "0.3.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/marbl/rukki/archive/refs/tags/v{{ version }}.tar.gz + sha256: 036360e6287dc2b7e28bfc7b49db4ca79e792417e75f4bcc926c02d4161625b6 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('rukki', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - {{ compiler('rust') }} + - make + +test: + commands: + - rukki --help + +about: + home: "https://github.com/marbl/rukki" + license: "Public Domain" + license_file: "README.licenses" + summary: "Extracting paths from assembly graphs." + doc_url: "https://github.com/marbl/rukki/blob/v{{ version }}/README.md" + dev_url: "https://github.com/marbl/rukki" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/rust-ncbitaxonomy/build.sh b/recipes/rust-ncbitaxonomy/build.sh index bfdd53f18dd16..07f397dca273a 100755 --- a/recipes/rust-ncbitaxonomy/build.sh +++ b/recipes/rust-ncbitaxonomy/build.sh @@ -1,4 +1,6 @@ -#!/bin/bash -euo +#!/bin/bash + +set -xeuo if [ "$(uname)" == "Darwin" ]; then # Apparently the Home variable isn't set correctly diff --git a/recipes/rust-ncbitaxonomy/meta.yaml b/recipes/rust-ncbitaxonomy/meta.yaml index 7d66502eb9824..103f0d6352d75 100644 --- a/recipes/rust-ncbitaxonomy/meta.yaml +++ b/recipes/rust-ncbitaxonomy/meta.yaml @@ -7,7 +7,9 @@ package: version: "{{ version }}" build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} source: url: "https://github.com/pvanheus/ncbitaxonomy/archive/{{ version }}.tar.gz" @@ -16,7 +18,7 @@ source: requirements: build: - {{ compiler('c') }} - - rust >=1.43 + - {{ compiler('rust') }} host: - sqlite run: @@ -32,5 +34,11 @@ about: home: https://github.com/pvanheus/ncbitaxonomy doc_url: "https://docs.rs/crate/ncbitaxonomy/{{ version }}" license: MIT + license_file: LICENSE summary: | A Rust crate for working with a local copy of the NCBI Taxonomy database, which provides utilities for taxonomic filtering. + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 \ No newline at end of file diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index dacd35cfbd8fd..6be4f7b7a92d2 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,7 @@ {% set name = "SACCHARIS" %} -{% set version = "2.0.1" %} -{% set hash = "b2bce5fb1d2c959df571735634de5b68fd175148978613e6fc0daa24b3e25df9" %} +{% set version = "2.0.1.dev21" %} +{% set hash = "1e5c4bb35414d1421f4debcf0ecb53cd62a853b40a887486a44c2c7a8929b113" %} + package: name: "{{ name|lower }}" diff --git a/recipes/sage-proteomics/build.sh b/recipes/sage-proteomics/build.sh index 0d6a1d40a3126..7e288ae106038 100644 --- a/recipes/sage-proteomics/build.sh +++ b/recipes/sage-proteomics/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include ${LDFLAGS}" @@ -8,4 +10,4 @@ export CXXFLAGS="${CXXFLAGS} -O3 -fcommon -I${PREFIX}/include ${LDFLAGS}" export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" # build statically linked binary with sage -RUST_BACKTRACE=1 cargo install --verbose -j 4 --root ${PREFIX} --path crates/sage-cli +RUST_BACKTRACE=1 cargo install --verbose -j ${CPU_COUNT} --root ${PREFIX} --path crates/sage-cli diff --git a/recipes/sage-proteomics/meta.yaml b/recipes/sage-proteomics/meta.yaml index 2e26967970fd3..185875e7a26e2 100644 --- a/recipes/sage-proteomics/meta.yaml +++ b/recipes/sage-proteomics/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('sage-proteomics', max_pin="x") }} @@ -18,8 +18,8 @@ source: requirements: build: - {{ compiler('c') }} + - {{ compiler('rust') }} host: - - rust >=1.70.0 test: commands: @@ -35,6 +35,9 @@ about: summary: "Proteomics searching so fast it feels like magic." extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - ypriverol - lazear diff --git a/recipes/sainsc/meta.yaml b/recipes/sainsc/meta.yaml new file mode 100644 index 0000000000000..d426091bed58c --- /dev/null +++ b/recipes/sainsc/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "sainsc" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sainsc-{{ version }}.tar.gz + sha256: 43afd7d2c9f1b8b891893cfe730175d0e01d5443b7f17981a233109df4cbb228 + +build: + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 2 + skip: True # [(osx and not arm64) or py<310] + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + build: + - {{ compiler('rust') }} + host: + - python + - setuptools >=61.0.0 + - setuptools-scm >=6.2 + - setuptools-rust >=1.7 + - pip + run: + - python + - anndata >=0.9 + - matplotlib-base + - matplotlib-scalebar + - numba >=0.44 + - numpy >=1.21 + - pandas + - polars >=1 + - scikit-image >=0.18 + - scipy >=1.9 + - seaborn >=0.11 + +test: + imports: + - sainsc + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/HiDiHlabs/sainsc + summary: Segmentation-free Analysis of In Situ Capture data + license: MIT + license_family: MIT + license_file: LICENSE + doc_url: https://sainsc.readthedocs.io/ + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - niklasmueboe diff --git a/recipes/sam2pairwise/build.sh b/recipes/sam2pairwise/build.sh new file mode 100644 index 0000000000000..4d70a6638a306 --- /dev/null +++ b/recipes/sam2pairwise/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin + +cd src +make CC=$CXX CXX=$CXX +cp sam2pairwise $PREFIX/bin diff --git a/recipes/sam2pairwise/meta.yaml b/recipes/sam2pairwise/meta.yaml new file mode 100644 index 0000000000000..fd0995c223f9b --- /dev/null +++ b/recipes/sam2pairwise/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "sam2pairwise" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +source: + url: https://github.com/mlafave/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 899d3db071cc248870bbedbdb39784de4c54c9a7888bc408022e809ace47ec0e + patches: + - patch.txt + +requirements: + build: + - {{ compiler('cxx') }} + - make + +test: + commands: + - sam2pairwise --version + +about: + home: https://github.com/mlafave/sam2pairwise + license: MIT + license_file: LICENSE + summary: 'sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read' + doc_url: https://github.com/mlafave/sam2pairwise/blob/master/README.md + dev_url: https://github.com/mlafave/sam2pairwise + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/sam2pairwise/patch.txt b/recipes/sam2pairwise/patch.txt new file mode 100644 index 0000000000000..35031e34c8af2 --- /dev/null +++ b/recipes/sam2pairwise/patch.txt @@ -0,0 +1,10 @@ +--- src/Makefile 2014-08-22 13:02:24.000000000 -0700 ++++ src/Makefile_new 2024-09-11 10:27:50.000000000 -0700 +@@ -1,5 +1,5 @@ +-CXX = g++ +-CC = g++ ++CXX ?= g++ ++CC ?= g++ + + sam2pairwise: sam2pairwise.o isolate_md.o shift_cigar.o shift_md.o translate_cigar.o translate_md.o + diff --git a/recipes/samestr/meta.yaml b/recipes/samestr/meta.yaml index 54f65bf516a7c..54a00dc7df83f 100644 --- a/recipes/samestr/meta.yaml +++ b/recipes/samestr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "samestr" %} -{% set version = "1.2024.2.post1" %} +{% set version = "1.2024.8" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d03c5f1fd89fd018409bcf332c3a95e752aca9fb47b88c617fad702581630bdd + sha256: e729a58652f019d5384f121565b2ca4faba19bee144af4d3bc88e6dfabc29a14 build: number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python run_exports: - {{ pin_subpackage('samestr', max_pin=None) }} @@ -29,7 +29,7 @@ requirements: - scipy ==1.10.0 - blast >=2.6.0 - muscle ==3.8.1551 - - mafft ==7.515 + - mafft ==7.525 - samtools ==0.1.19 test: diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index 4b3fddd767dd0..e0a4803383159 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.20" %} +{% set version = "1.21" %} package: name: samtools version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("samtools", max_pin="x") }} source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - sha256: c71be865e241613c2ca99679c074f1a0daeb55288af577db945bdabe3eb2cf10 + sha256: 05724b083a6b6f0305fcae5243a056cc36cf826309c3cb9347a6b89ee3fc5ada requirements: build: diff --git a/recipes/sansa/build.sh b/recipes/sansa/build.sh index dc2400afabae2..89d206cac27f5 100644 --- a/recipes/sansa/build.sh +++ b/recipes/sansa/build.sh @@ -1,3 +1,3 @@ #!/bin/sh -CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS" make CXX="${CXX}" prefix="${PREFIX}" install +CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS" make -j${CPU_COUNT} CXX="${CXX}" prefix="${PREFIX}" install diff --git a/recipes/sansa/build_failure.osx-64.yaml b/recipes/sansa/build_failure.osx-64.yaml deleted file mode 100644 index f0223f40aa68a..0000000000000 --- a/recipes/sansa/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 788a4a03f018442ca4759c62d776a93efa240672f1e911501e0ec7b926e3f3b7 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - ^ - src/markdup.h:432:38: note: in instantiation of template class 'sansa::SortSVEvents' requested here - sort(allsv.begin(), allsv.end(), SortSVEvents()); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/_build_env/bin/../include/c/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here - struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function - ^ - /opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/_build_env/bin/../include/c/v1/__config:1037:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' - # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED - ^ - /opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/_build_env/bin/../include/c/v1/__config:1022:49: note: expanded from macro '_LIBCPP_DEPRECATED' - # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) - ^ - In file included from src/sansa.cpp:14: - In file included from src/annotate.h:22: - src/parsedb.h:107:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] - bcf_write1(ofile, hdr_out, rec); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/htslib/vcf.h:270:33: note: expanded from macro 'bcf_write1' - #define bcf_write1(fp,h,v) bcf_write((fp),(h),(v)) - ^~~~~~~~~ ~~~~~~~~~~~~ - src/annotate.h:92:10: note: in instantiation of function template specialization 'sansa::parseDB>' requested here - if (!parseDB(c, svs)) { - ^ - src/annotate.h:231:12: note: in instantiation of function template specialization 'sansa::runAnnotate' requested here - return runAnnotate(c); - ^ - 11 warnings and 1 error generated. - make: *** [Makefile:53: src/sansa] Error 1 - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sansa-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sansa_1717639548819/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sansa-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sansa-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sansa-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - if [ -r src/htslib/Makefile ]; then cd src/htslib && autoreconf -i && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && make && make lib-static && cd ../../ && touch .htslib; fi - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sansa-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -std=c11 -isystem $SRC_DIR/src/htslib/ -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive -O3 -fno-tree-vectorize -DNDEBUG src/sansa.cpp src/edlib.cpp -o src/sansa -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/src/htslib/ -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -lhts -lz -llzma -lbz2 -Wl,-rpath,$SRC_DIR/src/htslib/ -# Last 100 lines of the build log. diff --git a/recipes/sansa/meta.yaml b/recipes/sansa/meta.yaml index 2673fcf314a4c..67c87723a5111 100644 --- a/recipes/sansa/meta.yaml +++ b/recipes/sansa/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.1" %} -{% set sha256 = "f43b088b8339d3ba395adf922d723b074e31f8bf548c9e9039cccace5acc60ee" %} +{% set version = "0.2.2" %} +{% set sha256 = "2bec3df6918a8dda9d0f5f766c5314137c18956e83601b93606ff2037f2662d4" %} package: name: sansa @@ -18,23 +18,18 @@ requirements: build: - make - {{ compiler('cxx') }} - - autoconf - - automake - - pkg-config - - clangdev - - llvm-openmp host: - - boost-cpp - - htslib - zlib - bzip2 - - clangdev - - llvm-openmp - run: + - libdeflate - boost-cpp - htslib + run: - zlib - bzip2 + - libdeflate + - boost-cpp + - htslib test: commands: @@ -46,3 +41,8 @@ about: license_family: BSD license_file: LICENSE summary: Structural variant annotation + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/savana/meta.yaml b/recipes/savana/meta.yaml index 8ba9b74b466b6..53a05b2658cd2 100644 --- a/recipes/savana/meta.yaml +++ b/recipes/savana/meta.yaml @@ -1,5 +1,5 @@ {% set name = "savana" %} -{% set version = "1.2.0" %} +{% set version = "1.2.2" %} package: name: "{{ name }}" @@ -7,10 +7,10 @@ package: source: url: "https://github.com/cortes-ciriano-lab/{{ name }}/archive/{{ version }}.tar.gz" - sha256: 25025d73628e282c7cd5fd6204befe9152d0d695ebd027b87831aa1338b83914 + sha256: c4a72c13d712930e8bc8e0865767c00708062edf4eec6f1bc951877c58f08380 build: - number: 1 + number: 0 noarch: python script: - "{{ PYTHON }} -m pip install . -vv" diff --git a/recipes/sawfish/build.sh b/recipes/sawfish/build.sh new file mode 100644 index 0000000000000..f427f2b39fda7 --- /dev/null +++ b/recipes/sawfish/build.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +# Sawfish already auto-extracts to bin directory, so just need to move it to PREFIX +cp -r bin "${PREFIX}"/ + diff --git a/recipes/sawfish/meta.yaml b/recipes/sawfish/meta.yaml new file mode 100644 index 0000000000000..a56f80957f6ca --- /dev/null +++ b/recipes/sawfish/meta.yaml @@ -0,0 +1,32 @@ +{% set name = "sawfish" %} +{% set version = "0.12.4" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/PacificBiosciences/sawfish/releases/download/v{{ version }}/sawfish-v{{ version }}-x86_64-unknown-linux-gnu.tar.gz + sha256: e42064108c70b66e208a24fcec77d66a85331025d09ac30f2c9bea0de3842c0f + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('sawfish', max_pin="x.x") }} + +test: + commands: + - sawfish --version + +about: + home: https://github.com/PacificBiosciences/sawfish + license: Pacific Biosciences Software License Agreement + summary: Structural variant discovery and genotyping from mapped PacBio HiFi data + +extra: + recipe-maintainers: + - ctsa + skip-lints: + - should_use_compilers + - should_be_noarch_generic diff --git a/recipes/scar/meta.yaml b/recipes/scar/meta.yaml index ed6eb33f81d7c..18d5c9ca181d9 100644 --- a/recipes/scar/meta.yaml +++ b/recipes/scar/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.0" %} -{% set sha256 = "f4a3ee980dcad4465d23e146e23605df61e4ebc016f2c7279820dcbc3ee111c1" %} +{% set version = "0.7.0" %} +{% set sha256 = "e3d75d2ee20fa5acce2db7456c00f9ad806e2355e2936dc7db2dcfff6038a3cb" %} package: name: scar diff --git a/recipes/scarches/meta.yaml b/recipes/scarches/meta.yaml new file mode 100644 index 0000000000000..f044a26e18a03 --- /dev/null +++ b/recipes/scarches/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "scarches" %} +{% set version = "0.6.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/scArches-{{ version }}.tar.gz + sha256: 187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('scarches', max_pin="x.x") }} + +requirements: + host: + - python + - pip + run: + - python + - scanpy >=1.6.0 + - anndata >=0.7.4 + - schpl >=1.0.0 + - h5py >=2.10.0 + - pytorch >=1.8.0 + - numpy >=1.19.2 + - scipy >=1.5.2 + - scikit-learn >=0.23.2 + - matplotlib-base >=3.3.1 + - pandas >=1.1.2 + - scvi-tools >=0.12.1 + - tqdm >=4.56.0 + - requests + - gdown + - leidenalg + - muon + +test: + imports: + - scarches + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/theislab/scarches + summary: Transfer learning with Architecture Surgery on Single-cell data + license: BSD-3-Clause + license_file: LICENSE + +extra: + identifiers: + - doi:10.1038/s41587-021-01001-7 + recipe-maintainers: + - jdblischak diff --git a/recipes/sccmec/build.sh b/recipes/sccmec/build.sh index aa318ca945110..5ca6a640acbd0 100644 --- a/recipes/sccmec/build.sh +++ b/recipes/sccmec/build.sh @@ -3,9 +3,18 @@ mkdir -p $PREFIX/bin ${PREFIX}/share/sccmec # Copy wrapper -chmod 755 bin/sccmec-bioconda +chmod 755 bin/sccmec-targets-bioconda +cp -f bin/sccmec-targets-bioconda $PREFIX/bin/sccmec-targets + +chmod 755 bin/sccmec-regions-bioconda +cp -f bin/sccmec-regions-bioconda $PREFIX/bin/sccmec-regions + +chmod 755 bin/sccmec bin/sccmec-bioconda +cp -f bin/sccmec $PREFIX/bin/sccmec-main cp -f bin/sccmec-bioconda $PREFIX/bin/sccmec # Copy schema (~100kb) -cp -f data/sccmec.yaml ${PREFIX}/share/sccmec -cp -f data/sccmec.fasta ${PREFIX}/share/sccmec +cp -f data/sccmec-targets.yaml ${PREFIX}/share/sccmec +cp -f data/sccmec-targets.fasta ${PREFIX}/share/sccmec +cp -f data/sccmec-regions.yaml ${PREFIX}/share/sccmec +cp -f data/sccmec-regions.fasta ${PREFIX}/share/sccmec diff --git a/recipes/sccmec/meta.yaml b/recipes/sccmec/meta.yaml index 166bd125861d4..02c1875f8ecb1 100644 --- a/recipes/sccmec/meta.yaml +++ b/recipes/sccmec/meta.yaml @@ -1,36 +1,40 @@ -{% set name="sccmec" %} -{% set version = "1.0.0" %} -{% set sha256 = "1bbddeec9a1fb2d340a8971dfa6a705e0beca80c3ef03483b52079f91e242b6a" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://github.com/rpetit3/sccmec/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 0 - noarch: generic - run_exports: - - {{ pin_subpackage(name, max_pin='x.x') }} - -requirements: - run: - - camlhmp >=0.1.0 - -test: - commands: - - sccmec --version - - sccmec --help - -about: - home: https://github.com/rpetit3/sccmec - license: MIT - license_file: LICENSE - summary: A tool for typing SCCmec cassettes in assemblies - -extra: - recipe-maintainers: - - rpetit3 +{% set name="sccmec" %} +{% set version = "1.2.0" %} +{% set sha256 = "b8ff1fb5f6d5d4c2bbfd3a5b95711ecd152638417558ecc98dc5e22724f06d8f" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/rpetit3/sccmec/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + run: + - camlhmp >=1.1.0 + +test: + commands: + - sccmec --version + - sccmec --help + - sccmec-targets --version + - sccmec-targets --help + - sccmec-regions --version + - sccmec-regions --help + +about: + home: https://github.com/rpetit3/sccmec + license: MIT + license_file: LICENSE + summary: A tool for typing SCCmec cassettes in assemblies + +extra: + recipe-maintainers: + - rpetit3 diff --git a/recipes/schpl/meta.yaml b/recipes/schpl/meta.yaml new file mode 100644 index 0000000000000..11814e500091c --- /dev/null +++ b/recipes/schpl/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "schpl" %} +{% set version = "1.0.5" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/scHPL-{{ version }}.tar.gz + sha256: 3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('schpl', max_pin="x") }} + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - numpy >=1.19.2 + - scipy >=1.5.2 + - scikit-learn >=0.23.2 + - pandas >=1.1.2,<2 + - python-newick >=1.0.0,<1.1.dev0 + - anndata >=0.7.4 + - matplotlib-base >=3.3.1 + - seaborn >=0.11.1 + +test: + imports: + - scHPL + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/lcmmichielsen/scHPL + summary: Hierarchical progressive learning pipeline for single-cell RNA-sequencing datasets + license: MIT + license_file: LICENSE + +extra: + identifiers: + - doi:10.1038/s41467-021-23196-8 + recipe-maintainers: + - jdblischak + - nictru + - lcmmichielsen diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index 98fde15171638..8fe28e48762f4 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scirpy" %} -{% set version = "0.17.2" %} +{% set version = "0.18.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 37dc159bb6d4f033039dde9073a69104f8445be4459cec4532fdcbf84eef13b3 + sha256: 7d8f5deb2f6d83aa6f719b051c2d7c8cd1fb27589b64796be4b1a64ec76a708e folder: "{{ name }}-{{ version }}" build: @@ -21,19 +21,18 @@ build: requirements: host: - - python >=3.9 + - python >=3.10 - hatchling - hatch-vcs run: - - python >=3.9 - - anndata >=0.9 + - python >=3.10 + - anndata >=0.9,<0.10.9 - awkward >=2.1.0 - mudata >=0.2.3 - scanpy >=1.9.3 - pandas >=1.5 - numpy >=1.17.0 - scipy - - parasail-python - scikit-learn - python-levenshtein - python-igraph >0.10.1|<0.10.0 diff --git a/recipes/scnic/build.sh b/recipes/scnic/build.sh deleted file mode 100644 index 601dac5b69ee5..0000000000000 --- a/recipes/scnic/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=/tmp/record.txt diff --git a/recipes/scnic/meta.yaml b/recipes/scnic/meta.yaml index 0694dc9b3d05e..29ce63c9daa93 100644 --- a/recipes/scnic/meta.yaml +++ b/recipes/scnic/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.3" %} +{% set version = "0.6.6" %} package: name: scnic @@ -6,45 +6,50 @@ package: source: url: https://github.com/lozuponelab/SCNIC/archive/{{ version }}.tar.gz - sha256: b0b6f9a1ba83e94d599e2ae5ca262acba2ad632512f6b179740e98d71a01236e + sha256: 754490880a31b067434a94c0bd4cbee6f067010511e5d7760b9ccbcbbddf0353 build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('scnic', max_pin="x.x") }} requirements: host: - python >=3 - - setuptools + - pip - pytest-runner run: - python >=3 - numpy - - scipy - - pandas + - scipy >=1.9.0,<=1.10.1 + - pandas >=1 - statsmodels - h5py - biom-format - - networkx >2 + - networkx >=2 - scikit-bio - fastspar - tqdm - matplotlib-base - - seaborn + - seaborn-base test: + imports: + - SCNIC command: - SCNIC_analysis.py --help - fastspar --help # verify fastspar working correctly about: home: https://github.com/lozuponelab/SCNIC - license: BSD + license: "BSD-3-Clause" + license_family: BSD license_file: LICENSE summary: "SCNIC: Sparse Cooccurence Network Investigation for Compositional data" + dev_url: https://github.com/lozuponelab/SCNIC extra: recipe-maintainers: - lozuponelab - skip-lints: - - missing_tests diff --git a/recipes/scoring-matrices/meta.yaml b/recipes/scoring-matrices/meta.yaml index abd5f86254259..b97fea1eea695 100644 --- a/recipes/scoring-matrices/meta.yaml +++ b/recipes/scoring-matrices/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 2192df3f5f8ecd144071858cc287c958d2a842cdc8cc082c13755dfefe2f66b8 build: - number: 0 + number: 1 skip: True # [py < 36] script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" run_exports: @@ -38,8 +38,8 @@ about: license: MIT license_family: MIT license_file: COPYING - summary: Dependency free, Cython-compatible scoring matrices to use with biological sequences. - doc_url: https://scoring-matrices.readthedocs.org/ + summary: "Dependency free, Cython-compatible scoring matrices to use with biological sequences." + doc_url: https://scoring-matrices.readthedocs.org dev_url: https://github.com/althonos/scoring-matrices extra: @@ -47,3 +47,4 @@ extra: - althonos additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/sdust/build.sh b/recipes/sdust/build.sh new file mode 100644 index 0000000000000..c495ad0379c1a --- /dev/null +++ b/recipes/sdust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +set -x -e + +mkdir -p "${PREFIX}/bin" + +make -j ${CPU_COUNT} CC="$CC" CFLAGS="${CFLAGS} -I${PREFIX}/include -L${PREFIX}/lib" + +chmod 0755 sdust + +cp -rf sdust "${PREFIX}/bin" diff --git a/recipes/sdust/meta.yaml b/recipes/sdust/meta.yaml new file mode 100644 index 0000000000000..f26962300d506 --- /dev/null +++ b/recipes/sdust/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "0.1" %} +{% set name = "sdust" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/lh3/sdust/archive/refs/tags/v{{ version }}.tar.gz + sha256: 0825a760fae884e65b2b024cc4f511e32e6c1698571c147daf5a61ba0dcac589 + +build: + number: 1 + run_exports: + - {{ pin_subpackage("sdust", max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + - zlib + +test: + commands: + - "sdust 2>&1 | grep 'Usage: sdust'" + +about: + home: "https://github.com/lh3/sdust" + dev_url: "https://github.com/lh3/sdust" + license: Unknown + summary: "Symmetric DUST for finding low-complexity regions in DNA sequences." + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - smeds diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 8cc42f01e9b8c..37ae4625b6021 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the searchgui.py file {% set name = "SearchGUI" %} -{% set version = "4.3.9" %} -{% set sha256 = "937898927c1727f72aad6a0fd1873324af5bc8eb946f79035d30b9407652032e" %} +{% set version = "4.3.11" %} +{% set sha256 = "5d1de05115e30f9d6a395c6990442efb37b497ecfff04873ff2af7849e11957f" %} {% set build = "0" %} package: @@ -23,13 +23,13 @@ source: requirements: host: - xtandem ==15.12.15.2 - - metamorpheus ==1.0.5 + - metamorpheus ==1.0.6 - blast >=2.14.0 run: - python - openjdk >=17 - xtandem ==15.12.15.2 - - metamorpheus ==1.0.5 + - metamorpheus ==1.0.6 - mono >=6.0.0 - fontconfig - fonts-conda-ecosystem @@ -46,12 +46,14 @@ test: - searchgui eu.isas.searchgui.cmd.SearchCLI -id_params "Identification_Parameters_default.par" -fasta_file "fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" -spectrum_files "searchgui_tinyspectra1.mgf" -xtandem 1 -output_folder "." -output_option 0 -output_data 1 about: - home: https://github.com/compomics/searchgui - license: Apache-2.0 + home: "https://github.com/compomics/searchgui" + license: "Apache-2.0" license_family: APACHE - summary: User-friendly graphical tool for using proteomics identification search engines + summary: "User-friendly graphical tool for using proteomics identification search engines." description: SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MetaMorpheus, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. + dev_url: "https://github.com/compomics/searchgui" + doc_url: "https://github.com/compomics/searchgui/blob/master/README.md" extra: notes: @@ -65,4 +67,4 @@ extra: - biotools:searchgui - usegalaxy-eu:search_gui - doi:10.1002/pmic.201000595 - extended-base: true ## precompiled packages + extended-base: True ## precompiled packages diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index 9f0af006eb888..911e0ab4542f6 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'SearchGUI-4.3.9.jar' +jar_file = 'SearchGUI-4.3.11.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] diff --git a/recipes/segalign-full/meta.yaml b/recipes/segalign-full/meta.yaml index 84bf15404adf9..9116ff7dd08a4 100644 --- a/recipes/segalign-full/meta.yaml +++ b/recipes/segalign-full/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_compatible('segalign-full', max_pin='x.x') }} @@ -24,16 +24,16 @@ test: - which faToTwoBit about: - home: https://github.com/gsneha26/SegAlign + home: https://github.com/galaxyproject/SegAlign summary: 'SegAlign: A Scalable GPU-Based Whole Genome Aligner' description: | SegAlign is a Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. license: MIT license_family: MIT - license_url: https://github.com/gsneha26/SegAlign/blob/main/LICENSE - doc_url: https://github.com/gsneha26/SegAlign/blob/main/README.md - dev_url: https://github.com/richard-burhans/SegAlign/blob/scoring/README.md + license_url: https://github.com/galaxyproject/SegAlign/blob/main/LICENSE + doc_url: https://github.com/galaxyproject/SegAlign/blob/main/README.md + dev_url: https://github.com/galaxyproject/SegAlign extra: identifiers: diff --git a/recipes/segalign-galaxy/meta.yaml b/recipes/segalign-galaxy/meta.yaml index 587bf1cacd24e..0912fc87c1272 100644 --- a/recipes/segalign-galaxy/meta.yaml +++ b/recipes/segalign-galaxy/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_compatible('segalign-galaxy', max_pin='x.x') }} @@ -25,16 +25,16 @@ test: - which faToTwoBit about: - home: https://github.com/gsneha26/SegAlign + home: https://github.com/galaxyproject/SegAlign summary: 'SegAlign: A Scalable GPU-Based Whole Genome Aligner' description: | SegAlign is a Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. license: MIT license_family: MIT - license_url: https://github.com/gsneha26/SegAlign/blob/main/LICENSE - doc_url: https://github.com/gsneha26/SegAlign/blob/main/README.md - dev_url: https://github.com/richard-burhans/SegAlign/blob/scoring/README.md + license_url: https://github.com/galaxyproject/SegAlign/blob/main/LICENSE + doc_url: https://github.com/galaxyproject/SegAlign/blob/main/README.md + dev_url: https://github.com/galaxyproject/SegAlign extra: identifiers: diff --git a/recipes/segul/meta.yaml b/recipes/segul/meta.yaml index a64eb2fd5a37c..98e5f7721f857 100644 --- a/recipes/segul/meta.yaml +++ b/recipes/segul/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.22.0" %} +{% set version = "0.22.1" %} package: name: segul @@ -6,7 +6,7 @@ package: source: url: https://github.com/hhandika/segul/archive/refs/tags/v{{ version }}.tar.gz - sha256: aa50dcfda557262f0a29a8e6be915c327392a10944492b21b42467306d53ed24 + sha256: 5d33058149e00551f219e6d92a9156d89643551c47fac18ed688aec022b8afdd build: number: 0 diff --git a/recipes/seismic-rna/meta.yaml b/recipes/seismic-rna/meta.yaml index 408e717537b7e..0ea99cde077e3 100644 --- a/recipes/seismic-rna/meta.yaml +++ b/recipes/seismic-rna/meta.yaml @@ -2,8 +2,8 @@ package: name: seismic-rna - version: 0.20.0 - + version: 0.20.1 + about: home: https://github.com/rouskinlab/seismic-rna license: GPL-3.0-only @@ -13,12 +13,12 @@ about: summary: SEISMIC-RNA software by the Rouskin Lab source: - url: https://github.com/rouskinlab/seismic-rna/archive/refs/tags/v0.20.0.tar.gz - sha256: 91ea9c7d23a85a0d9d035e41ee0782f892ea7e4f0df5af96317b7302a58c8de4 + url: https://github.com/rouskinlab/seismic-rna/archive/refs/tags/v0.20.1.tar.gz + sha256: b6d159119d394a9a92f74a886dc398a8479e4d890438bf2e19e2eee3eefaee24 build: noarch: python - number: 1 + number: 0 run_exports: - {{ pin_subpackage("seismic-rna", max_pin="x.x") }} @@ -29,22 +29,23 @@ requirements: - hatch >=1.12 run: - python >=3.10 - - bowtie2 >=2.5.1 + - bowtie2 >=2.5.4 - fastqc >=0.12.1 - - rnastructure >=6.3 - - samtools >=1.17 - - matplotlib-base >=3.6 + - rnastructure >=6.4 + - samtools >=1.20 + - matplotlib-base >=3.9 - brotli-python >=1.0 + - python-kaleido >=0.2.1 - click >=8.1 - - cutadapt >=4.4 + - cutadapt >=4.8 - fastqsplitter >=1.2 - - numpy >=1.23,<1.27 - - numba >=0.59 - - pandas >=1.5 - - plotly >=5.11 + - numpy >=1.26,<1.27 + - numba >=0.60 + - pandas >=2.2 + - plotly >=5.23 - pyyaml >=6.0 - - scipy >=1.9 - + - scipy >=1.13 + test: imports: - - seismicrna + - seismicrna \ No newline at end of file diff --git a/recipes/sepp/meta.yaml b/recipes/sepp/meta.yaml index 980e754e11f8c..9b675d94ae3f2 100644 --- a/recipes/sepp/meta.yaml +++ b/recipes/sepp/meta.yaml @@ -1,38 +1,35 @@ -{% set version = "4.5.1" %} -{% set sha256 = "51e052569ae89f586a1a94c804f09fe1b7910a3ffff7664e2005f18c7d3f717b" %} +{% set version = "4.5.5" %} +{% set sha256 = "af6b985bc16c96cd7c57bf78b3decce448f976aea612b3fad07b91697e4e1cfd" %} package: name: sepp version: '{{version}}' source: - - url: https://github.com/smirarab/sepp/archive/{{version}}.tar.gz + - url: https://github.com/smirarab/sepp/archive/v{{version}}.tar.gz sha256: '{{sha256}}' patches: - relocate.run-sepp.sh.patch - relocate.sepp.config.patch - # prevent python's setup to search for dendropy dependency via pip. - # Instead use dendropy provided by conda: - - nodeps.setup.py.patch build: - number: 4 + number: 0 run_exports: - {{ pin_subpackage('sepp', max_pin="x") }} requirements: host: - - python <=3.9 + - python <=3.10 - setuptools - pip - - dendropy <=4.5.1 + - dendropy - openjdk - - hmmer ==3.1b2 + - hmmer run: - - python <=3.9 - - dendropy <=4.5.1 + - python <=3.10 + - dendropy - openjdk - - hmmer ==3.1b2 + - hmmer - pasta # TODO: source bundled binaries as conda packages. # But pplacer / guppy are not available for OSX. diff --git a/recipes/sepp/nodeps.setup.py.patch b/recipes/sepp/nodeps.setup.py.patch index f93b859cf421e..f63161a7cd5d0 100644 --- a/recipes/sepp/nodeps.setup.py.patch +++ b/recipes/sepp/nodeps.setup.py.patch @@ -4,8 +4,8 @@ author_email="smirarab@gmail.com, namphuon@cs.utah.edu", license="General Public License (GPL)", -- install_requires=["dendropy >= 4.0.0"], +- install_requires=["dendropy >= 4.6.0"], + install_requires=[], provides=["sepp"], - scripts=["run_sepp.py", 'run_tipp.py', 'run_upp.py', 'run_abundance.py', - "split_sequences.py", "run_tipp_tool.py"], + scripts=["run_sepp.py", 'run_upp.py', "split_sequences.py"], + cmdclass={"config": ConfigSepp, "upp": ConfigUPP}, diff --git a/recipes/seq-hasher/build.sh b/recipes/seq-hasher/build.sh new file mode 100644 index 0000000000000..e5cb5faa26a8b --- /dev/null +++ b/recipes/seq-hasher/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash -euo + +set -xe + +# build statically linked binary with Rust +cargo-bundle-licenses --format yaml --output THIRDPARTY.yml +RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . \ No newline at end of file diff --git a/recipes/seq-hasher/meta.yaml b/recipes/seq-hasher/meta.yaml new file mode 100644 index 0000000000000..17be5a1eeac6e --- /dev/null +++ b/recipes/seq-hasher/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.1.0" %} + +package: + name: seq-hasher + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("seq-hasher", max_pin="x") }} + +source: + url: https://github.com/apcamargo/seq-hasher/archive/v{{ version }}.tar.gz + sha256: a017be3eae1a278bd38339cc4c53f406b7536a3f3d75adcc82e75c1e1daa8253 + +requirements: + build: + - {{ compiler('rust') }} + - cargo-bundle-licenses + host: + run: + +test: + commands: + - seq-hasher --help + +about: + home: https://github.com/apcamargo/seq-hasher + license: MIT + license_file: + - LICENSE + - THIRDPARTY.yml + + summary: > + Compute hash digests for DNA sequences in a FASTA file, with support for + circular permutations + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 \ No newline at end of file diff --git a/recipes/seqchromloader/meta.yaml b/recipes/seqchromloader/meta.yaml index 6c69d088838a2..a89e6961ea4a4 100644 --- a/recipes/seqchromloader/meta.yaml +++ b/recipes/seqchromloader/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqchromloader" %} -{% set version = "0.7.7" %} +{% set version = "0.7.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c4d37d0b8c91e0d666e7ae0a581884c113ed84862526b3621f86704668bb8b27 + sha256: 7b94212a2eb5d722fa13bf52c6aa8b3dc945e78806be01af025f8d33d9fc04cd build: number: 0 diff --git a/recipes/seqerakit/meta.yaml b/recipes/seqerakit/meta.yaml index 1c05abe525a1c..115b311960b83 100644 --- a/recipes/seqerakit/meta.yaml +++ b/recipes/seqerakit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqerakit" %} -{% set version = "0.4.8" %} +{% set version = "0.4.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqerakit-{{ version }}.tar.gz - sha256: 4d80b3e5230b1fbb29d191d36927fc59c696718447616cc9447cdf7bb5dafbbf + sha256: ecca8afc49498226a8c9ad81723a609ae324993e4352fd9561dd2ab657eff378 build: entry_points: diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml index dec9c542f81cc..9dfcd4bb28b7f 100644 --- a/recipes/seqfu/meta.yaml +++ b/recipes/seqfu/meta.yaml @@ -1,6 +1,6 @@ {% set name = "seqfu" %} -{% set version = "1.20.3" %} -{% set sha256 = "1b287b99f3f1ac7045f4d551e781d6780ce168ba8e0a7bfaa0f5490f32e15938" %} +{% set version = "1.22.2" %} +{% set sha256 = "0b66405ca98a80be614874fd1c1f651ecb410d953ac5070a0e93c77d2dbe1919" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/sequali/build_failure.osx-64.yaml b/recipes/sequali/build_failure.osx-64.yaml deleted file mode 100644 index a23733fbe04f1..0000000000000 --- a/recipes/sequali/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b82be46fe70a4476baf68c386ad04ec62bab54268efc685fda61370f10059d7f # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - clangxx: 16.0.6-default_ha3b9224_7 conda-forge - compiler-rt: 16.0.6-ha38d28d_2 conda-forge - compiler-rt_osx-64: 16.0.6-ha38d28d_2 conda-forge - icu: 73.2-hf5e326d_0 conda-forge - ld64_osx-64: 711-ha20a434_0 conda-forge - libclang-cpp16: 16.0.6-default_h4c8afb6_7 conda-forge - libcxx: 17.0.6-h88467a6_0 conda-forge - libexpat: 2.6.2-h73e2aa4_0 conda-forge - libffi: 3.4.2-h0d85af4_5 conda-forge - libiconv: 1.17-hd75f5a5_2 conda-forge - libllvm16: 16.0.6-hbedff68_3 conda-forge - libsqlite: 3.45.3-h92b6c6a_0 conda-forge - libxml2: 2.12.7-hfa5d230_0 conda-forge - libzlib: 1.3.1-h87427d6_1 conda-forge - llvm-tools: 16.0.6-hbedff68_3 conda-forge - ncurses: 6.5-h5846eda_0 conda-forge - openssl: 3.3.0-h87427d6_3 conda-forge - pip: 24.0-pyhd8ed1ab_0 conda-forge - python: 3.12.3-h1411813_0_cpython conda-forge - readline: 8.2-h9e318b2_1 conda-forge - setuptools: 70.0.0-pyhd8ed1ab_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - tk: 8.6.13-h1abcd95_1 conda-forge - tzdata: 2024a-h0c530f3_0 conda-forge - wheel: 0.43.0-pyhd8ed1ab_1 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.6-h915ae27_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: sequali-0.10.0_c43b38a212.tar.gz - Downloading https://pypi.io/packages/source/s/sequali/sequali-0.10.0.tar.gz - Success - /opt/mambaforge/envs/bioconda/conda-bld/sequali_1717523007406/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/python: No module named pip - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/sequali_1717523007406/work - Traceback (most recent call last): - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sequali_1717523007406/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sequali_1717523007406/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sequali_1717523007406/work - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - INFO: activate_clang_osx-64.sh made the following environmental changes: - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sequali-0.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sequali-0.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sequali_1717523007406/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 69fccabe0a7f7..6ea35930a5604 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.10.0" %} +{% set version = "0.11.1" %} package: name: "{{ name|lower }}" @@ -7,24 +7,26 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c43b38a212c80bfd3f44bb0beeb37f62c9cb298698f2c876e5231cfb6faa34e1 + sha256: d528a9a6eceace4fa8f1ef29625954a759928e7bab02348ef8f92887442f9527 build: - number: 1 + number: 2 entry_points: - sequali=sequali.__main__:main - sequali-report=sequali.__main__:sequali_report + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} run_exports: - {{ pin_subpackage('sequali', max_pin="x.x") }} - script: "{{ PYTHON }} -m pip install . -vv" - + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" requirements: build: - "{{ compiler('c') }}" - - pip host: - python + - pip + - setuptools-scm >=8.0 run: - pygal >=3.0.4 - python @@ -40,7 +42,7 @@ test: about: home: "https://github.com/rhpvorderman/sequali" - license: "GNU Affero General Public v3 or later (AGPLv3+)" + license: "AGPL-3.0-or-later" license_family: AGPL license_file: LICENSE summary: "Fast sequencing quality metrics" @@ -48,6 +50,10 @@ about: dev_url: "https://github.com/rhpvorderman/sequali" extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - rhpvorderman - + identifiers: + - doi:10.5281/zenodo.10854010 diff --git a/recipes/seqwish/build.sh b/recipes/seqwish/build.sh index 0b621bb26f65d..699332a22fd00 100644 --- a/recipes/seqwish/build.sh +++ b/recipes/seqwish/build.sh @@ -1,4 +1,7 @@ #!/bin/bash + +set -xe + export LIBRARY_PATH=${PREFIX}/lib export LD_LIBRARY_PATH=${PREFIX}/lib export CPATH=${PREFIX}/include @@ -6,7 +9,17 @@ export C_INCLUDE_PATH=${PREFIX}/include export CPLUS_INCLUDE_PATH=${PREFIX}/include export CPP_INCLUDE_PATH=${PREFIX}/include export CXX_INCLUDE_PATH=${PREFIX}/include -cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -cmake --build build + +EXTRA_FLAGS="-Ofast" + +case $(uname -m) in + x86_64) + EXTRA_FLAGS="${EXTRA_FLAGS} -march=sandybridge" + ;; + *) ;; +esac + +cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS="${EXTRA_FLAGS}" +cmake --build build -j ${CPU_COUNT} mkdir -p $PREFIX/bin mv bin/* $PREFIX/bin diff --git a/recipes/seqwish/meta.yaml b/recipes/seqwish/meta.yaml index 61ad99d0a7389..04cdcf32616b4 100644 --- a/recipes/seqwish/meta.yaml +++ b/recipes/seqwish/meta.yaml @@ -13,7 +13,7 @@ build: skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} - number: 0 + number: 1 requirements: build: @@ -40,6 +40,8 @@ about: summary: Alignment to variation graph inducer extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - AndreaGuarracino skip-lints: diff --git a/recipes/seurat-scripts/conda_build_config.yaml b/recipes/seurat-scripts/conda_build_config.yaml index 3eedcdc17af61..04b83d74f6c26 100644 --- a/recipes/seurat-scripts/conda_build_config.yaml +++ b/recipes/seurat-scripts/conda_build_config.yaml @@ -1,2 +1,2 @@ r_base: - - 4.0 + - 4.0.5 diff --git a/recipes/seurat-scripts/meta.yaml b/recipes/seurat-scripts/meta.yaml index 55cba16fa5424..15da9b60e8023 100644 --- a/recipes/seurat-scripts/meta.yaml +++ b/recipes/seurat-scripts/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.0.0" %} +{% set version = "4.4.0" %} package: name: seurat-scripts @@ -6,11 +6,13 @@ package: source: url: https://github.com/ebi-gene-expression-group/r-seurat-scripts/archive/{{ version }}.tar.gz - sha256: 2ee6f3bf471809efe8455131af763dfa17b84d0134a57cc9d33d7c347898dc29 + sha256: 907d30d3c2326565654af170670fc09b6bbda5fbfa356b17486a239ebf022bfb build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('seurat-scripts', max_pin="x.x") }} requirements: host: @@ -19,16 +21,17 @@ requirements: - r-optparse - libpng - r-cairo - - r-seurat =4.0.0 - - r-uwot <0.1.11 - r-workflowscriptscommon >=0.0.8 + - r-seurat <=4.4 - r-loom - r-svglite - bioconductor-scater - r-seuratdisk + - r-remotes - bioconductor-multtest - r-metap - pandoc + - bioconductor-limma - mscorefonts test: diff --git a/recipes/severus/meta.yaml b/recipes/severus/meta.yaml index 8f3899b47acaa..a8692261e10e3 100644 --- a/recipes/severus/meta.yaml +++ b/recipes/severus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1" %} +{% set version = "1.2" %} package: name: severus @@ -6,7 +6,7 @@ package: source: url: https://github.com/KolmogorovLab/Severus/archive/refs/tags/{{ version }}.tar.gz - sha256: 9479ff6c5ee09d28c047b7088414f5cc626cc77523940f2a22fa939506772d1d + sha256: 087566e5fb6f9156323771e46b9fe8d5f90aefb5bbb442cf1ed246dcb4f85847 build: number: 0 diff --git a/recipes/shasta/meta.yaml b/recipes/shasta/meta.yaml index fb4758f507aab..1cfc6b35d6b1e 100644 --- a/recipes/shasta/meta.yaml +++ b/recipes/shasta/meta.yaml @@ -1,6 +1,6 @@ {% set name = "shasta" %} -{% set version = "0.12.0" %} -{% set sha256 = "abbecf0662f52a55e13fcb09cd337b5768623929b7e8c5e3ccac9dde4a626623" %} +{% set version = "0.13.0" %} +{% set sha256 = "0f7c25579a7600d10f0ad92aaed2e3ed8d9f3450c53cba2293c3e6d8bceb02ca" %} package: name: "{{ name|lower }}" diff --git a/recipes/short-read-connector/meta.yaml b/recipes/short-read-connector/meta.yaml index b20e32de5f24b..cd9c0537505c8 100644 --- a/recipes/short-read-connector/meta.yaml +++ b/recipes/short-read-connector/meta.yaml @@ -7,8 +7,10 @@ source: md5: "2b7a3c9bdb5a3d3e2d3c9fdd9b496323" build: - number: 0 + number: 1 skip: True # [osx] + run_exports: + - {{ pin_subpackage('short-read-connector', max_pin="x") }} requirements: build: @@ -35,3 +37,7 @@ about: license_family: AGPL license_file: LICENSE summary: Short read connector enables the comparisons of two read sets + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/shortstack/meta.yaml b/recipes/shortstack/meta.yaml index 6d48ecdb909da..f473cd67cc6e1 100644 --- a/recipes/shortstack/meta.yaml +++ b/recipes/shortstack/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ShortStack" %} -{% set version = "4.0.4" %} -{% set sha256 = "62bd8424c95bacb85350fd9a23c9a6b446f6bee86770d08803b7fad0bb512ac2" %} +{% set version = "4.1.0" %} +{% set sha256 = "f138672d1f564cdd9dffe384bc84ca01bbd67b8e76a9d9f030b47a0e478f3fe1" %} package: name: {{ name|lower }} @@ -18,15 +18,15 @@ build: requirements: run: - - python >=3.10.8 - - samtools >=1.16 + - python >=3.12.3 + - samtools >=1.20 - bowtie >=1.3.1 - viennarna 2.* - tqdm - numpy - biopython - - strucvis - - shorttracks + - strucvis >=0.9 + - shorttracks >=1.2 - bedtools - cutadapt diff --git a/recipes/shorttracks/meta.yaml b/recipes/shorttracks/meta.yaml index 197302af4a89e..75081b308d1cb 100644 --- a/recipes/shorttracks/meta.yaml +++ b/recipes/shorttracks/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ShortTracks" %} -{% set version = "1.1" %} -{% set sha256 = "3cdc1f74c417f88d53c5d097f19dc341a6038b13190b7966f1e6be8624f66f0e" %} +{% set version = "1.2" %} +{% set sha256 = "e29ab660736a2da98eb7161e97636cf16d0c0b3161ed4e2e0d1b0914bddeccc6" %} package: name: {{ name|lower }} @@ -13,6 +13,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('shorttracks', max_pin="x") }} requirements: run: @@ -31,4 +33,4 @@ about: license_family: MIT license_file: LICENSE summary: 'ShortTracks : Useful length- and strand-based coverage files (bigwig) from small RNA-seq alignments (BAM)' - + dev_url: https://github.com/MikeAxtell/ShortTracks diff --git a/recipes/sigprofilerassignment/meta.yaml b/recipes/sigprofilerassignment/meta.yaml index 63705800193c8..d67c7198b9b00 100644 --- a/recipes/sigprofilerassignment/meta.yaml +++ b/recipes/sigprofilerassignment/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SigProfilerAssignment" %} -{% set version = "0.1.7" %} +{% set version = "0.1.8" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/SigProfilerAssignment-{{ version }}.tar.gz - sha256: f4522dccecb3a39792d4199aa730134c7cb9efa2f49e54d3d4b58915600fad02 + sha256: dc0deaf3d37570ed5557f829a2708d93c0c0d2feef99ae680c4222bb9e491f5f build: noarch: python diff --git a/recipes/sigprofilermatrixgenerator/meta.yaml b/recipes/sigprofilermatrixgenerator/meta.yaml index feea8811d72e4..01f51f62609da 100644 --- a/recipes/sigprofilermatrixgenerator/meta.yaml +++ b/recipes/sigprofilermatrixgenerator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SigProfilerMatrixGenerator" %} -{% set version = "1.2.27" %} +{% set version = "1.2.29" %} package: name: {{ name|lower }} @@ -7,13 +7,13 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/SigProfilerMatrixGenerator-{{ version }}.tar.gz - sha256: c25d3e4c3de14b7a758da8c5a54e53d591899938e71234b1ea44d66c4eec744b + sha256: cd00ae4f5c0bf916823b9bd76d75e09d804f4cb91a9c0e0be6af2f6887dcf503 build: entry_points: - SigProfilerMatrixGenerator=SigProfilerMatrixGenerator.scripts.SigProfilerMatrixGenerator_CLI:main_function noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} @@ -35,13 +35,12 @@ test: imports: - SigProfilerMatrixGenerator commands: - - pip check - SigProfilerMatrixGenerator install --help - requires: - - pip about: - home: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator.git - summary: SigProfiler matrix generator tool + home: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator + summary: "SigProfiler matrix generator tool." license: BSD-2-Clause + license_family: BSD license_file: LICENSE + dev_url: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator diff --git a/recipes/sigprofilerplotting/meta.yaml b/recipes/sigprofilerplotting/meta.yaml index 26a637ebc5fb5..efe1357184a46 100644 --- a/recipes/sigprofilerplotting/meta.yaml +++ b/recipes/sigprofilerplotting/meta.yaml @@ -1,29 +1,29 @@ -{% set name = "SigProfilerPlotting" %} -{% set version = "1.3.23" %} +{% set name = "sigProfilerPlotting" %} +{% set version = "1.3.24" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sigProfilerPlotting-{{ version }}.tar.gz - sha256: 867201902893dbca89444309229731b2294fdbf254dbd76ebd970ca36198b825 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sigprofilerplotting-{{ version }}.tar.gz + sha256: 99be52760ff9cac55d075035580d256a28e99e8dbd5a7c67f45f1451d4d8ffcd build: entry_points: - SigProfilerPlotting=sigProfilerPlotting.sigProfilerPlotting_CLI:main_function noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: host: - - python + - python >=3.7 - pip run: - - python + - python >=3.7 - matplotlib-base >=3.4.3 - pandas >=1.2.4,<2.0.0 - scikit-learn >=1.1.3 @@ -33,13 +33,13 @@ test: imports: - sigProfilerPlotting commands: - - pip check - SigProfilerPlotting plotSBS --help - requires: - - pip about: home: https://github.com/alexandrovlab/SigProfilerPlotting - summary: SigProfiler plotting tool + summary: "SigProfiler plotting tool." license: BSD-2-Clause + license_family: BSD license_file: LICENSE + dev_url: https://github.com/alexandrovlab/SigProfilerPlotting + doc_url: https://osf.io/2aj6t/wiki/home diff --git a/recipes/singlem/meta.yaml b/recipes/singlem/meta.yaml index c686add8750fa..122cb94531495 100644 --- a/recipes/singlem/meta.yaml +++ b/recipes/singlem/meta.yaml @@ -1,5 +1,5 @@ {% set name = "singlem" %} -{% set version = "0.18.2" %} +{% set version = "0.18.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8b1f1e51a8cebc4d6d2aa916c6ebb566b3828d3b4029d5831ac186b238d739dc + sha256: 2265476582ce418961072ee0eaaa70db60a888fdcda18c72828f6d0bf55530e8 build: number: 0 diff --git a/recipes/sizemeup/build.sh b/recipes/sizemeup/build.sh new file mode 100644 index 0000000000000..98412cd73fb29 --- /dev/null +++ b/recipes/sizemeup/build.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin ${PREFIX}/share/sizemeup + +# Install sizemup library +$PYTHON -m pip install --no-deps --ignore-installed -vv . + +# move main executable, and replace with wrapper +chmod 755 bin/sizemeup-bioconda +mv $PREFIX/bin/sizemeup $PREFIX/bin/sizemeup-main +cp -f bin/sizemeup-bioconda $PREFIX/bin/sizemeup + +# Copy genome size database (~100kb) +cp -f data/sizemeup-sizes.txt ${PREFIX}/share/sizemeup diff --git a/recipes/sizemeup/meta.yaml b/recipes/sizemeup/meta.yaml new file mode 100644 index 0000000000000..a9d8a6b435d66 --- /dev/null +++ b/recipes/sizemeup/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "sizemeup" %} +{% set version = "1.2.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/rpetit3/sizemeup/archive/v{{ version }}.tar.gz + sha256: 0ce574a492ec88bb4befba1c429e7f853afa859808f9606a642c722ce2564f68 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + host: + - python >=3.7 + - poetry + - pip + run: + - python >=3.7 + - requests + - rich-click >=1.6.0 + +test: + imports: + - sizemeup + commands: + - pip check + - sizemeup --version + - sizemeup --help + - sizemeup --query "Staphylococcus aureus" + - sizemeup -q 1280 + - sizemeup-build --help + requires: + - pip + +about: + home: https://github.com/rpetit3/sizemeup + summary: A simple tool to determine the genome size of an organism + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - rpetit3 diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index f6a8f34b16558..97a9ed1c65d7f 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ska2" %} -{% set version = "0.3.9" %} +{% set version = "0.3.11" %} package: name: {{ name|lower}} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/ska.rust/archive/v{{ version }}.tar.gz - sha256: e25a05c2c08a871feb5f9eca6993d9719a63a97323385353a58ba30fa829b5c1 + sha256: d58519c57db7c3a8c36015a435645e09b15be456e8ffabb175bcb3e3b7731e78 build: number: 0 diff --git a/recipes/skder/build.sh b/recipes/skder/build.sh index 77291308f3479..0761399e03b08 100644 --- a/recipes/skder/build.sh +++ b/recipes/skder/build.sh @@ -4,9 +4,10 @@ $PYTHON -m pip install . --ignore-installed --no-deps -vv mkdir -p ${PREFIX}/bin -# (re)-compile C++ programs -${CXX} -std=c++11 -o ${PREFIX}/bin/skDERcore src/skDER/skDERcore.cpp -${CXX} -std=c++11 -o ${PREFIX}/bin/skDERsum src/skDER/skDERsum.cpp +export LDFLAGS= + +${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/skDERsum src/skDER/skDERsum.cpp +${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/skDERcore src/skDER/skDERcore.cpp chmod +x ${PREFIX}/bin/skDERcore chmod +x ${PREFIX}/bin/skDERsum diff --git a/recipes/skder/meta.yaml b/recipes/skder/meta.yaml index c028bb34e45db..2e14329b862dd 100644 --- a/recipes/skder/meta.yaml +++ b/recipes/skder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skder" %} -{% set version = "1.2.3" %} +{% set version = "1.2.7" %} package: name: {{ name|lower }} @@ -7,13 +7,13 @@ package: source: url: https://github.com/raufs/skDER/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3089d3a60f1007101208b4aa4678133b979590521a497f36eb54c673088790d5 + sha256: 283e4a05d27afcff65564450d15150e6a9ad393b0a29b61802b6ab7e05197347 build: number: 0 skip: True # [py <= 39] run_exports: - - {{ pin_subpackage('skder', max_pin='x.x') }} + - {{ pin_subpackage('skder', max_pin='x') }} requirements: build: @@ -24,15 +24,15 @@ requirements: - pip - wget run: - - python =3.10 + - python >=3.10 - biopython - setuptools - skani - ncbi-genome-download - - pyfastx - wget - seaborn - matplotlib-base + - python-igraph - pandas - pyrodigal - cd-hit @@ -46,9 +46,11 @@ about: license: BSD-3-Clause license license_file: LICENSE license_family: BSD - summary: "skDER: efficient & high-resolution dereplication of microbial genomes" + summary: "skDER & CiDDER: efficient & high-resolution dereplication methods for microbial genomes" dev_url: https://github.com/raufs/skDER extra: additional-platforms: - linux-aarch64 + recipe-maintainers: + - raufs diff --git a/recipes/slow5tools/meta.yaml b/recipes/slow5tools/meta.yaml index 1886640a6b95d..4941e1c8f1dc6 100644 --- a/recipes/slow5tools/meta.yaml +++ b/recipes/slow5tools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "slow5tools" %} -{% set version = "1.2.0" %} +{% set version = "1.3.0" %} package: name: {{ name }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/hasindu2008/slow5tools/releases/download/v{{ version }}/slow5tools-v{{ version }}-release.tar.gz - sha256: ce9d198f8368e90f440fce974e798b7f521b0fe4f859caf9a452bba1ca5af2d4 + sha256: f7221285e0090a5ca05a75f5e70c51d093138b2c8ad658b2756c3c6e51097d5d build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('slow5tools', max_pin="x") }} diff --git a/recipes/smalt/build.sh b/recipes/smalt/build.sh index 3f8b3a68e0763..62bafd63bdae4 100644 --- a/recipes/smalt/build.sh +++ b/recipes/smalt/build.sh @@ -1,12 +1,12 @@ #!/bin/bash -set -ef -o pipefail +set -xef -o pipefail export CPPFLAGS="-I${PREFIX}/include" export LDFLAGS="-L${PREFIX}/lib" ./configure --prefix=$PREFIX -make +make -j ${CPU_COUNT} if [ -z "${OSX_ARCH}" ]; then make check diff --git a/recipes/smudgeplot/build.sh b/recipes/smudgeplot/build.sh index 758b23ba13f0e..7dd1d9fd55b4a 100644 --- a/recipes/smudgeplot/build.sh +++ b/recipes/smudgeplot/build.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash mkdir -p $PREFIX/bin diff --git a/recipes/smudgeplot/meta.yaml b/recipes/smudgeplot/meta.yaml index 3def4859d4580..9d41489cad4f2 100644 --- a/recipes/smudgeplot/meta.yaml +++ b/recipes/smudgeplot/meta.yaml @@ -1,16 +1,17 @@ -{% set version = "0.2.5" %} +{% set version = "0.3.0" %} package: name: smudgeplot version: {{ version }} build: - number: 4 - skip: True # [py2k] + number: 1 + run_exports: + - {{ pin_subpackage('smudgeplot', max_pin="x.x") }} source: url: https://github.com/KamilSJaron/smudgeplot/archive/v{{ version }}.tar.gz - sha256: 189c910b28e59d52f52ae1f7b2fc0c7e8c603525e4383e19753eccbb65afb5cc + sha256: b95b61e517de8f33c49910825a5c68e9a0d1e27cc33463939ef4c994e61dda92 requirements: build: @@ -30,6 +31,7 @@ requirements: - r-argparse - numpy - scipy + test: commands: - smudgeplot.py --version 2>&1 | grep 'Running' @@ -37,5 +39,12 @@ test: about: home: https://github.com/KamilSJaron/smudgeplot license: Apache-2.0 + license_family: APACHE license_file: LICENSE - summary: Inference of ploidy and heterozygosity structure using whole genome sequencing data + summary: "Inference of ploidy and heterozygosity structure using whole genome sequencing data." + dev_url: https://github.com/KamilSJaron/smudgeplot + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/snakemake-executor-plugin-drmaa/meta.yaml b/recipes/snakemake-executor-plugin-drmaa/meta.yaml index 7937a06afe146..dd409935a535d 100644 --- a/recipes/snakemake-executor-plugin-drmaa/meta.yaml +++ b/recipes/snakemake-executor-plugin-drmaa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-drmaa" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_drmaa-{{ version }}.tar.gz - sha256: 93ddefc3fcb5ee2241e4622d04fd1ffcfc58776ff9e723e958a0da2cc2c5fcb7 + sha256: 24fe16fc1f1e7ef75bc213cdb960b674bb130ec918a9f6106511a667ffc661b2 build: noarch: python diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml index e47a6fbc91962..1cc98c04baa22 100644 --- a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-googlebatch" %} -{% set version = "0.4.0" %} +{% set version = "0.5.0" %} # Upon version update, requirements have to be checked! package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz - sha256: ad1ebf74d6558bc5ea9d1849570fb3c5991413265c771d944e99aeb8c49217d2 + sha256: 242ddb2348db1837a0676e991b257e0924791d3dab20aa8f89d63c548adfd1cd build: noarch: python diff --git a/recipes/snakemake-executor-plugin-kubernetes/meta.yaml b/recipes/snakemake-executor-plugin-kubernetes/meta.yaml index c4ffe95046b1e..f302f655b0d07 100644 --- a/recipes/snakemake-executor-plugin-kubernetes/meta.yaml +++ b/recipes/snakemake-executor-plugin-kubernetes/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-kubernetes" %} -{% set version = "0.1.5" %} +{% set version = "0.2.1" %} # Upon version update, requirements have to be checked! package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_kubernetes-{{ version }}.tar.gz - sha256: 7984ef057c25ce1ff46ceac5839dfad01e2938faa649e59fa439e8154e8025eb + sha256: 476c423cb33b71bff2ed11d2ec0aace8bb76e1b9667b408880bcbe2c7fdbe6ef build: noarch: python diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index dcd161f2ac530..cd72d9426ad2d 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.9.0" %} +{% set version = "0.11.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 1d527dc8d09daa194b4ced3360d06bce61001bfa78471ff35bd421c818fa4101 + sha256: bce1df57900da71175c1c384dbc8f04d8bf8572717c0aaf95c32945a4c7a08d3 build: noarch: python diff --git a/recipes/snakemake-executor-plugin-tes/meta.yaml b/recipes/snakemake-executor-plugin-tes/meta.yaml new file mode 100644 index 0000000000000..2aaa1f6e115f1 --- /dev/null +++ b/recipes/snakemake-executor-plugin-tes/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "snakemake-executor-plugin-tes" %} +{% set version = "0.1.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_tes-{{ version }}.tar.gz + sha256: bbecd5c1e63a39e2ea84b752e8e4d68e64b16df686062f22e347cf97c7cd47b3 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + host: + - python >=3.11,<3.13 + - poetry-core + - pip + run: + - python >=3.11.0,<3.13 + - snakemake-interface-common >=1.14.0,<2.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 + - py-tes >=0.4.2,<0.5.0 + +test: + imports: + - snakemake_executor_plugin_tes + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-tes + summary: A Snakemake executor plugin for submitting jobs to a GA4GH TES cluster. + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 854fad21ef1e9..63b0ac8ef24ec 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.17.2" %} +{% set version = "1.17.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 7a2bba88df98c1a0a5cec89b835c62dd2e6e72c1fb8fd104fe73405c800b87c0 + sha256: cca6e2c728072a285a8e750f00fdd98d9c50063912184c41f8b89e4cab66c7b0 build: noarch: python diff --git a/recipes/snakemake-interface-storage-plugins/meta.yaml b/recipes/snakemake-interface-storage-plugins/meta.yaml index 377dfe94187ab..57fe560c93036 100644 --- a/recipes/snakemake-interface-storage-plugins/meta.yaml +++ b/recipes/snakemake-interface-storage-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-storage-plugins" %} -{% set version = "3.2.3" %} +{% set version = "3.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_storage_plugins-{{ version }}.tar.gz - sha256: b5be7c7dd0b4ec283bfc24f56070aa4047f67de44d8bc64c7aa9bf6ee590b27d + sha256: 203d8f794dfb37d568ad01a6c375fa8beac36df8e488c0f9b9f75984769c362a build: noarch: python diff --git a/recipes/snakemake-storage-plugin-azure/meta.yaml b/recipes/snakemake-storage-plugin-azure/meta.yaml index 1dbea32c465a1..09d9cb959f74e 100644 --- a/recipes/snakemake-storage-plugin-azure/meta.yaml +++ b/recipes/snakemake-storage-plugin-azure/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-azure" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_azure-{{ version }}.tar.gz - sha256: 5200670ee317a572aa8fe843847a3b9810da1584543b84f69b804b54802db11b + sha256: f1b0395e466fa2f6a20247a23c240b418240dbd6eaf7a55af3b34714594891f0 build: noarch: python diff --git a/recipes/snakemake-storage-plugin-fs/meta.yaml b/recipes/snakemake-storage-plugin-fs/meta.yaml index 579a4f5664acd..571c12e62ff7b 100644 --- a/recipes/snakemake-storage-plugin-fs/meta.yaml +++ b/recipes/snakemake-storage-plugin-fs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-fs" %} -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_fs-{{ version }}.tar.gz - sha256: 4f7ce1bf16d10510f8f4a2fde2ae22d047131020bd5efa603132dabfc85f444b + sha256: 8d8ead1883d7e670b1d34ea084f7c927bb4fab71fd8d221b7478680cc09a443e build: noarch: python diff --git a/recipes/snakemake-storage-plugin-gcs/meta.yaml b/recipes/snakemake-storage-plugin-gcs/meta.yaml index b269805339223..9228b2ed03517 100644 --- a/recipes/snakemake-storage-plugin-gcs/meta.yaml +++ b/recipes/snakemake-storage-plugin-gcs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-gcs" %} -{% set version = "1.0.0" %} +{% set version = "1.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_gcs-{{ version }}.tar.gz - sha256: a5ca15813a74ae18d41cc5dbde0792e2ec5bfc32e8615d458b41dded1b430e14 + sha256: ac6fc6aaf63ec6ae7453e1cb080e07da346ad4497bd2a87947c352f0fb311d31 build: noarch: python diff --git a/recipes/snakemake-storage-plugin-s3/meta.yaml b/recipes/snakemake-storage-plugin-s3/meta.yaml index 998e66cac163b..b0e4efbecbe32 100644 --- a/recipes/snakemake-storage-plugin-s3/meta.yaml +++ b/recipes/snakemake-storage-plugin-s3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-s3" %} -{% set version = "0.2.11" %} +{% set version = "0.2.12" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_s3-{{ version }}.tar.gz - sha256: edbac21ca22d2e674eaadf05f21c611891df37366d4fbd6a712d79172d788895 + sha256: 339bd425e18baabfb1404ab91dfe56a26499bf728fa3359fb4e0b17b287786a8 build: noarch: python diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 1081e75cde7ef..d1eb2d070650d 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,7 +1,7 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set name = "snakemake" %} -{% set version = "8.16.0" %} +{% set version = "8.20.5" %} package: name: {{ name }} @@ -9,7 +9,7 @@ package: source: url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz - sha256: 3906ae1a5e16b941755b61537a8d16e249106cbbeb0d40b9552933e96ff07af4 + sha256: 5b877b6cf9403397977b0ac0442a6e3aff70d8d893f74b586f988ff7e9c025d7 build: number: 0 @@ -103,11 +103,10 @@ outputs: - requests >=2.8.1 - reretry - smart_open >=4.0,<8.0 - - snakemake-interface-executor-plugins >=9.1.0,<10.0.0 + - snakemake-interface-executor-plugins >=9.2.0,<10.0.0 - snakemake-interface-common >=1.17.0,<2.0 - - snakemake-interface-storage-plugins >=3.1.0,<4.0 + - snakemake-interface-storage-plugins >=3.2.3,<4.0 - snakemake-interface-report-plugins >=1.0.0,<2.0.0 - - stopit - tabulate - throttler - toposort >=1.10,<2.0 diff --git a/recipes/snakeobjects/meta.yaml b/recipes/snakeobjects/meta.yaml index 381cf6f16f1b6..6eb4903c40099 100644 --- a/recipes/snakeobjects/meta.yaml +++ b/recipes/snakeobjects/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.1.2" %} +{% set version = "3.1.4" %} package: name: snakeobjects @@ -6,21 +6,23 @@ package: source: url: https://github.com/iossifovlab/snakeobjects/archive/refs/tags/{{ version }}.tar.gz - sha256: b95951c084c5d4ab047bb4dccbb2d7c1573bf9652eabde29b5c6fab93c1075e4 + sha256: 056d8edff46015a6813047f327ca1888c88ee012707e9400d6297e4eb7b00cf7 build: - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir -vvv . noarch: python number: 0 entry_points: - sobjects = snakeobjects.cli:cli + run_exports: + - {{ pin_subpackage('snakeobjects', max_pin="x") }} requirements: host: - - python + - python <3.12 - pip run: - - python + - python <3.12 - snakemake-minimal test: @@ -34,7 +36,9 @@ about: home: https://github.com/iossifovlab/snakeobjects summary: Snakeobjects, an object-oriented workflow management system based on snakemake license: MIT + license_family: MIT license_file: LICENSE + dev_url: https://github.com/iossifovlab/snakeobjects extra: maintainers: diff --git a/recipes/snp-pileup/meta.yaml b/recipes/snp-pileup/meta.yaml index 183350fbe75df..f601bcf01ad9c 100644 --- a/recipes/snp-pileup/meta.yaml +++ b/recipes/snp-pileup/meta.yaml @@ -10,8 +10,10 @@ source: sha256: '{{sha256}}' build: - number: 6 + number: 7 skip: True # [osx] + run_exports: + - {{ pin_subpackage('snp-pileup', max_pin="x.x") }} requirements: build: @@ -31,3 +33,7 @@ about: license: MIT summary: Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets license_family: MIT + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file diff --git a/recipes/solvebio/meta.yaml b/recipes/solvebio/meta.yaml index 03cd78b807a48..da8e049db6098 100644 --- a/recipes/solvebio/meta.yaml +++ b/recipes/solvebio/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.28.0" %} -{% set sha256 = "e7135df9c67eebaa34b54ce2f400d78a7e38b60c65185e8822b6987083baca8d" %} +{% set version = "2.29.1" %} +{% set sha256 = "e5e1e6eb044fb8300b64af768e1a1cae8ee66d665b55190daa44ec2489f7a2a6" %} package: name: solvebio diff --git a/recipes/sonicparanoid/meta.yaml b/recipes/sonicparanoid/meta.yaml index bbcd6ab1811bf..8a7c121c39ac8 100644 --- a/recipes/sonicparanoid/meta.yaml +++ b/recipes/sonicparanoid/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sonicparanoid" %} -{% set version = "2.0.7" %} -{% set sha256 = "634f4fa00d65c6c1c83a2bee35acaeabc097463d7b58099e523725b71e6d1a1b" %} +{% set version = "2.0.8" %} +{% set sha256 = "3649ca513f3ad72f495ccd3aa9871ca9e7bdc0bef21b4efa9e93eeae405c24c2" %} package: name: {{ name|lower }} diff --git a/recipes/sorted_nearest/build_failure.osx-64.yaml b/recipes/sorted_nearest/build_failure.osx-64.yaml deleted file mode 100644 index b28a52d273527..0000000000000 --- a/recipes/sorted_nearest/build_failure.osx-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 2fa8de914f4d17ddde8039fbe1761352a875d48f192b025f668e9186e0a4edc9 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: test failure -log: |2- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. - compiling .pyc files... - number of files: 54 - INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']' - INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']' - INFO: sysroot: '/opt/X11/' files: '[]' - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/sorted_nearest.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/tiles.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/k_nearest.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/max_disjoint_intervals.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/clusters.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/k_nearest_ties.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/windows.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/introns.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/annotate_clusters.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/merge_by.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/cluster_by.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - WARNING (sorted_nearest): interpreter (Python) package conda-forge/osx-64::python==3.9.19=h7a9c478_0_cpython in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) - Fixing permissions - INFO :: Time taken to mark (prefix) - 0 replacements in 0 files was 0.06 seconds - TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/sorted_nearest-0.0.39-py39h1841df5_2.tar.bz2 - Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/work' to '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/work_moved_sorted_nearest-0.0.39-py39h1841df5_2_osx-64' - shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/work_moved_sorted_nearest-0.0.39-py39h1841df5_2_osx-64) - Reloading output folder (local): ...working... done - Solving environment (_test_env): ...working... done - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - - - The following NEW packages will be INSTALLED: - - bzip2: 1.0.8-h10d778d_5 conda-forge - ca-certificates: 2024.6.2-h8857fd0_0 conda-forge - libblas: 3.9.0-22_osx64_openblas conda-forge - libcblas: 3.9.0-22_osx64_openblas conda-forge - libcxx: 17.0.6-h88467a6_0 conda-forge - libffi: 3.4.2-h0d85af4_5 conda-forge - libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge - libgfortran5: 13.2.0-h2873a65_3 conda-forge - liblapack: 3.9.0-22_osx64_openblas conda-forge - libopenblas: 0.3.27-openmp_hfef2a42_0 conda-forge - libsqlite: 3.46.0-h1b8f9f3_0 conda-forge - libzlib: 1.3.1-h87427d6_1 conda-forge - llvm-openmp: 18.1.7-h15ab845_0 conda-forge - ncurses: 6.5-h5846eda_0 conda-forge - numpy: 1.26.4-py39h28c39a1_0 conda-forge - openssl: 3.3.1-h87427d6_0 conda-forge - python: 3.9.19-h7a9c478_0_cpython conda-forge - python_abi: 3.9-4_cp39 conda-forge - readline: 8.2-h9e318b2_1 conda-forge - sorted_nearest: 0.0.39-py39h1841df5_2 local - tk: 8.6.13-h1abcd95_1 conda-forge - tzdata: 2024a-h0c530f3_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/test_tmp/run_test.py", line 2, in - import sorted_nearest - File "/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.9/site-packages/sorted_nearest/__init__.py", line 1, in - import pkg_resources - ModuleNotFoundError: No module named 'pkg_resources' - WARNING: Tests failed for sorted_nearest-0.0.39-py39h1841df5_2.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - TESTS FAILED: sorted_nearest-0.0.39-py39h1841df5_2.tar.bz2 - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/test_tmp - import: 'sorted_nearest' -# Last 100 lines of the build log. diff --git a/recipes/sorted_nearest/meta.yaml b/recipes/sorted_nearest/meta.yaml index d6a32c10c8df0..24a8e58adac2b 100644 --- a/recipes/sorted_nearest/meta.yaml +++ b/recipes/sorted_nearest/meta.yaml @@ -4,7 +4,6 @@ {% set hash_type = "sha256" %} {% set hash_value = "16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1" %} - package: name: '{{ name|lower }}' version: '{{ version }}' @@ -14,8 +13,10 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 2 - script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt" + number: 4 + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir" run_exports: - {{ pin_subpackage(name|lower, max_pin='x.x') }} @@ -24,10 +25,12 @@ requirements: - {{ compiler('c') }} host: - python - - setuptools + - pip - cython + - setuptools-scm >=6.2 run: - python + - setuptools # [osx and arm64] - numpy test: @@ -36,9 +39,13 @@ test: about: home: https://github.com/endrebak/sorted_nearest - license: BSD - summary: Find nearest interval. + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE.txt + summary: "Find nearest interval." + dev_url: https://github.com/endrebak/sorted_nearest extra: additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/spades/0001-change-verbosity-remove-expr.patch b/recipes/spades/0001-change-verbosity-remove-expr.patch index 5528c0a70e085..21bc5e5b9be11 100644 --- a/recipes/spades/0001-change-verbosity-remove-expr.patch +++ b/recipes/spades/0001-change-verbosity-remove-expr.patch @@ -1,7 +1,7 @@ diff -Naur pre_patch/spades_compile.sh post_patch/spades_compile.sh --- pre_patch/spades_compile.sh 2024-05-26 14:36:40 +++ post_patch/spades_compile.sh 2024-05-27 13:00:03 -@@ -36,10 +36,10 @@ +@@ -37,10 +37,10 @@ check_whether_OPTARG_is_an_integer() { } # return the argument first character @@ -14,12 +14,30 @@ diff -Naur pre_patch/spades_compile.sh post_patch/spades_compile.sh print_help() { echo -@@ -222,7 +222,7 @@ +@@ -221,11 +221,21 @@ else + ADDITIONAL_FLAGS="$ADDITIONAL_FLAGS -DSPADES_BUILD_INTERNAL=OFF" + fi - cd "$WORK_DIR" - cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $ADDITIONAL_FLAGS "$BASEDIR/src" +-cd "$WORK_DIR" +-cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $ADDITIONAL_FLAGS "$BASEDIR/src" -make -j $AMOUNT_OF_THREADS -+make -j $AMOUNT_OF_THREADS VERBOSE=1 - make install - cd "$PREFIX" +-make install +-cd "$PREFIX" ++if [[ `uname` == "Darwin" ]]; then ++ export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" ++ export CFLAGS="${CFLAGS} -Wunused-command-line-argument" ++ export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" ++else ++ export CONFIG_ARGS="" ++fi ++ ++cd "${WORK_DIR}" ++cmake -S "${BASEDIR}/src" -B . -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ ++ -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \ ++ -DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \ ++ -DCMAKE_C_FLAGS="${CFLAGS}" "${ADDITIONAL_FLAGS}" \ ++ "${CONFIG_ARGS}" ++cmake --build . --target install -j "${AMOUNT_OF_THREADS}" -v + if [ $RUN_TESTS = "y" ]; then + cd "$BASEDIR" diff --git a/recipes/spades/build.sh b/recipes/spades/build.sh index 60f586f3d392b..3b00666635bce 100644 --- a/recipes/spades/build.sh +++ b/recipes/spades/build.sh @@ -2,10 +2,9 @@ set -e -o pipefail -x -export LIBRARY_PATH=${PREFIX}/lib -export C_INCLUDE_PATH=${PREFIX}/include -export CPP_INCLUDE_PATH=${PREFIX}/include -export CFLAGS="${CFLAGS} -fcommon" -export CXXFLAGS="${CFLAGS} -fcommon" +export LIBRARY_PATH="${PREFIX}/lib" +export INCLUDE_PATH="${PREFIX}/include" +export CFLAGS="${CFLAGS} -O3 -fcommon" +export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include" -bash spades_compile.sh -rj4 -DSPADES_USE_NCBISDK=ON +PREFIX="${PREFIX}" bash spades_compile.sh -rj"${CPU_COUNT}" -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS="all" diff --git a/recipes/spades/build_failure.linux-aarch64.yaml b/recipes/spades/build_failure.linux-aarch64.yaml deleted file mode 100644 index aca6e6112608e..0000000000000 --- a/recipes/spades/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,33 +0,0 @@ -recipe_sha: 6be4333db8acfb6314096dc4462d291a25cfaa0039e0061049862257f52f80a1 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: CI unresponsive -reason: may be due to disk space -log: |- - 13:33:38 [32mBIOCONDA INFO [0m (OUT) [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o [0m - 13:33:38 [32mBIOCONDA INFO [0m (OUT) cd $SRC_DIR/build_spades/projects/ionhammer && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c++ -DBLAZE_CACHE_SIZE=33554432UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DUSE_GLIBCXX_PARALLEL=1 -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -I$SRC_DIR/src/projects/ionhammer -I$SRC_DIR/build_spades/_deps/zlib_ng-build -I$SRC_DIR/ext/src/zlib-ng -I$SRC_DIR/ext/src/mimalloc/include -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/ext/include/blaze/cmake/.. -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fcommon -fopenmp -O2 -g -DNDEBUG -std=gnu++17 -UNDEBUG -Wno-deprecated -g1 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c $SRC_DIR/src/projects/ionhammer/err_helper_table.cpp [0m - 13:33:41 [32mBIOCONDA INFO [0m (OUT) [ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o [0m - 13:33:41 [32mBIOCONDA INFO [0m (OUT) cd $SRC_DIR/build_spades/projects/ionhammer && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c++ -DBLAZE_CACHE_SIZE=33554432UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DUSE_GLIBCXX_PARALLEL=1 -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -I$SRC_DIR/src/projects/ionhammer -I$SRC_DIR/build_spades/_deps/zlib_ng-build -I$SRC_DIR/ext/src/zlib-ng -I$SRC_DIR/ext/src/mimalloc/include -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/ext/include/blaze/cmake/.. -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fcommon -fopenmp -O2 -g -DNDEBUG -std=gnu++17 -UNDEBUG -Wno-deprecated -g1 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -MF CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c $SRC_DIR/src/projects/ionhammer/config_struct.cpp [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) In file included from /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/kmer_helpers.h:20, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/reference.h:20, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/subcluster.hpp:15, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/subcluster.cpp:9: [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/valid_hkmer_generator.hpp: In instantiation of 'void ValidHKMerGenerator::Next() [with long unsigned int kK = 16]': [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/kmer_helpers.h:47:21: required from here [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/valid_hkmer_generator.hpp:227:17: warning: comparison is always true due to limited range of data type [-Wtype-limits] [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) 227 | if (pnucl != -1) { [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) | ~~~~~~^~~~~ [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) In file included from /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/special_functions/detail/bernoulli_details.hpp:11, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/special_functions/bernoulli.hpp:16, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/special_functions/gamma.hpp:35, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/special_functions/factorials.hpp:14, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/special_functions/binomial.hpp:14, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/gamma_poisson_model.hpp:16, [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) from /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/subcluster.hpp:19: [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/tools/toms748_solve.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> boost::math::tools::bracket_and_solve_root(F, const T&, T, bool, Tol, uintmax_t&, const Policy&) [with F = boost::math::detail::beta_inv_ab_t >; T = long double; Tol = eps_tolerance; Policy = boost::math::policies::policy; uintmax_t = long unsigned int]': [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/special_functions/detail/ibeta_inv_ab.hpp:155:46: required from 'T boost::math::detail::ibeta_inv_ab_imp(const T&, const T&, const T&, const T&, bool, const Policy&) [with T = long double; Policy = boost::math::policies::policy]' [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/special_functions/detail/ibeta_inv_ab.hpp:187:31: required from 'boost::math::tools::promote_args_t boost::math::ibeta_inva(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = policies::policy; tools::promote_args_t = double]' [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/special_functions/detail/ibeta_inv_ab.hpp:299:34: required from 'boost::math::tools::promote_args_t boost::math::ibeta_inva(RT1, RT2, RT3) [with RT1 = double; RT2 = double; RT3 = double; tools::promote_args_t = double]' [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/src/projects/ionhammer/gamma_poisson_model.hpp:127:35: required from here [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) /opt/conda/conda-bld/spades_1718371532226/work/ext/include/boost/math/tools/toms748_solve.hpp:502:17: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) 502 | std::pair bracket_and_solve_root(F f, const T& guess, T factor, bool rising, Tol tol, std::uintmax_t& max_iter, const Policy& pol) [0m - 13:33:43 [32mBIOCONDA INFO [0m (OUT) | ^~~~~~~~~~~~~~~~~~~~~~ [0m diff --git a/recipes/spades/build_failure.osx-64.yaml b/recipes/spades/build_failure.osx-64.yaml deleted file mode 100644 index 27f700c1275b3..0000000000000 --- a/recipes/spades/build_failure.osx-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 6be4333db8acfb6314096dc4462d291a25cfaa0039e0061049862257f52f80a1 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error -log: |2- - this->__append(__sz - __cs); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/work/src/../ext/include/llvm/Support/YAMLTraits.h:1976:13: note: in instantiation of member function 'std::vector::resize' requested here - seq.resize(index1); - ^ - In file included from /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/work/ext/src/llvm/YAMLTraits.cpp:9: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/work/src/../ext/include/llvm/Support/YAMLTraits.h:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/work/src/../ext/include/llvm/ADT/Optional.h:22: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/_build_env/bin/../include/c/v1/memory:886: - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/_build_env/bin/../include/c/v1/__memory/allocator.h:167:28: error: 'path' is unavailable: introduced in macOS 10.15 - see https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk - ::new ((void*)__p) _Up(_VSTD::forward<_Args>(__args)...); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/_build_env/bin/../include/c/v1/__memory/allocator_traits.h:296:13: note: in instantiation of function template specialization 'std::allocator::construct' requested here - __a.construct(__p, _VSTD::forward<_Args>(__args)...); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/_build_env/bin/../include/c/v1/__memory/uninitialized_algorithms.h:615:31: note: in instantiation of function template specialization 'std::allocator_traits>::construct' requested here - allocator_traits<_Alloc>::construct(__alloc, std::__to_address(__first2), std::move_if_noexcept(*__first1)); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/_build_env/bin/../include/c/v1/vector:1035:27: note: in instantiation of function template specialization 'std::__uninitialized_allocator_move_if_noexcept, std::reverse_iterator, std::reverse_iterator, std::reverse_iterator>' requested here - __v.__begin_ = std::__uninitialized_allocator_move_if_noexcept( - ^ - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/_build_env/bin/../include/c/v1/vector:1164:9: note: in instantiation of member function 'std::vector::__swap_out_circular_buffer' requested here - __swap_out_circular_buffer(__v); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/_build_env/bin/../include/c/v1/vector:1981:15: note: in instantiation of member function 'std::vector::__append' requested here - this->__append(__sz - __cs); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/work/src/../ext/include/llvm/Support/YAMLTraits.h:1976:13: note: in instantiation of member function 'std::vector::resize' requested here - seq.resize(index1); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/_build_env/bin/../include/c/v1/__filesystem/path.h:477:25: note: 'path' has been explicitly marked unavailable here - _LIBCPP_HIDE_FROM_ABI path(path&& __p) noexcept - ^ - 11 errors generated. - make[2]: *** [ext/llvm/CMakeFiles/llvm-support.dir/build.make:636: ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o] Error 1 - make[2]: *** Waiting for unfinished jobs.... - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c $SRC_DIR/ext/src/easel/esl_stats.c - [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c $SRC_DIR/ext/src/easel/esl_stopwatch.c - [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c $SRC_DIR/ext/src/easel/esl_stretchexp.c - [ 35%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o - cd $SRC_DIR/build_spades/ext/llvm && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -I$SRC_DIR/ext/src/llvm -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fcommon -fopenmp=libomp -stdlib=libc -O2 -g -DNDEBUG -std=gnu17 -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c $SRC_DIR/ext/src/llvm/WithColor.cpp - [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o -MF CMakeFiles/easel.dir/esl_subcmd.c.o.d -o CMakeFiles/easel.dir/esl_subcmd.c.o -c $SRC_DIR/ext/src/easel/esl_subcmd.c - [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c $SRC_DIR/ext/src/easel/esl_threads.c - [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c $SRC_DIR/ext/src/easel/esl_tree.c - [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_varint.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_varint.c.o -MF CMakeFiles/easel.dir/esl_varint.c.o.d -o CMakeFiles/easel.dir/esl_varint.c.o -c $SRC_DIR/ext/src/easel/esl_varint.c - [ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o - cd $SRC_DIR/build_spades/ext/llvm && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -I$SRC_DIR/ext/src/llvm -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fcommon -fopenmp=libomp -stdlib=libc -O2 -g -DNDEBUG -std=gnu17 -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c $SRC_DIR/ext/src/llvm/YAMLParser.cpp - [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c $SRC_DIR/ext/src/easel/esl_vectorops.c - [ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o - cd $SRC_DIR/build_spades/ext/llvm && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -I$SRC_DIR/ext/src/llvm -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fcommon -fopenmp=libomp -stdlib=libc -O2 -g -DNDEBUG -std=gnu17 -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c $SRC_DIR/ext/src/llvm/YAMLTraits.cpp - [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c $SRC_DIR/ext/src/easel/esl_weibull.c - [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c $SRC_DIR/ext/src/easel/esl_workqueue.c - [ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o - cd $SRC_DIR/build_spades/ext/llvm && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -I$SRC_DIR/ext/src/llvm -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fcommon -fopenmp=libomp -stdlib=libc -O2 -g -DNDEBUG -std=gnu17 -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c $SRC_DIR/ext/src/llvm/raw_os_ostream.cpp - [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o - make[1]: *** [CMakeFiles/Makefile2:1594: ext/llvm/CMakeFiles/llvm-support.dir/all] Error 2 - make: *** [Makefile:166: all] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c $SRC_DIR/ext/src/easel/esl_wuss.c - [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c $SRC_DIR/ext/src/easel/esl_sse.c - [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c $SRC_DIR/ext/src/easel/esl_avx.c - [ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o -MF CMakeFiles/easel.dir/esl_avx512.c.o.d -o CMakeFiles/easel.dir/esl_avx512.c.o -c $SRC_DIR/ext/src/easel/esl_avx512.c - [ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_neon.c.o - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/src/include -I$SRC_DIR/build_spades/include -I$SRC_DIR/src -I$SRC_DIR/src/common -isystem $SRC_DIR/src/../ext/include -isystem $SRC_DIR/ext/include -isystem $SRC_DIR/build_spades/ext/easel/include -isystem $SRC_DIR/ext/src/easel -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spades-4.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -fopenmp=libomp -O2 -g -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -UNDEBUG -Wno-deprecated -g1 -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_neon.c.o -MF CMakeFiles/easel.dir/esl_neon.c.o.d -o CMakeFiles/easel.dir/esl_neon.c.o -c $SRC_DIR/ext/src/easel/esl_neon.c - [ 38%] Linking C static library libeasel.a - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake - cd $SRC_DIR/build_spades/ext/easel && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alloc.c.o CMakeFiles/easel.dir/esl_alphabet.c.o CMakeFiles/easel.dir/esl_arr2.c.o CMakeFiles/easel.dir/esl_arr3.c.o CMakeFiles/easel.dir/esl_bitfield.c.o CMakeFiles/easel.dir/esl_buffer.c.o CMakeFiles/easel.dir/esl_cluster.c.o CMakeFiles/easel.dir/esl_composition.c.o CMakeFiles/easel.dir/esl_cpu.c.o CMakeFiles/easel.dir/esl_dirichlet.c.o CMakeFiles/easel.dir/esl_distance.c.o CMakeFiles/easel.dir/esl_dmatrix.c.o CMakeFiles/easel.dir/esl_dsqdata.c.o CMakeFiles/easel.dir/esl_exponential.c.o CMakeFiles/easel.dir/esl_fileparser.c.o CMakeFiles/easel.dir/esl_gamma.c.o CMakeFiles/easel.dir/esl_gencode.c.o CMakeFiles/easel.dir/esl_getopts.c.o CMakeFiles/easel.dir/esl_gev.c.o CMakeFiles/easel.dir/esl_graph.c.o CMakeFiles/easel.dir/esl_gumbel.c.o CMakeFiles/easel.dir/esl_heap.c.o CMakeFiles/easel.dir/esl_histogram.c.o CMakeFiles/easel.dir/esl_hmm.c.o CMakeFiles/easel.dir/esl_huffman.c.o CMakeFiles/easel.dir/esl_hyperexp.c.o CMakeFiles/easel.dir/esl_iset.c.o CMakeFiles/easel.dir/esl_json.c.o CMakeFiles/easel.dir/esl_keyhash.c.o CMakeFiles/easel.dir/esl_lognormal.c.o CMakeFiles/easel.dir/esl_matrixops.c.o CMakeFiles/easel.dir/esl_mem.c.o CMakeFiles/easel.dir/esl_minimizer.c.o CMakeFiles/easel.dir/esl_mixdchlet.c.o CMakeFiles/easel.dir/esl_mixgev.c.o CMakeFiles/easel.dir/esl_mpi.c.o CMakeFiles/easel.dir/esl_msa.c.o CMakeFiles/easel.dir/esl_msacluster.c.o CMakeFiles/easel.dir/esl_msafile.c.o CMakeFiles/easel.dir/esl_msafile2.c.o CMakeFiles/easel.dir/esl_msafile_a2m.c.o CMakeFiles/easel.dir/esl_msafile_afa.c.o CMakeFiles/easel.dir/esl_msafile_clustal.c.o CMakeFiles/easel.dir/esl_msafile_phylip.c.o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o CMakeFiles/easel.dir/esl_msafile_selex.c.o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o CMakeFiles/easel.dir/esl_msashuffle.c.o CMakeFiles/easel.dir/esl_msaweight.c.o CMakeFiles/easel.dir/esl_normal.c.o CMakeFiles/easel.dir/esl_paml.c.o CMakeFiles/easel.dir/esl_quicksort.c.o CMakeFiles/easel.dir/esl_random.c.o CMakeFiles/easel.dir/esl_rand64.c.o CMakeFiles/easel.dir/esl_randomseq.c.o CMakeFiles/easel.dir/esl_ratematrix.c.o CMakeFiles/easel.dir/esl_recorder.c.o CMakeFiles/easel.dir/esl_red_black.c.o CMakeFiles/easel.dir/esl_regexp.c.o CMakeFiles/easel.dir/esl_rootfinder.c.o CMakeFiles/easel.dir/esl_scorematrix.c.o CMakeFiles/easel.dir/esl_sq.c.o CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_ssi.c.o CMakeFiles/easel.dir/esl_stack.c.o CMakeFiles/easel.dir/esl_stats.c.o CMakeFiles/easel.dir/esl_stopwatch.c.o CMakeFiles/easel.dir/esl_stretchexp.c.o CMakeFiles/easel.dir/esl_subcmd.c.o CMakeFiles/easel.dir/esl_threads.c.o CMakeFiles/easel.dir/esl_tree.c.o CMakeFiles/easel.dir/esl_varint.c.o CMakeFiles/easel.dir/esl_vectorops.c.o CMakeFiles/easel.dir/esl_weibull.c.o CMakeFiles/easel.dir/esl_workqueue.c.o CMakeFiles/easel.dir/esl_wuss.c.o CMakeFiles/easel.dir/esl_sse.c.o CMakeFiles/easel.dir/esl_avx.c.o CMakeFiles/easel.dir/esl_avx512.c.o CMakeFiles/easel.dir/esl_neon.c.o - $BUILD_PREFIX/bin/llvm-ranlib libeasel.a - make[2]: Leaving directory '$SRC_DIR/build_spades' - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - [ 38%] Built target easel - make[2]: Leaving directory '$SRC_DIR/build_spades' - make[1]: Leaving directory '$SRC_DIR/build_spades' - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/spades_1718310310834/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/spades/conda_build_config.yaml b/recipes/spades/conda_build_config.yaml deleted file mode 100644 index 54efb0ce6b78c..0000000000000 --- a/recipes/spades/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -MACOSX_DEPLOYMENT_TARGET: - - 10.15 # [osx] \ No newline at end of file diff --git a/recipes/spades/meta.yaml b/recipes/spades/meta.yaml index bacd3f85ce2cd..a9621bd4904de 100644 --- a/recipes/spades/meta.yaml +++ b/recipes/spades/meta.yaml @@ -1,8 +1,9 @@ +{% set name = "spades" %} {% set version = "4.0.0" %} {% set sha256 = "07c02eb1d9d90f611ac73bdd30ddc242ed51b00c8a3757189e8a8137ad8cfb8b" %} package: - name: spades + name: {{ name }} version: {{ version }} source: @@ -12,31 +13,25 @@ source: - 0001-change-verbosity-remove-expr.patch build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('spades', max_pin="x") }} requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} - - llvm-openmp # [osx] - - libgomp # [linux] - cmake - make - pkg-config - - sysroot_linux-64 =2.17 # [linux] host: - llvm-openmp # [osx] - libgomp # [linux] - zlib - bzip2 - - sysroot_linux-64 =2.17 # [linux] run: - llvm-openmp # [osx] - libgomp # [linux] - - python >3.9 - - sysroot_linux-64 =2.17 # [linux] + - python >=3.8 test: commands: @@ -49,28 +44,26 @@ test: - spades-gbuilder 2>&1 | grep spades-gbuilder - spades.py --test && rm -rf spades_test - about: - home: http://ablab.github.io/spades/ - license: GPL-2.0-only + home: "https://github.com/ablab/spades" + license: "GPL-2.0-only" license_family: GPL license_file: LICENSE - summary: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. + summary: "SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies." description: | SPAdes (St. Petersburg genome assembler) is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. However, it might not be suitable for large genomes projects. SPAdes works with Ion Torrent, PacBio, Oxford Nanopore, and Illumina paired-end, mate-pairs and - single reads - - dev_url: https://github.com/ablab/spades - doc_url: http://ablab.github.io/spades/ - + single reads. + dev_url: "https://github.com/ablab/spades" + doc_url: "https://ablab.github.io/spades" extra: additional-platforms: - linux-aarch64 + - osx-arm64 recipe-maintainers: - druvus - notestaff @@ -82,5 +75,3 @@ extra: - doi:10.1101/gr.213959.116 - doi:10.1093/gigascience/giz100 - doi:10.1093/bioinformatics/btz349 - skip-lints: - - should_not_be_noarch_source diff --git a/recipes/spaln/makefile.patch b/recipes/spaln/makefile.patch index 05b4085926c03..e18b786e104b6 100644 --- a/recipes/spaln/makefile.patch +++ b/recipes/spaln/makefile.patch @@ -1,8 +1,8 @@ diff --git a/src/Makefile.in b/src/Makefile.in -index ed5cb96..2d837d0 100644 +index 7e0ab8d..bd09001 100644 --- a/src/Makefile.in +++ b/src/Makefile.in -@@ -1,19 +1,19 @@ +@@ -1,20 +1,20 @@ # Makefile.in for splan/sortgrcd # Copyright(c) Osamu Gotoh <> @@ -14,9 +14,10 @@ index ed5cb96..2d837d0 100644 +table_dir = $(PREFIX)/share/spaln/table +alndbs_dir = $(PREFIX)/share/spaln/alndbs +CXX = $(CXX) - #CXX = clang++ + # for MACOS uncomment below line + #CXX = clang++ -std=c++11 -CFLAGS = -O3 -march=native -+CFLAGS += -O3 ++CFLAGS = -O3 RANLIB = ranlib -LD = g++ +LD = $(CXX) diff --git a/recipes/spaln/meta.yaml b/recipes/spaln/meta.yaml index 98884708d7d91..897fbab3335c3 100644 --- a/recipes/spaln/meta.yaml +++ b/recipes/spaln/meta.yaml @@ -1,6 +1,6 @@ {% set name = "spaln" %} -{% set version = "3.0.4" %} -{% set sha256 = "6001a901e2e1ea5dbf19f34ee18b61ebd9afaf3a3c5107f937dd13e9b63ea870" %} +{% set version = "3.0.6" %} +{% set sha256 = "0b627609b69e0e1487cbb75ff564cfe3816c24da8552acbaf50bf19bce1c6490" %} package: name: {{ name|lower }} @@ -16,6 +16,7 @@ source: build: number: 0 + skip: True # [osx] run_exports: - {{ pin_subpackage('spaln', max_pin="x") }} @@ -58,3 +59,5 @@ extra: - doi:10.1093/nar/gks708 - doi:10.1093/bioinformatics/btl067 - usegalaxy-eu:spaln + additional-platforms: + - linux-aarch64 diff --git a/recipes/spaln/patch-makefile_ldflags b/recipes/spaln/patch-makefile_ldflags index 4b35645b7c204..fbf64ebdfc5fb 100644 --- a/recipes/spaln/patch-makefile_ldflags +++ b/recipes/spaln/patch-makefile_ldflags @@ -1,31 +1,22 @@ +diff --git a/src/Makefile.in b/src/Makefile.in +index 7e0ab8d..f6c7256 100644 --- a/src/Makefile.in +++ b/src/Makefile.in -@@ -23,8 +23,9 @@ PROG_F = fitild compild decompild plotild - PROG = $(PROG_B) $(PROG_A) $(PROG_F) - - STDH = stdtype.h --CLIB = clib.a -lpthread -lm -lz -+CLIB = clib.a - SLIB = sblib.a $(CLIB) -+LLIB = -lpthread -lm -lz - ULIB = ublib.a $(SLIB) - - BINDIR = $(DESTDIR)$(exec_prefix) -@@ -88,13 +89,13 @@ ls: +@@ -95,13 +95,13 @@ ls: ls $(SRC) $(HDR) spaln: spaln.cc blksrc.o $(SLIB) -- $(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(ILIB) +- $(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(LLIB) + $(CXX) $(LDFLAGS) -o $@ spaln.cc blksrc.o $(SLIB) $(LLIB) sortgrcd: sortgrcd.cc $(SLIB) -- $(CXX) -o $@ sortgrcd.cc $(SLIB) $(ILIB) +- $(CXX) -o $@ sortgrcd.cc $(SLIB) $(LLIB) + $(CXX) $(LDFLAGS) -o $@ sortgrcd.cc $(SLIB) $(LLIB) makdbs: makdbs.cc dbs.h seq.h bitpat.h $(SLIB) -- $(CXX) -o $@ makdbs.cc $(SLIB) $(ILIB) +- $(CXX) -o $@ makdbs.cc $(SLIB) $(LLIB) + $(CXX) $(LDFLAGS) -o $@ makdbs.cc $(SLIB) $(LLIB) makmdm: makmdm.cc mdm.h $(CLIB) -- $(CXX) -o $@ makmdm.cc $(CLIB) $(ILIB) +- $(CXX) -o $@ makmdm.cc $(CLIB) $(LLIB) + $(CXX) $(LDFLAGS) -o $@ makmdm.cc $(CLIB) $(LLIB) dvn: dvn.cc autocomp.h $(ULIB) - $(CXX) -o $@ dvn.cc $(ULIB) $(ILIB) + $(CXX) -o $@ dvn.cc $(ULIB) $(LLIB) diff --git a/recipes/spatialleiden/meta.yaml b/recipes/spatialleiden/meta.yaml new file mode 100644 index 0000000000000..b269d97634ff7 --- /dev/null +++ b/recipes/spatialleiden/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "spatialleiden" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/spatialleiden-{{ version }}.tar.gz + sha256: 9f2c9781a347423ba45d14a3e21eaeec1b9ca24bc26edf207fafa41fab71139b + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.10 + - setuptools >=61.0.0 + - setuptools-scm >=6.2 + - pip + run: + - python >=3.10 + - anndata + - igraph + - leidenalg >=0.10.2,<0.11.dev0 + - numpy >=1.21 + - scanpy + - scipy >=1.9 + +test: + imports: + - spatialleiden + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/HiDiHlabs/SpatialLeiden + summary: Implementation of multiplex Leiden for analysis of spatial omics data. + license: MIT + license_family: MIT + license_file: LICENSE + doc_url: https://spatialleiden.readthedocs.io/ + +extra: + recipe-maintainers: + - niklasmueboe + - shashwatsahay diff --git a/recipes/sphae/meta.yaml b/recipes/sphae/meta.yaml index ffd1cd3558f3d..d84b4dca29e66 100644 --- a/recipes/sphae/meta.yaml +++ b/recipes/sphae/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sphae" %} -{% set version = "1.4.3" %} +{% set version = "1.4.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/linsalrob/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 30b92bebe5538b52694a73614a932b12f46575ea5c857961815bbb9cec4c5db9 + sha256: 09d5de5da2e429b2de3734af7331b52fcadd185715d7f06e71eca4631afe2e91 build: number: 0 diff --git a/recipes/spoa/build.sh b/recipes/spoa/build.sh index 925752eeaca8e..1f0c524a7b06f 100644 --- a/recipes/spoa/build.sh +++ b/recipes/spoa/build.sh @@ -4,7 +4,7 @@ set -eoux pipefail export INCLUDES="-I{PREFIX}/include" export LIBPATH="-L${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CXXFLAGS="${CXXFLAGS} -O3" +export CXXFLAGS="${CXXFLAGS} -O3 -I{PREFIX}/include" case $(uname -m) in x86_64) @@ -13,21 +13,29 @@ case $(uname -m) in aarch64) SPOA_OPTS="-Dspoa_use_simde_nonvec=ON -DBUILD_TESTING=OFF" ;; + arm64) + SPOA_OPTS="-Dspoa_use_simde_nonvec=ON -DBUILD_TESTING=OFF" + ;; *) ;; esac +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi cmake -S . -B build \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ -DCMAKE_BUILD_TYPE=Release \ - -DBUILD_SHARED_LIBS=ON \ -Dspoa_install=ON \ -Dspoa_build_exe=ON \ - ${SPOA_OPTS} \ + "${SPOA_OPTS}" \ -Dspoa_use_simde=ON \ -Dspoa_use_simde_openmp=ON \ + -Dspoa_use_cereal=ON \ -DCMAKE_CXX_COMPILER="${CXX}" \ - -DCMAKE_CXX_FLAGS="${CXXFLAGS}" + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" "${CONFIG_ARGS}" cmake --build build/ --target install -j ${CPU_COUNT} -v diff --git a/recipes/spoa/meta.yaml b/recipes/spoa/meta.yaml index b4c53999344c7..ca3c358ba60bf 100644 --- a/recipes/spoa/meta.yaml +++ b/recipes/spoa/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -23,9 +23,10 @@ requirements: host: - zlib - simde - - libgomp # [linux] + - libgomp # [linux] - llvm-openmp # [osx] - - cpu_features + - cpu_features # [linux] + - cereal test: commands: @@ -34,12 +35,16 @@ test: about: home: 'https://github.com/rvaser/spoa' license: MIT + license_family: MIT license_file: LICENSE - summary: 'SIMD partial order alignment tool/library' + summary: 'SIMD partial order alignment tool/library.' + dev_url: 'https://github.com/rvaser/spoa' + doc_url: 'https://github.com/rvaser/spoa/blob/{{ version }}/README.md' extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - biotools:spoa - doi:10.1101/gr.214270.116 diff --git a/recipes/spreadgltools/meta.yaml b/recipes/spreadgltools/meta.yaml new file mode 100644 index 0000000000000..0cb09eeb3e772 --- /dev/null +++ b/recipes/spreadgltools/meta.yaml @@ -0,0 +1,60 @@ +{% set name ="SpreadGLtools" %} +{% set version ="1.1.0" %} +{% set sha256 ="de9319eb0cab7dcf042671c77fd473a7a03a8384ce7d476f10f89a8a100cbeec" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/GuyBaele/SpreadGL/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: python + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} + script: | + cd scripts + {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + host: + - python >=3.11 + - pip + run: + - python >=3.11 + - setuptools >=67.4.0 + - numpy >=1.23.2 + - pandas >=2.2.0 + - geojson >=3.0.1 + - pyproj >=3.4.1 + - dendropy >=4.5.2 + - geopandas >=0.12.2 + - rasterio >=1.3.6 + - rioxarray >=0.14.0 + - bottleneck >=1.3.7 + - gdal >=3.3.0 + +test: + commands: + - spread --help + - rates --help + - regions --help + - raster --help + - reprojection --help + - trimming --help + +about: + home: https://github.com/GuyBaele/SpreadGL + license: MIT + summary: 'Visualising pathogen dispersal in a high-performance browser application' + license_family: MIT + doc_url: https://github.com/GuyBaele/SpreadGL + +extra: + identifiers: + - doi:10.1101/2024.06.04.24308447 diff --git a/recipes/squigulator/build.sh b/recipes/squigulator/build.sh index 892f6dafecd1c..ef6581b36ea81 100644 --- a/recipes/squigulator/build.sh +++ b/recipes/squigulator/build.sh @@ -1,4 +1,7 @@ #!/bin/bash -make CC=$CC CXX=$CXX + +set -xe + +make -j ${CPU_COUNT} CC=$CC CXX=$CXX mkdir -p $PREFIX/bin cp squigulator $PREFIX/bin/squigulator diff --git a/recipes/squigulator/meta.yaml b/recipes/squigulator/meta.yaml index e55f517d8a142..087ddfe0ea226 100644 --- a/recipes/squigulator/meta.yaml +++ b/recipes/squigulator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "squigulator" %} -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} package: name: {{ name }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/hasindu2008/squigulator/releases/download/v{{ version }}/squigulator-v{{ version }}-release.tar.gz - sha256: fca1427fe609c20125e679459c1f509b320acf8a44887fa265649607d8a47789 + sha256: b8c895067308fd950581771c5ad80ce3af10a0264c55476145d0ef0a9d437bb7 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('squigulator', max_pin="x") }} @@ -38,3 +38,7 @@ about: summary: A tool for simulating nanopore raw signal data description: 'squigulator is a tool for simulating nanopore raw signal data.' +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/squirrel/meta.yaml b/recipes/squirrel/meta.yaml new file mode 100644 index 0000000000000..1040946001e9f --- /dev/null +++ b/recipes/squirrel/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.10" %} +{% set name = "squirrel" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/aineniamh/squirrel/archive/refs/tags/{{ version }}.tar.gz + sha256: f59e433906b995004f4e266235b0cfd58d80a08fd63c776d86c1846c8565254e + +build: + number: 0 + noarch: python + script: python -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - python ==3.10 + - pip + run: + - python ==3.10 + - biopython >=1.74 + - minimap2 >=2.16 + - snakemake-minimal ==7.32 + - matplotlib-base >=3.3.1 + - seaborn + - gofasta + - baltic + - mako ==1.2 + - pandas + - iqtree >=2.1 + - jclusterfunk >=0.0.25 + +test: + commands: + - squirrel --help + +about: + home: https://github.com/aineniamh/squirrel + license: GPL-3.0-only + license_family: GPL3 + license_file: LICENSE + summary: Some QUIck Reconstruction to Resolve Evolutionary Links + diff --git a/recipes/sra-tools/build.sh b/recipes/sra-tools/build.sh index 5b55bd0ccec80..272542a5bdabe 100755 --- a/recipes/sra-tools/build.sh +++ b/recipes/sra-tools/build.sh @@ -4,12 +4,6 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 -DH5_USE_110_API -D_FILE_OFFSET_BITS=64 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" -echo "compiling sra-tools" -if [[ ${OSTYPE} == "darwin"* ]]; then - export CFLAGS="${CFLAGS} -DTARGET_OS_OSX" - export CXXFLAGS="${CXXFLAGS} -DTARGET_OS_OSX" -fi - mkdir -p obj/ngs/ngs-java/javadoc/ngs-doc # prevent error on OSX @@ -18,22 +12,32 @@ mkdir -p obj/ngs/ngs-java/javadoc/ngs-doc # prevent error on OSX export SRA_BUILD_DIR=${SRC_DIR}/build_sratools mkdir -p ${SRA_BUILD_DIR} +echo "Compiling sra-tools" if [[ "$(uname)" == "Darwin" ]]; then - export VDB_INC="${SRC_DIR}/ncbi-vdb/interfaces" + export VDB_INC="${SRC_DIR}/ncbi-vdb/interfaces" + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" + export CFLAGS="${CFLAGS} -DTARGET_OS_OSX" + export CXXFLAGS="${CXXFLAGS} -DTARGET_OS_OSX" else - export VDB_INC="${PREFIX}/include" + export VDB_INC="${PREFIX}/include" + export CONFIG_ARGS="" fi cmake -S sra-tools/ -B build_sratools/ \ - -DVDB_BINDIR="${PREFIX}" \ - -DVDB_LIBDIR="${PREFIX}/lib64" \ - -DVDB_INCDIR="${VDB_INC}" \ - -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ - -DCMAKE_BUILD_TYPE=Release \ - -DCMAKE_CXX_COMPILER="${CXX}" \ - -DCMAKE_CXX_FLAGS="${CXXFLAGS}" - -cmake --build build_sratools/ --target install -j ${CPU_COUNT} -v + -DVDB_BINDIR="${PREFIX}" \ + -DVDB_LIBDIR="${PREFIX}/lib" \ + -DVDB_INCDIR="${VDB_INC}" \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_INSTALL_LIBDIR="${PREFIX}/lib" \ + -DCMAKE_C_COMPILER="${CC}" \ + -DCMAKE_C_FLAGS="${CFLAGS}" \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + "${CONFIG_ARGS}" + +cmake --build build_sratools/ --target install -j "${CPU_COUNT}" -v # Strip package version from binary names diff --git a/recipes/sra-tools/meta.yaml b/recipes/sra-tools/meta.yaml index b05af8f4b98c5..00633aae7b54e 100644 --- a/recipes/sra-tools/meta.yaml +++ b/recipes/sra-tools/meta.yaml @@ -15,7 +15,7 @@ source: folder: ncbi-vdb # [osx] build: - number: 0 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -55,14 +55,16 @@ test: about: home: "https://github.com/ncbi/sra-tools" - license: Public Domain + license: "Public Domain" summary: "The SRA Toolkit and SDK from NCBI." description: | - The SRA Toolkit and SDK from NCBI is a collection of tools and libraries - for using data in the INSDC Sequence Read Archives. + "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries + for using data in the INSDC Sequence Read Archives." dev_url: "https://github.com/ncbi/sra-tools" doc_url: "https://github.com/ncbi/sra-tools/wiki" extra: notes: 'After installation, you should run the configuration tool: ./vdb-config -i. This tool will setup your download/cache area for downloaded files and references.' + identifiers: + - biotools:sra-tools diff --git a/recipes/srnamapper/build.sh b/recipes/srnamapper/build.sh index f84b5edcffa02..4c383967d7913 100644 --- a/recipes/srnamapper/build.sh +++ b/recipes/srnamapper/build.sh @@ -1,8 +1,9 @@ #!/bin/bash +set -xe # zlib hack -make CC=$CC INCLUDES="-I$PREFIX/include" CFLAGS+="-g -Wall -O2 -L$PREFIX/lib" +make -j ${CPU_COUNT} CC=$CC INCLUDES="-I$PREFIX/include" CFLAGS+="-g -Wall -O2 -L$PREFIX/lib" chmod +x srnaMapper mkdir -p ${PREFIX}/bin cp -f srnaMapper ${PREFIX}/bin diff --git a/recipes/srnamapper/meta.yaml b/recipes/srnamapper/meta.yaml index 70a63aa2fddb7..517d9908d7844 100644 --- a/recipes/srnamapper/meta.yaml +++ b/recipes/srnamapper/meta.yaml @@ -1,16 +1,19 @@ {% set name = "srnaMapper" %} -{% set version = "1.0.8" %} +{% set version = "1.0.11" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} source: - url: https://github.com/mzytnicki/srnaMapper/archive/refs/tags/{{ version }}.tar.gz - sha256: 389fb960add27a3cfef5d52329711976ff7954cbca589f4c67f60f66bd64ce2a + git_url: https://github.com/mzytnicki/srnaMapper.git + git_rev: {{ version }} + sha256: 582b2f891ae181cf9754cd5d8968dc1eafa0f1d5978d7f8d588f1136a005e467 requirements: build: @@ -33,5 +36,11 @@ test: - srnaMapper -h extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + skip-lints: + - uses_vcs_url + - missing_hash recipe-maintainers: - mzytnicki diff --git a/recipes/starcatpy/meta.yaml b/recipes/starcatpy/meta.yaml new file mode 100644 index 0000000000000..9e1f0b2f4600e --- /dev/null +++ b/recipes/starcatpy/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "starcatpy" %} +{% set version = "1.0.8" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/starcatpy-{{ version }}.tar.gz + sha256: 7ebdc81623cef595ef8a9eaa2bc2a1cc04addcf4238367e83f2f35c01fc5baba + +build: + entry_points: + - starcat = starcat:main + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + number: 0 + run_exports: + - {{ pin_subpackage('starcatpy', max_pin="x") }} + +requirements: + host: + - python + - pip + run: + - python + - scikit-learn >=1.0 + - anndata + - pandas + - numpy + - scipy + - pyyaml + - requests + +test: + imports: + - starcat + commands: + - starcat --help + +about: + home: https://github.com/immunogenomics/starCAT + summary: "Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs." + license: MIT + license_family: MIT + license_file: LICENSE + dev_url: https://github.com/immunogenomics/starCAT diff --git a/recipes/straglr/meta.yaml b/recipes/straglr/meta.yaml index 88b99b723b0dd..12c98c8e8497c 100644 --- a/recipes/straglr/meta.yaml +++ b/recipes/straglr/meta.yaml @@ -1,13 +1,13 @@ {% set name = "straglr" %} -{% set version = "1.5.1" %} +{% set version = "1.5.2" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/bcgsc/straglr/archive/refs/tags/v1.5.1.tar.gz - sha256: 8c65247e9329f5c0b51b83cbf595089efc1d5f4783fc7e8346c05b93e9bc8abe + url: https://github.com/bcgsc/straglr/archive/refs/tags/v1.5.2.tar.gz + sha256: ab04d95e7c5e9465bdf565ad14bd0f46a20482df365b4e8fecd65adb04cf6614 build: noarch: python diff --git a/recipes/strainr2/build.sh b/recipes/strainr2/build.sh index 1e72ed4dfcb40..ff3d646a151fa 100644 --- a/recipes/strainr2/build.sh +++ b/recipes/strainr2/build.sh @@ -2,17 +2,17 @@ mkdir -p "${PREFIX}/bin" -${CC} ${SRC_DIR}/subcontig.c -o subcontig -${CC} ${SRC_DIR}/hashcounter.c -o hashcounter +${CC} ${SRC_DIR}/src/subcontig.c -O3 -o subcontig +${CC} ${SRC_DIR}/src/hashcounter.c -I$PREFIX/include -L$PREFIX/lib -O3 -o hashcounter -lz -chmod +x $SRC_DIR/PreProcessR +chmod +x $SRC_DIR/src/PreProcessR chmod +x $SRC_DIR/subcontig chmod +x $SRC_DIR/hashcounter -chmod +x $SRC_DIR/Plot.R -chmod +x $SRC_DIR/StrainR +chmod +x $SRC_DIR/src/Plot.R +chmod +x $SRC_DIR/src/StrainR -cp $SRC_DIR/PreProcessR ${PREFIX}/bin/ +cp $SRC_DIR/src/PreProcessR ${PREFIX}/bin/ cp $SRC_DIR/subcontig ${PREFIX}/bin/ cp $SRC_DIR/hashcounter ${PREFIX}/bin/ -cp $SRC_DIR/Plot.R ${PREFIX}/bin/ -cp $SRC_DIR/StrainR ${PREFIX}/bin/ +cp $SRC_DIR/src/Plot.R ${PREFIX}/bin/ +cp $SRC_DIR/src/StrainR ${PREFIX}/bin/ diff --git a/recipes/strainr2/meta.yaml b/recipes/strainr2/meta.yaml index d92319912b1b0..fb508093f4d78 100644 --- a/recipes/strainr2/meta.yaml +++ b/recipes/strainr2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.0" %} +{% set version = "2.1.0" %} package: name: strainr2 @@ -6,10 +6,10 @@ package: source: url: https://github.com/BisanzLab/StrainR2/archive/v{{ version }}.tar.gz - sha256: 00ddd426e6d27e461c806282107503d93472a93c71c24e82069bf78be1d31a89 + sha256: 4683de73b3a6cb1c764a0e3adfd92e0eca61aa14dee09e87b9a75af5053e1eb0 build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("strainr2", max_pin="x") }} @@ -20,6 +20,7 @@ requirements: - r-base >=4.2.0 - r-optparse - r-tidyverse + - zlib run: - bbmap - fastp diff --git a/recipes/strainy/meta.yaml b/recipes/strainy/meta.yaml new file mode 100644 index 0000000000000..756fcdc9d5669 --- /dev/null +++ b/recipes/strainy/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.1" %} +{% set name = "strainy" %} + + +package: + name: strainy + version: {{ version }} + + +source: + url: https://github.com/katerinakazantseva/strainy/archive/refs/tags/{{ version }}.tar.gz + sha256: bdbac3961fa840344ac67e249de8f6d4114e0796c5b40bb5535d8e59f4dc63d1 + + +build: + number: 1 + noarch: python + script: {{ PYTHON }} -m pip install -vv . + run_exports: + - {{ pin_subpackage("strainy", max_pin="x") }} + + +requirements: + host: + - python + run: + - python >=3.8 + - samtools >=1.14 + - bcftools >=1.14 + - minimap2 + - pygraphviz + - matplotlib-base + - biopython + - python-edlib + - networkx >=2.6,<3.4 + - gfapy + - karateclub + - numpy >=1.24,<1.27 + - pandas >=1.3,<3 + - pysam >=0.20,<0.23 + - scipy >=1.8,<1.13 + - flye + + +test: + commands: + - strainy -h + +about: + home: https://github.com/katerinakazantseva/strainy + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: assembly-based metagenomic strain phasing using long reads diff --git a/recipes/strangepg/build.sh b/recipes/strangepg/build.sh index 08e12b16862ae..3040da4a94b98 100644 --- a/recipes/strangepg/build.sh +++ b/recipes/strangepg/build.sh @@ -1,4 +1,7 @@ -#!/bin/bash +#!/bin/bash -eu + +set -xe + export CFLAGS="$CFLAGS -I${PREFIX}/include" export LDFLAGS="$LDFLAGS -ldl -lpthread" -make -j install +make -j ${CPU_COUNT} install diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml index 5305080d13612..65e4fdeb2edb7 100644 --- a/recipes/strangepg/meta.yaml +++ b/recipes/strangepg/meta.yaml @@ -1,20 +1,25 @@ {% set name = "strangepg" %} -{% set version = "0.8.0" %} -{% set ref = "55e8fba29e9e0259f5d950df477d1850eb4f3163" %} +{% set version = "0.8.6" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/qwx9/{{ name }}/archive/{{ ref }}.tar.gz - sha256: a8210b50f6ceda7dc6edd05a771d8645523a05d43d01fc7d15bb36ad86d4ffc9 + url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz + sha256: 4023cc790bac53696cf5f62a18c6eafc12e5209eaebf21d921e9865cd5812b5a build: number: 0 skip: True # [not linux] run_exports: - {{ pin_subpackage('strangepg', max_pin=None) }} + ignore_run_exports: + - libxcb + - xorg-libxau + - xorg-libxdmcp + - xorg-libxext + - xorg-libxfixes requirements: build: @@ -26,21 +31,23 @@ requirements: - {{ cdt('libdrm-devel') }} - {{ cdt('libglvnd-glx') }} # [cdt_name != 'cos6'] host: + - xorg-libx11 + - xorg-libxcursor + - xorg-libxi + run: + - libxcb - xorg-libx11 - xorg-libxau - - xorg-libxcb - xorg-libxcursor - xorg-libxdmcp - xorg-libxext - xorg-libxfixes - xorg-libxi - xorg-libxrandr - run: test: - commands: - - which strpg - - which strawk + source_files: + - cmd/main.awk about: home: https://github.com/qwx9/{{ name }} @@ -50,6 +57,8 @@ about: license_file: LICENSE extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - qwx9 container: diff --git a/recipes/strangepg/run_test.sh b/recipes/strangepg/run_test.sh new file mode 100644 index 0000000000000..0093b29f85b73 --- /dev/null +++ b/recipes/strangepg/run_test.sh @@ -0,0 +1,6 @@ +#!/bin/sh -e +# https://github.com/bioconda/bioconda-recipes/pull/29042#issuecomment-864465780 + +strangepg -h 2>/dev/null +strangepg /dev/mordor 2>/dev/null || [[ $? == 1 ]] +echo | strawk -f cmd/main.awk diff --git a/recipes/stranger/meta.yaml b/recipes/stranger/meta.yaml index 7c22e48e2acc5..cddbaa9d4f343 100644 --- a/recipes/stranger/meta.yaml +++ b/recipes/stranger/meta.yaml @@ -1,5 +1,5 @@ {% set name = "stranger" %} -{% set version = "0.9.1" %} +{% set version = "0.9.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b9322384836e46ed9373fdb30b4e7656ea59d6b293f22692a1b9125b6cb8ca76 + sha256: f27c705b53e27098907f6ff8710ee817408baf75ea26720423bfbf1a2383f013 build: number: 0 diff --git a/recipes/strdust/build.sh b/recipes/strdust/build.sh index 8c7b6970ffe7c..24fd00d92cbae 100644 --- a/recipes/strdust/build.sh +++ b/recipes/strdust/build.sh @@ -1,6 +1,9 @@ #!/bin/bash -euo -export CFLAGS="${CFLAGS} -fcommon" -export CXXFLAGS="${CFLAGS} -fcommon" + +export INCLUDE_PATH="${PREFIX}/include" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 -fcommon" +export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include" # build statically linked binary with Rust -RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . +RUST_BACKTRACE=1 cargo install --verbose --root "${PREFIX}" --path . diff --git a/recipes/strdust/meta.yaml b/recipes/strdust/meta.yaml index 281601c6ed233..e4f6df68ce9c7 100644 --- a/recipes/strdust/meta.yaml +++ b/recipes/strdust/meta.yaml @@ -1,30 +1,32 @@ {% set name = "strdust" %} -{% set version = "0.8.0" %} +{% set version = "0.8.2" %} package: name: {{ name }} version: {{ version }} +source: + url: https://github.com/wdecoster/STRdust/archive/refs/tags/v{{ version }}.tar.gz + sha256: 4fd97b05b22870c70a9d41dbcb2f106836f009e3db39bce47921ab6aa9bff100 + build: number: 0 run_exports: - {{ pin_subpackage('strdust', max_pin="x.x") }} -source: - url: https://github.com/wdecoster/strdust/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1b1e0ce34852961066f67020e44ed1716dfb1744488eb9b42b97f6516997cd38 - requirements: build: - - {{ compiler('rust') }} + - {{ compiler('rust') }} - autoconf + - automake + - libtool - make - {{ compiler('cxx') }} - pkg-config - cmake host: + - clangdev - zlib - - clang test: commands: @@ -37,3 +39,8 @@ about: license_file: LICENSE summary: "Tandem repeat genotyper for long reads." dev_url: "https://github.com/wdecoster/STRdust" + doc_url: "https://github.com/wdecoster/STRdust/blob/v{{ version }}/README.md" + +extra: + additional-platforms: + - osx-arm64 diff --git a/recipes/strucvis/meta.yaml b/recipes/strucvis/meta.yaml index 679eba2dab7d6..14469db9d4f0b 100644 --- a/recipes/strucvis/meta.yaml +++ b/recipes/strucvis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "strucVis" %} -{% set version = "0.8" %} -{% set sha256 = "bf14366b9e1b9b983d531de4c6b894adbc9a446461aa7c8c4ce7627f02f88903" %} +{% set version = "0.9" %} +{% set sha256 = "a10a0a7d3fd66bf8e9966fd76ef521c33e8bba0fcb5b474f30a8a6c6533d93d8" %} package: name: {{ name|lower }} diff --git a/recipes/superdsm/meta.yaml b/recipes/superdsm/meta.yaml index d1a32ebbd7551..c534684f4dabe 100644 --- a/recipes/superdsm/meta.yaml +++ b/recipes/superdsm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SuperDSM" %} -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} {% set repo_url = "https://github.com/BMCV/SuperDSM" %} {% set docs_url = "https://superdsm.readthedocs.io" %} @@ -9,7 +9,7 @@ package: source: url: "{{ repo_url }}/archive/refs/tags/v{{ version }}.zip" - sha256: 45907ac09bd6fc150bce816194a1d09cccab42b02a418b9387e00bcb89e0ba3f + sha256: a46a150298a8c611b6ed18bebcf67fe1fc98895760acc70291fb5ca3fe435ea5 build: number: 0 @@ -20,26 +20,28 @@ build: requirements: host: - - python >=3.6,<3.11 + - python >=3.11 - pip - setuptools run: - - python >=3.6,<3.11 + - python >=3.11 - blas =*=mkl - ipython >=7.31.1 - - numpy >=1.18,<2.0 - - scipy >=1.6.3,<2.0 - - scikit-image >=0.18,<=0.19 + - numpy >=1.26,<2.0 + - scipy >=1.13.1,<1.14 + - scikit-image >=0.24.0 - dill >=0.3.2 - - cvxopt >=1.2.6,<2.0 - - cvxpy >=1.1.13,<2.0 + - cvxopt >=1.3.2,<2.0 + - cvxpy >=1.5.3,<2.0 - matplotlib-base >=3.0,<4.0 - mkl >=2020.0 - - ray-core >=0.8.7,<1.7 + - ray-core >=0.8.7 + - imagecodecs >=2024.6.1 + - repype >=1.0.0,<1.1 test: commands: - - python -m superdsm.batch --help + - python -m superdsm --help about: home: "{{ repo_url }}" diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index 28541bd233a37..672db509362e9 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version = "4.4.0" %} +{% set version = "4.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: 331d0740a8cebf29a231d5ead35cda164fc74d7d3a8470803e623f2c33e897b5 + sha256: b8e3b58f4ae054cd2047a931d9c239f7497b9435ce9da72d4a673ddaab89e40e build: noarch: python diff --git a/recipes/t1k/meta.yaml b/recipes/t1k/meta.yaml index d1a157c3a6e45..0e4865512483a 100644 --- a/recipes/t1k/meta.yaml +++ b/recipes/t1k/meta.yaml @@ -5,7 +5,7 @@ package: version: '{{ version }}' build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('t1k', max_pin="x") }} @@ -24,6 +24,7 @@ requirements: run: - perl - python + - curl test: commands: diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index 23b03ecb70bdd..1d2bc89eb43f5 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.26" %} +{% set version = "0.1.1" %} package: name: tcdemux @@ -7,10 +7,10 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: 120b57d54d9fd30e96186c4d11f25691bd54e758e1d7dde99b24868bd2788e59 + sha256: 945c8acef0f68a8bbbd0449ca77a6408e7e2eb2b85c54812931282b8783cdb8f build: - number: 1 + number: 0 noarch: python script: {{ PYTHON }} -m pip install --ignore-installed . run_exports: diff --git a/recipes/telometer/meta.yaml b/recipes/telometer/meta.yaml index 2480b9109616a..541254d534130 100644 --- a/recipes/telometer/meta.yaml +++ b/recipes/telometer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "telometer" %} -{% set version = "0.81" %} +{% set version = "1.1" %} package: name: "{{ name|lower }}" @@ -7,13 +7,13 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/telometer-{{ version }}.tar.gz" - sha256: 88e3f4d0c4018d83f6406be6ecf772a9ea232eab774a8a268bb3b0d427707da3 + sha256: 28f3256263be23e06f68cee0ddb9a3c942dc4cd7674389ce8e5f3c09ba4e17f3 build: number: 0 noarch: python entry_points: - - telometer=telometer:calculate_telomere_length + - telometer=telometer:run_telometer script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -27,6 +27,9 @@ requirements: - pysam - pandas - regex + - samtools + - minimap2 + - scipy test: imports: @@ -38,13 +41,10 @@ about: home: https://github.com/santiago-es/Telometer license: MIT license_family: MIT - license_file: LICENSE.txt + license_file: "LICENSE.txt" summary: "A simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data." dev_url: https://github.com/santiago-es/Telometer - - - extra: recipe-maintainers: - santiago-es diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 6a3ccb82537e6..1451e942c5aca 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.13" %} +{% set version = "1.0.16" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 772b10381901f9bbebc63588ae67c16676462393b8c9a5f886eab32ad13aa7ea + sha256: 85cf6d180db38166bb7ccd14af8c3813e2b3fa0d5026cac76bce8867492563f7 build: noarch: python @@ -29,7 +29,7 @@ requirements: - cutadapt >=4.0 - matplotlib-base >=3.7 - networkx >=2.4,!=2.8.3,!=2.8.4 - - pydot + - pydot <3 - python >=3.8 - rapidfuzz >=2.4.0 - sqlalchemy >=2.0 diff --git a/recipes/tiberius/build.sh b/recipes/tiberius/build.sh new file mode 100644 index 0000000000000..7db29bf46afdf --- /dev/null +++ b/recipes/tiberius/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +mkdir -p ${PREFIX}/bin +cp -R $SRC_DIR/bin/* ${PREFIX}/bin/ +chmod +x ${PREFIX}/bin/tiberius.py +ln -s ${PREFIX}/bin/tiberius.py ${PREFIX}/bin/tiberius +sed -i '1s|^|#!/usr/bin/env python3\n|' ${PREFIX}/bin/tiberius \ No newline at end of file diff --git a/recipes/tiberius/meta.yaml b/recipes/tiberius/meta.yaml new file mode 100644 index 0000000000000..74d57de25be23 --- /dev/null +++ b/recipes/tiberius/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "tiberius" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/Gaius-Augustus/Tiberius/archive/refs/tags/v{{ version }}.tar.gz + sha256: 05fc993a72a1881bac2ec85ae412d2a186daf9d5a2bebb60237c8437b3a68da0 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - python + - pip + run: + - python >=3.7 + - pip + - tensorflow + - transformers + - pyBigWig + - biopython + - bcbio-gff + - requests + - jax + - jaxlib + +test: + commands: + - tiberius -h + +about: + home: https://github.com/Gaius-Augustus/Tiberius + license: MIT + license_file: LICENSE + summary: | + Tiberius is a programme for quantifying and analysing genetic sequence data. \ No newline at end of file diff --git a/recipes/tigmint/build.sh b/recipes/tigmint/build.sh index 3ac3bac6a3b56..061cabb433050 100644 --- a/recipes/tigmint/build.sh +++ b/recipes/tigmint/build.sh @@ -1,6 +1,10 @@ #!/bin/bash set -eux -o pipefail +if [[ ${target_platform} =~ linux.* ]]; then + export CXXFLAGS="${CXXFLAGS} -fopenmp" +fi + make -C src mkdir -p ${PREFIX}/bin/ diff --git a/recipes/tigmint/meta.yaml b/recipes/tigmint/meta.yaml index 7c4c77a4824a0..f7042d839b8b9 100644 --- a/recipes/tigmint/meta.yaml +++ b/recipes/tigmint/meta.yaml @@ -10,8 +10,10 @@ source: sha256: 8e7b5d424ff69d5da7b117bef9996463b02205078ce0fb6e3074ca6c9933efa9 build: - number: 2 - skip: True # [py<38] + number: 3 + skip: True #[(py>38 or py<38) and (arm64 or aarch64)] + run_exports: + - {{ pin_subpackage("tigmint", max_pin="x") }} requirements: @@ -48,15 +50,15 @@ test: about: home: https://bcgsc.github.io/tigmint/ - license: GNU General Public v3 (GPLv3) - license_family: GPL3 -# license_file: LICENSE + license: GPL-3.0 + license_file: LICENSE summary: Correct misassemblies using linked or long reads dev_url: https://github.com/bcgsc/tigmint doc_url: https://github.com/bcgsc/tigmint#readme extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - doi:10.1101/304253 - recipe-maintainers: - - sjackman diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index d3b5a1c418492..ae769341e2447 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.1.9" %} +{% set version = "3.2.1.10" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: cd859ae51d14d243dd9c3000d5aa5e9e9a6920643b7b5eafdaedbc88d5214a4d + sha256: 126537079ea9fef743b0d2575d4e6cafac1351c465de7bbf0b0ec2b080748e34 build: number: 0 diff --git a/recipes/tooldistillator/meta.yaml b/recipes/tooldistillator/meta.yaml index 278963cd3d1f7..286e22cf02b85 100644 --- a/recipes/tooldistillator/meta.yaml +++ b/recipes/tooldistillator/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.9" %} -{% set sha256 = "e2b52e29971ef0da84d9bb8370db060dbc6c58fc61e509e852d297b3d7648817" %} +{% set version = "0.9.1" %} +{% set sha256 = "54e107b0ffa3bde988ca9a77cb3c74111f463f33b8c161c652990953a4cdc4c2" %} context: {} diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml index f9d01beea308f..6283ba23ae3bd 100644 --- a/recipes/toulligqc/meta.yaml +++ b/recipes/toulligqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "toulligqc" %} -{% set version = "2.5.6" %} +{% set version = "2.7.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 1b6087ccb927e0da6ff8f9c82c166de02d41bc55df9b9d7fc9edf264aec009f9 + sha256: 243eea4259e83ff0570e70b65b3b406212fe51356e9e376ab3ff5a27258d46ac build: number: 0 @@ -20,18 +20,21 @@ build: requirements: host: - - python >=3.10.0 + - python >=3.11 + - pip run: - - h5py >=3.7.0 + - h5py >=3.10.0 - matplotlib-base >=3.6.3 - - numpy >=1.24.2 - - scipy >=1.10.1 - - pandas >=1.5.3 + - numpy >=1.26.4 + - scipy >=1.11.4 + - pandas >=2.1.4 - plotly >=5.15.0 - - pysam >=0.21.0 - - python >=3.10.0 - - scikit-learn >=1.2.1 - - tqdm >=4.64.1 + - pysam >=0.22.0 + - python >=3.11 + - scikit-learn >=1.4.1 + - tqdm >=4.66.2 + - pod5 >=0.3.15 + #- ezcharts ==0.7.6 test: imports: @@ -40,6 +43,14 @@ test: - toulligqc --help about: - home: https://github.com/GenomicParisCentre/toulligQC - license: CECILL-2.1 - summary: A post sequencing QC tool for Oxford Nanopore sequencers + home: "https://github.com/GenomicParisCentre/toulligQC" + license: "GPL-3.0-or-later" + license_family: GPL3 + license_file: "LICENSE.txt" + summary: "A post sequencing QC tool for Oxford Nanopore sequencers." + dev_url: "https://github.com/GenomicParisCentre/toulligQC" + doc_url: "https://github.com/GenomiqueENS/toulligQC/blob/v{{ version }}/README.md" + +extra: + identifiers: + - biotools:ToulligQC diff --git a/recipes/tr-trimmer/build.sh b/recipes/tr-trimmer/build.sh new file mode 100644 index 0000000000000..e5cb5faa26a8b --- /dev/null +++ b/recipes/tr-trimmer/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash -euo + +set -xe + +# build statically linked binary with Rust +cargo-bundle-licenses --format yaml --output THIRDPARTY.yml +RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . \ No newline at end of file diff --git a/recipes/tr-trimmer/meta.yaml b/recipes/tr-trimmer/meta.yaml new file mode 100644 index 0000000000000..5e5e01cfaad7d --- /dev/null +++ b/recipes/tr-trimmer/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.1.0" %} + +package: + name: tr-trimmer + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("tr-trimmer", max_pin="x") }} + +source: + url: https://github.com/apcamargo/tr-trimmer/archive/v{{ version }}.tar.gz + sha256: ff063dcf3dbe23bee3c9f0d47808c0859fd79ccf0caed20642ebc0e4e38e917c + +requirements: + build: + - {{ compiler('rust') }} + - cargo-bundle-licenses + host: + run: + +test: + commands: + - tr-trimmer --help + +about: + home: https://github.com/apcamargo/tr-trimmer + license: MIT + license_file: + - LICENSE + - THIRDPARTY.yml + summary: Identify and trim terminal repeats from sequences in FASTA files + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 \ No newline at end of file diff --git a/recipes/tracegroomer/meta.yaml b/recipes/tracegroomer/meta.yaml index b85ee45217450..cba5bd1371551 100644 --- a/recipes/tracegroomer/meta.yaml +++ b/recipes/tracegroomer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tracegroomer" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/tracegroomer-{{ version }}.tar.gz - sha256: d81c872e9ca5f52d10413c4b9c0aff3aa54cc977125b531229dd8a1e4e6a5cdf + sha256: be87034d1ac14622ff361c39e363a842ace6d40ab3a70be62a9a38e29a593c70 build: entry_points: diff --git a/recipes/trackplot/meta.yaml b/recipes/trackplot/meta.yaml index ffc35783b502b..0be965226ae10 100644 --- a/recipes/trackplot/meta.yaml +++ b/recipes/trackplot/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trackplot" %} -{% set version = "0.4.0" %} +{% set version = "0.5.1" %} package: name: trackplot @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3d9e07e7270401a91db8730dc3675a003dafdcc3b73c4c157beee2c82743a61a + sha256: 686735f647e9ffdaab6dad02b56d483385142421928381b2c3d075d9a610ba52 build: noarch: python diff --git a/recipes/tracs/meta.yaml b/recipes/tracs/meta.yaml new file mode 100644 index 0000000000000..c0f21db61532b --- /dev/null +++ b/recipes/tracs/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.0.1" %} +{% set name = "tracs" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz + sha256: ea54a443c2a1a2bda7bb4dc9b79f79ffe5bfffc340ef8e6cc61f1df249ba4e5c + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('tracs', max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - python >=3.12 + - pip + - pybind11 + - boost-cpp + - zlib + - llvm-openmp + run: + - python >=3.12 + - numpy + - pandas + - sourmash + - joblib + - ncbi-genome-download + - pyfastx + - tqdm + - scipy + - plotly + - samtools + - htsbox + - minimap2 + +test: + imports: + - tracs + commands: + - tracs --help + - tracs --version + - tracs align --help + - tracs combine --help + - tracs distance --help + - tracs threshold --help + - tracs cluster --help + - tracs build-db --help + - tracs pipe --help + +about: + home: https://github.com/gtonkinhill/tracs + license: MIT + license_family: MIT + license_file: LICENSE + summary: 'Tracs - Fast pairwise transmission inference from single genome and/or metagenomic data' + doc_url: https://github.com/gtonkinhill/tracs/tree/main/docs diff --git a/recipes/tracy/build.sh b/recipes/tracy/build.sh index 2f754987f29e7..38a203670614e 100644 --- a/recipes/tracy/build.sh +++ b/recipes/tracy/build.sh @@ -1,7 +1,3 @@ #!/bin/bash -set -xe - -make all CXX=$CXX CXXFLAGS="-D__STDC_FORMAT_MACROS -I${SRC_DIR}/src/sdslLite/include -L${SRC_DIR}/src/sdslLite/lib -I${PREFIX}/include -L${PREFIX}/lib -Isrc/jlib/ -std=c++14" -j ${CPU_COUNT} -mkdir -p $PREFIX/bin -cp src/tracy $PREFIX/bin +CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS -I${SRC_DIR}/src/sdslLite/include -L${SRC_DIR}/src/sdslLite/lib -I${PREFIX}/include -L${PREFIX}/lib -Isrc/jlib/ -std=c++17" make -j${CPU_COUNT} CXX="${CXX}" prefix="${PREFIX}" install diff --git a/recipes/tracy/meta.yaml b/recipes/tracy/meta.yaml index ee530f591de05..64b4ec6a20b6f 100644 --- a/recipes/tracy/meta.yaml +++ b/recipes/tracy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.6" %} -{% set sha256 = "68bb079d9c05c98d7de1bf044e6c4da6a409d8f2abc8b96038b1782bc5497c5e" %} +{% set version = "0.7.8" %} +{% set sha256 = "9bac46e97ec43b85f12d1958abbc8f329f2dca8c3c363e67d8dff09b29260ea0" %} package: name: tracy @@ -13,7 +13,7 @@ source: git_rev: a654b57 build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage("tracy", max_pin="x.x") }} @@ -22,20 +22,16 @@ requirements: build: - make - {{ compiler('cxx') }} - - cmake >=3.10 + - cmake - autoconf - automake - pkg-config - - clangdev - - llvm-openmp host: - zlib - bzip2 - libdeflate - boost-cpp - htslib - - clangdev - - llvm-openmp run: - zlib - bzip2 diff --git a/recipes/transanno/build.sh b/recipes/transanno/build.sh new file mode 100644 index 0000000000000..a19f8c827c782 --- /dev/null +++ b/recipes/transanno/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash -e + +# build statically linked binary with Rust +RUST_BACKTRACE=1 \ + C_INCLUDE_PATH=$PREFIX/include \ + LIBRARY_PATH=$PREFIX/lib \ + cargo build --release + +mkdir $PREFIX/bin +cp $SRC_DIR/target/*/release/transanno $PREFIX/bin/transanno +chmod a+x $PREFIX/bin/transanno diff --git a/recipes/transanno/meta.yaml b/recipes/transanno/meta.yaml new file mode 100644 index 0000000000000..dbc207425ea00 --- /dev/null +++ b/recipes/transanno/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.4.5" %} +{% set sha256 = "f800ef6d9eff31aad6e00bbe963fd0c57a9ba9036c676a972ceefd9d1cdfbdc9" %} +{% set name = "transanno" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +source: + url: https://github.com/informationsea/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler('rust') }} + +test: + commands: + - transanno --help + +about: + home: https://github.com/informationsea/{{ name }} + license: GPL-3.0-only + license_family: GPL + license_file: LICENSE + summary: "accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies" + +extra: + additional-platforms: + - osx-arm64 + - linux-aarch64 diff --git a/recipes/transannot/build.sh b/recipes/transannot/build.sh index ae429591a47eb..8f7d428ac11e6 100644 --- a/recipes/transannot/build.sh +++ b/recipes/transannot/build.sh @@ -1,6 +1,11 @@ -#!/bin/bash -e +#!/bin/bash -ex -set -xe +mkdir -p build && pushd build + +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" case $(uname -m) in aarch64) @@ -11,8 +16,17 @@ case $(uname -m) in ;; esac -mkdir build -cd build -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 "${ARCH_OPTS}" -DVERSION_OVERRIDE="${PKG_VERSION}" .. -make -j${CPU_COUNT} ${VERBOSE_CM} -make install +if [ "$(uname)" == "Darwin" ]; then + export CMAKE_EXTRA="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER -Wno-dev" +else + export CMAKE_EXTRA="-Wno-dev" +fi + +cmake -S .. -B . -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=RELEASE \ + -DHAVE_TESTS=0 -DHAVE_MPI=0 "${ARCH_OPTS}" \ + -DVERSION_OVERRIDE="${PKG_VERSION}" \ + "${CMAKE_EXTRA}" + +cmake --build . --target install -j ${CPU_COUNT} -v +popd diff --git a/recipes/transannot/meta.yaml b/recipes/transannot/meta.yaml index 068bb67a93dbe..315da17189512 100644 --- a/recipes/transannot/meta.yaml +++ b/recipes/transannot/meta.yaml @@ -1,49 +1,49 @@ -{% set version = "3-70b2a60" %} -{% set sha256 = "3b1d2f28362004378528755b8b4e0b8dc45b51cc60562816258bdf16d9cda08d" %} +{% set name = "transannot" %} +{% set version = "3.0.0" %} +{% set sha256 = "6835fc3cc77aafd273abc8f2b4d8213b251b199ff7dd5ae9fa7e1dd19579ae41" %} package: - name: transannot - version: {{ version|replace("-", ".") }} + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/soedinglab/{{ name }}/archive/refs/tags/3-e15e316.tar.gz + sha256: {{ sha256 }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('transannot', max_pin="x") }} -source: - url: https://github.com/soedinglab/transannot/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} - requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - cmake - make + host: - llvm-openmp # [osx] - libgomp # [linux] - host: - - perl - gawk - zlib - bzip2 run: - aria2 - wget - - gawk - - zlib - - bzip2 + - perl test: commands: - - transannot > /dev/null + - "transannot > /dev/null" about: - home: https://github.com/soedinglab/transannot - summary: "TransAnnot: a fast transcriptome annotation pipeline" - license: GPL-3.0-or-later - license_family: GPL - license_file: LICENSE.md + home: "https://github.com/soedinglab/transannot" + summary: "TransAnnot: a fast transcriptome annotation pipeline." + license: "GPL-3.0-or-later" + license_family: GPL3 + license_file: "LICENSE.md" + dev_url: "https://github.com/soedinglab/transannot" + doc_url: "https://github.com/soedinglab/transannot/blob/master/README.md" extra: identifiers: diff --git a/recipes/treesimulator/meta.yaml b/recipes/treesimulator/meta.yaml index 247f0a7959257..2e652c8857735 100644 --- a/recipes/treesimulator/meta.yaml +++ b/recipes/treesimulator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "treesimulator" %} -{% set version = "0.1.22" %} +{% set version = "0.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2ea8d07b1ef98590b1477c322d8a06efabf63f39ac7d9ff0f75f6063e48898c8 + sha256: 599507b62cce4d8f77a850fc0f84d003d13530ec39960afdf1efcf356df16176 build: number: 0 diff --git a/recipes/treetime/meta.yaml b/recipes/treetime/meta.yaml index ae44e4a810ad5..96041b068c5e5 100644 --- a/recipes/treetime/meta.yaml +++ b/recipes/treetime/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.11.3" %} -{% set sha256 = "c19b336691fcf3fddbb2b0e55000ff6d4aafca1f2bdf75b4ab39631a57a73e2b" %} +{% set version = "0.11.4" %} +{% set sha256 = "0b41c4a60e020ad7888693ebc4e7f8001df977243154bf577f1567a48f71b31c" %} package: name: treetime @@ -11,7 +11,7 @@ source: build: noarch: python - number: 1 + number: 0 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vvv entry_points: - treetime = treetime.__main__:main diff --git a/recipes/trgt/build.sh b/recipes/trgt/build.sh deleted file mode 100644 index 65c729ab1d289..0000000000000 --- a/recipes/trgt/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env bash - -mkdir -p "${PREFIX}"/bin -gunzip *.gz -mv trvz* trvz -mv trgt* trgt -chmod +x trvz -chmod +x trgt -cp trvz "${PREFIX}"/bin/ -cp trgt "${PREFIX}"/bin/ - diff --git a/recipes/trgt/meta.yaml b/recipes/trgt/meta.yaml index 030c04cde40a0..bb87d98169589 100644 --- a/recipes/trgt/meta.yaml +++ b/recipes/trgt/meta.yaml @@ -1,35 +1,39 @@ {% set name = "trgt" %} -{% set version = "0.9.0" %} -{% set trgt_sha256 = "fba2edb311c2ea4f15ae1e0f1b464ae470a73f803d12630b8ea6dbeeff3cc3f9" %} -{% set trvz_sha256 = "08dcb1e5ca9d317140f26d635b323d12a8384b1263fda542e293effb2ca81280" %} +{% set version = "1.2.0" %} +{% set trgt_sha256 = "5dec0943d3400fd1677236fa35737e5a442a486fac55188029c3c9164edb3d23" %} package: name: {{ name }} version: {{ version }} -source: - - url: https://github.com/PacificBiosciences/trgt/releases/download/v{{ version }}/trgt-v{{ version }}-linux_x86_64.gz - sha256: {{ trgt_sha256 }} - - url: https://github.com/PacificBiosciences/trgt/releases/download/v{{ version }}/trvz-v{{ version }}-linux_x86_64.gz - sha256: {{ trvz_sha256 }} +source: + - url: https://github.com/PacificBiosciences/trgt/releases/download/v{{ version }}/trgt-v{{ version }}-x86_64-unknown-linux-gnu.tar.gz # [linux64] + sha256: {{ trgt_sha256 }} # [linux64] about: home: https://github.com/PacificBiosciences/trgt - license: BSD-3-Clause-Clear + license: Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md) summary: Tandem repeat genotyping and visualization from PacBio HiFi data -extra: - recipe-maintainers: - - zeeev - - williamrowell - build: number: 0 - noarch: generic + skip: true # [not linux64] + noarch: false + script: + - mkdir -p ${PREFIX}/bin + - cp trgt ${PREFIX}/bin/ + - chmod +x ${PREFIX}/bin/trgt run_exports: - {{ pin_subpackage('trgt', max_pin="x") }} test: commands: - trgt --version - - trvz --version + +extra: + recipe-maintainers: + - zeeev + - williamrowell + - tmokveld + skip-lints: + - should_be_noarch_generic diff --git a/recipes/tribal/meta.yaml b/recipes/tribal/meta.yaml new file mode 100644 index 0000000000000..dfc122ff0d268 --- /dev/null +++ b/recipes/tribal/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "TRIBAL" %} +{% set version = "0.1.1" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://github.com/elkebir-group/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 3859295c1e615ce9ce5d34e73c9dea33a08a105a502096e7640e0feeda83756e + +build: + number: 1 + run_exports: + - {{ pin_subpackage('tribal', max_pin='x.x') }} + script: + - "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" + - $CC -c tribal/dnapars/phylip.c -o tribal/dnapars/phylip.o -fcommon + - $CC -c tribal/dnapars/seq.c -o tribal/dnapars/seq.o -fcommon + - $CC -c tribal/dnapars/dnapars.c -o tribal/dnapars/dnapars.o -fcommon + - $CC tribal/dnapars/seq.o tribal/dnapars/phylip.o tribal/dnapars/dnapars.o -lm -o $PREFIX/bin/dnapars + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - python >=3.9,<3.11 + - pip + - setuptools + run: + - python >=3.9,<3.11 + - numpy >=1.26,<2.0 + - pandas + - networkx >=3.1 + - pygraphviz >=1.10 + - ete3 >=3.1.2 + - mafft ==7.526 + - glpk >=5.0 + - pyomo >=6.7 + - biopython >=1.81 + +test: + imports: + - tribal + commands: + - tribal --help + - tribal preprocess -h + - tribal fit -h + +about: + home: "https://github.com/elkebir-group/TRIBAL" + doc_url: "https://elkebir-group.github.io/TRIBAL" + license: "BSD-3-Clause" + summary: "TRIBAL is a package to infer B cell lineage trees from single-cell RNA sequencing data." + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/tribal/run_test.py b/recipes/tribal/run_test.py new file mode 100644 index 0000000000000..74c8489f92072 --- /dev/null +++ b/recipes/tribal/run_test.py @@ -0,0 +1,21 @@ +""" +Vignette to demonstrate the capabilities of the tribal package. +""" + +from tribal.preprocess import preprocess +from tribal import df, roots +from tribal import Tribal + + +if __name__ == "__main__": + + isotypes = ['IGHM', 'IGHG3', 'IGHG1', 'IGHA1','IGHG2','IGHG4','IGHE','IGHA2'] + + #test that dnapars installed correctly by running it during preprocessing + clonotypes, df_filt = preprocess(df, roots,isotypes, cores=3, verbose=True ) + + #test that the tribal package is working + tr = Tribal(n_isotypes=len(isotypes), verbose=True, restarts=1, niter=15) + + #run in refinement mode + shm_score, csr_likelihood, best_scores, transmat = tr.fit(clonotypes=clonotypes, mode="refinement", cores=6) \ No newline at end of file diff --git a/recipes/trimal/build.sh b/recipes/trimal/build.sh index 3b76620205a47..32fa745b57afe 100644 --- a/recipes/trimal/build.sh +++ b/recipes/trimal/build.sh @@ -1,11 +1,18 @@ -#!/bin/sh - -cd source -make CC="${CXX}" FLAGS="${CPPFLAGS} ${CXXFLAGS}" -j ${CPU_COUNT} +#!/bin/bash mkdir -p $PREFIX/bin -cp readal $PREFIX/bin -cp statal $PREFIX/bin -cp trimal $PREFIX/bin +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" +export CXXFLAGS="${CXXFLAGS} -O3" + +cd source +make CC="${CXX}" FLAGS="${CPPFLAGS} ${CXXFLAGS}" -j "${CPU_COUNT}" + +cp -f readal $PREFIX/bin +cp -f statal $PREFIX/bin +cp -f trimal $PREFIX/bin +chmod 0755 $PREFIX/bin/readal +chmod 0755 $PREFIX/bin/statal +chmod 0755 $PREFIX/bin/trimal diff --git a/recipes/trimal/meta.yaml b/recipes/trimal/meta.yaml index 659a5cb83b357..49ab7cd5dc61d 100644 --- a/recipes/trimal/meta.yaml +++ b/recipes/trimal/meta.yaml @@ -1,13 +1,16 @@ +{% set name = "trimal" %} +{% set version = "1.5.0" %} + package: - name: trimal - version: "1.5.0" + name: {{ name }} + version: {{ version }} source: - url: https://github.com/inab/trimal/archive/v1.5.0.tar.gz - md5: 414cebd328157f63704e49a592645286 + url: https://github.com/inab/trimal/archive/refs/tags/v{{ version }}.tar.gz + sha256: 3fba2e07bffb7290c34e713a052d0f0ff1ce0792861740a8cec46f40685c6d73 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('trimal', max_pin='x') }} @@ -15,7 +18,6 @@ requirements: build: - make - {{ compiler('cxx') }} - run: test: commands: @@ -26,10 +28,15 @@ test: about: home: 'https://trimal.readthedocs.io' summary: 'A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment' - license: GNU General Public License v3 or later (GPLv3+) + license: "GPL-3.0-or-later" + license_family: GPL3 + dev_url: "https://github.com/inab/trimal" + doc_url: "https://trimal.readthedocs.io" extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - biotools:trimAl + - doi:10.1093/bioinformatics/btp348 diff --git a/recipes/trnascan-se/build.sh b/recipes/trnascan-se/build.sh index f4f88fa388ac6..e3460852a2275 100644 --- a/recipes/trnascan-se/build.sh +++ b/recipes/trnascan-se/build.sh @@ -1,5 +1,6 @@ #!/bin/bash +export M4="${BUILD_PREFIX}/bin/m4" export INCLUDE_PATH=${PREFIX}/include export LIBRARY_PATH=${PREFIX}/lib export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" @@ -7,7 +8,10 @@ export CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}" sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' tRNAscan-SE.src sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' src/instman.pl +rm -rf *.bak +rm -rf src/*.bak +autoreconf -if ./configure CC="${CC}" CFLAGS="${CFLAGS}" --prefix="${PREFIX}" make diff --git a/recipes/trnascan-se/meta.yaml b/recipes/trnascan-se/meta.yaml index 5d8c1c2ed9f80..48596fa090ce3 100644 --- a/recipes/trnascan-se/meta.yaml +++ b/recipes/trnascan-se/meta.yaml @@ -1,16 +1,18 @@ {% set name = "tRNAscan-SE" %} {% set version = "2.0.12" %} -{% set sha256 = "96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251" %} +{% set sha256 = "4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('trnascan-se', max_pin="x") }} source: - url: http://trna.ucsc.edu/software/trnascan-se-{{ version }}.tar.gz + url: https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} patches: - patches/libdir.patch @@ -21,6 +23,7 @@ requirements: - make - autoconf - automake + - libtool host: - perl run: @@ -32,13 +35,18 @@ test: - tRNAscan-SE -h about: - home: "http://lowelab.ucsc.edu/tRNAscan-SE/" - license: GPLv3 + home: "https://lowelab.ucsc.edu/tRNAscan-SE/" + license: "GPL-3.0-or-later" + license_family: GPL3 license_file: LICENSE summary: tRNA detection in large-scale genomic sequences - doc_url: "http://lowelab.ucsc.edu/tRNAscan-SE/help.html" + doc_url: "https://lowelab.ucsc.edu/tRNAscan-SE/help.html" + dev_url: "https://github.com/UCSC-LoweLab/tRNAscan-SE" extra: identifiers: - biotools:trnascan-se - doi:10.1093/nar/gkab688 + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/trust4/meta.yaml b/recipes/trust4/meta.yaml index 9781bf90f5806..39d3efbb30704 100644 --- a/recipes/trust4/meta.yaml +++ b/recipes/trust4/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: trust4 version: '{{ version }}' build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('trust4', max_pin="x") }} source: url: https://github.com/liulab-dfci/TRUST4/archive/v{{ version }}.tar.gz - sha256: 99bfd50a742598e6a5fbf6318b0fadeec811f635bc1d7f5f49315b64a708c378 + sha256: c369ca538143b7aaf56d8d9d34f5c1024eaca425f1e2b8c845c78c2a29e6fbfb requirements: build: diff --git a/recipes/truvari/meta.yaml b/recipes/truvari/meta.yaml index a87cbf94c0803..12ca13de958ae 100644 --- a/recipes/truvari/meta.yaml +++ b/recipes/truvari/meta.yaml @@ -1,6 +1,6 @@ {% set name = "truvari" %} -{% set version = "4.3.0" %} -{% set sha256 = "cb25b3e8163584b51dec06356b89f193674e4388891e29b56c7e5b6f4bb63779" %} +{% set version = "4.3.1" %} +{% set sha256 = "aeb1bec08ad5fbd6a515c76806dfc4c3e67240fb89825049288f29935d49cf54" %} package: name: {{ name|lower }} diff --git a/recipes/ucsc-addcols/build.sh b/recipes/ucsc-addcols/build.sh index 8a3ac9a9447cd..880241ad96660 100644 --- a/recipes/ucsc-addcols/build.sh +++ b/recipes/ucsc-addcols/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/addCols && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/addCols "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/addCols" +cp bin/addCols "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/addCols" diff --git a/recipes/ucsc-addcols/meta.yaml b/recipes/ucsc-addcols/meta.yaml index e75b5b93e7d1d..63fadaf3b0f19 100644 --- a/recipes/ucsc-addcols/meta.yaml +++ b/recipes/ucsc-addcols/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-addcols" %} {% set program = "addCols" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-ameme/build.sh b/recipes/ucsc-ameme/build.sh index 85f44dbbbfe3c..9d9cf92f41ee3 100644 --- a/recipes/ucsc-ameme/build.sh +++ b/recipes/ucsc-ameme/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/ameme && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/ameme "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/ameme" +cp bin/ameme "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/ameme" diff --git a/recipes/ucsc-ameme/meta.yaml b/recipes/ucsc-ameme/meta.yaml index 55193a0bb388c..7b92909aa8ed1 100644 --- a/recipes/ucsc-ameme/meta.yaml +++ b/recipes/ucsc-ameme/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ameme" %} {% set program = "ameme" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-autodtd/build.sh b/recipes/ucsc-autodtd/build.sh index 1f36af8025753..ebab5b497694d 100644 --- a/recipes/ucsc-autodtd/build.sh +++ b/recipes/ucsc-autodtd/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/autoDtd && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/autoDtd "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/autoDtd" +cp bin/autoDtd "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/autoDtd" diff --git a/recipes/ucsc-autodtd/meta.yaml b/recipes/ucsc-autodtd/meta.yaml index e68e033f37830..597fe094769b6 100644 --- a/recipes/ucsc-autodtd/meta.yaml +++ b/recipes/ucsc-autodtd/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-autodtd" %} {% set program = "autoDtd" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-autosql/build.sh b/recipes/ucsc-autosql/build.sh index 9b7d4357f7341..ee0b575e35b97 100644 --- a/recipes/ucsc-autosql/build.sh +++ b/recipes/ucsc-autosql/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/autoSql && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/autoSql "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/autoSql" +cp bin/autoSql "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/autoSql" diff --git a/recipes/ucsc-autosql/meta.yaml b/recipes/ucsc-autosql/meta.yaml index 87e2d555f0df2..b2a651b3b5a58 100644 --- a/recipes/ucsc-autosql/meta.yaml +++ b/recipes/ucsc-autosql/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-autosql" %} {% set program = "autoSql" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-autoxml/build.sh b/recipes/ucsc-autoxml/build.sh index 5476f6f1d0a83..73dfe37c83820 100644 --- a/recipes/ucsc-autoxml/build.sh +++ b/recipes/ucsc-autoxml/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/autoXml && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/autoXml "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/autoXml" +cp bin/autoXml "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/autoXml" diff --git a/recipes/ucsc-autoxml/meta.yaml b/recipes/ucsc-autoxml/meta.yaml index 9c3792b8558d4..c5328653b9315 100644 --- a/recipes/ucsc-autoxml/meta.yaml +++ b/recipes/ucsc-autoxml/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-autoxml" %} {% set program = "autoXml" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-avecols/build.sh b/recipes/ucsc-avecols/build.sh index b9727be3692ee..eb3ce0613441f 100644 --- a/recipes/ucsc-avecols/build.sh +++ b/recipes/ucsc-avecols/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/aveCols && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/aveCols "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/aveCols" +cp bin/aveCols "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/aveCols" diff --git a/recipes/ucsc-avecols/meta.yaml b/recipes/ucsc-avecols/meta.yaml index 0d1e71052c40e..1845792fc30ac 100644 --- a/recipes/ucsc-avecols/meta.yaml +++ b/recipes/ucsc-avecols/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-avecols" %} {% set program = "aveCols" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-axtchain/build.sh b/recipes/ucsc-axtchain/build.sh index 0cf99f309dc17..1765bb92a55e3 100644 --- a/recipes/ucsc-axtchain/build.sh +++ b/recipes/ucsc-axtchain/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/axtChain && make) -cp bin/axtChain "$PREFIX/bin" -chmod +x "$PREFIX/bin/axtChain" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/axtChain && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/axtChain "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtChain" diff --git a/recipes/ucsc-axtchain/include.patch b/recipes/ucsc-axtchain/include.patch index e4831ef2dea13..edc04d0dc2f64 100644 --- a/recipes/ucsc-axtchain/include.patch +++ b/recipes/ucsc-axtchain/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-axtchain/meta.yaml b/recipes/ucsc-axtchain/meta.yaml index 72064fd875b92..8bdb49a164a0d 100644 --- a/recipes/ucsc-axtchain/meta.yaml +++ b/recipes/ucsc-axtchain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axtchain" %} {% set program = "axtChain" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,27 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Chain together axt alignments." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-axtsort/build.sh b/recipes/ucsc-axtsort/build.sh index 496cf5dcb35d8..f8296a72424f0 100644 --- a/recipes/ucsc-axtsort/build.sh +++ b/recipes/ucsc-axtsort/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/mouseStuff/axtSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/axtSort "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/axtSort" +cp bin/axtSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtSort" diff --git a/recipes/ucsc-axtsort/meta.yaml b/recipes/ucsc-axtsort/meta.yaml index 4c4b3f7e611c5..41b575334e20f 100644 --- a/recipes/ucsc-axtsort/meta.yaml +++ b/recipes/ucsc-axtsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axtsort" %} {% set program = "axtSort" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-axtswap/build.sh b/recipes/ucsc-axtswap/build.sh index c15f336ce33a1..002d003249880 100644 --- a/recipes/ucsc-axtswap/build.sh +++ b/recipes/ucsc-axtswap/build.sh @@ -2,7 +2,7 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -11,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/mouseStuff/axtSwap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/axtSwap "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/axtSwap" +cp bin/axtSwap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtSwap" diff --git a/recipes/ucsc-axtswap/meta.yaml b/recipes/ucsc-axtswap/meta.yaml index a432cdd091d15..af74691f328d2 100644 --- a/recipes/ucsc-axtswap/meta.yaml +++ b/recipes/ucsc-axtswap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axtswap" %} {% set program = "axtSwap" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-axttomaf/build.sh b/recipes/ucsc-axttomaf/build.sh index 9b86c892dc16a..8aff3ba3ee73e 100644 --- a/recipes/ucsc-axttomaf/build.sh +++ b/recipes/ucsc-axttomaf/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/axtToMaf && make) -cp bin/axtToMaf "$PREFIX/bin" -chmod +x "$PREFIX/bin/axtToMaf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/axtToMaf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/axtToMaf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtToMaf" diff --git a/recipes/ucsc-axttomaf/include.patch b/recipes/ucsc-axttomaf/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-axttomaf/include.patch +++ b/recipes/ucsc-axttomaf/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-axttomaf/meta.yaml b/recipes/ucsc-axttomaf/meta.yaml index c4c3506781e5f..9fad27f9b6c48 100644 --- a/recipes/ucsc-axttomaf/meta.yaml +++ b/recipes/ucsc-axttomaf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axttomaf" %} {% set program = "axtToMaf" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from axt to maf format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-axttopsl/build.sh b/recipes/ucsc-axttopsl/build.sh index d34c31e9c40dd..53d90bfeef68a 100644 --- a/recipes/ucsc-axttopsl/build.sh +++ b/recipes/ucsc-axttopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/axtToPsl && make) -cp bin/axtToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/axtToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/axtToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/axtToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtToPsl" diff --git a/recipes/ucsc-axttopsl/include.patch b/recipes/ucsc-axttopsl/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-axttopsl/include.patch +++ b/recipes/ucsc-axttopsl/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-axttopsl/meta.yaml b/recipes/ucsc-axttopsl/meta.yaml index d3c5108e5d1c7..b6873169ffcc3 100644 --- a/recipes/ucsc-axttopsl/meta.yaml +++ b/recipes/ucsc-axttopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axttopsl" %} {% set program = "axtToPsl" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,27 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert axt to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bamtopsl/build.sh b/recipes/ucsc-bamtopsl/build.sh index ce701d375c18f..c68078409abcb 100644 --- a/recipes/ucsc-bamtopsl/build.sh +++ b/recipes/ucsc-bamtopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bamToPsl && make) -cp bin/bamToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/bamToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bamToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bamToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bamToPsl" diff --git a/recipes/ucsc-bamtopsl/build_failure.linux-aarch64.yaml b/recipes/ucsc-bamtopsl/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..94614dba9e19b --- /dev/null +++ b/recipes/ucsc-bamtopsl/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: cabd65b4a582750389dddd801a4cb10eeace0ae27e187a087c070a8ab41e7a12 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o rmskOut.o -c rmskOut.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o rmskOut2.o -c rmskOut2.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o rnaGene.o -c rnaGene.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o sage.o -c sage.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem 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trackHub.o -c trackHub.c + trackDbCustom.c: In function 'trackDbInclude': + trackDbCustom.c:294:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=] + 294 | splitPath(raFile, incFile, NULL, NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]' + trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]' + trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]' + In file included from trackDbCustom.c:9: + ../../inc/common.h:1139:6: note: in a call to function 'splitPath' + 1139 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 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-L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleUtils.o -c wiggleUtils.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wikiLink.o -c wikiLink.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskAlignBed.o -c bigRmskAlignBed.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskBed.o -c bigRmskBed.c + mkdir -p ../../lib/aarch64 + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o web.o -c web.c + ar rcus ../../lib/aarch64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o bigRmskAlignBed.o bigRmskBed.o + cd kent/src/utils/bamToPsl + make CC=/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/aarch64-conda-linux-gnu-cc CXX= 'CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/work=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib' 'CXXFLAGS= -I/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib' -j 4 + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -o bamToPsl.o -c bamToPsl.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/bamToPsl bamToPsl.o ../../lib/aarch64/jkweb.a -L$PREFIX/lib -lmysqlclient -lstdc -lrt -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -lpthread $PREFIX/lib/libssl.a $PREFIX/lib/libcrypto.a -ldl ../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz + /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(bamFile.o): in function bamFetchAlreadyOpen': + /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:207: undefined reference to cram_get_Md5' + /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:207: undefined reference to cram_get_Md5' + /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:214: undefined reference to cram_get_ref_url' + /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:214: undefined reference to cram_get_ref_url' + /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:215: undefined reference to cram_get_cache_dir' + /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:215: undefined reference to cram_get_cache_dir' + /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(bamFile.o): in function bamAndIndexFetchPlus': + /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:257: undefined reference to cram_set_cache_url' + /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:257: undefined reference to cram_set_cache_url' + collect2: error: ld returned 1 exit status + make: *** [../../inc/userApp.mk:32: /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/work/bin/bamToPsl] Error 1 + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-bamtopsl/include.patch b/recipes/ucsc-bamtopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bamtopsl/include.patch +++ b/recipes/ucsc-bamtopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bamtopsl/meta.yaml b/recipes/ucsc-bamtopsl/meta.yaml index 3ab6ea6912eda..24249d39cd741 100644 --- a/recipes/ucsc-bamtopsl/meta.yaml +++ b/recipes/ucsc-bamtopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bamtopsl" %} {% set program = "bamToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert a bam file to a psl and optionally also a fasta file that contains the reads." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedclip/build.sh b/recipes/ucsc-bedclip/build.sh index a0d9457e75286..7899ca0c8a07a 100644 --- a/recipes/ucsc-bedclip/build.sh +++ b/recipes/ucsc-bedclip/build.sh @@ -1,22 +1,21 @@ #!/bin/bash -if [ $(arch) = "aarch64" ] -then - export CFLAGS+=" -O3 " - export CPPFLAGS+=" -O3 " -else - export MACHTYPE=x86_64 -fi +set -xe +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" - -mkdir -p "$PREFIX/bin" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bedClip && make) -cp bin/bedClip "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedClip" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedClip && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedClip "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedClip" diff --git a/recipes/ucsc-bedclip/include.patch b/recipes/ucsc-bedclip/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedclip/include.patch +++ b/recipes/ucsc-bedclip/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedclip/meta.yaml b/recipes/ucsc-bedclip/meta.yaml index b985207becc8a..3dcd15559784f 100644 --- a/recipes/ucsc-bedclip/meta.yaml +++ b/recipes/ucsc-bedclip/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedclip" %} {% set program = "bedClip" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -12,13 +12,12 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" - - "patch1.patch" build: skip: True # [osx] - number: 4 + number: 0 run_exports: - - {{ pin_subpackage("ucsc-bedclip", max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -28,25 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} + +about: + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Remove lines from bed file that refer to off-chromosome locations." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 - -about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Remove lines from bed file that refer to off-chromosome locations." diff --git a/recipes/ucsc-bedcommonregions/build.sh b/recipes/ucsc-bedcommonregions/build.sh index 2ec002da3d943..8184ab80f550d 100644 --- a/recipes/ucsc-bedcommonregions/build.sh +++ b/recipes/ucsc-bedcommonregions/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bedCommonRegions && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedCommonRegions "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedCommonRegions" +cp bin/bedCommonRegions "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedCommonRegions" diff --git a/recipes/ucsc-bedcommonregions/meta.yaml b/recipes/ucsc-bedcommonregions/meta.yaml index 78698cd3f1e32..7e61e49095f09 100644 --- a/recipes/ucsc-bedcommonregions/meta.yaml +++ b/recipes/ucsc-bedcommonregions/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedcommonregions" %} {% set program = "bedCommonRegions" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedcoverage/build.sh b/recipes/ucsc-bedcoverage/build.sh index e7cb194b48474..d9dd530db9deb 100644 --- a/recipes/ucsc-bedcoverage/build.sh +++ b/recipes/ucsc-bedcoverage/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/bedCoverage && make) -cp bin/bedCoverage "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedCoverage" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/bedCoverage && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedCoverage "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedCoverage" diff --git a/recipes/ucsc-bedcoverage/include.patch b/recipes/ucsc-bedcoverage/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedcoverage/include.patch +++ b/recipes/ucsc-bedcoverage/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedcoverage/meta.yaml b/recipes/ucsc-bedcoverage/meta.yaml index ec874780ff0ec..237bcd0ba115c 100644 --- a/recipes/ucsc-bedcoverage/meta.yaml +++ b/recipes/ucsc-bedcoverage/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedcoverage" %} {% set program = "bedCoverage" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Analyse coverage by bed files - chromosome by " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-bedextendranges/build.sh b/recipes/ucsc-bedextendranges/build.sh index f136ad15518a5..7027ce1284eba 100644 --- a/recipes/ucsc-bedextendranges/build.sh +++ b/recipes/ucsc-bedextendranges/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/bedExtendRanges && make) -cp bin/bedExtendRanges "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedExtendRanges" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bedExtendRanges && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedExtendRanges "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedExtendRanges" diff --git a/recipes/ucsc-bedextendranges/include.patch b/recipes/ucsc-bedextendranges/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedextendranges/include.patch +++ b/recipes/ucsc-bedextendranges/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedextendranges/meta.yaml b/recipes/ucsc-bedextendranges/meta.yaml index 8b388ba115445..b0278a6067f83 100644 --- a/recipes/ucsc-bedextendranges/meta.yaml +++ b/recipes/ucsc-bedextendranges/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedextendranges" %} {% set program = "bedExtendRanges" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "extend length of entries in bed 6+ data to be at least the given length," + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-bedgeneparts/build.sh b/recipes/ucsc-bedgeneparts/build.sh index f1399eb250589..c1d170f184800 100644 --- a/recipes/ucsc-bedgeneparts/build.sh +++ b/recipes/ucsc-bedgeneparts/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bedGeneParts && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedGeneParts "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedGeneParts" +cp bin/bedGeneParts "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedGeneParts" diff --git a/recipes/ucsc-bedgeneparts/meta.yaml b/recipes/ucsc-bedgeneparts/meta.yaml index 8685b3fe9e52b..de9f72681bcd3 100644 --- a/recipes/ucsc-bedgeneparts/meta.yaml +++ b/recipes/ucsc-bedgeneparts/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedgeneparts" %} {% set program = "bedGeneParts" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedgraphpack/build.sh b/recipes/ucsc-bedgraphpack/build.sh index 35f9f4a4071a5..3600d25ac86be 100644 --- a/recipes/ucsc-bedgraphpack/build.sh +++ b/recipes/ucsc-bedgraphpack/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bedGraphPack && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedGraphPack "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedGraphPack" +cp bin/bedGraphPack "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedGraphPack" diff --git a/recipes/ucsc-bedgraphpack/meta.yaml b/recipes/ucsc-bedgraphpack/meta.yaml index 81da67b2ef311..d950f7ed9e88e 100644 --- a/recipes/ucsc-bedgraphpack/meta.yaml +++ b/recipes/ucsc-bedgraphpack/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedgraphpack" %} {% set program = "bedGraphPack" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedgraphtobigwig/build.sh b/recipes/ucsc-bedgraphtobigwig/build.sh index a41225d70c23a..5d7368f71bdd2 100644 --- a/recipes/ucsc-bedgraphtobigwig/build.sh +++ b/recipes/ucsc-bedgraphtobigwig/build.sh @@ -1,17 +1,21 @@ #!/bin/bash + +set -xe + mkdir -p "${PREFIX}/bin" -export MACHTYPE=x86_64 -export BINDIR=`pwd`/bin +export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" -export LD_LIBRARY_PATH="${PREFIX}/lib" -export LDFLAGS="-L${PREFIX}/lib" -export CFLAGS="-I${PREFIX}/include ${LDFLAGS}" -export CXXFLAGS="-I${PREFIX}/include ${LDFLAGS}" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" mkdir -p "${BINDIR}" -cd ${SRC_DIR}/kent/src/lib && make CC=${CC} CXX=${CXX} CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -cd ${SRC_DIR}/kent/src/htslib && make CC=${CC} CXX=${CXX} CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -cd ${SRC_DIR}/kent/src/jkOwnLib && make CC=${CC} CXX=${CXX} CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -cd ${SRC_DIR}/kent/src/utils/bedGraphToBigWig && make CC=${CC} CXX=${CXX} CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -cp ${SRC_DIR}/bin/bedGraphToBigWig "${PREFIX}/bin" -chmod +x "${PREFIX}/bin/bedGraphToBigWig" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedGraphToBigWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedGraphToBigWig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedGraphToBigWig" diff --git a/recipes/ucsc-bedgraphtobigwig/include.patch b/recipes/ucsc-bedgraphtobigwig/include.patch index b4b153480032c..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedgraphtobigwig/include.patch +++ b/recipes/ucsc-bedgraphtobigwig/include.patch @@ -1,24 +1,24 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml index 9aec6cf66f7a4..ea2f56db02e67 100644 --- a/recipes/ucsc-bedgraphtobigwig/meta.yaml +++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml @@ -1,21 +1,21 @@ {% set package = "ucsc-bedgraphtobigwig" %} {% set program = "bedGraphToBigWig" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" version: "{{ version }}" source: - url: "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" sha256: "{{ sha256 }}" patches: - "include.patch" - - "patch1.patch" build: - number: 1 + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -23,29 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static - - openssl - zlib + run: - libpng - libuuid - - openssl + - mysql-connector-c + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} + +about: + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Convert a bedGraph file to bigWig format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 - -about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert a bedGraph file to bigWig format." diff --git a/recipes/ucsc-bedintersect/build.sh b/recipes/ucsc-bedintersect/build.sh index 463e5ef29d12d..e8735ba8125e6 100644 --- a/recipes/ucsc-bedintersect/build.sh +++ b/recipes/ucsc-bedintersect/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/bedIntersect && make) -cp bin/bedIntersect "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedIntersect" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/bedIntersect && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedIntersect "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedIntersect" diff --git a/recipes/ucsc-bedintersect/include.patch b/recipes/ucsc-bedintersect/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedintersect/include.patch +++ b/recipes/ucsc-bedintersect/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedintersect/meta.yaml b/recipes/ucsc-bedintersect/meta.yaml index 8f70102146641..5ed61c6ad927f 100644 --- a/recipes/ucsc-bedintersect/meta.yaml +++ b/recipes/ucsc-bedintersect/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedintersect" %} {% set program = "bedIntersect" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Intersect two bed files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-beditemoverlapcount/build.sh b/recipes/ucsc-beditemoverlapcount/build.sh index bfb85d4baf7e3..9e731e0e7b060 100644 --- a/recipes/ucsc-beditemoverlapcount/build.sh +++ b/recipes/ucsc-beditemoverlapcount/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/bedItemOverlapCount && make) -cp bin/bedItemOverlapCount "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedItemOverlapCount" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/bedItemOverlapCount && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedItemOverlapCount "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedItemOverlapCount" diff --git a/recipes/ucsc-beditemoverlapcount/include.patch b/recipes/ucsc-beditemoverlapcount/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-beditemoverlapcount/include.patch +++ b/recipes/ucsc-beditemoverlapcount/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-beditemoverlapcount/meta.yaml b/recipes/ucsc-beditemoverlapcount/meta.yaml index 5fa66226d97c3..bdb5fb822e3a5 100644 --- a/recipes/ucsc-beditemoverlapcount/meta.yaml +++ b/recipes/ucsc-beditemoverlapcount/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-beditemoverlapcount" %} {% set program = "bedItemOverlapCount" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "count number of times a base is overlapped by the" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-bedjointaboffset/build.sh b/recipes/ucsc-bedjointaboffset/build.sh index b0fa55386a339..66c35a7548a83 100644 --- a/recipes/ucsc-bedjointaboffset/build.sh +++ b/recipes/ucsc-bedjointaboffset/build.sh @@ -1,4 +1,7 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -cp kent/src/utils/bedJoinTabOffset "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedJoinTabOffset" + +set -xe + +mkdir -p "${PREFIX}/bin" +cp kent/src/utils/bedJoinTabOffset "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedJoinTabOffset" diff --git a/recipes/ucsc-bedjointaboffset/build_failure.linux-64.yaml b/recipes/ucsc-bedjointaboffset/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a7938f2cf850d --- /dev/null +++ b/recipes/ucsc-bedjointaboffset/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e012ba21d33790d74fa3bd1b6883d0278e83a96dc5f265d468abf3d43927b632 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + sysroot_linux-64: 2.17-h4a8ded7_16 conda-forge + tzdata: 2024a-h8827d51_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: userApps.v469.src_3f95b26ccc.tgz + Downloading http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v469.src.tgz + Success + Extracting download + Applying patch: /opt/recipe/include.patch + Applying patch: /opt/recipe/include.patch with args: + ['-Np0', '-i', '/tmp/tmpj88djt1f/include.patch.native', '--binary'] + checking file kent/src/inc/common.mk + Hunk #1 succeeded at 21 (offset 4 lines). + checking file kent/src/utils/bedJoinTabOffset.py + checking file kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed + patching file kent/src/inc/common.mk + Hunk #1 succeeded at 21 (offset 4 lines). + patching file kent/src/utils/bedJoinTabOffset.py + patching file kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed + Patch analysis gives: + [[ RA--D0L-VE ]] - [[ include.patch ]] + + Key: + + R :: Reversible A :: Applicable + Y :: Build-prefix patch in use M :: Minimal, non-amalgamated + D :: Dry-runnable N :: Patch level (1 is preferred) + L :: Patch level not-ambiguous O :: Patch applies without offsets + V :: Patch applies without fuzz E :: Patch applies without emitting to stderr + + source tree in: /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/work + export PREFIX=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/_build_env + export SRC_DIR=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bedjointaboffset-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bedjointaboffset-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + mkdir -p /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin + cp kent/src/utils/bedJoinTabOffset /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin + cp: omitting directory 'kent/src/utils/bedJoinTabOffset' + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-bedjointaboffset/build_failure.linux-aarch64.yaml b/recipes/ucsc-bedjointaboffset/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..e9b919aba5c68 --- /dev/null +++ b/recipes/ucsc-bedjointaboffset/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e012ba21d33790d74fa3bd1b6883d0278e83a96dc5f265d468abf3d43927b632 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + sysroot_linux-aarch64: 2.17-h5b4a56d_16 conda-forge + tzdata: 2024a-h8827d51_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: userApps.v469.src_3f95b26ccc.tgz + Downloading http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v469.src.tgz + Success + Extracting download + Applying patch: /opt/recipe/include.patch + Applying patch: /opt/recipe/include.patch with args: + ['-Np0', '-i', '/tmp/tmp7zu2_wri/include.patch.native', '--binary'] + checking file kent/src/inc/common.mk + Hunk #1 succeeded at 21 (offset 4 lines). + checking file kent/src/utils/bedJoinTabOffset.py + checking file kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed + patching file kent/src/inc/common.mk + Hunk #1 succeeded at 21 (offset 4 lines). + patching file kent/src/utils/bedJoinTabOffset.py + patching file kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed + Patch analysis gives: + [[ RA--D0L-VE ]] - [[ include.patch ]] + + Key: + + R :: Reversible A :: Applicable + Y :: Build-prefix patch in use M :: Minimal, non-amalgamated + D :: Dry-runnable N :: Patch level (1 is preferred) + L :: Patch level not-ambiguous O :: Patch applies without offsets + V :: Patch applies without fuzz E :: Patch applies without emitting to stderr + + source tree in: /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792053044/work + export PREFIX=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792053044/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792053044/_build_env + export SRC_DIR=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792053044/work + INFO: activate-binutils_linux-aarch64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip + INFO: activate-gcc_linux-aarch64.sh made the following environmental changes: + BUILD=aarch64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bedjointaboffset-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=aarch64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=aarch64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bedjointaboffset-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + mkdir -p /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792053044/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin + cp kent/src/utils/bedJoinTabOffset /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792053044/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin + cp: omitting directory 'kent/src/utils/bedJoinTabOffset' + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792053044/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-bedjointaboffset/include.patch b/recipes/ucsc-bedjointaboffset/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedjointaboffset/include.patch +++ b/recipes/ucsc-bedjointaboffset/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedjointaboffset/meta.yaml b/recipes/ucsc-bedjointaboffset/meta.yaml index 5fb1d736c7504..850769f638b08 100644 --- a/recipes/ucsc-bedjointaboffset/meta.yaml +++ b/recipes/ucsc-bedjointaboffset/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedjointaboffset" %} {% set program = "bedJoinTabOffset" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,16 +15,25 @@ source: build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: + - {{ compiler('c') }} host: + - libpng + - libuuid + - mysql-connector-c + - libopenssl-static + - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - python - zlib @@ -37,3 +46,12 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "given a bed file and tab file where each have a column with matching values: first get the value of column0, the offset and line length from inTabFile. Then go over the bed file, use the name field and append its offset and length to the bed file as two separate fields. Write the new bed file to outBed." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedpileups/build.sh b/recipes/ucsc-bedpileups/build.sh index f1aa76b9a3b4c..d49b45360aa4d 100644 --- a/recipes/ucsc-bedpileups/build.sh +++ b/recipes/ucsc-bedpileups/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bedPileUps && make) -cp bin/bedPileUps "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedPileUps" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedPileUps && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedPileUps "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedPileUps" diff --git a/recipes/ucsc-bedpileups/include.patch b/recipes/ucsc-bedpileups/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedpileups/include.patch +++ b/recipes/ucsc-bedpileups/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedpileups/meta.yaml b/recipes/ucsc-bedpileups/meta.yaml index b3e70a97e2c18..f75c721a2889f 100644 --- a/recipes/ucsc-bedpileups/meta.yaml +++ b/recipes/ucsc-bedpileups/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedpileups" %} {% set program = "bedPileUps" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Find (exact) overlaps if any in bed input" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedremoveoverlap/build.sh b/recipes/ucsc-bedremoveoverlap/build.sh index 971f4a5ace1d1..ee59fd0ba4298 100644 --- a/recipes/ucsc-bedremoveoverlap/build.sh +++ b/recipes/ucsc-bedremoveoverlap/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bedRemoveOverlap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedRemoveOverlap "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedRemoveOverlap" +cp bin/bedRemoveOverlap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedRemoveOverlap" diff --git a/recipes/ucsc-bedremoveoverlap/meta.yaml b/recipes/ucsc-bedremoveoverlap/meta.yaml index a35d8341dbdbd..40e11ffca0e67 100644 --- a/recipes/ucsc-bedremoveoverlap/meta.yaml +++ b/recipes/ucsc-bedremoveoverlap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedremoveoverlap" %} {% set program = "bedRemoveOverlap" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedrestricttopositions/build.sh b/recipes/ucsc-bedrestricttopositions/build.sh index e27e6ecc54f19..82f7323e39f3d 100644 --- a/recipes/ucsc-bedrestricttopositions/build.sh +++ b/recipes/ucsc-bedrestricttopositions/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bedRestrictToPositions && make) -cp bin/bedRestrictToPositions "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedRestrictToPositions" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedRestrictToPositions && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedRestrictToPositions "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedRestrictToPositions" diff --git a/recipes/ucsc-bedrestricttopositions/include.patch b/recipes/ucsc-bedrestricttopositions/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedrestricttopositions/include.patch +++ b/recipes/ucsc-bedrestricttopositions/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedrestricttopositions/meta.yaml b/recipes/ucsc-bedrestricttopositions/meta.yaml index 1c9117bdb25e3..ab068a46f57fb 100644 --- a/recipes/ucsc-bedrestricttopositions/meta.yaml +++ b/recipes/ucsc-bedrestricttopositions/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedrestricttopositions" %} {% set program = "bedRestrictToPositions" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedsort/build.sh b/recipes/ucsc-bedsort/build.sh index 7a161baafe158..308bd9a232ed2 100644 --- a/recipes/ucsc-bedsort/build.sh +++ b/recipes/ucsc-bedsort/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd kent/src/hg/lib && USE_HIC=0 make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/bedSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedSort "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedSort" +cp bin/bedSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedSort" diff --git a/recipes/ucsc-bedsort/include.patch b/recipes/ucsc-bedsort/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedsort/include.patch +++ b/recipes/ucsc-bedsort/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedsort/meta.yaml b/recipes/ucsc-bedsort/meta.yaml index 832d257a70c12..416d0f783723e 100644 --- a/recipes/ucsc-bedsort/meta.yaml +++ b/recipes/ucsc-bedsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedsort" %} {% set program = "bedSort" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,9 +14,10 @@ source: - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage('ucsc-bedsort', max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -28,11 +29,13 @@ requirements: - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -41,11 +44,14 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Sort a .bed file by chrom,chromStart" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-bedtobigbed/build.sh b/recipes/ucsc-bedtobigbed/build.sh index fb722163f7ad1..2b2c5a16aad45 100644 --- a/recipes/ucsc-bedtobigbed/build.sh +++ b/recipes/ucsc-bedtobigbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bedToBigBed && make) -cp bin/bedToBigBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedToBigBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedToBigBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedToBigBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedToBigBed" diff --git a/recipes/ucsc-bedtobigbed/include.patch b/recipes/ucsc-bedtobigbed/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedtobigbed/include.patch +++ b/recipes/ucsc-bedtobigbed/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bedtobigbed/meta.yaml b/recipes/ucsc-bedtobigbed/meta.yaml index dc6ece24ed64b..156f4100092c2 100644 --- a/recipes/ucsc-bedtobigbed/meta.yaml +++ b/recipes/ucsc-bedtobigbed/meta.yaml @@ -1,25 +1,21 @@ {% set package = "ucsc-bedtobigbed" %} {% set program = "bedToBigBed" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 - skip: True # [osx] - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -27,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert bed file to bigBed. (bbi version: 4)" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Convert bed file to bigBed. (BigBed version: 4)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedtogenepred/build.sh b/recipes/ucsc-bedtogenepred/build.sh index aa966fdb34201..163f8a5c60726 100644 --- a/recipes/ucsc-bedtogenepred/build.sh +++ b/recipes/ucsc-bedtogenepred/build.sh @@ -1,21 +1,21 @@ #!/bin/bash -set -xe +set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p $BINDIR +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/bedToGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedToGenePred "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedToGenePred" +cp bin/bedToGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedToGenePred" diff --git a/recipes/ucsc-bedtogenepred/meta.yaml b/recipes/ucsc-bedtogenepred/meta.yaml index 0e5ba571827a5..1fc76c92ba6db 100644 --- a/recipes/ucsc-bedtogenepred/meta.yaml +++ b/recipes/ucsc-bedtogenepred/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedtogenepred" %} {% set program = "bedToGenePred" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,7 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: -# - linux-aarch64 # linking fails with `undefined reference to `cram_get_Md5'` and few more functions \ No newline at end of file + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-bedtopsl/build.sh b/recipes/ucsc-bedtopsl/build.sh index dcab9d7776a97..27fed78f2e79a 100644 --- a/recipes/ucsc-bedtopsl/build.sh +++ b/recipes/ucsc-bedtopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/bedToPsl && make) -cp bin/bedToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bedToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedToPsl" diff --git a/recipes/ucsc-bedtopsl/include.patch b/recipes/ucsc-bedtopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedtopsl/include.patch +++ b/recipes/ucsc-bedtopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedtopsl/meta.yaml b/recipes/ucsc-bedtopsl/meta.yaml index 07b6858631fe6..bf6d5446c806b 100644 --- a/recipes/ucsc-bedtopsl/meta.yaml +++ b/recipes/ucsc-bedtopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedtopsl" %} {% set program = "bedToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert bed format files to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedweedoverlapping/build.sh b/recipes/ucsc-bedweedoverlapping/build.sh index 002beb540c1dd..08ebc84a92e93 100644 --- a/recipes/ucsc-bedweedoverlapping/build.sh +++ b/recipes/ucsc-bedweedoverlapping/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/bedWeedOverlapping && make) -cp bin/bedWeedOverlapping "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedWeedOverlapping" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bedWeedOverlapping && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedWeedOverlapping "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedWeedOverlapping" diff --git a/recipes/ucsc-bedweedoverlapping/include.patch b/recipes/ucsc-bedweedoverlapping/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedweedoverlapping/include.patch +++ b/recipes/ucsc-bedweedoverlapping/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedweedoverlapping/meta.yaml b/recipes/ucsc-bedweedoverlapping/meta.yaml index bc6676b987bb3..e372114ed5e4b 100644 --- a/recipes/ucsc-bedweedoverlapping/meta.yaml +++ b/recipes/ucsc-bedweedoverlapping/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedweedoverlapping" %} {% set program = "bedWeedOverlapping" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter out beds that overlap a 'weed.bed' file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bigbedinfo/build.sh b/recipes/ucsc-bigbedinfo/build.sh index 15cf1c6b82b8a..420bee013e254 100644 --- a/recipes/ucsc-bigbedinfo/build.sh +++ b/recipes/ucsc-bigbedinfo/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigBedInfo && make -j ${CPU_COUNT}) -cp bin/bigBedInfo "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigBedInfo" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigBedInfo && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigBedInfo "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigBedInfo" diff --git a/recipes/ucsc-bigbedinfo/include.patch b/recipes/ucsc-bigbedinfo/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigbedinfo/include.patch +++ b/recipes/ucsc-bigbedinfo/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigbedinfo/meta.yaml b/recipes/ucsc-bigbedinfo/meta.yaml index 93110c41fe8eb..964aa7c634c8e 100644 --- a/recipes/ucsc-bigbedinfo/meta.yaml +++ b/recipes/ucsc-bigbedinfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigbedinfo" %} {% set program = "bigBedInfo" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Show information about a bigBed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigbednameditems/build.sh b/recipes/ucsc-bigbednameditems/build.sh index 3d04dd5bf568e..777c54b464f56 100644 --- a/recipes/ucsc-bigbednameditems/build.sh +++ b/recipes/ucsc-bigbednameditems/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigBedNamedItems && make -j ${CPU_COUNT}) -cp bin/bigBedNamedItems "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigBedNamedItems" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigBedNamedItems && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigBedNamedItems "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigBedNamedItems" diff --git a/recipes/ucsc-bigbednameditems/include.patch b/recipes/ucsc-bigbednameditems/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigbednameditems/include.patch +++ b/recipes/ucsc-bigbednameditems/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigbednameditems/meta.yaml b/recipes/ucsc-bigbednameditems/meta.yaml index c3514f0bfc7ae..eb9e9631ab382 100644 --- a/recipes/ucsc-bigbednameditems/meta.yaml +++ b/recipes/ucsc-bigbednameditems/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigbednameditems" %} {% set program = "bigBedNamedItems" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract item of given name from bigBed" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigbedsummary/build.sh b/recipes/ucsc-bigbedsummary/build.sh index cfb822b0daef1..89e7a9c76ffeb 100644 --- a/recipes/ucsc-bigbedsummary/build.sh +++ b/recipes/ucsc-bigbedsummary/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigBedSummary && make -j ${CPU_COUNT}) -cp bin/bigBedSummary "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigBedSummary" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigBedSummary && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigBedSummary "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigBedSummary" diff --git a/recipes/ucsc-bigbedsummary/include.patch b/recipes/ucsc-bigbedsummary/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigbedsummary/include.patch +++ b/recipes/ucsc-bigbedsummary/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigbedsummary/meta.yaml b/recipes/ucsc-bigbedsummary/meta.yaml index 5a3a07fb3aa8c..528d9716a3817 100644 --- a/recipes/ucsc-bigbedsummary/meta.yaml +++ b/recipes/ucsc-bigbedsummary/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigbedsummary" %} {% set program = "bigBedSummary" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract summary information from a bigBed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigbedtobed/build.sh b/recipes/ucsc-bigbedtobed/build.sh index 557d263987d51..dea44fa59530b 100644 --- a/recipes/ucsc-bigbedtobed/build.sh +++ b/recipes/ucsc-bigbedtobed/build.sh @@ -2,15 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigBedToBed && make -j ${CPU_COUNT}) -cp bin/bigBedToBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigBedToBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigBedToBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigBedToBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigBedToBed" diff --git a/recipes/ucsc-bigbedtobed/include.patch b/recipes/ucsc-bigbedtobed/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigbedtobed/include.patch +++ b/recipes/ucsc-bigbedtobed/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigbedtobed/meta.yaml b/recipes/ucsc-bigbedtobed/meta.yaml index 2572fb5c4f7a8..708bb43118bd2 100644 --- a/recipes/ucsc-bigbedtobed/meta.yaml +++ b/recipes/ucsc-bigbedtobed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigbedtobed" %} {% set program = "bigBedToBed" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,7 +23,6 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid @@ -44,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from bigBed to ascii bed format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigmaftomaf/build.sh b/recipes/ucsc-bigmaftomaf/build.sh index 291b1bb07748e..fbed7ad379763 100644 --- a/recipes/ucsc-bigmaftomaf/build.sh +++ b/recipes/ucsc-bigmaftomaf/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/hg/utils/bigMafToMaf && make -j ${CPU_COUNT}) -cp bin/bigMafToMaf "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigMafToMaf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bigMafToMaf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigMafToMaf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigMafToMaf" diff --git a/recipes/ucsc-bigmaftomaf/include.patch b/recipes/ucsc-bigmaftomaf/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigmaftomaf/include.patch +++ b/recipes/ucsc-bigmaftomaf/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigmaftomaf/meta.yaml b/recipes/ucsc-bigmaftomaf/meta.yaml index 08fb94982d426..f59a7e70f7d81 100644 --- a/recipes/ucsc-bigmaftomaf/meta.yaml +++ b/recipes/ucsc-bigmaftomaf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigmaftomaf" %} {% set program = "bigMafToMaf" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert bigMaf to maf file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigpsltopsl/build.sh b/recipes/ucsc-bigpsltopsl/build.sh index f6e9e3b240bef..ea6e4221c1466 100644 --- a/recipes/ucsc-bigpsltopsl/build.sh +++ b/recipes/ucsc-bigpsltopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/hg/utils/bigPslToPsl && make -j ${CPU_COUNT}) -cp bin/bigPslToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigPslToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bigPslToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigPslToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigPslToPsl" diff --git a/recipes/ucsc-bigpsltopsl/include.patch b/recipes/ucsc-bigpsltopsl/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigpsltopsl/include.patch +++ b/recipes/ucsc-bigpsltopsl/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigpsltopsl/meta.yaml b/recipes/ucsc-bigpsltopsl/meta.yaml index d8b8df1c6ec46..515aa553be985 100644 --- a/recipes/ucsc-bigpsltopsl/meta.yaml +++ b/recipes/ucsc-bigpsltopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigpsltopsl" %} {% set program = "bigPslToPsl" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert bigPsl file to psl" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigaverageoverbed/build.sh b/recipes/ucsc-bigwigaverageoverbed/build.sh index 36ed74547fa9e..9044dbe5feb95 100644 --- a/recipes/ucsc-bigwigaverageoverbed/build.sh +++ b/recipes/ucsc-bigwigaverageoverbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigAverageOverBed && make -j ${CPU_COUNT}) -cp bin/bigWigAverageOverBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigAverageOverBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigAverageOverBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigAverageOverBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigAverageOverBed" diff --git a/recipes/ucsc-bigwigaverageoverbed/include.patch b/recipes/ucsc-bigwigaverageoverbed/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigaverageoverbed/include.patch +++ b/recipes/ucsc-bigwigaverageoverbed/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigwigaverageoverbed/meta.yaml b/recipes/ucsc-bigwigaverageoverbed/meta.yaml index a3d7862dd2f63..e2e1bb8da3cce 100644 --- a/recipes/ucsc-bigwigaverageoverbed/meta.yaml +++ b/recipes/ucsc-bigwigaverageoverbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigaverageoverbed" %} {% set program = "bigWigAverageOverBed" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Compute average score of big wig over each bed, which may have introns." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigcat/build.sh b/recipes/ucsc-bigwigcat/build.sh index de0b41cfd02d2..c76176d286e9f 100644 --- a/recipes/ucsc-bigwigcat/build.sh +++ b/recipes/ucsc-bigwigcat/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigCat && make -j ${CPU_COUNT}) -cp bin/bigWigCat "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigCat" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigCat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigCat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigCat" diff --git a/recipes/ucsc-bigwigcat/include.patch b/recipes/ucsc-bigwigcat/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigcat/include.patch +++ b/recipes/ucsc-bigwigcat/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigwigcat/meta.yaml b/recipes/ucsc-bigwigcat/meta.yaml index 17562ee0872e2..f314a3ed65b9a 100644 --- a/recipes/ucsc-bigwigcat/meta.yaml +++ b/recipes/ucsc-bigwigcat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigcat" %} {% set program = "bigWigCat" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "merge non-overlapping bigWig files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigcluster/build.sh b/recipes/ucsc-bigwigcluster/build.sh index 765d6480a8b74..dfff70dd0b0a7 100644 --- a/recipes/ucsc-bigwigcluster/build.sh +++ b/recipes/ucsc-bigwigcluster/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigCluster && make -j ${CPU_COUNT}) -cp bin/bigWigCluster "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigCluster" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigCluster && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigCluster "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigCluster" diff --git a/recipes/ucsc-bigwigcluster/include.patch b/recipes/ucsc-bigwigcluster/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigcluster/include.patch +++ b/recipes/ucsc-bigwigcluster/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigwigcluster/meta.yaml b/recipes/ucsc-bigwigcluster/meta.yaml index 850d0384ba104..b385ad7c28da7 100644 --- a/recipes/ucsc-bigwigcluster/meta.yaml +++ b/recipes/ucsc-bigwigcluster/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigcluster" %} {% set program = "bigWigCluster" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Cluster bigWigs using a hacTree" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigcorrelate/build.sh b/recipes/ucsc-bigwigcorrelate/build.sh index 0d57ea8b1e3de..f4b5ede22c371 100644 --- a/recipes/ucsc-bigwigcorrelate/build.sh +++ b/recipes/ucsc-bigwigcorrelate/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigCorrelate && make -j ${CPU_COUNT}) -cp bin/bigWigCorrelate "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigCorrelate" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigCorrelate && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigCorrelate "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigCorrelate" diff --git a/recipes/ucsc-bigwigcorrelate/include.patch b/recipes/ucsc-bigwigcorrelate/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigcorrelate/include.patch +++ b/recipes/ucsc-bigwigcorrelate/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigwigcorrelate/meta.yaml b/recipes/ucsc-bigwigcorrelate/meta.yaml index 069403ca75dcb..0b51d8e1375da 100644 --- a/recipes/ucsc-bigwigcorrelate/meta.yaml +++ b/recipes/ucsc-bigwigcorrelate/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigcorrelate" %} {% set program = "bigWigCorrelate" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Correlate bigWig files, optionally only on target regions." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwiginfo/build.sh b/recipes/ucsc-bigwiginfo/build.sh index 70406d184f47e..6a25548f42c46 100644 --- a/recipes/ucsc-bigwiginfo/build.sh +++ b/recipes/ucsc-bigwiginfo/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd kent/src/hg/lib && USE_HIC=0 make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bigWigInfo && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bigWigInfo "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bigWigInfo" +cp bin/bigWigInfo "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigInfo" diff --git a/recipes/ucsc-bigwiginfo/include.patch b/recipes/ucsc-bigwiginfo/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwiginfo/include.patch +++ b/recipes/ucsc-bigwiginfo/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bigwiginfo/meta.yaml b/recipes/ucsc-bigwiginfo/meta.yaml index e338cf6643131..844216cdcde7e 100644 --- a/recipes/ucsc-bigwiginfo/meta.yaml +++ b/recipes/ucsc-bigwiginfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwiginfo" %} {% set program = "bigWigInfo" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,6 +14,7 @@ source: - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -28,11 +29,13 @@ requirements: - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -41,11 +44,14 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Print out information about bigWig file." dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-bigwigmerge/build.sh b/recipes/ucsc-bigwigmerge/build.sh index be5b9c0fd7dd6..c2f18065057b5 100644 --- a/recipes/ucsc-bigwigmerge/build.sh +++ b/recipes/ucsc-bigwigmerge/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bigWigMerge && make) -cp bin/bigWigMerge "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigMerge" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigMerge && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigMerge "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigMerge" diff --git a/recipes/ucsc-bigwigmerge/include.patch b/recipes/ucsc-bigwigmerge/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigmerge/include.patch +++ b/recipes/ucsc-bigwigmerge/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bigwigmerge/meta.yaml b/recipes/ucsc-bigwigmerge/meta.yaml index f88912eece11c..96f88d832b3ee 100644 --- a/recipes/ucsc-bigwigmerge/meta.yaml +++ b/recipes/ucsc-bigwigmerge/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigmerge" %} {% set program = "bigWigMerge" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Merge together multiple bigWigs into a single output bedGraph." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bigwigsummary/build.sh b/recipes/ucsc-bigwigsummary/build.sh index bc10870454d00..522db94f18c2b 100644 --- a/recipes/ucsc-bigwigsummary/build.sh +++ b/recipes/ucsc-bigwigsummary/build.sh @@ -1,13 +1,28 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigSummary && make -j ${CPU_COUNT}) -cp bin/bigWigSummary "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigSummary" + +mkdir -p "${BINDIR}" + +if [[ "$(uname)" == Darwin ]]; then + export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" + export CFLAGS="${CFLAGS} -Wno-unused-command-line-argument" +fi + +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigSummary && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigSummary "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigSummary" diff --git a/recipes/ucsc-bigwigsummary/htmshell.patch b/recipes/ucsc-bigwigsummary/htmshell.patch deleted file mode 100644 index 1e6f87375ed01..0000000000000 --- a/recipes/ucsc-bigwigsummary/htmshell.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 -+++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 -@@ -713,7 +713,7 @@ - puts("Status: 400\r"); - puts("Content-Type: text/plain; charset=UTF-8\r"); - puts("\r"); --if (format != NULL && args != NULL) -+if (format != NULL) - { - vfprintf(stdout, format, args); - fprintf(stdout, "\n"); diff --git a/recipes/ucsc-bigwigsummary/include.macos.patch b/recipes/ucsc-bigwigsummary/include.macos.patch new file mode 100644 index 0000000000000..979f87005a72e --- /dev/null +++ b/recipes/ucsc-bigwigsummary/include.macos.patch @@ -0,0 +1,27 @@ +--- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} +-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include + + # to check for Mac OSX Darwin specifics: + UNAME_S := $(shell uname -s) +--- a/kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ b/kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +@@ -1,4 +1,4 @@ +-KENT_INC=-I../../../inc ++KENT_INC=-I../../../inc -I${PREFIX}/include + + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o +--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + # expMatrixToBarchartBed + """ + Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. diff --git a/recipes/ucsc-bigwigsummary/include.patch b/recipes/ucsc-bigwigsummary/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigsummary/include.patch +++ b/recipes/ucsc-bigwigsummary/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigsummary/meta.yaml b/recipes/ucsc-bigwigsummary/meta.yaml index ca2ca18d6646b..390d49e449180 100644 --- a/recipes/ucsc-bigwigsummary/meta.yaml +++ b/recipes/ucsc-bigwigsummary/meta.yaml @@ -1,54 +1,62 @@ {% set package = "ucsc-bigwigsummary" %} {% set program = "bigWigSummary" %} -{% set version = "448" %} -{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - include.patch # [linux] + - include.macos.patch # [osx] build: - number: 1 - skip: True # [osx] + number: 2 run_exports: - - {{ pin_subpackage(package|lower, max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - {{ compiler('cxx') }} - - binutils # [linux] + - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl + - mariadb-connector-c - libopenssl-static + - clangdev # [osx] - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - mariadb-connector-c + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract summary information from a bigWig file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-bigwigtobedgraph/build.sh b/recipes/ucsc-bigwigtobedgraph/build.sh index 4d79a8a8afcb7..d9ee8a1c48c9c 100644 --- a/recipes/ucsc-bigwigtobedgraph/build.sh +++ b/recipes/ucsc-bigwigtobedgraph/build.sh @@ -2,15 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigToBedGraph && make -j ${CPU_COUNT}) -cp bin/bigWigToBedGraph "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigToBedGraph" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigToBedGraph && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigToBedGraph "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigToBedGraph" diff --git a/recipes/ucsc-bigwigtobedgraph/include.patch b/recipes/ucsc-bigwigtobedgraph/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigtobedgraph/include.patch +++ b/recipes/ucsc-bigwigtobedgraph/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigtobedgraph/meta.yaml b/recipes/ucsc-bigwigtobedgraph/meta.yaml index 03565119fb3c5..3cc5185b0c350 100644 --- a/recipes/ucsc-bigwigtobedgraph/meta.yaml +++ b/recipes/ucsc-bigwigtobedgraph/meta.yaml @@ -1,22 +1,21 @@ {% set package = "ucsc-bigwigtobedgraph" %} {% set program = "bigWigToBedGraph" %} -{% set version = "448" %} -{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -24,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence + exec bit, because the individual packages have no unified behavior - - test -x $PREFIX/bin/{{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from bigWig to bedGraph format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigtowig/build.sh b/recipes/ucsc-bigwigtowig/build.sh index a437ceb086a47..a1977c231e86f 100644 --- a/recipes/ucsc-bigwigtowig/build.sh +++ b/recipes/ucsc-bigwigtowig/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigToWig && make -j ${CPU_COUNT}) -cp bin/bigWigToWig "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigToWig" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigToWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigToWig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigToWig" diff --git a/recipes/ucsc-bigwigtowig/include.patch b/recipes/ucsc-bigwigtowig/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigtowig/include.patch +++ b/recipes/ucsc-bigwigtowig/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigtowig/meta.yaml b/recipes/ucsc-bigwigtowig/meta.yaml index 31e4bcee47493..af93e4083efd4 100644 --- a/recipes/ucsc-bigwigtowig/meta.yaml +++ b/recipes/ucsc-bigwigtowig/meta.yaml @@ -1,54 +1,57 @@ {% set package = "ucsc-bigwigtowig" %} {% set program = "bigWigToWig" %} -{% set version = "448" %} -{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 skip: True # [osx] + number: 0 run_exports: - - {{ pin_subpackage(package, max_pin="x") }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert bigWig to wig. This will keep more of the same structure of the original wig than bigWigToBedGraph does, but still will break up large stepped sections into smaller ones." + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Convert bigWig to wig. This will keep more of the same structure of the" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-blasttopsl/build.sh b/recipes/ucsc-blasttopsl/build.sh index 529365f0499e5..4e504991b1d17 100644 --- a/recipes/ucsc-blasttopsl/build.sh +++ b/recipes/ucsc-blasttopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/blastToPsl && make) -cp bin/blastToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/blastToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/blastToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/blastToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/blastToPsl" diff --git a/recipes/ucsc-blasttopsl/include.patch b/recipes/ucsc-blasttopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-blasttopsl/include.patch +++ b/recipes/ucsc-blasttopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-blasttopsl/meta.yaml b/recipes/ucsc-blasttopsl/meta.yaml index c50f577a4a6af..905368c1cacaa 100644 --- a/recipes/ucsc-blasttopsl/meta.yaml +++ b/recipes/ucsc-blasttopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-blasttopsl" %} {% set program = "blastToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert blast alignments to PSLs." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-blat/build.sh b/recipes/ucsc-blat/build.sh index 90db359833d44..abeab8ea7afd6 100644 --- a/recipes/ucsc-blat/build.sh +++ b/recipes/ucsc-blat/build.sh @@ -1,18 +1,21 @@ #!/bin/bash -export USE_HIC=0 + +set -xe + mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) -export BINDIR=`pwd`/bin +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p ${BINDIR} -(cd ${SRC_DIR}/kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd ${SRC_DIR}/kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd ${SRC_DIR}/kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd ${SRC_DIR}/kent/src/blat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f ${SRC_DIR}/bin/blat "${PREFIX}/bin" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/blat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/blat "${PREFIX}/bin" chmod 0755 "${PREFIX}/bin/blat" diff --git a/recipes/ucsc-blat/include.patch b/recipes/ucsc-blat/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-blat/include.patch +++ b/recipes/ucsc-blat/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-blat/meta.yaml b/recipes/ucsc-blat/meta.yaml index 089b3c02933a3..3a050f884b74b 100644 --- a/recipes/ucsc-blat/meta.yaml +++ b/recipes/ucsc-blat/meta.yaml @@ -1,38 +1,41 @@ {% set package = "ucsc-blat" %} {% set program = "blat" %} -{% set version = "468" %} -{% set sha256 = "f57b49be7e4eeb0719ac9414ca8878f93916fc3eb8dd408c8f7e076a999d1ca8" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch + - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage('ucsc-blat', max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid + - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -41,11 +44,14 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" - summary: "Standalone BLAT v. 39x1 fast sequence search command line tool" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Standalone BLAT v. 36x2 fast sequence search command line tool" dev_url: "https://github.com/ucscGenomeBrowser/kent" - doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-catdir/build.sh b/recipes/ucsc-catdir/build.sh index 615f2c28219a0..59b45dc68486c 100644 --- a/recipes/ucsc-catdir/build.sh +++ b/recipes/ucsc-catdir/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/catDir && make) -cp bin/catDir "$PREFIX/bin" -chmod +x "$PREFIX/bin/catDir" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/catDir && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/catDir "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/catDir" diff --git a/recipes/ucsc-catdir/include.patch b/recipes/ucsc-catdir/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-catdir/include.patch +++ b/recipes/ucsc-catdir/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-catdir/meta.yaml b/recipes/ucsc-catdir/meta.yaml index ec99f3e160dc9..9443ff4922d67 100644 --- a/recipes/ucsc-catdir/meta.yaml +++ b/recipes/ucsc-catdir/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-catdir" %} {% set program = "catDir" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "concatenate files in directory to stdout." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-catuncomment/build.sh b/recipes/ucsc-catuncomment/build.sh index e633331bb5d99..a6488e4ee3858 100644 --- a/recipes/ucsc-catuncomment/build.sh +++ b/recipes/ucsc-catuncomment/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/catUncomment && make) -cp bin/catUncomment "$PREFIX/bin" -chmod +x "$PREFIX/bin/catUncomment" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/catUncomment && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/catUncomment "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/catUncomment" diff --git a/recipes/ucsc-catuncomment/include.patch b/recipes/ucsc-catuncomment/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-catuncomment/include.patch +++ b/recipes/ucsc-catuncomment/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-catuncomment/meta.yaml b/recipes/ucsc-catuncomment/meta.yaml index 0eb80f7890c09..4e34d400fbd36 100644 --- a/recipes/ucsc-catuncomment/meta.yaml +++ b/recipes/ucsc-catuncomment/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-catuncomment" %} {% set program = "catUncomment" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Concatenate input removing lines that start with '#'" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainantirepeat/build.sh b/recipes/ucsc-chainantirepeat/build.sh index 4b96355a7cca0..42129d7ba0d38 100644 --- a/recipes/ucsc-chainantirepeat/build.sh +++ b/recipes/ucsc-chainantirepeat/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainAntiRepeat && make) -cp bin/chainAntiRepeat "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainAntiRepeat" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainAntiRepeat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainAntiRepeat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainAntiRepeat" diff --git a/recipes/ucsc-chainantirepeat/include.patch b/recipes/ucsc-chainantirepeat/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainantirepeat/include.patch +++ b/recipes/ucsc-chainantirepeat/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainantirepeat/meta.yaml b/recipes/ucsc-chainantirepeat/meta.yaml index c08a1b271ba4a..0ecd147dd4112 100644 --- a/recipes/ucsc-chainantirepeat/meta.yaml +++ b/recipes/ucsc-chainantirepeat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainantirepeat" %} {% set program = "chainAntiRepeat" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,28 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Get rid of chains that are primarily the results of repeats and degenerate DNA" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainbridge/build_failure.linux-64.yaml b/recipes/ucsc-chainbridge/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1f1c6c15a3d8c --- /dev/null +++ b/recipes/ucsc-chainbridge/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bc36f2b7ef37442f8cc79f3a7908cc9386a0df209151113d2954fe44e791a92e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o tigrOperon.o -c tigrOperon.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o tilingPath.o -c tilingPath.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o traceInfo.o -c traceInfo.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackDb.o -c trackDb.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackDbCustom.o -c trackDbCustom.c + trackDbCustom.c: In function 'trackDbInclude': + trackDbCustom.c:294:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=] + 294 | splitPath(raFile, incFile, NULL, NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]' + trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]' + trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]' + In file included from trackDbCustom.c:8: + ../../inc/common.h:1104:6: note: in a call to function 'splitPath' + 1104 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackHub.o -c trackHub.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 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-I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackTable.o -c trackTable.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackVersion.o -c trackVersion.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 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-I$PREFIX/include/libpng16 -I$PREFIX/include -o variome.o -c variome.c + ar rcus ../../lib/x86_64/jkhgap.a acemblyClass.o adjacency.o affyAllExonProbe.o affyAtlas.o affy10KDetails.o affy120KDetails.o affyOffset.o affyPairs.o agp.o agpFrag.o agpGap.o alignSeqSizes.o altGraph.o altGraphX.o ancientRref.o annoFormatVep.o annoGratorGpVar.o annoGrateWigDb.o annoStreamDb.o annoStreamDbFactorSource.o annoStreamDbPslPlus.o annoStreamWig.o api.o atomDb.o autoUpgrade.o axtInfo.o axtLib.o bactigPos.o hgBam.o barChartBed.o barChartCategory.o barChartUi.o barChartData.o barChartSample.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bigBedFind.o bigBedLabel.o bigGenePred.o bigPsl.o bigTransMap.o bioImage.o blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o cart.o cartDb.o cartJson.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o 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web.o ncRna.o wgRna.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o yaleGencodeAssoc.o zdobnovSynt.o oreganno.o oregannoUi.o gvUi.o gv.o omicia.o protVar.o pgSnp.o alignInfo.o cddInfo.o loweutils.o cddDesc.o arCOGs.o arcogdesc.o geneTree.o megablastInfo.o pgPhenoAssoc.o pgSiftPred.o pgPolyphenPred.o userRegions.o variome.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-chainbridge-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -o chainBridge.o -c chainBridge.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/chainBridge chainBridge.o ../../../lib/x86_64/jkOwnLib.a ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -L$PREFIX/lib -lmysqlclient -lstdc -lrt -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz + /opt/conda/conda-bld/ucsc-chainbridge_1724782613970/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(htmshell.o):/usr/local/src/conda/ucsc-chainbridge-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-chainbridge-377/kent/src/lib/../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-chainbridge_1724782613970/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(portimpl.o):/usr/local/src/conda/ucsc-chainbridge-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-chainbridge-377/kent/src/lib/../inc/htmshell.h:163: first defined here + collect2: error: ld returned 1 exit status + make: *** [../../../inc/userApp.mk:31: /opt/conda/conda-bld/ucsc-chainbridge_1724782613970/work/bin/chainBridge] Error 1 + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-chainbridge_1724782613970/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-chainfilter/build.sh b/recipes/ucsc-chainfilter/build.sh index 6ed9ac45b5549..10d08403f1c62 100644 --- a/recipes/ucsc-chainfilter/build.sh +++ b/recipes/ucsc-chainfilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainFilter && make) -cp bin/chainFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainFilter" diff --git a/recipes/ucsc-chainfilter/include.patch b/recipes/ucsc-chainfilter/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainfilter/include.patch +++ b/recipes/ucsc-chainfilter/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainfilter/meta.yaml b/recipes/ucsc-chainfilter/meta.yaml index eb41f55eb619f..950b6e95f0bba 100644 --- a/recipes/ucsc-chainfilter/meta.yaml +++ b/recipes/ucsc-chainfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainfilter" %} {% set program = "chainFilter" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,28 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter chain files. Output goes to standard out." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainmergesort/build.sh b/recipes/ucsc-chainmergesort/build.sh index afd3f10975fbc..d6577def526dc 100644 --- a/recipes/ucsc-chainmergesort/build.sh +++ b/recipes/ucsc-chainmergesort/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainMergeSort && make) -cp bin/chainMergeSort "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainMergeSort" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainMergeSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainMergeSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainMergeSort" diff --git a/recipes/ucsc-chainmergesort/include.patch b/recipes/ucsc-chainmergesort/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainmergesort/include.patch +++ b/recipes/ucsc-chainmergesort/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainmergesort/meta.yaml b/recipes/ucsc-chainmergesort/meta.yaml index a8116c2079423..ae45368e76907 100644 --- a/recipes/ucsc-chainmergesort/meta.yaml +++ b/recipes/ucsc-chainmergesort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainmergesort" %} {% set program = "chainMergeSort" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,28 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Combine sorted files into larger sorted file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainnet/build.sh b/recipes/ucsc-chainnet/build.sh index d374b876a973a..f90815a193a1d 100644 --- a/recipes/ucsc-chainnet/build.sh +++ b/recipes/ucsc-chainnet/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainNet && make) -cp bin/chainNet "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainNet" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainNet && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainNet "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainNet" diff --git a/recipes/ucsc-chainnet/include.patch b/recipes/ucsc-chainnet/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainnet/include.patch +++ b/recipes/ucsc-chainnet/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainnet/meta.yaml b/recipes/ucsc-chainnet/meta.yaml index 070f24c45a620..55b46b9d727b0 100644 --- a/recipes/ucsc-chainnet/meta.yaml +++ b/recipes/ucsc-chainnet/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainnet" %} {% set program = "chainNet" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,27 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make alignment nets out of chains" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainprenet/build.sh b/recipes/ucsc-chainprenet/build.sh index 63ca58dde82ac..30c78ac9541a4 100644 --- a/recipes/ucsc-chainprenet/build.sh +++ b/recipes/ucsc-chainprenet/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainPreNet && make) -cp bin/chainPreNet "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainPreNet" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainPreNet && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainPreNet "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainPreNet" diff --git a/recipes/ucsc-chainprenet/include.patch b/recipes/ucsc-chainprenet/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainprenet/include.patch +++ b/recipes/ucsc-chainprenet/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chainprenet/meta.yaml b/recipes/ucsc-chainprenet/meta.yaml index 748d450bbaa02..02c19c160aef0 100644 --- a/recipes/ucsc-chainprenet/meta.yaml +++ b/recipes/ucsc-chainprenet/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainprenet" %} {% set program = "chainPreNet" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Remove chains that don't have a chance of being netted" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainsort/build.sh b/recipes/ucsc-chainsort/build.sh index aa1b99bc6019b..2ebbff9ed471a 100644 --- a/recipes/ucsc-chainsort/build.sh +++ b/recipes/ucsc-chainsort/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainSort && make) -cp bin/chainSort "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainSort" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainSort" diff --git a/recipes/ucsc-chainsort/include.patch b/recipes/ucsc-chainsort/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainsort/include.patch +++ b/recipes/ucsc-chainsort/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-chainsort/meta.yaml b/recipes/ucsc-chainsort/meta.yaml index 3864af0708530..93c9d98b79b37 100644 --- a/recipes/ucsc-chainsort/meta.yaml +++ b/recipes/ucsc-chainsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainsort" %} {% set program = "chainSort" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -17,34 +17,41 @@ build: skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage("ucsc-chainsort", max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Sort chains. By default sorts by score." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainsplit/build.sh b/recipes/ucsc-chainsplit/build.sh index 904b5af20b961..86485b0bf816f 100644 --- a/recipes/ucsc-chainsplit/build.sh +++ b/recipes/ucsc-chainsplit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainSplit && make) -cp bin/chainSplit "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainSplit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainSplit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainSplit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainSplit" diff --git a/recipes/ucsc-chainsplit/include.patch b/recipes/ucsc-chainsplit/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainsplit/include.patch +++ b/recipes/ucsc-chainsplit/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chainsplit/meta.yaml b/recipes/ucsc-chainsplit/meta.yaml index 879198f6e1dc9..8904f36ce5819 100644 --- a/recipes/ucsc-chainsplit/meta.yaml +++ b/recipes/ucsc-chainsplit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainsplit" %} {% set program = "chainSplit" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split chains up by target or query sequence" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainstitchid/build.sh b/recipes/ucsc-chainstitchid/build.sh index 5a737a5c85003..10dfddf7ed04e 100644 --- a/recipes/ucsc-chainstitchid/build.sh +++ b/recipes/ucsc-chainstitchid/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainStitchId && make) -cp bin/chainStitchId "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainStitchId" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainStitchId && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainStitchId "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainStitchId" diff --git a/recipes/ucsc-chainstitchid/include.patch b/recipes/ucsc-chainstitchid/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainstitchid/include.patch +++ b/recipes/ucsc-chainstitchid/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chainstitchid/meta.yaml b/recipes/ucsc-chainstitchid/meta.yaml index 2001b5df994a4..ef2cfd4aeacd6 100644 --- a/recipes/ucsc-chainstitchid/meta.yaml +++ b/recipes/ucsc-chainstitchid/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainstitchid" %} {% set program = "chainStitchId" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Join chain fragments with the same chain ID into a single" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainswap/build.sh b/recipes/ucsc-chainswap/build.sh index 361d0fad14946..8eb218a29a95a 100644 --- a/recipes/ucsc-chainswap/build.sh +++ b/recipes/ucsc-chainswap/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainSwap && make) -cp bin/chainSwap "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainSwap" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainSwap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainSwap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainSwap" diff --git a/recipes/ucsc-chainswap/include.patch b/recipes/ucsc-chainswap/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainswap/include.patch +++ b/recipes/ucsc-chainswap/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chainswap/meta.yaml b/recipes/ucsc-chainswap/meta.yaml index a4781ec42be5d..4e91525fb6b79 100644 --- a/recipes/ucsc-chainswap/meta.yaml +++ b/recipes/ucsc-chainswap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainswap" %} {% set program = "chainSwap" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Swap target and query in chain" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chaintoaxt/build.sh b/recipes/ucsc-chaintoaxt/build.sh index 183b350517e6a..04441646d7916 100644 --- a/recipes/ucsc-chaintoaxt/build.sh +++ b/recipes/ucsc-chaintoaxt/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainToAxt && make) -cp bin/chainToAxt "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainToAxt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainToAxt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainToAxt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainToAxt" diff --git a/recipes/ucsc-chaintoaxt/include.patch b/recipes/ucsc-chaintoaxt/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chaintoaxt/include.patch +++ b/recipes/ucsc-chaintoaxt/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chaintoaxt/meta.yaml b/recipes/ucsc-chaintoaxt/meta.yaml index b9c5445fd18b2..77d4ae748c889 100644 --- a/recipes/ucsc-chaintoaxt/meta.yaml +++ b/recipes/ucsc-chaintoaxt/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chaintoaxt" %} {% set program = "chainToAxt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from chain to axt file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chaintopsl/build.sh b/recipes/ucsc-chaintopsl/build.sh index 73cc58fd9a243..744cad97874af 100644 --- a/recipes/ucsc-chaintopsl/build.sh +++ b/recipes/ucsc-chaintopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainToPsl && make) -cp bin/chainToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainToPsl" diff --git a/recipes/ucsc-chaintopsl/include.patch b/recipes/ucsc-chaintopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chaintopsl/include.patch +++ b/recipes/ucsc-chaintopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chaintopsl/meta.yaml b/recipes/ucsc-chaintopsl/meta.yaml index 0bc996af09ba1..ced6ca5ebea90 100644 --- a/recipes/ucsc-chaintopsl/meta.yaml +++ b/recipes/ucsc-chaintopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chaintopsl" %} {% set program = "chainToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert chain file to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chaintopslbasic/build.sh b/recipes/ucsc-chaintopslbasic/build.sh index 0c1f25b1e30dc..4f3b66b44fedb 100644 --- a/recipes/ucsc-chaintopslbasic/build.sh +++ b/recipes/ucsc-chaintopslbasic/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainToPslBasic && make) -cp bin/chainToPslBasic "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainToPslBasic" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainToPslBasic && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainToPslBasic "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainToPslBasic" diff --git a/recipes/ucsc-chaintopslbasic/include.patch b/recipes/ucsc-chaintopslbasic/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chaintopslbasic/include.patch +++ b/recipes/ucsc-chaintopslbasic/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chaintopslbasic/meta.yaml b/recipes/ucsc-chaintopslbasic/meta.yaml index fba9f93d81f94..9a9683eff74f7 100644 --- a/recipes/ucsc-chaintopslbasic/meta.yaml +++ b/recipes/ucsc-chaintopslbasic/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chaintopslbasic" %} {% set program = "chainToPslBasic" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Basic conversion chain file to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-checkagpandfa/build.sh b/recipes/ucsc-checkagpandfa/build.sh index 73ca488d61f8f..ad3b4d10ece14 100644 --- a/recipes/ucsc-checkagpandfa/build.sh +++ b/recipes/ucsc-checkagpandfa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/gigAssembler/checkAgpAndFa && make) -cp bin/checkAgpAndFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/checkAgpAndFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/gigAssembler/checkAgpAndFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/checkAgpAndFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/checkAgpAndFa" diff --git a/recipes/ucsc-checkagpandfa/include.patch b/recipes/ucsc-checkagpandfa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-checkagpandfa/include.patch +++ b/recipes/ucsc-checkagpandfa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-checkagpandfa/meta.yaml b/recipes/ucsc-checkagpandfa/meta.yaml index 602c1b2589e17..5a739b8c2d0db 100644 --- a/recipes/ucsc-checkagpandfa/meta.yaml +++ b/recipes/ucsc-checkagpandfa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-checkagpandfa" %} {% set program = "checkAgpAndFa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "takes a .agp file and .fa file and ensures that they are in synch" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-checkcoveragegaps/build.sh b/recipes/ucsc-checkcoveragegaps/build.sh index ef5ebe0df0a02..eb941d1941048 100644 --- a/recipes/ucsc-checkcoveragegaps/build.sh +++ b/recipes/ucsc-checkcoveragegaps/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/checkCoverageGaps && make) -cp bin/checkCoverageGaps "$PREFIX/bin" -chmod +x "$PREFIX/bin/checkCoverageGaps" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/checkCoverageGaps && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/checkCoverageGaps "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/checkCoverageGaps" diff --git a/recipes/ucsc-checkcoveragegaps/include.patch b/recipes/ucsc-checkcoveragegaps/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-checkcoveragegaps/include.patch +++ b/recipes/ucsc-checkcoveragegaps/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-checkcoveragegaps/meta.yaml b/recipes/ucsc-checkcoveragegaps/meta.yaml index b3d0db6ae4843..cc86c26c9b7a9 100644 --- a/recipes/ucsc-checkcoveragegaps/meta.yaml +++ b/recipes/ucsc-checkcoveragegaps/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-checkcoveragegaps" %} {% set program = "checkCoverageGaps" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Check for biggest gap in coverage for a list of tracks." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-checkhgfindspec/build.sh b/recipes/ucsc-checkhgfindspec/build.sh index c89af8112bd23..a1d8fa895c2af 100644 --- a/recipes/ucsc-checkhgfindspec/build.sh +++ b/recipes/ucsc-checkhgfindspec/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/checkHgFindSpec && make) -cp bin/checkHgFindSpec "$PREFIX/bin" -chmod +x "$PREFIX/bin/checkHgFindSpec" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/checkHgFindSpec && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/checkHgFindSpec "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/checkHgFindSpec" diff --git a/recipes/ucsc-checkhgfindspec/build_failure.linux-64.yaml b/recipes/ucsc-checkhgfindspec/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0d3815ba92acf --- /dev/null +++ b/recipes/ucsc-checkhgfindspec/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: df8d57e37d78b7409b8c609e4b204bd41d195d67802921500989e57e12b65d07 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~~~ + qaSeq.c: In function 'qaFastReadNext': + qaSeq.c:195:1: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] + 195 | strncpy(name, s, sizeof(name)); + | ^~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o quickLift.o -c quickLift.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o quickLiftChain.o -c quickLiftChain.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o rankProp.o -c rankProp.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o refLink.o -c refLink.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o refSeqStatus.o -c refSeqStatus.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o rikenCluster.o -c rikenCluster.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include 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splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trashDir.o -c trashDir.c + 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-fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txEdgeBed.o -c txEdgeBed.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txGraph.o -c txGraph.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txInfo.o -c txInfo.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txRnaAccs.o -c txRnaAccs.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o variantProjector.o -c variantProjector.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vcfUi.o -c vcfUi.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vegaInfo.o -c vegaInfo.c + sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestHeader.html > jWestHeader.h + sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestBanner.html > jWestBanner.h + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigAsciiToBinary.o -c wigAsciiToBinary.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigDataStream.o -c wigDataStream.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggle.o -c wiggle.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleCart.o -c wiggleCart.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleUtils.o -c wiggleUtils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wikiLink.o -c wikiLink.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskAlignBed.o -c bigRmskAlignBed.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskBed.o -c bigRmskBed.c + mkdir -p ../../lib/x86_64 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o web.o -c web.c + ar rcus ../../lib/x86_64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o bigRmskAlignBed.o bigRmskBed.o + cd kent/src/hg/checkHgFindSpec + make CC=/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_build_env/bin/x86_64-conda-linux-gnu-cc CXX= 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/work=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -L/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -L/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib' 'CXXFLAGS= -I/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -L/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -L/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib' -j 4 + make: *** No rule to make target '../../lib/x86_64/jkhgapcgi.a', needed by '/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/work/bin/checkHgFindSpec'. Stop. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-checkhgfindspec_1724792872911/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-checkhgfindspec/build_failure.linux-aarch64.yaml b/recipes/ucsc-checkhgfindspec/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..968e091213191 --- /dev/null +++ b/recipes/ucsc-checkhgfindspec/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: df8d57e37d78b7409b8c609e4b204bd41d195d67802921500989e57e12b65d07 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~~~ + qaSeq.c: In function 'qaFastReadNext': + qaSeq.c:195:1: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] + 195 | strncpy(name, s, sizeof(name)); + | ^~~~~~~ + 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-Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackDbCustom.o -c trackDbCustom.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackHub.o -c trackHub.c + trackDbCustom.c: In function 'trackDbInclude': + trackDbCustom.c:294:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=] + 294 | splitPath(raFile, incFile, NULL, NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]' + trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]' + trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]' + In file included from trackDbCustom.c:9: + ../../inc/common.h:1139:6: note: in a call to function 'splitPath' + 1139 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix 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-D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trashDir.o -c trashDir.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txAliDiff.o -c txAliDiff.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txCluster.o -c txCluster.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txCommon.o -c txCommon.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txEdgeBed.o -c txEdgeBed.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txGraph.o -c txGraph.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txInfo.o -c txInfo.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txRnaAccs.o -c txRnaAccs.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o variantProjector.o -c variantProjector.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common 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-DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vegaInfo.o -c vegaInfo.c + sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestHeader.html > jWestHeader.h + sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestBanner.html > jWestBanner.h + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigAsciiToBinary.o -c wigAsciiToBinary.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigDataStream.o -c wigDataStream.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggle.o -c wiggle.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleCart.o -c wiggleCart.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleUtils.o -c wiggleUtils.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wikiLink.o -c wikiLink.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskAlignBed.o -c bigRmskAlignBed.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskBed.o -c bigRmskBed.c + mkdir -p ../../lib/aarch64 + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o web.o -c web.c + ar rcus ../../lib/aarch64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o bigRmskAlignBed.o bigRmskBed.o + cd kent/src/hg/checkHgFindSpec + make CC=/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_build_env/bin/aarch64-conda-linux-gnu-cc CXX= 'CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/work=/usr/local/src/conda/ucsc-checkhgfindspec-469 -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -L/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -L/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib' 'CXXFLAGS= -I/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -L/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib -L/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib' -j 4 + make: *** No rule to make target '../../lib/aarch64/jkhgapcgi.a', needed by '/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/work/bin/checkHgFindSpec'. Stop. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-checkhgfindspec_1724786009370/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-checkhgfindspec/include.patch b/recipes/ucsc-checkhgfindspec/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-checkhgfindspec/include.patch +++ b/recipes/ucsc-checkhgfindspec/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-checkhgfindspec/meta.yaml b/recipes/ucsc-checkhgfindspec/meta.yaml index 7d0c1b14e7bda..344ee0e75f466 100644 --- a/recipes/ucsc-checkhgfindspec/meta.yaml +++ b/recipes/ucsc-checkhgfindspec/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-checkhgfindspec" %} {% set program = "checkHgFindSpec" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "test and describe search specs in hgFindSpec tables." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-checktablecoords/build.sh b/recipes/ucsc-checktablecoords/build.sh index 32521004ac2cd..91bb2e088ce06 100644 --- a/recipes/ucsc-checktablecoords/build.sh +++ b/recipes/ucsc-checktablecoords/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/checkTableCoords && make) -cp bin/checkTableCoords "$PREFIX/bin" -chmod +x "$PREFIX/bin/checkTableCoords" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/checkTableCoords && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/checkTableCoords "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/checkTableCoords" diff --git a/recipes/ucsc-checktablecoords/include.patch b/recipes/ucsc-checktablecoords/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-checktablecoords/include.patch +++ b/recipes/ucsc-checktablecoords/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-checktablecoords/meta.yaml b/recipes/ucsc-checktablecoords/meta.yaml index 791004d8305d7..adb7ea668615a 100644 --- a/recipes/ucsc-checktablecoords/meta.yaml +++ b/recipes/ucsc-checktablecoords/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-checktablecoords" %} {% set program = "checkTableCoords" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "check invariants on genomic coords in table(s)." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-chopfalines/build.sh b/recipes/ucsc-chopfalines/build.sh index ee55545a7dfb8..a58ab6b37ac2a 100644 --- a/recipes/ucsc-chopfalines/build.sh +++ b/recipes/ucsc-chopfalines/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/chopFaLines && make) -cp bin/chopFaLines "$PREFIX/bin" -chmod +x "$PREFIX/bin/chopFaLines" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/chopFaLines && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chopFaLines "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chopFaLines" diff --git a/recipes/ucsc-chopfalines/include.patch b/recipes/ucsc-chopfalines/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chopfalines/include.patch +++ b/recipes/ucsc-chopfalines/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chopfalines/meta.yaml b/recipes/ucsc-chopfalines/meta.yaml index 82f95f1e65f16..55a8833c00e82 100644 --- a/recipes/ucsc-chopfalines/meta.yaml +++ b/recipes/ucsc-chopfalines/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chopfalines" %} {% set program = "chopFaLines" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Read in FA file with long lines and rewrite it with shorter lines" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chromgraphfrombin/build.sh b/recipes/ucsc-chromgraphfrombin/build.sh index f4e4f1cd6a5c7..abe23d1d58239 100644 --- a/recipes/ucsc-chromgraphfrombin/build.sh +++ b/recipes/ucsc-chromgraphfrombin/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/chromGraphFromBin && make) -cp bin/chromGraphFromBin "$PREFIX/bin" -chmod +x "$PREFIX/bin/chromGraphFromBin" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/chromGraphFromBin && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chromGraphFromBin "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chromGraphFromBin" diff --git a/recipes/ucsc-chromgraphfrombin/include.patch b/recipes/ucsc-chromgraphfrombin/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chromgraphfrombin/include.patch +++ b/recipes/ucsc-chromgraphfrombin/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chromgraphfrombin/meta.yaml b/recipes/ucsc-chromgraphfrombin/meta.yaml index d5fee658365da..81ed418950a54 100644 --- a/recipes/ucsc-chromgraphfrombin/meta.yaml +++ b/recipes/ucsc-chromgraphfrombin/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chromgraphfrombin" %} {% set program = "chromGraphFromBin" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert chromGraph binary to ascii format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-chromgraphtobin/build.sh b/recipes/ucsc-chromgraphtobin/build.sh index 3cfddf7a01494..e48eda9b05ff5 100644 --- a/recipes/ucsc-chromgraphtobin/build.sh +++ b/recipes/ucsc-chromgraphtobin/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/chromGraphToBin && make) -cp bin/chromGraphToBin "$PREFIX/bin" -chmod +x "$PREFIX/bin/chromGraphToBin" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/chromGraphToBin && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chromGraphToBin "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chromGraphToBin" diff --git a/recipes/ucsc-chromgraphtobin/include.patch b/recipes/ucsc-chromgraphtobin/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chromgraphtobin/include.patch +++ b/recipes/ucsc-chromgraphtobin/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chromgraphtobin/meta.yaml b/recipes/ucsc-chromgraphtobin/meta.yaml index 3e585a0142a8f..3ca7a67b56d0a 100644 --- a/recipes/ucsc-chromgraphtobin/meta.yaml +++ b/recipes/ucsc-chromgraphtobin/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chromgraphtobin" %} {% set program = "chromGraphToBin" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make binary version of chromGraph." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-clustergenes/build_failure.linux-64.yaml b/recipes/ucsc-clustergenes/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6f6b3fc542fb7 --- /dev/null +++ b/recipes/ucsc-clustergenes/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7301658b2a9a152f5678e10ce66f847a6c66e265570df1b26bdf41f4d8183b78 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]' + trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]' + trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]' + In file included from trackDbCustom.c:8: + ../../inc/common.h:1104:6: note: in a call to function 'splitPath' + 1104 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-clustergenes-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackHub.o -c trackHub.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-clustergenes-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackLayout.o -c trackLayout.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include 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gtexGeneBed.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueData.o gtexTissueMedian.o gtexUi.o gwasCatalog.o hAnno.o haplotypes.o hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o hapmapSnps.o hapmapSnpsCombined.o hashJoin.o hCommon.o hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgGene.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o HInv.o hubConnect.o hubSearchText.o hui.o humanParalog.o imageClone.o indelShift.o interact.o interactUi.o isochores.o ispyTables.o itemAttr.o itemConf.o itemDetailsHtml.o jalview.o jaxOrtholog.o jaxQTL.o jaxQTL3.o jksql.o joiner.o jsHelper.o kg1ToKg2.o jgiGene.o joinMixer.o kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o lav.o ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o llaInfo.o longRange.o lrg.o lsSnpPdb.o lsSnpPdbChimera.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mammalPsg.o mapSts.o mathWig.o mcnBreakpoints.o mdb.o metaChromGraph.o microarray.o minChromSize.o minGeneInfo.o mrnaMisMatch.o mouseOrtho.o mouseSyn.o mouseSynWhd.o mysqlTableStatus.o ncbiRefLink.o ncbiRefSeqLink.o netAlign.o netCart.o nonCodingUi.o omimTitle.o ooUtils.o orthoAlleles.o pal.o pbStamp.o pcrResult.o pepPred.o peptideAtlasPeptide.o plasEndPairs.o polyGenotype.o protFeat.o pscreen.o pseudoGeneLink.o pslReader.o pslWScore.o putaInfo.o qaSeq.o rangeTreeFile.o rankProp.o recombRate.o recombRateRat.o recombRateMouse.o refLink.o refSeqStatus.o rgdQtl.o riken.o rhMapZfishInfo.o rikenBest.o rikenCluster.o rmskOut.o rmskAlign.o rmskJoined.o rmskOut2.o rnaFold.o rnaGene.o rnaGroup.o rnaHybridization.o rnaPLFold.o tRNAs.o gbRNAs.o snoRNAs.o lowelabPfamHit.o lowelabArkinOperonScore.o lowelabTIGROperonScore.o rnaSecStr.o tfbsConsFactors.o roughAli.o transMapStuff.o transMapInfo.o transMapGene.o transMapSrc.o sage.o sageCounts.o sageExp.o samAlignment.o sample.o sanger22extra.o sangerGene.o sangerGeneToWBGeneID.o sargassoSeaXra.o scopDes.o scoredRef.o search.o seqWindow.o sessionThumbnail.o sgdAbundance.o sgdClone.o sgdDescription.o sgdOther.o simpleNucDiff.o simpleRepeat.o snakeUi.o snp.o snp125.o snp125CodingCoordless.o snp132Ext.o snpExceptions.o snpFasta.o snpMap.o snpTmp.o snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o soTerm.o spDb.o splignAlign.o sqlSanity.o stanMad.o stsAlias.o stsInfo.o stsInfo2.o stsInfoMouse.o stsInfoMouseNew.o stsInfoRat.o stsMap.o stsMapMouse.o stsMapMouseNew.o stsMapRat.o stsMarker.o suggest.o switchDbTss.o synMap.o synteny100000.o syntenyBerk.o syntenySanger.o sqlProg.o tfbsCons.o tfbsConsSites.o tablesTables.o tableDescriptions.o tableStatus.o targetDb.o tfbsConsMap.o tagRepo.o taxonDivision.o taxonGeneticCode.o taxonName.o taxonNode.o taxonXref.o tigrCmrGene.o tigrOperon.o tilingPath.o traceInfo.o trackDb.o trackDbCustom.o trackHub.o trackLayout.o trackTable.o trackVersion.o trashDir.o transRegCode.o transRegCodeCondition.o transRegCodeProbe.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txEdgeOrtho.o txGraph.o txInfo.o txRnaAccs.o ucscRetroInfo.o ucscRetroOrtho.o validateGisaid.o variant.o variantProjector.o vcfUi.o vegaInfo.o vegaInfoZfish.o visiGene.o vntr.o wabAli.o web.o ncRna.o wgRna.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o yaleGencodeAssoc.o zdobnovSynt.o oreganno.o oregannoUi.o gvUi.o gv.o omicia.o protVar.o pgSnp.o alignInfo.o cddInfo.o loweutils.o cddDesc.o arCOGs.o arcogdesc.o geneTree.o megablastInfo.o pgPhenoAssoc.o pgSiftPred.o pgPolyphenPred.o userRegions.o variome.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-clustergenes-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -o clusterGenes.o -c clusterGenes.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/clusterGenes clusterGenes.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -L$PREFIX/lib -lmysqlclient -lstdc -lrt -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(trackHub.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(web.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(wikiLink.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(cart.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(hPrint.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(bamFile.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(htmlPage.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(htmshell.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(portimpl.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-clustergenes-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + collect2: error: ld returned 1 exit status + make: *** [../../../inc/userApp.mk:31: /opt/conda/conda-bld/ucsc-clustergenes_1724781208821/work/bin/clusterGenes] Error 1 + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-clustergenes_1724781208821/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-coltransform/build.sh b/recipes/ucsc-coltransform/build.sh index a98809f9c583c..17f4d40047c93 100644 --- a/recipes/ucsc-coltransform/build.sh +++ b/recipes/ucsc-coltransform/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/colTransform && make) -cp bin/colTransform "$PREFIX/bin" -chmod +x "$PREFIX/bin/colTransform" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/colTransform && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/colTransform "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/colTransform" diff --git a/recipes/ucsc-coltransform/include.patch b/recipes/ucsc-coltransform/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-coltransform/include.patch +++ b/recipes/ucsc-coltransform/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-coltransform/meta.yaml b/recipes/ucsc-coltransform/meta.yaml index 8db80ad0ad41b..46a6ce6c314fa 100644 --- a/recipes/ucsc-coltransform/meta.yaml +++ b/recipes/ucsc-coltransform/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-coltransform" %} {% set program = "colTransform" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add and/or multiply column by constant." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-countchars/build.sh b/recipes/ucsc-countchars/build.sh index e2c225cd7ebe3..ab3cb84cb1983 100644 --- a/recipes/ucsc-countchars/build.sh +++ b/recipes/ucsc-countchars/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/countChars && make) -cp bin/countChars "$PREFIX/bin" -chmod +x "$PREFIX/bin/countChars" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/countChars && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/countChars "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/countChars" diff --git a/recipes/ucsc-countchars/include.patch b/recipes/ucsc-countchars/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-countchars/include.patch +++ b/recipes/ucsc-countchars/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-countchars/meta.yaml b/recipes/ucsc-countchars/meta.yaml index a5edbbf355e7d..3191991de187e 100644 --- a/recipes/ucsc-countchars/meta.yaml +++ b/recipes/ucsc-countchars/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-countchars" %} {% set program = "countChars" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Count the number of occurrences of a particular char" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-crtreeindexbed/build.sh b/recipes/ucsc-crtreeindexbed/build.sh index a5c31fd2e8f40..32c54dab05cde 100644 --- a/recipes/ucsc-crtreeindexbed/build.sh +++ b/recipes/ucsc-crtreeindexbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/crTreeIndexBed && make) -cp bin/crTreeIndexBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/crTreeIndexBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/crTreeIndexBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/crTreeIndexBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/crTreeIndexBed" diff --git a/recipes/ucsc-crtreeindexbed/include.patch b/recipes/ucsc-crtreeindexbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-crtreeindexbed/include.patch +++ b/recipes/ucsc-crtreeindexbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-crtreeindexbed/meta.yaml b/recipes/ucsc-crtreeindexbed/meta.yaml index b27fbf72f00c6..59945d6280836 100644 --- a/recipes/ucsc-crtreeindexbed/meta.yaml +++ b/recipes/ucsc-crtreeindexbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-crtreeindexbed" %} {% set program = "crTreeIndexBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create an index for a bed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-crtreesearchbed/build.sh b/recipes/ucsc-crtreesearchbed/build.sh index a12dde560da6c..3ff4031d4a04a 100644 --- a/recipes/ucsc-crtreesearchbed/build.sh +++ b/recipes/ucsc-crtreesearchbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/crTreeSearchBed && make) -cp bin/crTreeSearchBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/crTreeSearchBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/crTreeSearchBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/crTreeSearchBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/crTreeSearchBed" diff --git a/recipes/ucsc-crtreesearchbed/include.patch b/recipes/ucsc-crtreesearchbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-crtreesearchbed/include.patch +++ b/recipes/ucsc-crtreesearchbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-crtreesearchbed/meta.yaml b/recipes/ucsc-crtreesearchbed/meta.yaml index 2066d7d3f5600..cf88771bb980d 100644 --- a/recipes/ucsc-crtreesearchbed/meta.yaml +++ b/recipes/ucsc-crtreesearchbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-crtreesearchbed" %} {% set program = "crTreeSearchBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Search a crTree indexed bed file and print all items that overlap query." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-dbsnoop/build.sh b/recipes/ucsc-dbsnoop/build.sh index 262a37a241c74..aa3011731bccf 100644 --- a/recipes/ucsc-dbsnoop/build.sh +++ b/recipes/ucsc-dbsnoop/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/schema/dbSnoop && make) -cp bin/dbSnoop "$PREFIX/bin" -chmod +x "$PREFIX/bin/dbSnoop" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/schema/dbSnoop && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/dbSnoop "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/dbSnoop" diff --git a/recipes/ucsc-dbsnoop/include.patch b/recipes/ucsc-dbsnoop/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-dbsnoop/include.patch +++ b/recipes/ucsc-dbsnoop/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-dbsnoop/meta.yaml b/recipes/ucsc-dbsnoop/meta.yaml index e72dffb9fd650..b20c4a5c34f80 100644 --- a/recipes/ucsc-dbsnoop/meta.yaml +++ b/recipes/ucsc-dbsnoop/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-dbsnoop" %} {% set program = "dbSnoop" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Produce an overview of a database." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-dbtrash/build.sh b/recipes/ucsc-dbtrash/build.sh index 486a57847c65e..9052d214175ac 100644 --- a/recipes/ucsc-dbtrash/build.sh +++ b/recipes/ucsc-dbtrash/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/dbTrash && make) -cp bin/dbTrash "$PREFIX/bin" -chmod +x "$PREFIX/bin/dbTrash" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/dbTrash && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/dbTrash "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/dbTrash" diff --git a/recipes/ucsc-dbtrash/include.patch b/recipes/ucsc-dbtrash/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-dbtrash/include.patch +++ b/recipes/ucsc-dbtrash/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-dbtrash/meta.yaml b/recipes/ucsc-dbtrash/meta.yaml index 66ad1fd75c48d..4270a211766bf 100644 --- a/recipes/ucsc-dbtrash/meta.yaml +++ b/recipes/ucsc-dbtrash/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-dbtrash" %} {% set program = "dbTrash" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "drop tables from a database older than specified N hours" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-endsinlf/build_failure.linux-64.yaml b/recipes/ucsc-endsinlf/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c207bddc849c7 --- /dev/null +++ b/recipes/ucsc-endsinlf/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9dd147853f61d5e67e767ed724974f0baf58c1fffa7e30799c31880431f172b7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o tigrOperon.o -c tigrOperon.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o tilingPath.o -c tilingPath.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o traceInfo.o -c traceInfo.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 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trackDbCustom.c + trackDbCustom.c: In function 'trackDbInclude': + trackDbCustom.c:294:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=] + 294 | splitPath(raFile, incFile, NULL, NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]' + trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]' + trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]' + In file included from trackDbCustom.c:8: + ../../inc/common.h:1104:6: note: in a call to function 'splitPath' + 1104 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 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-I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o cddDesc.o -c cddDesc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o arCOGs.o -c arCOGs.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o arcogdesc.o -c arcogdesc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o geneTree.o -c geneTree.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o megablastInfo.o -c megablastInfo.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgPhenoAssoc.o -c pgPhenoAssoc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgSiftPred.o -c pgSiftPred.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgPolyphenPred.o -c pgPolyphenPred.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o userRegions.o -c userRegions.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o variome.o -c variome.c + ar rcus ../../lib/x86_64/jkhgap.a acemblyClass.o adjacency.o affyAllExonProbe.o affyAtlas.o affy10KDetails.o affy120KDetails.o affyOffset.o affyPairs.o agp.o agpFrag.o agpGap.o alignSeqSizes.o altGraph.o altGraphX.o ancientRref.o annoFormatVep.o annoGratorGpVar.o annoGrateWigDb.o annoStreamDb.o annoStreamDbFactorSource.o annoStreamDbPslPlus.o annoStreamWig.o api.o atomDb.o autoUpgrade.o axtInfo.o axtLib.o bactigPos.o hgBam.o barChartBed.o barChartCategory.o barChartUi.o barChartData.o barChartSample.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bigBedFind.o bigBedLabel.o bigGenePred.o bigPsl.o bigTransMap.o bioImage.o blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o cart.o cartDb.o cartJson.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o ccdsInfo.o ccdsNotes.o ccdsGeneMap.o celeraCoverage.o celeraDupPositive.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgh.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chicken13kInfo.o chromBins.o chromAlias.o chr18deletions.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o codeBlast.o codeBlastScore.o cogs.o cogsxra.o columnInfo.o contigAcc.o coordConv.o cnpIafrate.o cnpIafrate2.o cnpLocke.o cnpRedon.o cnpSebat.o cnpSebat2.o cnpSharp2.o cnpSharpCutoff.o cnpSharpSample.o cnpSharp.o cpgIsland.o cpgIslandExt.o ctgPos.o ctgPos2.o customComposite.o bedDetail.o cgiApoptosis.o customAdjacency.o customFactory.o customPp.o customTrack.o cutter.o cv.o cytoBand.o dbDb.o dbRIP.o dbSnpRs.o defaultDb.o delConrad2.o delHinds2.o dgv.o dgvPlus.o dless.o dnaMotifSql.o dnaMarkovSql.o dnaProbe.o dv.o dvBed.o dvXref2.o easyGene.o ec.o ecCode.o ecAttribute.o ecAttributeCode.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfo.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/pairedTagAlign.o encode/peptideMapping.o encode/tagAlign.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode/wgEncodeGencodePolyAFeature.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeCell.o encode/encodeExp.o encode3/encode2Manifest.o encode3/encode3Valid.o ensFace.o ensInfo.o ensPhusionBlast.o ensXRefZfish.o est3.o estOrientInfo.o estPair.o exoFish.o expData.o expRecord.o exprBed.o facetField.o factorSource.o fbTables.o featureBits.o fileUi.o findKGAlias.o findKGProtAlias.o fishClones.o flyBase2004Xref.o flyBaseSwissProt.o flyreg.o flyreg2.o gbExtFile.o gbWarn.o gbMiscDiff.o gbProtAnn.o gcPercent.o gbSeq.o genbank.o genbankBlackList.o gencodeGeneClass.o gencodeIntron.o genMapDb.o geneBands.o geneCheck.o geneCheckDetails.o geneCheckWidget.o geneGraph.o genePred.o genePredReader.o geneSimilarities.o genoLay.o genomeRangeTreeFile.o genomicDups.o genomicSuperDups.o geoMirror.o ggCluster.o ggDbIo.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o goa.o goaPart.o googleAnalytics.o gpFx.o growthCondition.o grp.o gtexAse.o gtexBoxplot.o gtexEqtlCluster.o gtexInfo.o gtexDonor.o gtexGeneBed.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueData.o gtexTissueMedian.o gtexUi.o gwasCatalog.o hAnno.o haplotypes.o hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o hapmapSnps.o hapmapSnpsCombined.o hashJoin.o hCommon.o hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgGene.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o HInv.o hubConnect.o hubSearchText.o hui.o humanParalog.o imageClone.o indelShift.o interact.o interactUi.o isochores.o ispyTables.o itemAttr.o itemConf.o itemDetailsHtml.o jalview.o jaxOrtholog.o jaxQTL.o jaxQTL3.o jksql.o joiner.o jsHelper.o kg1ToKg2.o jgiGene.o joinMixer.o kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o lav.o ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o llaInfo.o longRange.o lrg.o lsSnpPdb.o lsSnpPdbChimera.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mammalPsg.o mapSts.o mathWig.o mcnBreakpoints.o mdb.o metaChromGraph.o microarray.o minChromSize.o minGeneInfo.o mrnaMisMatch.o mouseOrtho.o mouseSyn.o mouseSynWhd.o mysqlTableStatus.o ncbiRefLink.o ncbiRefSeqLink.o netAlign.o netCart.o nonCodingUi.o omimTitle.o ooUtils.o orthoAlleles.o pal.o pbStamp.o pcrResult.o pepPred.o peptideAtlasPeptide.o plasEndPairs.o polyGenotype.o protFeat.o pscreen.o pseudoGeneLink.o pslReader.o pslWScore.o putaInfo.o qaSeq.o rangeTreeFile.o rankProp.o recombRate.o recombRateRat.o recombRateMouse.o refLink.o refSeqStatus.o rgdQtl.o riken.o rhMapZfishInfo.o rikenBest.o rikenCluster.o rmskOut.o rmskAlign.o rmskJoined.o rmskOut2.o rnaFold.o rnaGene.o rnaGroup.o rnaHybridization.o rnaPLFold.o tRNAs.o gbRNAs.o snoRNAs.o lowelabPfamHit.o lowelabArkinOperonScore.o lowelabTIGROperonScore.o rnaSecStr.o tfbsConsFactors.o roughAli.o transMapStuff.o transMapInfo.o transMapGene.o transMapSrc.o sage.o sageCounts.o sageExp.o samAlignment.o sample.o sanger22extra.o sangerGene.o sangerGeneToWBGeneID.o sargassoSeaXra.o scopDes.o scoredRef.o search.o seqWindow.o sessionThumbnail.o sgdAbundance.o sgdClone.o sgdDescription.o sgdOther.o simpleNucDiff.o simpleRepeat.o snakeUi.o snp.o snp125.o snp125CodingCoordless.o snp132Ext.o snpExceptions.o snpFasta.o snpMap.o snpTmp.o snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o soTerm.o spDb.o splignAlign.o sqlSanity.o stanMad.o stsAlias.o stsInfo.o stsInfo2.o stsInfoMouse.o stsInfoMouseNew.o stsInfoRat.o stsMap.o stsMapMouse.o stsMapMouseNew.o stsMapRat.o stsMarker.o suggest.o switchDbTss.o synMap.o synteny100000.o syntenyBerk.o syntenySanger.o sqlProg.o tfbsCons.o tfbsConsSites.o tablesTables.o tableDescriptions.o tableStatus.o targetDb.o tfbsConsMap.o tagRepo.o taxonDivision.o taxonGeneticCode.o taxonName.o taxonNode.o taxonXref.o tigrCmrGene.o tigrOperon.o tilingPath.o traceInfo.o trackDb.o trackDbCustom.o trackHub.o trackLayout.o trackTable.o trackVersion.o trashDir.o transRegCode.o transRegCodeCondition.o transRegCodeProbe.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txEdgeOrtho.o txGraph.o txInfo.o txRnaAccs.o ucscRetroInfo.o ucscRetroOrtho.o validateGisaid.o variant.o variantProjector.o vcfUi.o vegaInfo.o vegaInfoZfish.o visiGene.o vntr.o wabAli.o web.o ncRna.o wgRna.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o yaleGencodeAssoc.o zdobnovSynt.o oreganno.o oregannoUi.o gvUi.o gv.o omicia.o protVar.o pgSnp.o alignInfo.o cddInfo.o loweutils.o cddDesc.o arCOGs.o arcogdesc.o geneTree.o megablastInfo.o pgPhenoAssoc.o pgSiftPred.o pgPolyphenPred.o userRegions.o variome.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -o endsInLf.o -c endsInLf.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/endsInLf endsInLf.o ../../lib/x86_64/jkweb.a -L$PREFIX/lib -lmysqlclient -lstdc -lrt -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -lpthread -lssl -lcrypto ../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz -lm + /opt/conda/conda-bld/ucsc-endsinlf_1724783725175/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../lib/x86_64/jkweb.a(htmshell.o):/usr/local/src/conda/ucsc-endsinlf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-endsinlf-377/kent/src/lib/../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-endsinlf_1724783725175/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../lib/x86_64/jkweb.a(portimpl.o):/usr/local/src/conda/ucsc-endsinlf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-endsinlf-377/kent/src/lib/../inc/htmshell.h:163: first defined here + collect2: error: ld returned 1 exit status + make: *** [../../inc/userApp.mk:31: /opt/conda/conda-bld/ucsc-endsinlf_1724783725175/work/bin/endsInLf] Error 1 + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-endsinlf_1724783725175/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-estorient/build.sh b/recipes/ucsc-estorient/build.sh index 5566c5e5ad866..d7641fd6d458b 100644 --- a/recipes/ucsc-estorient/build.sh +++ b/recipes/ucsc-estorient/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/estOrient && make) -cp bin/estOrient "$PREFIX/bin" -chmod +x "$PREFIX/bin/estOrient" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/estOrient && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/estOrient "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/estOrient" diff --git a/recipes/ucsc-estorient/include.patch b/recipes/ucsc-estorient/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-estorient/include.patch +++ b/recipes/ucsc-estorient/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-estorient/meta.yaml b/recipes/ucsc-estorient/meta.yaml index 9d1af8682029d..5c3d11569e838 100644 --- a/recipes/ucsc-estorient/meta.yaml +++ b/recipes/ucsc-estorient/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-estorient" %} {% set program = "estOrient" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,27 +27,35 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Read ESTs from a database and determine orientation based on estOrientInfo table or direction in gbCdnaInfo table. Update PSLs so that the strand reflects the direction of transcription. By default, PSLs where the direction can't be determined are dropped. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-expmatrixtobarchartbed/build.sh b/recipes/ucsc-expmatrixtobarchartbed/build.sh index 1a0f89d979c8a..4d969ac373b84 100644 --- a/recipes/ucsc-expmatrixtobarchartbed/build.sh +++ b/recipes/ucsc-expmatrixtobarchartbed/build.sh @@ -1,4 +1,7 @@ #!/bin/bash + +set -xe + mkdir -p "$PREFIX/bin" -cp kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/expMatrixToBarchartBed" +cp kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/expMatrixToBarchartBed" diff --git a/recipes/ucsc-expmatrixtobarchartbed/include.patch b/recipes/ucsc-expmatrixtobarchartbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-expmatrixtobarchartbed/include.patch +++ b/recipes/ucsc-expmatrixtobarchartbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-expmatrixtobarchartbed/meta.yaml b/recipes/ucsc-expmatrixtobarchartbed/meta.yaml index d553009fe4404..ad965a7733d42 100644 --- a/recipes/ucsc-expmatrixtobarchartbed/meta.yaml +++ b/recipes/ucsc-expmatrixtobarchartbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-expmatrixtobarchartbed" %} {% set program = "expMatrixToBarchartBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,16 +15,25 @@ source: build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: + - {{ compiler('c') }} host: + - libpng + - libuuid + - mysql-connector-c + - libopenssl-static + - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - python - zlib @@ -40,3 +49,12 @@ about: Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-faalign/build.sh b/recipes/ucsc-faalign/build.sh index a2075d4dccc91..ab0abc9c5a13a 100644 --- a/recipes/ucsc-faalign/build.sh +++ b/recipes/ucsc-faalign/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faAlign && make) -cp bin/faAlign "$PREFIX/bin" -chmod +x "$PREFIX/bin/faAlign" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faAlign && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faAlign "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faAlign" diff --git a/recipes/ucsc-faalign/include.patch b/recipes/ucsc-faalign/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-faalign/include.patch +++ b/recipes/ucsc-faalign/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-faalign/meta.yaml b/recipes/ucsc-faalign/meta.yaml index bce04cc6ed964..e5bb10fb1e460 100644 --- a/recipes/ucsc-faalign/meta.yaml +++ b/recipes/ucsc-faalign/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-faalign" %} {% set program = "faAlign" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Align two fasta files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-facmp/build.sh b/recipes/ucsc-facmp/build.sh index 63045c9a3e2b8..a5d4d479e44b0 100644 --- a/recipes/ucsc-facmp/build.sh +++ b/recipes/ucsc-facmp/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faCmp && make) -cp bin/faCmp "$PREFIX/bin" -chmod +x "$PREFIX/bin/faCmp" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faCmp && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faCmp "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faCmp" diff --git a/recipes/ucsc-facmp/include.patch b/recipes/ucsc-facmp/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-facmp/include.patch +++ b/recipes/ucsc-facmp/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-facmp/meta.yaml b/recipes/ucsc-facmp/meta.yaml index c418a4cb1aea9..7a45c7f7ff32d 100644 --- a/recipes/ucsc-facmp/meta.yaml +++ b/recipes/ucsc-facmp/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-facmp" %} {% set program = "faCmp" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Compare two .fa files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-facount/build.sh b/recipes/ucsc-facount/build.sh index 728b733768684..3c2c36f703f08 100644 --- a/recipes/ucsc-facount/build.sh +++ b/recipes/ucsc-facount/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faCount && make) -cp bin/faCount "$PREFIX/bin" -chmod +x "$PREFIX/bin/faCount" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faCount && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faCount "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faCount" diff --git a/recipes/ucsc-facount/include.patch b/recipes/ucsc-facount/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-facount/include.patch +++ b/recipes/ucsc-facount/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-facount/meta.yaml b/recipes/ucsc-facount/meta.yaml index cdadf370f0701..e09912d257d02 100644 --- a/recipes/ucsc-facount/meta.yaml +++ b/recipes/ucsc-facount/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-facount" %} {% set program = "faCount" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "count base statistics and CpGs in FA files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fafilter/build.sh b/recipes/ucsc-fafilter/build.sh index 35517aac7e251..967758179cadb 100644 --- a/recipes/ucsc-fafilter/build.sh +++ b/recipes/ucsc-fafilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faFilter && make) -cp bin/faFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/faFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faFilter" diff --git a/recipes/ucsc-fafilter/include.patch b/recipes/ucsc-fafilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fafilter/include.patch +++ b/recipes/ucsc-fafilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fafilter/meta.yaml b/recipes/ucsc-fafilter/meta.yaml index de8020cd7496a..ee67056366443 100644 --- a/recipes/ucsc-fafilter/meta.yaml +++ b/recipes/ucsc-fafilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fafilter" %} {% set program = "faFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter fa records, selecting ones that match the specified conditions" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fafiltern/build.sh b/recipes/ucsc-fafiltern/build.sh index 772564ca3074e..e7a910bc26cad 100644 --- a/recipes/ucsc-fafiltern/build.sh +++ b/recipes/ucsc-fafiltern/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faFilterN && make) -cp bin/faFilterN "$PREFIX/bin" -chmod +x "$PREFIX/bin/faFilterN" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faFilterN && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faFilterN "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faFilterN" diff --git a/recipes/ucsc-fafiltern/include.patch b/recipes/ucsc-fafiltern/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fafiltern/include.patch +++ b/recipes/ucsc-fafiltern/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fafiltern/meta.yaml b/recipes/ucsc-fafiltern/meta.yaml index d6d0f1112e23a..64f3693d3df25 100644 --- a/recipes/ucsc-fafiltern/meta.yaml +++ b/recipes/ucsc-fafiltern/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fafiltern" %} {% set program = "faFilterN" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Get rid of sequences with too many N's" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fafrag/build.sh b/recipes/ucsc-fafrag/build.sh index cc8217d202654..bbde61befd833 100644 --- a/recipes/ucsc-fafrag/build.sh +++ b/recipes/ucsc-fafrag/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faFrag && make) -cp bin/faFrag "$PREFIX/bin" -chmod +x "$PREFIX/bin/faFrag" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faFrag && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faFrag "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faFrag" diff --git a/recipes/ucsc-fafrag/include.patch b/recipes/ucsc-fafrag/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fafrag/include.patch +++ b/recipes/ucsc-fafrag/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fafrag/meta.yaml b/recipes/ucsc-fafrag/meta.yaml index 74dbeee693c2e..63fbd2a2bc5cf 100644 --- a/recipes/ucsc-fafrag/meta.yaml +++ b/recipes/ucsc-fafrag/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fafrag" %} {% set program = "faFrag" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract a piece of DNA from a .fa file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fanoise/build.sh b/recipes/ucsc-fanoise/build.sh index 2c1848ec9a9dc..4b96dc8e7a9ad 100644 --- a/recipes/ucsc-fanoise/build.sh +++ b/recipes/ucsc-fanoise/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faNoise && make) -cp bin/faNoise "$PREFIX/bin" -chmod +x "$PREFIX/bin/faNoise" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faNoise && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faNoise "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faNoise" diff --git a/recipes/ucsc-fanoise/include.patch b/recipes/ucsc-fanoise/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fanoise/include.patch +++ b/recipes/ucsc-fanoise/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fanoise/meta.yaml b/recipes/ucsc-fanoise/meta.yaml index a89d4b85524be..6ba0418b05532 100644 --- a/recipes/ucsc-fanoise/meta.yaml +++ b/recipes/ucsc-fanoise/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fanoise" %} {% set program = "faNoise" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add noise to .fa file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-faonerecord/build.sh b/recipes/ucsc-faonerecord/build.sh index d2a4c53e9f283..af644537f494a 100644 --- a/recipes/ucsc-faonerecord/build.sh +++ b/recipes/ucsc-faonerecord/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faOneRecord && make) -cp bin/faOneRecord "$PREFIX/bin" -chmod +x "$PREFIX/bin/faOneRecord" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faOneRecord && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faOneRecord "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faOneRecord" diff --git a/recipes/ucsc-faonerecord/include.patch b/recipes/ucsc-faonerecord/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-faonerecord/include.patch +++ b/recipes/ucsc-faonerecord/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-faonerecord/meta.yaml b/recipes/ucsc-faonerecord/meta.yaml index 761f7d83bdc1a..d52e42e40b317 100644 --- a/recipes/ucsc-faonerecord/meta.yaml +++ b/recipes/ucsc-faonerecord/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-faonerecord" %} {% set program = "faOneRecord" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract a single record from a .FA file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fapolyasizes/build.sh b/recipes/ucsc-fapolyasizes/build.sh index 2a7659a5c4a58..383f0fdc8416b 100644 --- a/recipes/ucsc-fapolyasizes/build.sh +++ b/recipes/ucsc-fapolyasizes/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faPolyASizes && make) -cp bin/faPolyASizes "$PREFIX/bin" -chmod +x "$PREFIX/bin/faPolyASizes" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faPolyASizes && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faPolyASizes "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faPolyASizes" diff --git a/recipes/ucsc-fapolyasizes/include.patch b/recipes/ucsc-fapolyasizes/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fapolyasizes/include.patch +++ b/recipes/ucsc-fapolyasizes/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fapolyasizes/meta.yaml b/recipes/ucsc-fapolyasizes/meta.yaml index 55df8ed83732c..6dac4793b6b2e 100644 --- a/recipes/ucsc-fapolyasizes/meta.yaml +++ b/recipes/ucsc-fapolyasizes/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fapolyasizes" %} {% set program = "faPolyASizes" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "get poly A sizes" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-farandomize/build.sh b/recipes/ucsc-farandomize/build.sh index 10bcbaa61dec2..992f3baa9537f 100644 --- a/recipes/ucsc-farandomize/build.sh +++ b/recipes/ucsc-farandomize/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faRandomize && make) -cp bin/faRandomize "$PREFIX/bin" -chmod +x "$PREFIX/bin/faRandomize" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faRandomize && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faRandomize "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faRandomize" diff --git a/recipes/ucsc-farandomize/include.patch b/recipes/ucsc-farandomize/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-farandomize/include.patch +++ b/recipes/ucsc-farandomize/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-farandomize/meta.yaml b/recipes/ucsc-farandomize/meta.yaml index 400b9d8b2578e..7a357380b6102 100644 --- a/recipes/ucsc-farandomize/meta.yaml +++ b/recipes/ucsc-farandomize/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-farandomize" %} {% set program = "faRandomize" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Program to create random fasta records" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-farc/build.sh b/recipes/ucsc-farc/build.sh index d68de0a45c997..5efc3188c34d8 100644 --- a/recipes/ucsc-farc/build.sh +++ b/recipes/ucsc-farc/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faRc && make) -cp bin/faRc "$PREFIX/bin" -chmod +x "$PREFIX/bin/faRc" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faRc && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faRc "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faRc" diff --git a/recipes/ucsc-farc/include.patch b/recipes/ucsc-farc/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-farc/include.patch +++ b/recipes/ucsc-farc/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-farc/meta.yaml b/recipes/ucsc-farc/meta.yaml index 544410aef81d7..59ad4f779fb2c 100644 --- a/recipes/ucsc-farc/meta.yaml +++ b/recipes/ucsc-farc/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-farc" %} {% set program = "faRc" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Reverse complement a FA file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fasize/build.sh b/recipes/ucsc-fasize/build.sh index 08610aaa04451..42e777e285924 100644 --- a/recipes/ucsc-fasize/build.sh +++ b/recipes/ucsc-fasize/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faSize && make) -cp bin/faSize "$PREFIX/bin" -chmod +x "$PREFIX/bin/faSize" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faSize && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faSize "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faSize" diff --git a/recipes/ucsc-fasize/include.patch b/recipes/ucsc-fasize/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fasize/include.patch +++ b/recipes/ucsc-fasize/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fasize/meta.yaml b/recipes/ucsc-fasize/meta.yaml index 295546709d3a1..e5ca815518a66 100644 --- a/recipes/ucsc-fasize/meta.yaml +++ b/recipes/ucsc-fasize/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fasize" %} {% set program = "faSize" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "print total base count in fa files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fasomerecords/build.sh b/recipes/ucsc-fasomerecords/build.sh index b61bf19685404..94dda243aec45 100644 --- a/recipes/ucsc-fasomerecords/build.sh +++ b/recipes/ucsc-fasomerecords/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faSomeRecords && make) -cp bin/faSomeRecords "$PREFIX/bin" -chmod +x "$PREFIX/bin/faSomeRecords" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faSomeRecords && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faSomeRecords "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faSomeRecords" diff --git a/recipes/ucsc-fasomerecords/include.patch b/recipes/ucsc-fasomerecords/include.patch index e4831ef2dea13..edc04d0dc2f64 100644 --- a/recipes/ucsc-fasomerecords/include.patch +++ b/recipes/ucsc-fasomerecords/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-fasomerecords/meta.yaml b/recipes/ucsc-fasomerecords/meta.yaml index 507bf2b0b7cd6..86fe4dda5cbc4 100644 --- a/recipes/ucsc-fasomerecords/meta.yaml +++ b/recipes/ucsc-fasomerecords/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fasomerecords" %} {% set program = "faSomeRecords" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,27 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract multiple fa records" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fasplit/build.sh b/recipes/ucsc-fasplit/build.sh index bf837fd78a605..ed7f37ba92c85 100644 --- a/recipes/ucsc-fasplit/build.sh +++ b/recipes/ucsc-fasplit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faSplit && make) -cp bin/faSplit "$PREFIX/bin" -chmod +x "$PREFIX/bin/faSplit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faSplit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faSplit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faSplit" diff --git a/recipes/ucsc-fasplit/include.patch b/recipes/ucsc-fasplit/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fasplit/include.patch +++ b/recipes/ucsc-fasplit/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fasplit/meta.yaml b/recipes/ucsc-fasplit/meta.yaml index 1758efe8fe7d9..9b811fc0a565c 100644 --- a/recipes/ucsc-fasplit/meta.yaml +++ b/recipes/ucsc-fasplit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fasplit" %} {% set program = "faSplit" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split an fa file into several files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fastqstatsandsubsample/build.sh b/recipes/ucsc-fastqstatsandsubsample/build.sh index a06ee6dcb3901..56efb5ed3f796 100644 --- a/recipes/ucsc-fastqstatsandsubsample/build.sh +++ b/recipes/ucsc-fastqstatsandsubsample/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/fastqStatsAndSubsample && make) -cp bin/fastqStatsAndSubsample "$PREFIX/bin" -chmod +x "$PREFIX/bin/fastqStatsAndSubsample" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/fastqStatsAndSubsample && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/fastqStatsAndSubsample "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/fastqStatsAndSubsample" diff --git a/recipes/ucsc-fastqstatsandsubsample/include.patch b/recipes/ucsc-fastqstatsandsubsample/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fastqstatsandsubsample/include.patch +++ b/recipes/ucsc-fastqstatsandsubsample/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fastqstatsandsubsample/meta.yaml b/recipes/ucsc-fastqstatsandsubsample/meta.yaml index fa874a86c6770..ccdb6bfc69d23 100644 --- a/recipes/ucsc-fastqstatsandsubsample/meta.yaml +++ b/recipes/ucsc-fastqstatsandsubsample/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fastqstatsandsubsample" %} {% set program = "fastqStatsAndSubsample" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Go through a fastq file doing sanity checks and collecting stats" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fastqtofa/build.sh b/recipes/ucsc-fastqtofa/build.sh index a0eb7afc81495..0d73cb307256b 100644 --- a/recipes/ucsc-fastqtofa/build.sh +++ b/recipes/ucsc-fastqtofa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/fastqToFa && make) -cp bin/fastqToFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/fastqToFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/fastqToFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/fastqToFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/fastqToFa" diff --git a/recipes/ucsc-fastqtofa/include.patch b/recipes/ucsc-fastqtofa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fastqtofa/include.patch +++ b/recipes/ucsc-fastqtofa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fastqtofa/meta.yaml b/recipes/ucsc-fastqtofa/meta.yaml index d2bcf5a600ff4..5bc623ded2330 100644 --- a/recipes/ucsc-fastqtofa/meta.yaml +++ b/recipes/ucsc-fastqtofa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fastqtofa" %} {% set program = "fastqToFa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from fastq to fasta format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fatofastq/build.sh b/recipes/ucsc-fatofastq/build.sh index 69dd94f808370..821b6b535ce86 100644 --- a/recipes/ucsc-fatofastq/build.sh +++ b/recipes/ucsc-fatofastq/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faToFastq && make) -cp bin/faToFastq "$PREFIX/bin" -chmod +x "$PREFIX/bin/faToFastq" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faToFastq && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faToFastq "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faToFastq" diff --git a/recipes/ucsc-fatofastq/include.patch b/recipes/ucsc-fatofastq/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fatofastq/include.patch +++ b/recipes/ucsc-fatofastq/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fatofastq/meta.yaml b/recipes/ucsc-fatofastq/meta.yaml index 31b3b7709b9d3..e2ecba2ff9675 100644 --- a/recipes/ucsc-fatofastq/meta.yaml +++ b/recipes/ucsc-fatofastq/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatofastq" %} {% set program = "faToFastq" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert fa to fastq format, just faking quality values." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fatotab/build.sh b/recipes/ucsc-fatotab/build.sh index 6bdeebad8ed7b..1939aa14b9372 100644 --- a/recipes/ucsc-fatotab/build.sh +++ b/recipes/ucsc-fatotab/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faToTab && make) -cp bin/faToTab "$PREFIX/bin" -chmod +x "$PREFIX/bin/faToTab" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faToTab && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faToTab "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faToTab" diff --git a/recipes/ucsc-fatotab/include.patch b/recipes/ucsc-fatotab/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fatotab/include.patch +++ b/recipes/ucsc-fatotab/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fatotab/meta.yaml b/recipes/ucsc-fatotab/meta.yaml index a5106bdd93cd2..c7901931785a1 100644 --- a/recipes/ucsc-fatotab/meta.yaml +++ b/recipes/ucsc-fatotab/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatotab" %} {% set program = "faToTab" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert fa file to tab separated file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fatotwobit/build.sh b/recipes/ucsc-fatotwobit/build.sh index cd1c569ec1e88..47d1b7225bb5c 100644 --- a/recipes/ucsc-fatotwobit/build.sh +++ b/recipes/ucsc-fatotwobit/build.sh @@ -1,13 +1,28 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faToTwoBit && make) -cp bin/faToTwoBit "$PREFIX/bin" -chmod +x "$PREFIX/bin/faToTwoBit" + +mkdir -p "${BINDIR}" + +if [[ "$(uname)" == Darwin ]]; then + export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" + export CFLAGS="${CFLAGS} -Wno-unused-command-line-argument" +fi + +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faToTwoBit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faToTwoBit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faToTwoBit" diff --git a/recipes/ucsc-fatotwobit/htmshell.patch b/recipes/ucsc-fatotwobit/htmshell.patch deleted file mode 100644 index 1e6f87375ed01..0000000000000 --- a/recipes/ucsc-fatotwobit/htmshell.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 -+++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 -@@ -713,7 +713,7 @@ - puts("Status: 400\r"); - puts("Content-Type: text/plain; charset=UTF-8\r"); - puts("\r"); --if (format != NULL && args != NULL) -+if (format != NULL) - { - vfprintf(stdout, format, args); - fprintf(stdout, "\n"); diff --git a/recipes/ucsc-fatotwobit/include.macos.patch b/recipes/ucsc-fatotwobit/include.macos.patch new file mode 100644 index 0000000000000..979f87005a72e --- /dev/null +++ b/recipes/ucsc-fatotwobit/include.macos.patch @@ -0,0 +1,27 @@ +--- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} +-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include + + # to check for Mac OSX Darwin specifics: + UNAME_S := $(shell uname -s) +--- a/kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ b/kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +@@ -1,4 +1,4 @@ +-KENT_INC=-I../../../inc ++KENT_INC=-I../../../inc -I${PREFIX}/include + + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o +--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + # expMatrixToBarchartBed + """ + Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. diff --git a/recipes/ucsc-fatotwobit/include.patch b/recipes/ucsc-fatotwobit/include.patch index e9c8621194325..35fd16a3d9090 100644 --- a/recipes/ucsc-fatotwobit/include.patch +++ b/recipes/ucsc-fatotwobit/include.patch @@ -1,32 +1,32 @@ ---- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +--- a/kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ b/kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 @@ -147,4 +147,4 @@ - L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl + L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl else ifneq ($(wildcard /opt/local/lib/libssl.a),) L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- a/kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ b/kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 @@ -1,4 +1,4 @@ -KENT_INC=-I../../../inc +KENT_INC=-I../../../inc -I${PREFIX}/include straw: straw.o cStraw.o ld -r -o ../straw.o straw.o cStraw.o ---- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fatotwobit/meta.yaml b/recipes/ucsc-fatotwobit/meta.yaml index 4a21a851c4e54..0a74ff24cf3fc 100644 --- a/recipes/ucsc-fatotwobit/meta.yaml +++ b/recipes/ucsc-fatotwobit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatotwobit" %} {% set program = "faToTwoBit" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -11,47 +11,49 @@ source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" sha256: "{{ sha256 }}" patches: - - "include.patch" - - htmshell.patch + - include.patch # [linux] + - include.macos.patch # [osx] build: - skip: True # [osx] number: 2 - ignore_run_exports: - - libpng - - libuuid run_exports: - - {{ pin_subpackage("ucsc-fatotwobit", max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - {{ compiler('cxx') }} - - binutils # [linux] + - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - - zlib >=1.3.1,<2.0a0 + - clangdev # [osx] + - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert DNA from fasta to 2bit format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-fatrans/build.sh b/recipes/ucsc-fatrans/build.sh index a781ab3d9c5fb..2e4768dfe353f 100644 --- a/recipes/ucsc-fatrans/build.sh +++ b/recipes/ucsc-fatrans/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faTrans && make) -cp bin/faTrans "$PREFIX/bin" -chmod +x "$PREFIX/bin/faTrans" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faTrans && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faTrans "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faTrans" diff --git a/recipes/ucsc-fatrans/include.patch b/recipes/ucsc-fatrans/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fatrans/include.patch +++ b/recipes/ucsc-fatrans/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fatrans/meta.yaml b/recipes/ucsc-fatrans/meta.yaml index 39e117aec53d2..51811a6159fa7 100644 --- a/recipes/ucsc-fatrans/meta.yaml +++ b/recipes/ucsc-fatrans/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatrans" %} {% set program = "faTrans" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Translate DNA .fa file to peptide" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-featurebits/build.sh b/recipes/ucsc-featurebits/build.sh index 0aab0a6b5bf92..917a51e28eb88 100644 --- a/recipes/ucsc-featurebits/build.sh +++ b/recipes/ucsc-featurebits/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/featureBits && make) -cp bin/featureBits "$PREFIX/bin" -chmod +x "$PREFIX/bin/featureBits" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/featureBits && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/featureBits "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/featureBits" diff --git a/recipes/ucsc-featurebits/include.patch b/recipes/ucsc-featurebits/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-featurebits/include.patch +++ b/recipes/ucsc-featurebits/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-featurebits/meta.yaml b/recipes/ucsc-featurebits/meta.yaml index 24e41aeb3841b..8dd37713562a8 100644 --- a/recipes/ucsc-featurebits/meta.yaml +++ b/recipes/ucsc-featurebits/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-featurebits" %} {% set program = "featureBits" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Correlate tables via bitmap projections. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-fetchchromsizes/build.sh b/recipes/ucsc-fetchchromsizes/build.sh index 60cb967c7e192..f37dd6327039f 100644 --- a/recipes/ucsc-fetchchromsizes/build.sh +++ b/recipes/ucsc-fetchchromsizes/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -mkdir -p $PREFIX/bin +set -xe -cp -f kent/src/utils/userApps/fetchChromSizes $PREFIX/bin -chmod 0755 $PREFIX/bin/fetchChromSizes +cp kent/src/utils/userApps/fetchChromSizes ${PREFIX}/bin +chmod 0755 ${PREFIX}/bin/fetchChromSizes diff --git a/recipes/ucsc-fetchchromsizes/include.patch b/recipes/ucsc-fetchchromsizes/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-fetchchromsizes/include.patch +++ b/recipes/ucsc-fetchchromsizes/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fetchchromsizes/meta.yaml b/recipes/ucsc-fetchchromsizes/meta.yaml index e93d20580f61f..cfe061d194d38 100644 --- a/recipes/ucsc-fetchchromsizes/meta.yaml +++ b/recipes/ucsc-fetchchromsizes/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fetchchromsizes" %} {% set program = "fetchChromSizes" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,26 +14,28 @@ source: - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage('ucsc-fetchchromsizes', max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -42,7 +44,7 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" + license: "Varies; see http://genome.ucsc.edu/license" summary: " used to fetch chrom.sizes information from UCSC for the given " @@ -50,5 +52,8 @@ used to fetch chrom.sizes information from UCSC for the given doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-findmotif/build.sh b/recipes/ucsc-findmotif/build.sh index c83f19994c25b..e0a729b566822 100644 --- a/recipes/ucsc-findmotif/build.sh +++ b/recipes/ucsc-findmotif/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/findMotif && make) -cp bin/findMotif "$PREFIX/bin" -chmod +x "$PREFIX/bin/findMotif" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/findMotif && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/findMotif "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/findMotif" diff --git a/recipes/ucsc-findmotif/include.patch b/recipes/ucsc-findmotif/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-findmotif/include.patch +++ b/recipes/ucsc-findmotif/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-findmotif/meta.yaml b/recipes/ucsc-findmotif/meta.yaml index 3ad718a71fc72..7a216c91b07df 100644 --- a/recipes/ucsc-findmotif/meta.yaml +++ b/recipes/ucsc-findmotif/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-findmotif" %} {% set program = "findMotif" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "find specified motif in sequence" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-gaptolift/build.sh b/recipes/ucsc-gaptolift/build.sh index ed5e7af6dd119..3e35b9508f85a 100644 --- a/recipes/ucsc-gaptolift/build.sh +++ b/recipes/ucsc-gaptolift/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/gapToLift && make) -cp bin/gapToLift "$PREFIX/bin" -chmod +x "$PREFIX/bin/gapToLift" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/gapToLift && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gapToLift "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gapToLift" diff --git a/recipes/ucsc-gaptolift/include.patch b/recipes/ucsc-gaptolift/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-gaptolift/include.patch +++ b/recipes/ucsc-gaptolift/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-gaptolift/meta.yaml b/recipes/ucsc-gaptolift/meta.yaml index b30683d4565e8..d966465836968 100644 --- a/recipes/ucsc-gaptolift/meta.yaml +++ b/recipes/ucsc-gaptolift/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-gaptolift" %} {% set program = "gapToLift" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create lift file from gap table(s)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredcheck/build.sh b/recipes/ucsc-genepredcheck/build.sh index b6524788d6ce9..2e78923fd14a7 100644 --- a/recipes/ucsc-genepredcheck/build.sh +++ b/recipes/ucsc-genepredcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/hg/genePredCheck && make -j ${CPU_COUNT}) -cp bin/genePredCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredCheck" diff --git a/recipes/ucsc-genepredcheck/include.patch b/recipes/ucsc-genepredcheck/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredcheck/include.patch +++ b/recipes/ucsc-genepredcheck/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-genepredcheck/meta.yaml b/recipes/ucsc-genepredcheck/meta.yaml index 3431a4e7693ad..db9f5b2a78bcd 100644 --- a/recipes/ucsc-genepredcheck/meta.yaml +++ b/recipes/ucsc-genepredcheck/meta.yaml @@ -1,57 +1,56 @@ {% set package = "ucsc-genepredcheck" %} {% set program = "genePredCheck" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 2 - skip: True # [osx] + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} - ignore_run_exports: - - libpng - - libuuid requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: # just check for existence and exec bit, because the individual packages have no unified behavior - - test -x $PREFIX/bin/{{ program }} + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Validate genePred files or tables" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "validate genePred files or tables" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: - - linux-aarch64 \ No newline at end of file + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredfilter/build.sh b/recipes/ucsc-genepredfilter/build.sh index 740a38a92b847..43aedb3dafe58 100644 --- a/recipes/ucsc-genepredfilter/build.sh +++ b/recipes/ucsc-genepredfilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/genePredFilter && make) -cp bin/genePredFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/genePredFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredFilter" diff --git a/recipes/ucsc-genepredfilter/include.patch b/recipes/ucsc-genepredfilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredfilter/include.patch +++ b/recipes/ucsc-genepredfilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredfilter/meta.yaml b/recipes/ucsc-genepredfilter/meta.yaml index bbdbe7224a9b2..555cc71621d1a 100644 --- a/recipes/ucsc-genepredfilter/meta.yaml +++ b/recipes/ucsc-genepredfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredfilter" %} {% set program = "genePredFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "filter a genePred file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredhisto/build.sh b/recipes/ucsc-genepredhisto/build.sh index eae0a8415e1ce..7cbdc5550a941 100644 --- a/recipes/ucsc-genepredhisto/build.sh +++ b/recipes/ucsc-genepredhisto/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredHisto && make) -cp bin/genePredHisto "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredHisto" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredHisto && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredHisto "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredHisto" diff --git a/recipes/ucsc-genepredhisto/include.patch b/recipes/ucsc-genepredhisto/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredhisto/include.patch +++ b/recipes/ucsc-genepredhisto/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredhisto/meta.yaml b/recipes/ucsc-genepredhisto/meta.yaml index 2c5afb13865f9..26ea81c76bb67 100644 --- a/recipes/ucsc-genepredhisto/meta.yaml +++ b/recipes/ucsc-genepredhisto/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredhisto" %} {% set program = "genePredHisto" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "get data for generating histograms from a genePred file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredsinglecover/build.sh b/recipes/ucsc-genepredsinglecover/build.sh index cc6aa8cdea7b8..69a1610ac29a2 100644 --- a/recipes/ucsc-genepredsinglecover/build.sh +++ b/recipes/ucsc-genepredsinglecover/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredSingleCover && make) -cp bin/genePredSingleCover "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredSingleCover" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredSingleCover && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredSingleCover "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredSingleCover" diff --git a/recipes/ucsc-genepredsinglecover/include.patch b/recipes/ucsc-genepredsinglecover/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredsinglecover/include.patch +++ b/recipes/ucsc-genepredsinglecover/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredsinglecover/meta.yaml b/recipes/ucsc-genepredsinglecover/meta.yaml index c5feab4138c2a..7da1658b06ae8 100644 --- a/recipes/ucsc-genepredsinglecover/meta.yaml +++ b/recipes/ucsc-genepredsinglecover/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredsinglecover" %} {% set program = "genePredSingleCover" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create single-coverage genePred files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredtobed/build.sh b/recipes/ucsc-genepredtobed/build.sh index 73f68a12d7a6a..c2d189f5935c0 100644 --- a/recipes/ucsc-genepredtobed/build.sh +++ b/recipes/ucsc-genepredtobed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredToBed && make) -cp bin/genePredToBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredToBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToBed" diff --git a/recipes/ucsc-genepredtobed/include.patch b/recipes/ucsc-genepredtobed/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtobed/include.patch +++ b/recipes/ucsc-genepredtobed/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-genepredtobed/meta.yaml b/recipes/ucsc-genepredtobed/meta.yaml index ce54339cf9111..3bec9a4e9fa8e 100644 --- a/recipes/ucsc-genepredtobed/meta.yaml +++ b/recipes/ucsc-genepredtobed/meta.yaml @@ -1,25 +1,21 @@ {% set package = "ucsc-genepredtobed" %} {% set program = "genePredToBed" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 - skip: True # [osx] - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -27,31 +23,34 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from genePred to bed format. Does not yet handle genePredExt" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: - - linux-aarch64 \ No newline at end of file + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredtobiggenepred/build.sh b/recipes/ucsc-genepredtobiggenepred/build.sh index baf17c6b537f2..22cb9a1a3f13f 100644 --- a/recipes/ucsc-genepredtobiggenepred/build.sh +++ b/recipes/ucsc-genepredtobiggenepred/build.sh @@ -2,15 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/hg/utils/genePredToBigGenePred && make -j ${CPU_COUNT}) -cp bin/genePredToBigGenePred "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToBigGenePred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/genePredToBigGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToBigGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToBigGenePred" diff --git a/recipes/ucsc-genepredtobiggenepred/include.patch b/recipes/ucsc-genepredtobiggenepred/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtobiggenepred/include.patch +++ b/recipes/ucsc-genepredtobiggenepred/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-genepredtobiggenepred/meta.yaml b/recipes/ucsc-genepredtobiggenepred/meta.yaml index 7c13583979a71..a1246916eef6c 100644 --- a/recipes/ucsc-genepredtobiggenepred/meta.yaml +++ b/recipes/ucsc-genepredtobiggenepred/meta.yaml @@ -1,46 +1,41 @@ {% set package = "ucsc-genepredtobiggenepred" %} {% set program = "genePredToBigGenePred" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 2 - skip: True # [osx] + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} - ignore_run_exports: - - libpng - - libuuid requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: @@ -48,10 +43,14 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Converts genePred or genePredExt to bigGenePred input (bed format with extra fields)" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "converts genePred or genePredExt to bigGenePred input (bed format with extra fields)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: - - linux-aarch64 + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredtofakepsl/build.sh b/recipes/ucsc-genepredtofakepsl/build.sh index 03cf481ed9fae..0cbaf2644b10f 100644 --- a/recipes/ucsc-genepredtofakepsl/build.sh +++ b/recipes/ucsc-genepredtofakepsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredToFakePsl && make) -cp bin/genePredToFakePsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToFakePsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredToFakePsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToFakePsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToFakePsl" diff --git a/recipes/ucsc-genepredtofakepsl/include.patch b/recipes/ucsc-genepredtofakepsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtofakepsl/include.patch +++ b/recipes/ucsc-genepredtofakepsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredtofakepsl/meta.yaml b/recipes/ucsc-genepredtofakepsl/meta.yaml index 6dd0dbfb20747..db76e2c25d187 100644 --- a/recipes/ucsc-genepredtofakepsl/meta.yaml +++ b/recipes/ucsc-genepredtofakepsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredtofakepsl" %} {% set program = "genePredToFakePsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create a psl of fake-mRNA aligned to gene-preds from a file or table." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredtogtf/build.sh b/recipes/ucsc-genepredtogtf/build.sh index 626b3eed43b01..2eacfa5aca0fe 100644 --- a/recipes/ucsc-genepredtogtf/build.sh +++ b/recipes/ucsc-genepredtogtf/build.sh @@ -2,15 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/hg/genePredToGtf && make -j ${CPU_COUNT}) -cp bin/genePredToGtf "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToGtf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredToGtf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToGtf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToGtf" diff --git a/recipes/ucsc-genepredtogtf/include.patch b/recipes/ucsc-genepredtogtf/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtogtf/include.patch +++ b/recipes/ucsc-genepredtogtf/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-genepredtogtf/meta.yaml b/recipes/ucsc-genepredtogtf/meta.yaml index 4283d807812f0..63feeb7475766 100644 --- a/recipes/ucsc-genepredtogtf/meta.yaml +++ b/recipes/ucsc-genepredtogtf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredtogtf" %} {% set program = "genePredToGtf" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,14 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert genePred table or file to gtf." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: - - linux-aarch64 \ No newline at end of file + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredtomafframes/build.sh b/recipes/ucsc-genepredtomafframes/build.sh index 3c6c10a9fad99..d0914e9e23d2e 100644 --- a/recipes/ucsc-genepredtomafframes/build.sh +++ b/recipes/ucsc-genepredtomafframes/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredToMafFrames && make) -cp bin/genePredToMafFrames "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToMafFrames" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredToMafFrames && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToMafFrames "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToMafFrames" diff --git a/recipes/ucsc-genepredtomafframes/include.patch b/recipes/ucsc-genepredtomafframes/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtomafframes/include.patch +++ b/recipes/ucsc-genepredtomafframes/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredtomafframes/meta.yaml b/recipes/ucsc-genepredtomafframes/meta.yaml index de319b6994200..a2198b27e22c8 100644 --- a/recipes/ucsc-genepredtomafframes/meta.yaml +++ b/recipes/ucsc-genepredtomafframes/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredtomafframes" %} {% set program = "genePredToMafFrames" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create mafFrames tables from a genePreds" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-genepredtoprot/build.sh b/recipes/ucsc-genepredtoprot/build.sh index 45cad43fa314d..0e997669e739d 100644 --- a/recipes/ucsc-genepredtoprot/build.sh +++ b/recipes/ucsc-genepredtoprot/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/genePredToProt && make) -cp bin/genePredToProt "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToProt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/genePredToProt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToProt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToProt" diff --git a/recipes/ucsc-genepredtoprot/include.patch b/recipes/ucsc-genepredtoprot/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtoprot/include.patch +++ b/recipes/ucsc-genepredtoprot/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredtoprot/meta.yaml b/recipes/ucsc-genepredtoprot/meta.yaml index b04d00344ff6f..415939a3f7ac5 100644 --- a/recipes/ucsc-genepredtoprot/meta.yaml +++ b/recipes/ucsc-genepredtoprot/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredtoprot" %} {% set program = "genePredToProt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create protein sequences by translating gene annotations" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-gensub2/build.sh b/recipes/ucsc-gensub2/build.sh index c2fb30cfe1ea8..7eea99522dd3e 100644 --- a/recipes/ucsc-gensub2/build.sh +++ b/recipes/ucsc-gensub2/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/gensub2 "$PREFIX/bin" -chmod +x "$PREFIX/bin/gensub2" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/gensub2 "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gensub2" diff --git a/recipes/ucsc-gensub2/include.patch b/recipes/ucsc-gensub2/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-gensub2/include.patch +++ b/recipes/ucsc-gensub2/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-gensub2/meta.yaml b/recipes/ucsc-gensub2/meta.yaml index 9dbd6efb84cd5..5b1d1ebc67a8d 100644 --- a/recipes/ucsc-gensub2/meta.yaml +++ b/recipes/ucsc-gensub2/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-gensub2" %} {% set program = "gensub2" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-getrna/build.sh b/recipes/ucsc-getrna/build.sh index a143abd3f5d49..68c77a40cd7d3 100644 --- a/recipes/ucsc-getrna/build.sh +++ b/recipes/ucsc-getrna/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/getRna && make) -cp bin/getRna "$PREFIX/bin" -chmod +x "$PREFIX/bin/getRna" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/getRna && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/getRna "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/getRna" diff --git a/recipes/ucsc-getrna/include.patch b/recipes/ucsc-getrna/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-getrna/include.patch +++ b/recipes/ucsc-getrna/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-getrna/meta.yaml b/recipes/ucsc-getrna/meta.yaml index 2762bd242def6..a513246dfff19 100644 --- a/recipes/ucsc-getrna/meta.yaml +++ b/recipes/ucsc-getrna/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-getrna" %} {% set program = "getRna" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Get mrna for GenBank or RefSeq sequences found in a database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-getrnapred/build.sh b/recipes/ucsc-getrnapred/build.sh index 8fc3876e2eba3..1285faed92b52 100644 --- a/recipes/ucsc-getrnapred/build.sh +++ b/recipes/ucsc-getrnapred/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/getRnaPred && make) -cp bin/getRnaPred "$PREFIX/bin" -chmod +x "$PREFIX/bin/getRnaPred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/getRnaPred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/getRnaPred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/getRnaPred" diff --git a/recipes/ucsc-getrnapred/include.patch b/recipes/ucsc-getrnapred/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-getrnapred/include.patch +++ b/recipes/ucsc-getrnapred/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-getrnapred/meta.yaml b/recipes/ucsc-getrnapred/meta.yaml index 456e7a2e36ce1..511717e689efd 100644 --- a/recipes/ucsc-getrnapred/meta.yaml +++ b/recipes/ucsc-getrnapred/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-getrnapred" %} {% set program = "getRnaPred" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Get virtual RNA for gene predictions" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-gff3togenepred/build.sh b/recipes/ucsc-gff3togenepred/build.sh index 6ffa740fe32c1..98a30d0537b93 100644 --- a/recipes/ucsc-gff3togenepred/build.sh +++ b/recipes/ucsc-gff3togenepred/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/hg/utils/gff3ToGenePred && make -j ${CPU_COUNT}) -cp bin/gff3ToGenePred "$PREFIX/bin" -chmod +x "$PREFIX/bin/gff3ToGenePred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/gff3ToGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gff3ToGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gff3ToGenePred" diff --git a/recipes/ucsc-gff3togenepred/include.patch b/recipes/ucsc-gff3togenepred/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-gff3togenepred/include.patch +++ b/recipes/ucsc-gff3togenepred/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-gff3togenepred/meta.yaml b/recipes/ucsc-gff3togenepred/meta.yaml index 184186af9a4d2..c16b7d914188d 100644 --- a/recipes/ucsc-gff3togenepred/meta.yaml +++ b/recipes/ucsc-gff3togenepred/meta.yaml @@ -1,57 +1,56 @@ {% set package = "ucsc-gff3togenepred" %} {% set program = "gff3ToGenePred" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 2 - skip: True # [osx] + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} - ignore_run_exports: - - libpng - - libuuid requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: # just check for existence and exec bit, because the individual packages have no unified behavior - - test -x $PREFIX/bin/{{ program }} + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert a GFF3 file to a genePred file" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "convert a GFF3 file to a genePred file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: - - linux-aarch64 \ No newline at end of file + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-gff3topsl/build.sh b/recipes/ucsc-gff3topsl/build.sh index 0af0b67a67fa0..1480a1a5c4c6c 100644 --- a/recipes/ucsc-gff3topsl/build.sh +++ b/recipes/ucsc-gff3topsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/gff3ToPsl && make) -cp bin/gff3ToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/gff3ToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/gff3ToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gff3ToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gff3ToPsl" diff --git a/recipes/ucsc-gff3topsl/include.patch b/recipes/ucsc-gff3topsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-gff3topsl/include.patch +++ b/recipes/ucsc-gff3topsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-gff3topsl/meta.yaml b/recipes/ucsc-gff3topsl/meta.yaml index 4a1ea66855d54..6b6d7a265cea8 100644 --- a/recipes/ucsc-gff3topsl/meta.yaml +++ b/recipes/ucsc-gff3topsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-gff3topsl" %} {% set program = "gff3ToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert a GFF3 CIGAR file to a PSL file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-gmtime/build.sh b/recipes/ucsc-gmtime/build.sh index df84f2bc8be6f..f9fdd83658185 100644 --- a/recipes/ucsc-gmtime/build.sh +++ b/recipes/ucsc-gmtime/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/timing/gmtime && make) -cp bin/gmtime "$PREFIX/bin" -chmod +x "$PREFIX/bin/gmtime" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/timing/gmtime && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gmtime "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gmtime" diff --git a/recipes/ucsc-gmtime/include.patch b/recipes/ucsc-gmtime/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-gmtime/include.patch +++ b/recipes/ucsc-gmtime/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-gmtime/meta.yaml b/recipes/ucsc-gmtime/meta.yaml index 3a363611db7b8..be7f2efb84739 100644 --- a/recipes/ucsc-gmtime/meta.yaml +++ b/recipes/ucsc-gmtime/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-gmtime" %} {% set program = "gmtime" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert unix timestamp to date string" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-gtftogenepred/build.sh b/recipes/ucsc-gtftogenepred/build.sh index 49f68076bbb2e..80a3ce55a4aa6 100644 --- a/recipes/ucsc-gtftogenepred/build.sh +++ b/recipes/ucsc-gtftogenepred/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/gtfToGenePred && make) -cp bin/gtfToGenePred "$PREFIX/bin" -chmod +x "$PREFIX/bin/gtfToGenePred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/gtfToGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gtfToGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gtfToGenePred" diff --git a/recipes/ucsc-gtftogenepred/include.patch b/recipes/ucsc-gtftogenepred/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-gtftogenepred/include.patch +++ b/recipes/ucsc-gtftogenepred/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-gtftogenepred/meta.yaml b/recipes/ucsc-gtftogenepred/meta.yaml index 87ed2f492e9cb..813e6c2d6a6b6 100644 --- a/recipes/ucsc-gtftogenepred/meta.yaml +++ b/recipes/ucsc-gtftogenepred/meta.yaml @@ -1,57 +1,56 @@ {% set package = "ucsc-gtftogenepred" %} {% set program = "gtfToGenePred" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 - skip: True # [osx] - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - - {{ pin_subpackage(package|lower, max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert a GTF file to a genePred" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "convert a GTF file to a genePred" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: - - linux-aarch64 \ No newline at end of file + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-headrest/build.sh b/recipes/ucsc-headrest/build.sh index e663809978aba..42931e2fdcda4 100644 --- a/recipes/ucsc-headrest/build.sh +++ b/recipes/ucsc-headrest/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/headRest && make) -cp bin/headRest "$PREFIX/bin" -chmod +x "$PREFIX/bin/headRest" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/headRest && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/headRest "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/headRest" diff --git a/recipes/ucsc-headrest/include.patch b/recipes/ucsc-headrest/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-headrest/include.patch +++ b/recipes/ucsc-headrest/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-headrest/meta.yaml b/recipes/ucsc-headrest/meta.yaml index ca8f56ff645ef..5544ab7e8edc7 100644 --- a/recipes/ucsc-headrest/meta.yaml +++ b/recipes/ucsc-headrest/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-headrest" %} {% set program = "headRest" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Return all *but* the first N lines of a file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgbbidblink/build.sh b/recipes/ucsc-hgbbidblink/build.sh index 6da58add15c6a..bd30d4f90abf3 100644 --- a/recipes/ucsc-hgbbidblink/build.sh +++ b/recipes/ucsc-hgbbidblink/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgBbiDbLink && make) -cp bin/hgBbiDbLink "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgBbiDbLink" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgBbiDbLink && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgBbiDbLink "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgBbiDbLink" diff --git a/recipes/ucsc-hgbbidblink/include.patch b/recipes/ucsc-hgbbidblink/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgbbidblink/include.patch +++ b/recipes/ucsc-hgbbidblink/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgbbidblink/meta.yaml b/recipes/ucsc-hgbbidblink/meta.yaml index b1ad270d2c719..45c299a6c87ee 100644 --- a/recipes/ucsc-hgbbidblink/meta.yaml +++ b/recipes/ucsc-hgbbidblink/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgbbidblink" %} {% set program = "hgBbiDbLink" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add table that just contains a pointer to a bbiFile to database. This program " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgfakeagp/build.sh b/recipes/ucsc-hgfakeagp/build.sh index da41fc2e586e1..03d106363c3f0 100644 --- a/recipes/ucsc-hgfakeagp/build.sh +++ b/recipes/ucsc-hgfakeagp/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgFakeAgp && make) -cp bin/hgFakeAgp "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgFakeAgp" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgFakeAgp && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgFakeAgp "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgFakeAgp" diff --git a/recipes/ucsc-hgfakeagp/include.patch b/recipes/ucsc-hgfakeagp/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgfakeagp/include.patch +++ b/recipes/ucsc-hgfakeagp/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgfakeagp/meta.yaml b/recipes/ucsc-hgfakeagp/meta.yaml index a8f5f3d17ac1e..457365f7fa59a 100644 --- a/recipes/ucsc-hgfakeagp/meta.yaml +++ b/recipes/ucsc-hgfakeagp/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgfakeagp" %} {% set program = "hgFakeAgp" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create fake AGP file by looking at N's" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgfindspec/build.sh b/recipes/ucsc-hgfindspec/build.sh index 86c10fc48027c..f02b401cba046 100644 --- a/recipes/ucsc-hgfindspec/build.sh +++ b/recipes/ucsc-hgfindspec/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgFindSpec && make) -cp bin/hgFindSpec "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgFindSpec" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgFindSpec && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgFindSpec "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgFindSpec" diff --git a/recipes/ucsc-hgfindspec/include.patch b/recipes/ucsc-hgfindspec/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgfindspec/include.patch +++ b/recipes/ucsc-hgfindspec/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgfindspec/meta.yaml b/recipes/ucsc-hgfindspec/meta.yaml index fa2b4eca2f34b..02d2bf103bd22 100644 --- a/recipes/ucsc-hgfindspec/meta.yaml +++ b/recipes/ucsc-hgfindspec/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgfindspec" %} {% set program = "hgFindSpec" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create hgFindSpec table from trackDb.ra files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hggcpercent/build.sh b/recipes/ucsc-hggcpercent/build.sh index 769b86221d65f..0f13041348d4e 100644 --- a/recipes/ucsc-hggcpercent/build.sh +++ b/recipes/ucsc-hggcpercent/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/hg/makeDb/hgGcPercent && make -j ${CPU_COUNT}) -cp bin/hgGcPercent "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgGcPercent" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgGcPercent && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgGcPercent "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgGcPercent" diff --git a/recipes/ucsc-hggcpercent/include.patch b/recipes/ucsc-hggcpercent/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-hggcpercent/include.patch +++ b/recipes/ucsc-hggcpercent/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-hggcpercent/meta.yaml b/recipes/ucsc-hggcpercent/meta.yaml index 9317978520057..8e1740f1de060 100644 --- a/recipes/ucsc-hggcpercent/meta.yaml +++ b/recipes/ucsc-hggcpercent/meta.yaml @@ -1,22 +1,21 @@ {% set package = "ucsc-hggcpercent" %} {% set program = "hgGcPercent" %} -{% set version = "448" %} -{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -24,31 +23,34 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: # just check for existence and exec bit, because the individual packages have no unified behavior - - test -x $PREFIX/bin/{{ program }} + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Calculate GC Percentage in 20kb windows" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: - - linux-aarch64 \ No newline at end of file + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hggoldgapgl/build_failure.linux-64.yaml b/recipes/ucsc-hggoldgapgl/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..2e5116388d48d --- /dev/null +++ b/recipes/ucsc-hggoldgapgl/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b3c6555b75999218c1585469a88df713fb1380afa8ca1f8f708ae3c4c4f06a67 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o protVar.o -c protVar.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgSnp.o -c pgSnp.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o alignInfo.o -c alignInfo.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o cddInfo.o -c cddInfo.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o loweutils.o -c loweutils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o cddDesc.o -c cddDesc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o arCOGs.o -c arCOGs.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o arcogdesc.o -c arcogdesc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o geneTree.o -c geneTree.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o megablastInfo.o -c megablastInfo.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgPhenoAssoc.o -c pgPhenoAssoc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgSiftPred.o -c pgSiftPred.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgPolyphenPred.o -c pgPolyphenPred.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o userRegions.o -c userRegions.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o variome.o -c variome.c + ar rcus ../../lib/x86_64/jkhgap.a acemblyClass.o adjacency.o affyAllExonProbe.o affyAtlas.o affy10KDetails.o affy120KDetails.o affyOffset.o affyPairs.o agp.o agpFrag.o agpGap.o alignSeqSizes.o altGraph.o altGraphX.o ancientRref.o annoFormatVep.o annoGratorGpVar.o annoGrateWigDb.o annoStreamDb.o annoStreamDbFactorSource.o annoStreamDbPslPlus.o annoStreamWig.o api.o atomDb.o autoUpgrade.o axtInfo.o axtLib.o bactigPos.o hgBam.o barChartBed.o barChartCategory.o barChartUi.o barChartData.o barChartSample.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bigBedFind.o bigBedLabel.o bigGenePred.o bigPsl.o bigTransMap.o bioImage.o blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o cart.o cartDb.o cartJson.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o ccdsInfo.o ccdsNotes.o ccdsGeneMap.o celeraCoverage.o celeraDupPositive.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgh.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chicken13kInfo.o chromBins.o chromAlias.o chr18deletions.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o codeBlast.o codeBlastScore.o cogs.o cogsxra.o columnInfo.o contigAcc.o coordConv.o cnpIafrate.o cnpIafrate2.o cnpLocke.o cnpRedon.o cnpSebat.o cnpSebat2.o cnpSharp2.o cnpSharpCutoff.o cnpSharpSample.o cnpSharp.o cpgIsland.o cpgIslandExt.o ctgPos.o ctgPos2.o customComposite.o bedDetail.o cgiApoptosis.o customAdjacency.o customFactory.o customPp.o customTrack.o cutter.o cv.o cytoBand.o dbDb.o dbRIP.o dbSnpRs.o defaultDb.o delConrad2.o delHinds2.o dgv.o dgvPlus.o dless.o dnaMotifSql.o dnaMarkovSql.o dnaProbe.o dv.o dvBed.o dvXref2.o easyGene.o ec.o ecCode.o ecAttribute.o ecAttributeCode.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfo.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/pairedTagAlign.o encode/peptideMapping.o encode/tagAlign.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode/wgEncodeGencodePolyAFeature.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeCell.o encode/encodeExp.o encode3/encode2Manifest.o encode3/encode3Valid.o ensFace.o ensInfo.o ensPhusionBlast.o ensXRefZfish.o est3.o estOrientInfo.o estPair.o exoFish.o expData.o expRecord.o exprBed.o facetField.o factorSource.o fbTables.o featureBits.o fileUi.o findKGAlias.o findKGProtAlias.o fishClones.o flyBase2004Xref.o flyBaseSwissProt.o flyreg.o flyreg2.o gbExtFile.o gbWarn.o gbMiscDiff.o gbProtAnn.o gcPercent.o gbSeq.o genbank.o genbankBlackList.o gencodeGeneClass.o gencodeIntron.o genMapDb.o geneBands.o geneCheck.o geneCheckDetails.o geneCheckWidget.o geneGraph.o genePred.o genePredReader.o geneSimilarities.o genoLay.o genomeRangeTreeFile.o genomicDups.o genomicSuperDups.o geoMirror.o ggCluster.o ggDbIo.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o goa.o goaPart.o googleAnalytics.o gpFx.o growthCondition.o grp.o gtexAse.o gtexBoxplot.o gtexEqtlCluster.o gtexInfo.o gtexDonor.o gtexGeneBed.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueData.o gtexTissueMedian.o gtexUi.o gwasCatalog.o hAnno.o haplotypes.o hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o hapmapSnps.o hapmapSnpsCombined.o hashJoin.o hCommon.o hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgGene.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o HInv.o hubConnect.o hubSearchText.o hui.o humanParalog.o imageClone.o indelShift.o interact.o interactUi.o isochores.o ispyTables.o itemAttr.o itemConf.o itemDetailsHtml.o jalview.o jaxOrtholog.o jaxQTL.o jaxQTL3.o jksql.o joiner.o jsHelper.o kg1ToKg2.o jgiGene.o joinMixer.o kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o lav.o ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o llaInfo.o longRange.o lrg.o lsSnpPdb.o lsSnpPdbChimera.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mammalPsg.o mapSts.o mathWig.o mcnBreakpoints.o mdb.o metaChromGraph.o microarray.o minChromSize.o minGeneInfo.o mrnaMisMatch.o mouseOrtho.o mouseSyn.o mouseSynWhd.o mysqlTableStatus.o ncbiRefLink.o ncbiRefSeqLink.o netAlign.o netCart.o nonCodingUi.o omimTitle.o ooUtils.o orthoAlleles.o pal.o pbStamp.o pcrResult.o pepPred.o peptideAtlasPeptide.o plasEndPairs.o polyGenotype.o protFeat.o pscreen.o pseudoGeneLink.o pslReader.o pslWScore.o putaInfo.o qaSeq.o rangeTreeFile.o rankProp.o recombRate.o recombRateRat.o recombRateMouse.o refLink.o refSeqStatus.o rgdQtl.o riken.o rhMapZfishInfo.o rikenBest.o rikenCluster.o rmskOut.o rmskAlign.o rmskJoined.o rmskOut2.o rnaFold.o rnaGene.o rnaGroup.o rnaHybridization.o rnaPLFold.o tRNAs.o gbRNAs.o snoRNAs.o lowelabPfamHit.o lowelabArkinOperonScore.o lowelabTIGROperonScore.o rnaSecStr.o tfbsConsFactors.o roughAli.o transMapStuff.o transMapInfo.o transMapGene.o transMapSrc.o sage.o sageCounts.o sageExp.o samAlignment.o sample.o sanger22extra.o sangerGene.o sangerGeneToWBGeneID.o sargassoSeaXra.o scopDes.o scoredRef.o search.o seqWindow.o sessionThumbnail.o sgdAbundance.o sgdClone.o sgdDescription.o sgdOther.o simpleNucDiff.o simpleRepeat.o snakeUi.o snp.o snp125.o snp125CodingCoordless.o snp132Ext.o snpExceptions.o snpFasta.o snpMap.o snpTmp.o snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o soTerm.o spDb.o splignAlign.o sqlSanity.o stanMad.o stsAlias.o stsInfo.o stsInfo2.o stsInfoMouse.o stsInfoMouseNew.o stsInfoRat.o stsMap.o stsMapMouse.o stsMapMouseNew.o stsMapRat.o stsMarker.o suggest.o switchDbTss.o synMap.o synteny100000.o syntenyBerk.o syntenySanger.o sqlProg.o tfbsCons.o tfbsConsSites.o tablesTables.o tableDescriptions.o tableStatus.o targetDb.o tfbsConsMap.o tagRepo.o taxonDivision.o taxonGeneticCode.o taxonName.o taxonNode.o taxonXref.o tigrCmrGene.o tigrOperon.o tilingPath.o traceInfo.o trackDb.o trackDbCustom.o trackHub.o trackLayout.o trackTable.o trackVersion.o trashDir.o transRegCode.o transRegCodeCondition.o transRegCodeProbe.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txEdgeOrtho.o txGraph.o txInfo.o txRnaAccs.o ucscRetroInfo.o ucscRetroOrtho.o validateGisaid.o variant.o variantProjector.o vcfUi.o vegaInfo.o vegaInfoZfish.o visiGene.o vntr.o wabAli.o web.o ncRna.o wgRna.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o yaleGencodeAssoc.o zdobnovSynt.o oreganno.o oregannoUi.o gvUi.o gv.o omicia.o protVar.o pgSnp.o alignInfo.o cddInfo.o loweutils.o cddDesc.o arCOGs.o arcogdesc.o geneTree.o megablastInfo.o pgPhenoAssoc.o pgSiftPred.o pgPolyphenPred.o userRegions.o variome.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -o hgGoldGapGl.o -c hgGoldGapGl.c + hgGoldGapGl.c: In function 'makeGoldAndGap': + hgGoldGapGl.c:213:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=] + 213 | splitPath(agpName, dir, chrom, ext); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + hgGoldGapGl.c:213:5: note: referencing argument 2 of type 'char[512]' + hgGoldGapGl.c:213:5: note: referencing argument 3 of type 'char[128]' + hgGoldGapGl.c:213:5: note: referencing argument 4 of type 'char[64]' + In file included from hgGoldGapGl.c:5: + ../../../inc/common.h:1104:6: note: in a call to function 'splitPath' + 1104 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + hgGoldGapGl.c: In function 'makeGl': + hgGoldGapGl.c:305:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=] + 305 | splitPath(glFileName, dir, chrom, ext); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + hgGoldGapGl.c:305:5: note: referencing argument 2 of type 'char[512]' + hgGoldGapGl.c:305:5: note: referencing argument 3 of type 'char[128]' + hgGoldGapGl.c:305:5: note: referencing argument 4 of type 'char[64]' + ../../../inc/common.h:1104:6: note: in a call to function 'splitPath' + 1104 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + hgGoldGapGl.c: In function 'makeGoldAndGap': + hgGoldGapGl.c:216:26: warning: '_gold' directive writing 5 bytes into a region of size between 1 and 128 [-Wformat-overflow=] + 216 | sprintf(goldName, "%s_gold", chrom); + | ^~~~~ + hgGoldGapGl.c:216:5: note: 'sprintf' output between 6 and 133 bytes into a destination of size 128 + 216 | sprintf(goldName, "%s_gold", chrom); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + hgGoldGapGl.c:217:25: warning: '_gap' directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=] + 217 | sprintf(gapName, "%s_gap", chrom); + | ^~~~ + hgGoldGapGl.c:217:5: note: 'sprintf' output between 5 and 132 bytes into a destination of size 128 + 217 | sprintf(gapName, "%s_gap", chrom); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + hgGoldGapGl.c: In function 'makeGl': + hgGoldGapGl.c:306:25: warning: '_gl' directive writing 3 bytes into a region of size between 1 and 128 [-Wformat-overflow=] + 306 | sprintf(glTable, "%s_gl", chrom); + | ^~~ + hgGoldGapGl.c:306:5: note: 'sprintf' output between 4 and 131 bytes into a destination of size 128 + 306 | sprintf(glTable, "%s_gl", chrom); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + hgGoldGapGl.c: In function 'makeCloneVerHash': + hgGoldGapGl.c:338:5: warning: '__builtin_strncpy' specified bound 32 equals destination size [-Wstringop-truncation] + 338 | strncpy(acc, row[0], sizeof(acc)); + | ^~~~~~~ + hgGoldGapGl.c: In function 'hgGoldGapGl': + hgGoldGapGl.c:394:37: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=] + 394 | sprintf(pathName, "%s/%s", ooDir, chrFi->name); + | ^ + hgGoldGapGl.c:394:13: note: 'sprintf' output 2 or more bytes (assuming 513) into a destination of size 512 + 394 | sprintf(pathName, "%s/%s", ooDir, chrFi->name); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hggoldgapgl-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -o ntContig.o -c ntContig.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/hgGoldGapGl \ + hgGoldGapGl.o ntContig.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz -L$PREFIX/lib -lmysqlclient -lstdc -lrt -lm + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(trackHub.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(web.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(wikiLink.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(cart.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(hPrint.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(bamFile.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(htmlPage.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(htmshell.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(portimpl.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hggoldgapgl-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + collect2: error: ld returned 1 exit status + make: *** [makefile:14: hgGoldGapGl] Error 1 + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-hggoldgapgl_1724781897900/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-hgloadbed/build.sh b/recipes/ucsc-hgloadbed/build.sh index 6c0b79016fe23..62d56d66a98c7 100644 --- a/recipes/ucsc-hgloadbed/build.sh +++ b/recipes/ucsc-hgloadbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadBed && make) -cp bin/hgLoadBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadBed" diff --git a/recipes/ucsc-hgloadbed/include.patch b/recipes/ucsc-hgloadbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadbed/include.patch +++ b/recipes/ucsc-hgloadbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadbed/meta.yaml b/recipes/ucsc-hgloadbed/meta.yaml index c14a6b24bfc5f..d10d7a94dec54 100644 --- a/recipes/ucsc-hgloadbed/meta.yaml +++ b/recipes/ucsc-hgloadbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadbed" %} {% set program = "hgLoadBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a generic bed file into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgloadchain/build.sh b/recipes/ucsc-hgloadchain/build.sh index 7733176a98e61..0836ef0a2b3a4 100644 --- a/recipes/ucsc-hgloadchain/build.sh +++ b/recipes/ucsc-hgloadchain/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadChain && make) -cp bin/hgLoadChain "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadChain" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadChain && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadChain "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadChain" diff --git a/recipes/ucsc-hgloadchain/include.patch b/recipes/ucsc-hgloadchain/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadchain/include.patch +++ b/recipes/ucsc-hgloadchain/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadchain/meta.yaml b/recipes/ucsc-hgloadchain/meta.yaml index a37db8bb33d55..b251f71789efa 100644 --- a/recipes/ucsc-hgloadchain/meta.yaml +++ b/recipes/ucsc-hgloadchain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadchain" %} {% set program = "hgLoadChain" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a generic Chain file into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgloadmaf/build.sh b/recipes/ucsc-hgloadmaf/build.sh index 2ae0cbe492abd..6e858c951b003 100644 --- a/recipes/ucsc-hgloadmaf/build.sh +++ b/recipes/ucsc-hgloadmaf/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadMaf && make) -cp bin/hgLoadMaf "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadMaf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadMaf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadMaf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadMaf" diff --git a/recipes/ucsc-hgloadmaf/include.patch b/recipes/ucsc-hgloadmaf/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadmaf/include.patch +++ b/recipes/ucsc-hgloadmaf/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadmaf/meta.yaml b/recipes/ucsc-hgloadmaf/meta.yaml index 19b53f7e81296..b16d0a55d7962 100644 --- a/recipes/ucsc-hgloadmaf/meta.yaml +++ b/recipes/ucsc-hgloadmaf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadmaf" %} {% set program = "hgLoadMaf" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a maf file index into the database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgloadnet/build.sh b/recipes/ucsc-hgloadnet/build.sh index afd005fbf3b31..44361aee149dc 100644 --- a/recipes/ucsc-hgloadnet/build.sh +++ b/recipes/ucsc-hgloadnet/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadNet && make) -cp bin/hgLoadNet "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadNet" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadNet && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadNet "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadNet" diff --git a/recipes/ucsc-hgloadnet/include.patch b/recipes/ucsc-hgloadnet/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadnet/include.patch +++ b/recipes/ucsc-hgloadnet/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadnet/meta.yaml b/recipes/ucsc-hgloadnet/meta.yaml index 29d2d37aa891a..34ae43d661357 100644 --- a/recipes/ucsc-hgloadnet/meta.yaml +++ b/recipes/ucsc-hgloadnet/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadnet" %} {% set program = "hgLoadNet" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a generic net file into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgloadout/build.sh b/recipes/ucsc-hgloadout/build.sh index bcbdfa0686952..19021359dacaf 100644 --- a/recipes/ucsc-hgloadout/build.sh +++ b/recipes/ucsc-hgloadout/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadOut && make) -cp bin/hgLoadOut "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadOut" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadOut && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadOut "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadOut" diff --git a/recipes/ucsc-hgloadout/include.patch b/recipes/ucsc-hgloadout/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadout/include.patch +++ b/recipes/ucsc-hgloadout/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadout/meta.yaml b/recipes/ucsc-hgloadout/meta.yaml index 589de17eb66f8..f1abed39bf9f8 100644 --- a/recipes/ucsc-hgloadout/meta.yaml +++ b/recipes/ucsc-hgloadout/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadout" %} {% set program = "hgLoadOut" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "load RepeatMasker .out files into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgloadoutjoined/build.sh b/recipes/ucsc-hgloadoutjoined/build.sh index 52f973bd6094f..1dd85c8321304 100644 --- a/recipes/ucsc-hgloadoutjoined/build.sh +++ b/recipes/ucsc-hgloadoutjoined/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadOutJoined && make) -cp bin/hgLoadOutJoined "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadOutJoined" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadOutJoined && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadOutJoined "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadOutJoined" diff --git a/recipes/ucsc-hgloadoutjoined/include.patch b/recipes/ucsc-hgloadoutjoined/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadoutjoined/include.patch +++ b/recipes/ucsc-hgloadoutjoined/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadoutjoined/meta.yaml b/recipes/ucsc-hgloadoutjoined/meta.yaml index 7a8f58d48adf8..530efb471e395 100644 --- a/recipes/ucsc-hgloadoutjoined/meta.yaml +++ b/recipes/ucsc-hgloadoutjoined/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadoutjoined" %} {% set program = "hgLoadOutJoined" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "load new style (2014) RepeatMasker .out files into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgloadsqltab/build.sh b/recipes/ucsc-hgloadsqltab/build.sh index 6b583d73e1561..943bf9b400cec 100644 --- a/recipes/ucsc-hgloadsqltab/build.sh +++ b/recipes/ucsc-hgloadsqltab/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadSqlTab && make) -cp bin/hgLoadSqlTab "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadSqlTab" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadSqlTab && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadSqlTab "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadSqlTab" diff --git a/recipes/ucsc-hgloadsqltab/include.patch b/recipes/ucsc-hgloadsqltab/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadsqltab/include.patch +++ b/recipes/ucsc-hgloadsqltab/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadsqltab/meta.yaml b/recipes/ucsc-hgloadsqltab/meta.yaml index a66bbbbb50a27..1ae390c3c6a3f 100644 --- a/recipes/ucsc-hgloadsqltab/meta.yaml +++ b/recipes/ucsc-hgloadsqltab/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadsqltab" %} {% set program = "hgLoadSqlTab" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load table into database from SQL and text files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgloadwiggle/build.sh b/recipes/ucsc-hgloadwiggle/build.sh index 8530d3cc9a930..5a8736a672f80 100644 --- a/recipes/ucsc-hgloadwiggle/build.sh +++ b/recipes/ucsc-hgloadwiggle/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadWiggle && make) -cp bin/hgLoadWiggle "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadWiggle" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadWiggle && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadWiggle "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadWiggle" diff --git a/recipes/ucsc-hgloadwiggle/include.patch b/recipes/ucsc-hgloadwiggle/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadwiggle/include.patch +++ b/recipes/ucsc-hgloadwiggle/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadwiggle/meta.yaml b/recipes/ucsc-hgloadwiggle/meta.yaml index 6859a90c405b5..e8e2571e9013b 100644 --- a/recipes/ucsc-hgloadwiggle/meta.yaml +++ b/recipes/ucsc-hgloadwiggle/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadwiggle" %} {% set program = "hgLoadWiggle" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a wiggle track definition into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgspeciesrna/build.sh b/recipes/ucsc-hgspeciesrna/build.sh index b6858f027c0a5..1af260d069942 100644 --- a/recipes/ucsc-hgspeciesrna/build.sh +++ b/recipes/ucsc-hgspeciesrna/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/hgSpeciesRna && make) -cp bin/hgSpeciesRna "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgSpeciesRna" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/hgSpeciesRna && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgSpeciesRna "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgSpeciesRna" diff --git a/recipes/ucsc-hgspeciesrna/include.patch b/recipes/ucsc-hgspeciesrna/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgspeciesrna/include.patch +++ b/recipes/ucsc-hgspeciesrna/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgspeciesrna/meta.yaml b/recipes/ucsc-hgspeciesrna/meta.yaml index 5970a38722898..26e0337c640e6 100644 --- a/recipes/ucsc-hgspeciesrna/meta.yaml +++ b/recipes/ucsc-hgspeciesrna/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgspeciesrna" %} {% set program = "hgSpeciesRna" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create fasta file with RNA from one species" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgsqldump/build.sh b/recipes/ucsc-hgsqldump/build.sh index 80671787650fb..dbee464b271c9 100644 --- a/recipes/ucsc-hgsqldump/build.sh +++ b/recipes/ucsc-hgsqldump/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/hgsqldump && make) -cp bin/hgsqldump "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgsqldump" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/hgsqldump && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgsqldump "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgsqldump" diff --git a/recipes/ucsc-hgsqldump/include.patch b/recipes/ucsc-hgsqldump/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgsqldump/include.patch +++ b/recipes/ucsc-hgsqldump/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgsqldump/meta.yaml b/recipes/ucsc-hgsqldump/meta.yaml index 9b1ffe0672543..cf837117dbedc 100644 --- a/recipes/ucsc-hgsqldump/meta.yaml +++ b/recipes/ucsc-hgsqldump/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgsqldump" %} {% set program = "hgsqldump" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Execute mysqldump using passwords from .hg.conf" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgtrackdb/build.sh b/recipes/ucsc-hgtrackdb/build.sh index e1b8ac6e65c4f..106bc9b2835e1 100644 --- a/recipes/ucsc-hgtrackdb/build.sh +++ b/recipes/ucsc-hgtrackdb/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgTrackDb && make) -cp bin/hgTrackDb "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgTrackDb" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgTrackDb && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgTrackDb "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgTrackDb" diff --git a/recipes/ucsc-hgtrackdb/build_failure.linux-64.yaml b/recipes/ucsc-hgtrackdb/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1a5cc3996bd96 --- /dev/null +++ b/recipes/ucsc-hgtrackdb/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4f8702f06ec982e425c34372c9753e61d8588e2d622c1c37d09bde19d1f58d12 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections 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-I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o refLink.o -c refLink.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o refSeqStatus.o -c refSeqStatus.c + 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-I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackDbCache.o -c trackDbCache.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackDbCustom.o -c trackDbCustom.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackHub.o -c trackHub.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong 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-fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trashDir.o -c trashDir.c + trackDbCustom.c: In function 'trackDbInclude': + trackDbCustom.c:294:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=] + 294 | splitPath(raFile, incFile, NULL, NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]' + trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]' + trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]' + In file included from trackDbCustom.c:9: + ../../inc/common.h:1139:6: note: in a call to function 'splitPath' + 1139 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat 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-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vcfUi.o -c vcfUi.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vegaInfo.o -c vegaInfo.c + sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestHeader.html > jWestHeader.h + sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestBanner.html > jWestBanner.h + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigAsciiToBinary.o -c wigAsciiToBinary.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigDataStream.o -c wigDataStream.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggle.o -c wiggle.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleCart.o -c wiggleCart.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleUtils.o -c wiggleUtils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wikiLink.o -c wikiLink.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskAlignBed.o -c bigRmskAlignBed.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskBed.o -c bigRmskBed.c + mkdir -p ../../lib/x86_64 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o web.o -c web.c + ar rcus ../../lib/x86_64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o bigRmskAlignBed.o bigRmskBed.o + cd kent/src/hg/makeDb/hgTrackDb + make CC=/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_build_env/bin/x86_64-conda-linux-gnu-cc CXX= 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/work=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -L/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -L/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib' 'CXXFLAGS= -I/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -L/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -L/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib' -j 4 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgtrackdb-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -o hgTrackDb.o -c hgTrackDb.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/hgTrackDb hgTrackDb.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -L$PREFIX/lib -lmysqlclient -lstdc -lrt -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -lpthread $PREFIX/lib/libssl.a $PREFIX/lib/libcrypto.a -ldl ../../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz + /opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(knetUdc.o): in function knetUdcInstall': + /usr/local/src/conda/ucsc-hgtrackdb-469/kent/src/lib/knetUdc.c:80: undefined reference to knet_init_alt' + collect2: error: ld returned 1 exit status + make: *** [../../../inc/userApp.mk:32: /opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/work/bin/hgTrackDb] Error 1 + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-hgtrackdb_1724797961927/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-hgtrackdb/include.patch b/recipes/ucsc-hgtrackdb/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgtrackdb/include.patch +++ b/recipes/ucsc-hgtrackdb/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgtrackdb/meta.yaml b/recipes/ucsc-hgtrackdb/meta.yaml index dc17c36ddfcd2..551b65375b5f2 100644 --- a/recipes/ucsc-hgtrackdb/meta.yaml +++ b/recipes/ucsc-hgtrackdb/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgtrackdb" %} {% set program = "hgTrackDb" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create trackDb table from text files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hgvstovcf/build_failure.linux-64.yaml b/recipes/ucsc-hgvstovcf/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5246ca5955a05 --- /dev/null +++ b/recipes/ucsc-hgvstovcf/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e623fe095996910ce2886e5861e4c5768349d26229f9006821887f1c8468ad5d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]' + trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]' + trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]' + In file included from trackDbCustom.c:8: + ../../inc/common.h:1104:6: note: in a call to function 'splitPath' + 1104 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgvstovcf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackHub.o -c trackHub.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgvstovcf-377 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-I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackTable.o -c trackTable.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgvstovcf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackVersion.o -c trackVersion.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 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-I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txCluster.o -c txCluster.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hgvstovcf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txCommon.o -c txCommon.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections 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../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -L$PREFIX/lib -lmysqlclient -lstdc -lrt -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(trackHub.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(web.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(wikiLink.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(cart.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkhgap.a(hPrint.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(bamFile.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(htmlPage.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(htmshell.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(portimpl.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../../lib/x86_64/jkhgap.a(hui.o):/usr/local/src/conda/ucsc-hgvstovcf-377/kent/src/hg/lib/../../inc/htmshell.h:163: first defined here + collect2: error: ld returned 1 exit status + make: *** [../../../inc/userApp.mk:31: /opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/work/bin/hgvsToVcf] Error 1 + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-hgvstovcf_1724784085089/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-htmlcheck/build.sh b/recipes/ucsc-htmlcheck/build.sh index b99b826297c80..10020a3222df5 100644 --- a/recipes/ucsc-htmlcheck/build.sh +++ b/recipes/ucsc-htmlcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/htmlCheck && make) -cp bin/htmlCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/htmlCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/htmlCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/htmlCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/htmlCheck" diff --git a/recipes/ucsc-htmlcheck/include.patch b/recipes/ucsc-htmlcheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-htmlcheck/include.patch +++ b/recipes/ucsc-htmlcheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-htmlcheck/meta.yaml b/recipes/ucsc-htmlcheck/meta.yaml index 2fb806db88e37..edc5c0b821f24 100644 --- a/recipes/ucsc-htmlcheck/meta.yaml +++ b/recipes/ucsc-htmlcheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-htmlcheck" %} {% set program = "htmlCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Do a little reading and verification of html file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hubcheck/build.sh b/recipes/ucsc-hubcheck/build.sh index f680c4c42c14b..42f264921d821 100644 --- a/recipes/ucsc-hubcheck/build.sh +++ b/recipes/ucsc-hubcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/hubCheck && make) -cp bin/hubCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/hubCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/hubCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hubCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hubCheck" diff --git a/recipes/ucsc-hubcheck/build_failure.linux-64.yaml b/recipes/ucsc-hubcheck/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b57fb59a51175 --- /dev/null +++ b/recipes/ucsc-hubcheck/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5f43f332bdb133a6b645f4a426f312cc7de49c205454fad3f075e2b4cd58541c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o quickLift.o -c quickLift.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong 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-I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackVersion.o -c trackVersion.c + trackDbCustom.c: In function 'trackDbInclude': + trackDbCustom.c:294:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=] + 294 | splitPath(raFile, incFile, NULL, NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]' + trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]' + trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]' + In file included from trackDbCustom.c:9: + ../../inc/common.h:1139:6: note: in a call to function 'splitPath' + 1139 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], + | ^~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include 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-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txEdgeBed.o -c txEdgeBed.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txGraph.o -c txGraph.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txInfo.o -c txInfo.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o txRnaAccs.o -c txRnaAccs.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o variantProjector.o -c variantProjector.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vcfUi.o -c vcfUi.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vegaInfo.o -c vegaInfo.c + sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestHeader.html > jWestHeader.h + sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestBanner.html > jWestBanner.h + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigAsciiToBinary.o -c wigAsciiToBinary.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigDataStream.o -c wigDataStream.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggle.o -c wiggle.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleCart.o -c wiggleCart.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleUtils.o -c wiggleUtils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wikiLink.o -c wikiLink.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskAlignBed.o -c bigRmskAlignBed.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o bigRmskBed.o -c bigRmskBed.c + mkdir -p ../../lib/x86_64 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o web.o -c web.c + ar rcus ../../lib/x86_64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o bigRmskAlignBed.o bigRmskBed.o + cd kent/src/hg/utils/hubCheck + make CC=/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_build_env/bin/x86_64-conda-linux-gnu-cc CXX= 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/work=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib' 'CXXFLAGS= -I/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib' -j 4 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-hubcheck-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -o hubCheck.o -c hubCheck.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/hubCheck hubCheck.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -lpthread $PREFIX/lib/libssl.a $PREFIX/lib/libcrypto.a -ldl ../../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz -L$PREFIX/lib -lmysqlclient -lstdc -lrt -lm + /opt/conda/conda-bld/ucsc-hubcheck_1724797987261/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../../lib/x86_64/jkweb.a(knetUdc.o): in function knetUdcInstall': + /usr/local/src/conda/ucsc-hubcheck-469/kent/src/lib/knetUdc.c:80: undefined reference to knet_init_alt' + collect2: error: ld returned 1 exit status + make: *** [makefile:12: hubCheck] Error 1 + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-hubcheck_1724797987261/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/ucsc-hubcheck/include.patch b/recipes/ucsc-hubcheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hubcheck/include.patch +++ b/recipes/ucsc-hubcheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hubcheck/meta.yaml b/recipes/ucsc-hubcheck/meta.yaml index a7bbbafd799af..5a3c63cb34566 100644 --- a/recipes/ucsc-hubcheck/meta.yaml +++ b/recipes/ucsc-hubcheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hubcheck" %} {% set program = "hubCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Check a track data hub for integrity." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-hubpubliccheck/build.sh b/recipes/ucsc-hubpubliccheck/build.sh index e44de2a3b03aa..9e62440c60826 100644 --- a/recipes/ucsc-hubpubliccheck/build.sh +++ b/recipes/ucsc-hubpubliccheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/hubPublicCheck && make) -cp bin/hubPublicCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/hubPublicCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/hubPublicCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hubPublicCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hubPublicCheck" diff --git a/recipes/ucsc-hubpubliccheck/include.patch b/recipes/ucsc-hubpubliccheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hubpubliccheck/include.patch +++ b/recipes/ucsc-hubpubliccheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hubpubliccheck/meta.yaml b/recipes/ucsc-hubpubliccheck/meta.yaml index cca7bfbd24adb..f0a4cc1d4f97e 100644 --- a/recipes/ucsc-hubpubliccheck/meta.yaml +++ b/recipes/ucsc-hubpubliccheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hubpubliccheck" %} {% set program = "hubPublicCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "checks that the labels in hubPublic match what is in the hub labels" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-ixixx/build.sh b/recipes/ucsc-ixixx/build.sh index e4ce4fe68f1ae..961320e7fd96d 100644 --- a/recipes/ucsc-ixixx/build.sh +++ b/recipes/ucsc-ixixx/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd kent/src/hg/lib && USE_HIC=0 make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/index/ixIxx && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/ixIxx "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/ixIxx" +cp bin/ixIxx "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/ixIxx" diff --git a/recipes/ucsc-ixixx/include.patch b/recipes/ucsc-ixixx/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-ixixx/include.patch +++ b/recipes/ucsc-ixixx/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ixixx/meta.yaml b/recipes/ucsc-ixixx/meta.yaml index 67d8022a455c2..12e29c5de07c1 100644 --- a/recipes/ucsc-ixixx/meta.yaml +++ b/recipes/ucsc-ixixx/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ixixx" %} {% set program = "ixIxx" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,26 +14,28 @@ source: - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage('ucsc-ixixx', max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -42,11 +44,14 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create indices for simple line-oriented file of format " dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-lavtoaxt/build.sh b/recipes/ucsc-lavtoaxt/build.sh index 053f95a6d6f0c..28b7382f0f659 100644 --- a/recipes/ucsc-lavtoaxt/build.sh +++ b/recipes/ucsc-lavtoaxt/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/lavToAxt && make) -cp bin/lavToAxt "$PREFIX/bin" -chmod +x "$PREFIX/bin/lavToAxt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/lavToAxt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/lavToAxt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/lavToAxt" diff --git a/recipes/ucsc-lavtoaxt/include.patch b/recipes/ucsc-lavtoaxt/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-lavtoaxt/include.patch +++ b/recipes/ucsc-lavtoaxt/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-lavtoaxt/meta.yaml b/recipes/ucsc-lavtoaxt/meta.yaml index e1c9793a5521a..06c0cafe88b92 100644 --- a/recipes/ucsc-lavtoaxt/meta.yaml +++ b/recipes/ucsc-lavtoaxt/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-lavtoaxt" %} {% set program = "lavToAxt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert blastz lav file to an axt file (which includes sequence)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-lavtopsl/build.sh b/recipes/ucsc-lavtopsl/build.sh index 6bc1639458228..f3bad35b19a90 100644 --- a/recipes/ucsc-lavtopsl/build.sh +++ b/recipes/ucsc-lavtopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/lavToPsl && make) -cp bin/lavToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/lavToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/lavToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/lavToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/lavToPsl" diff --git a/recipes/ucsc-lavtopsl/include.patch b/recipes/ucsc-lavtopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-lavtopsl/include.patch +++ b/recipes/ucsc-lavtopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-lavtopsl/meta.yaml b/recipes/ucsc-lavtopsl/meta.yaml index e561090f1335f..cfc2c04b24fa7 100644 --- a/recipes/ucsc-lavtopsl/meta.yaml +++ b/recipes/ucsc-lavtopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-lavtopsl" %} {% set program = "lavToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert blastz lav to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-ldhggene/build.sh b/recipes/ucsc-ldhggene/build.sh index f03594d189cf0..bcfee33c689a7 100644 --- a/recipes/ucsc-ldhggene/build.sh +++ b/recipes/ucsc-ldhggene/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/ldHgGene && make) -cp bin/ldHgGene "$PREFIX/bin" -chmod +x "$PREFIX/bin/ldHgGene" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/ldHgGene && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/ldHgGene "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/ldHgGene" diff --git a/recipes/ucsc-ldhggene/include.patch b/recipes/ucsc-ldhggene/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-ldhggene/include.patch +++ b/recipes/ucsc-ldhggene/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ldhggene/meta.yaml b/recipes/ucsc-ldhggene/meta.yaml index 629f7cfa8254a..aec3b9faa2050 100644 --- a/recipes/ucsc-ldhggene/meta.yaml +++ b/recipes/ucsc-ldhggene/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ldhggene" %} {% set program = "ldHgGene" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "load database with gene predictions from a gff file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-liftover/build.sh b/recipes/ucsc-liftover/build.sh index 189c409009472..50f0e8474db9a 100644 --- a/recipes/ucsc-liftover/build.sh +++ b/recipes/ucsc-liftover/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j${CPU_COUNT}) -(cd kent/src/htslib && make -j${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j${CPU_COUNT}) -(cd kent/src/hg/lib && make -j${CPU_COUNT}) -(cd kent/src/hg/liftOver && make -j${CPU_COUNT}) -cp bin/liftOver "$PREFIX/bin" -chmod +x "$PREFIX/bin/liftOver" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/liftOver && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/liftOver "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/liftOver" diff --git a/recipes/ucsc-liftover/include.patch b/recipes/ucsc-liftover/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-liftover/include.patch +++ b/recipes/ucsc-liftover/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-liftover/meta.yaml b/recipes/ucsc-liftover/meta.yaml index 4d953bf48e005..a38bea325585b 100644 --- a/recipes/ucsc-liftover/meta.yaml +++ b/recipes/ucsc-liftover/meta.yaml @@ -1,25 +1,21 @@ {% set package = "ucsc-liftover" %} {% set program = "liftOver" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 - skip: True # [osx] - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -27,31 +23,34 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Move annotations from one assembly to another" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: - additional-platforms: - - linux-aarch64 \ No newline at end of file + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-liftup/build.sh b/recipes/ucsc-liftup/build.sh index 5a638019c0676..1a14a6cb069d0 100644 --- a/recipes/ucsc-liftup/build.sh +++ b/recipes/ucsc-liftup/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/liftUp && make) -cp bin/liftUp "$PREFIX/bin" -chmod +x "$PREFIX/bin/liftUp" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/liftUp && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/liftUp "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/liftUp" diff --git a/recipes/ucsc-liftup/include.patch b/recipes/ucsc-liftup/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-liftup/include.patch +++ b/recipes/ucsc-liftup/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-liftup/meta.yaml b/recipes/ucsc-liftup/meta.yaml index 87acba1d33d82..b61c25d8102ca 100644 --- a/recipes/ucsc-liftup/meta.yaml +++ b/recipes/ucsc-liftup/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-liftup" %} {% set program = "liftUp" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-linestora/build.sh b/recipes/ucsc-linestora/build.sh index 945e02d5d447d..eb58c0fc0db43 100644 --- a/recipes/ucsc-linestora/build.sh +++ b/recipes/ucsc-linestora/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/raToLines/linesToRa && make) -cp bin/linesToRa "$PREFIX/bin" -chmod +x "$PREFIX/bin/linesToRa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/raToLines/linesToRa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/linesToRa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/linesToRa" diff --git a/recipes/ucsc-linestora/include.patch b/recipes/ucsc-linestora/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-linestora/include.patch +++ b/recipes/ucsc-linestora/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-linestora/meta.yaml b/recipes/ucsc-linestora/meta.yaml index 58fd0d3a47e68..8929fdad5aeff 100644 --- a/recipes/ucsc-linestora/meta.yaml +++ b/recipes/ucsc-linestora/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-linestora" %} {% set program = "linesToRa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "generate .ra format from lines with pipe-separated fields" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-localtime/build.sh b/recipes/ucsc-localtime/build.sh index 5e4271dc0c297..b0b32fe905438 100644 --- a/recipes/ucsc-localtime/build.sh +++ b/recipes/ucsc-localtime/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/timing/localtime && make) -cp bin/localtime "$PREFIX/bin" -chmod +x "$PREFIX/bin/localtime" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/timing/localtime && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/localtime "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/localtime" diff --git a/recipes/ucsc-localtime/include.patch b/recipes/ucsc-localtime/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-localtime/include.patch +++ b/recipes/ucsc-localtime/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-localtime/meta.yaml b/recipes/ucsc-localtime/meta.yaml index fe6a48b0afb65..9a5bb720eea6a 100644 --- a/recipes/ucsc-localtime/meta.yaml +++ b/recipes/ucsc-localtime/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-localtime" %} {% set program = "localtime" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert unix timestamp to date string" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafaddirows/build.sh b/recipes/ucsc-mafaddirows/build.sh index e7d550df0494d..cac297e03b3d9 100644 --- a/recipes/ucsc-mafaddirows/build.sh +++ b/recipes/ucsc-mafaddirows/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafAddIRows && make) -cp bin/mafAddIRows "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafAddIRows" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafAddIRows && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafAddIRows "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafAddIRows" diff --git a/recipes/ucsc-mafaddirows/include.patch b/recipes/ucsc-mafaddirows/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafaddirows/include.patch +++ b/recipes/ucsc-mafaddirows/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafaddirows/meta.yaml b/recipes/ucsc-mafaddirows/meta.yaml index 5d99df62b05d9..1678cf8b45d74 100644 --- a/recipes/ucsc-mafaddirows/meta.yaml +++ b/recipes/ucsc-mafaddirows/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafaddirows" %} {% set program = "mafAddIRows" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "add 'i' rows to a maf" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafaddqrows/build.sh b/recipes/ucsc-mafaddqrows/build.sh index 2a500dafaef18..ed596762c367a 100644 --- a/recipes/ucsc-mafaddqrows/build.sh +++ b/recipes/ucsc-mafaddqrows/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafAddQRows && make) -cp bin/mafAddQRows "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafAddQRows" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafAddQRows && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafAddQRows "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafAddQRows" diff --git a/recipes/ucsc-mafaddqrows/include.patch b/recipes/ucsc-mafaddqrows/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafaddqrows/include.patch +++ b/recipes/ucsc-mafaddqrows/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafaddqrows/meta.yaml b/recipes/ucsc-mafaddqrows/meta.yaml index f9017087a7315..852353ae2d074 100644 --- a/recipes/ucsc-mafaddqrows/meta.yaml +++ b/recipes/ucsc-mafaddqrows/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafaddqrows" %} {% set program = "mafAddQRows" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add quality data to a maf" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafcoverage/build.sh b/recipes/ucsc-mafcoverage/build.sh index 348d70bc50d75..468207ac0d869 100644 --- a/recipes/ucsc-mafcoverage/build.sh +++ b/recipes/ucsc-mafcoverage/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafCoverage && make) -cp bin/mafCoverage "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafCoverage" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafCoverage && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafCoverage "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafCoverage" diff --git a/recipes/ucsc-mafcoverage/include.patch b/recipes/ucsc-mafcoverage/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafcoverage/include.patch +++ b/recipes/ucsc-mafcoverage/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafcoverage/meta.yaml b/recipes/ucsc-mafcoverage/meta.yaml index 098e92ad735b5..e4a133f4200cc 100644 --- a/recipes/ucsc-mafcoverage/meta.yaml +++ b/recipes/ucsc-mafcoverage/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafcoverage" %} {% set program = "mafCoverage" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Analyse coverage by maf files - chromosome by " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-maffetch/build.sh b/recipes/ucsc-maffetch/build.sh index 645c5ada6b7fd..05845f691ae3f 100644 --- a/recipes/ucsc-maffetch/build.sh +++ b/recipes/ucsc-maffetch/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafFetch && make) -cp bin/mafFetch "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafFetch" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafFetch && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafFetch "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafFetch" diff --git a/recipes/ucsc-maffetch/include.patch b/recipes/ucsc-maffetch/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maffetch/include.patch +++ b/recipes/ucsc-maffetch/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maffetch/meta.yaml b/recipes/ucsc-maffetch/meta.yaml index 0bcc9b3c66e88..9090dbba9ad87 100644 --- a/recipes/ucsc-maffetch/meta.yaml +++ b/recipes/ucsc-maffetch/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maffetch" %} {% set program = "mafFetch" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "get overlapping records from an MAF using an index table" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-maffilter/build.sh b/recipes/ucsc-maffilter/build.sh index 1456dd4eba626..9843b09843d39 100644 --- a/recipes/ucsc-maffilter/build.sh +++ b/recipes/ucsc-maffilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafFilter && make) -cp bin/mafFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafFilter" diff --git a/recipes/ucsc-maffilter/include.patch b/recipes/ucsc-maffilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maffilter/include.patch +++ b/recipes/ucsc-maffilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maffilter/meta.yaml b/recipes/ucsc-maffilter/meta.yaml index 7663b1c8a008c..fe2bdf5d06413 100644 --- a/recipes/ucsc-maffilter/meta.yaml +++ b/recipes/ucsc-maffilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maffilter" %} {% set program = "mafFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter out maf files. Output goes to standard out" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maffrag/build.sh b/recipes/ucsc-maffrag/build.sh index f2386fc8ed4df..d9960af580f54 100644 --- a/recipes/ucsc-maffrag/build.sh +++ b/recipes/ucsc-maffrag/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafFrag && make) -cp bin/mafFrag "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafFrag" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafFrag && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafFrag "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafFrag" diff --git a/recipes/ucsc-maffrag/include.patch b/recipes/ucsc-maffrag/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maffrag/include.patch +++ b/recipes/ucsc-maffrag/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maffrag/meta.yaml b/recipes/ucsc-maffrag/meta.yaml index f65ce536626f5..be0547277cd93 100644 --- a/recipes/ucsc-maffrag/meta.yaml +++ b/recipes/ucsc-maffrag/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maffrag" %} {% set program = "mafFrag" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract maf sequences for a region from database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-maffrags/build.sh b/recipes/ucsc-maffrags/build.sh index b058c5853bc14..1e18fa9821f72 100644 --- a/recipes/ucsc-maffrags/build.sh +++ b/recipes/ucsc-maffrags/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafFrags && make) -cp bin/mafFrags "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafFrags" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafFrags && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafFrags "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafFrags" diff --git a/recipes/ucsc-maffrags/include.patch b/recipes/ucsc-maffrags/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maffrags/include.patch +++ b/recipes/ucsc-maffrags/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maffrags/meta.yaml b/recipes/ucsc-maffrags/meta.yaml index 21cd93f53f83e..34d81f233584a 100644 --- a/recipes/ucsc-maffrags/meta.yaml +++ b/recipes/ucsc-maffrags/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maffrags" %} {% set program = "mafFrags" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Collect MAFs from regions specified in a 6 column bed file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-mafgene/build.sh b/recipes/ucsc-mafgene/build.sh index 6ef25dbca5c93..b3fd8c73fa645 100644 --- a/recipes/ucsc-mafgene/build.sh +++ b/recipes/ucsc-mafgene/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafGene && make) -cp bin/mafGene "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafGene" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafGene && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafGene "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafGene" diff --git a/recipes/ucsc-mafgene/include.patch b/recipes/ucsc-mafgene/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafgene/include.patch +++ b/recipes/ucsc-mafgene/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafgene/meta.yaml b/recipes/ucsc-mafgene/meta.yaml index 9912fd7602673..00c8dcbf6fd3c 100644 --- a/recipes/ucsc-mafgene/meta.yaml +++ b/recipes/ucsc-mafgene/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafgene" %} {% set program = "mafGene" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "output protein alignments using maf and genePred" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-mafmefirst/build.sh b/recipes/ucsc-mafmefirst/build.sh index 4363fc2b59ba9..6ffa033237548 100644 --- a/recipes/ucsc-mafmefirst/build.sh +++ b/recipes/ucsc-mafmefirst/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafMeFirst && make) -cp bin/mafMeFirst "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafMeFirst" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafMeFirst && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafMeFirst "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafMeFirst" diff --git a/recipes/ucsc-mafmefirst/include.patch b/recipes/ucsc-mafmefirst/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafmefirst/include.patch +++ b/recipes/ucsc-mafmefirst/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafmefirst/meta.yaml b/recipes/ucsc-mafmefirst/meta.yaml index e48007351af53..4ee6e4b03ce1e 100644 --- a/recipes/ucsc-mafmefirst/meta.yaml +++ b/recipes/ucsc-mafmefirst/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafmefirst" %} {% set program = "mafMeFirst" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Move component to top if it is one of the named ones. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maforder/build.sh b/recipes/ucsc-maforder/build.sh index cefff99c5bdf1..a89bd8868c424 100644 --- a/recipes/ucsc-maforder/build.sh +++ b/recipes/ucsc-maforder/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafOrder && make) -cp bin/mafOrder "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafOrder" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafOrder && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafOrder "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafOrder" diff --git a/recipes/ucsc-maforder/include.patch b/recipes/ucsc-maforder/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maforder/include.patch +++ b/recipes/ucsc-maforder/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maforder/meta.yaml b/recipes/ucsc-maforder/meta.yaml index 54bfd559eb179..ad84eab22d85c 100644 --- a/recipes/ucsc-maforder/meta.yaml +++ b/recipes/ucsc-maforder/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maforder" %} {% set program = "mafOrder" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "order components within a maf file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafranges/build.sh b/recipes/ucsc-mafranges/build.sh index 0441760e4d982..e1687873c6d65 100644 --- a/recipes/ucsc-mafranges/build.sh +++ b/recipes/ucsc-mafranges/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafRanges && make) -cp bin/mafRanges "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafRanges" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafRanges && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafRanges "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafRanges" diff --git a/recipes/ucsc-mafranges/include.patch b/recipes/ucsc-mafranges/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafranges/include.patch +++ b/recipes/ucsc-mafranges/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafranges/meta.yaml b/recipes/ucsc-mafranges/meta.yaml index 6510d41b8bb8e..66d3c977d9dc7 100644 --- a/recipes/ucsc-mafranges/meta.yaml +++ b/recipes/ucsc-mafranges/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafranges" %} {% set program = "mafRanges" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract ranges of target (or query) coverage from maf and " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafsinregion/build.sh b/recipes/ucsc-mafsinregion/build.sh index 3e8ea07de6c37..4fb3f28a5e560 100644 --- a/recipes/ucsc-mafsinregion/build.sh +++ b/recipes/ucsc-mafsinregion/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafsInRegion && make) -cp bin/mafsInRegion "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafsInRegion" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafsInRegion && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafsInRegion "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafsInRegion" diff --git a/recipes/ucsc-mafsinregion/include.patch b/recipes/ucsc-mafsinregion/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafsinregion/include.patch +++ b/recipes/ucsc-mafsinregion/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafsinregion/meta.yaml b/recipes/ucsc-mafsinregion/meta.yaml index 81d418c4524e2..48415aa8bb4dc 100644 --- a/recipes/ucsc-mafsinregion/meta.yaml +++ b/recipes/ucsc-mafsinregion/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafsinregion" %} {% set program = "mafsInRegion" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract MAFS in a genomic region" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafspecieslist/build.sh b/recipes/ucsc-mafspecieslist/build.sh index fb5f2c9fc419c..b55e48756c1d1 100644 --- a/recipes/ucsc-mafspecieslist/build.sh +++ b/recipes/ucsc-mafspecieslist/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafSpeciesList && make) -cp bin/mafSpeciesList "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafSpeciesList" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafSpeciesList && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafSpeciesList "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafSpeciesList" diff --git a/recipes/ucsc-mafspecieslist/include.patch b/recipes/ucsc-mafspecieslist/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafspecieslist/include.patch +++ b/recipes/ucsc-mafspecieslist/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafspecieslist/meta.yaml b/recipes/ucsc-mafspecieslist/meta.yaml index db844606494ed..39fea6c3f3bcf 100644 --- a/recipes/ucsc-mafspecieslist/meta.yaml +++ b/recipes/ucsc-mafspecieslist/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafspecieslist" %} {% set program = "mafSpeciesList" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Scan maf and output all species used in it." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafspeciessubset/build.sh b/recipes/ucsc-mafspeciessubset/build.sh index 57941b4e15733..f1c3303a4e9d3 100644 --- a/recipes/ucsc-mafspeciessubset/build.sh +++ b/recipes/ucsc-mafspeciessubset/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafSpeciesSubset && make) -cp bin/mafSpeciesSubset "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafSpeciesSubset" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafSpeciesSubset && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafSpeciesSubset "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafSpeciesSubset" diff --git a/recipes/ucsc-mafspeciessubset/include.patch b/recipes/ucsc-mafspeciessubset/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafspeciessubset/include.patch +++ b/recipes/ucsc-mafspeciessubset/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafspeciessubset/meta.yaml b/recipes/ucsc-mafspeciessubset/meta.yaml index 29994a6b0c59f..566864c8adf9a 100644 --- a/recipes/ucsc-mafspeciessubset/meta.yaml +++ b/recipes/ucsc-mafspeciessubset/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafspeciessubset" %} {% set program = "mafSpeciesSubset" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract a maf that just has a subset of species." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafsplit/build.sh b/recipes/ucsc-mafsplit/build.sh index 16a94db036ce9..c95e8038cb565 100644 --- a/recipes/ucsc-mafsplit/build.sh +++ b/recipes/ucsc-mafsplit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafSplit && make) -cp bin/mafSplit "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafSplit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafSplit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafSplit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafSplit" diff --git a/recipes/ucsc-mafsplit/include.patch b/recipes/ucsc-mafsplit/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafsplit/include.patch +++ b/recipes/ucsc-mafsplit/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafsplit/meta.yaml b/recipes/ucsc-mafsplit/meta.yaml index 57c217ce78e8b..8fb771c78e0c5 100644 --- a/recipes/ucsc-mafsplit/meta.yaml +++ b/recipes/ucsc-mafsplit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafsplit" %} {% set program = "mafSplit" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split multiple alignment files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafsplitpos/build.sh b/recipes/ucsc-mafsplitpos/build.sh index 3c410b8870dc6..755b371f59363 100644 --- a/recipes/ucsc-mafsplitpos/build.sh +++ b/recipes/ucsc-mafsplitpos/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafSplitPos && make) -cp bin/mafSplitPos "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafSplitPos" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafSplitPos && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafSplitPos "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafSplitPos" diff --git a/recipes/ucsc-mafsplitpos/include.patch b/recipes/ucsc-mafsplitpos/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafsplitpos/include.patch +++ b/recipes/ucsc-mafsplitpos/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafsplitpos/meta.yaml b/recipes/ucsc-mafsplitpos/meta.yaml index 8c0fb2d4ad59c..77c67139a4334 100644 --- a/recipes/ucsc-mafsplitpos/meta.yaml +++ b/recipes/ucsc-mafsplitpos/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafsplitpos" %} {% set program = "mafSplitPos" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Pick positions to split multiple alignment input files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-maftoaxt/build.sh b/recipes/ucsc-maftoaxt/build.sh index d1c547e94566a..915b30b593cce 100644 --- a/recipes/ucsc-maftoaxt/build.sh +++ b/recipes/ucsc-maftoaxt/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafToAxt && make) -cp bin/mafToAxt "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafToAxt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafToAxt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafToAxt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafToAxt" diff --git a/recipes/ucsc-maftoaxt/include.patch b/recipes/ucsc-maftoaxt/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maftoaxt/include.patch +++ b/recipes/ucsc-maftoaxt/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maftoaxt/meta.yaml b/recipes/ucsc-maftoaxt/meta.yaml index 30844b9a378a5..2e31d3a08bf55 100644 --- a/recipes/ucsc-maftoaxt/meta.yaml +++ b/recipes/ucsc-maftoaxt/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maftoaxt" %} {% set program = "mafToAxt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from maf to axt format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maftobigmaf/build.sh b/recipes/ucsc-maftobigmaf/build.sh index b8f624f13c557..9e78fbddae397 100644 --- a/recipes/ucsc-maftobigmaf/build.sh +++ b/recipes/ucsc-maftobigmaf/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/mafToBigMaf && make) -cp bin/mafToBigMaf "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafToBigMaf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/mafToBigMaf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafToBigMaf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafToBigMaf" diff --git a/recipes/ucsc-maftobigmaf/include.patch b/recipes/ucsc-maftobigmaf/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maftobigmaf/include.patch +++ b/recipes/ucsc-maftobigmaf/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maftobigmaf/meta.yaml b/recipes/ucsc-maftobigmaf/meta.yaml index 823170338eb05..e99a1f9fec06f 100644 --- a/recipes/ucsc-maftobigmaf/meta.yaml +++ b/recipes/ucsc-maftobigmaf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maftobigmaf" %} {% set program = "mafToBigMaf" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Put ucsc standard maf file into bigMaf format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maftopsl/build.sh b/recipes/ucsc-maftopsl/build.sh index c9de71f45a5ed..3889b11a30b41 100644 --- a/recipes/ucsc-maftopsl/build.sh +++ b/recipes/ucsc-maftopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafToPsl && make) -cp bin/mafToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafToPsl" diff --git a/recipes/ucsc-maftopsl/include.patch b/recipes/ucsc-maftopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maftopsl/include.patch +++ b/recipes/ucsc-maftopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maftopsl/meta.yaml b/recipes/ucsc-maftopsl/meta.yaml index b47c1683b1e3b..ede1d2177c11c 100644 --- a/recipes/ucsc-maftopsl/meta.yaml +++ b/recipes/ucsc-maftopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maftopsl" %} {% set program = "mafToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert maf to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maftosnpbed/build.sh b/recipes/ucsc-maftosnpbed/build.sh index d85e46296e96a..50318d5b9132e 100644 --- a/recipes/ucsc-maftosnpbed/build.sh +++ b/recipes/ucsc-maftosnpbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafToSnpBed && make) -cp bin/mafToSnpBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafToSnpBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafToSnpBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafToSnpBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafToSnpBed" diff --git a/recipes/ucsc-maftosnpbed/include.patch b/recipes/ucsc-maftosnpbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maftosnpbed/include.patch +++ b/recipes/ucsc-maftosnpbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maftosnpbed/meta.yaml b/recipes/ucsc-maftosnpbed/meta.yaml index ec50b9371c946..46d27f2eb21d2 100644 --- a/recipes/ucsc-maftosnpbed/meta.yaml +++ b/recipes/ucsc-maftosnpbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maftosnpbed" %} {% set program = "mafToSnpBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "finds SNPs in MAF and builds a bed with their functional consequence" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-maketablelist/build.sh b/recipes/ucsc-maketablelist/build.sh index 5511e7edf2d17..637891a953eb6 100644 --- a/recipes/ucsc-maketablelist/build.sh +++ b/recipes/ucsc-maketablelist/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/makeTableList && make) -cp bin/makeTableList "$PREFIX/bin" -chmod +x "$PREFIX/bin/makeTableList" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/makeTableList && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/makeTableList "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/makeTableList" diff --git a/recipes/ucsc-maketablelist/include.patch b/recipes/ucsc-maketablelist/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maketablelist/include.patch +++ b/recipes/ucsc-maketablelist/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maketablelist/meta.yaml b/recipes/ucsc-maketablelist/meta.yaml index bed1d94da6a3d..b11002a961035 100644 --- a/recipes/ucsc-maketablelist/meta.yaml +++ b/recipes/ucsc-maketablelist/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maketablelist" %} {% set program = "makeTableList" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-maskoutfa/build.sh b/recipes/ucsc-maskoutfa/build.sh index 2f24ecb8fe45d..27e2043807128 100644 --- a/recipes/ucsc-maskoutfa/build.sh +++ b/recipes/ucsc-maskoutfa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/maskOutFa && make) -cp bin/maskOutFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/maskOutFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/maskOutFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/maskOutFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/maskOutFa" diff --git a/recipes/ucsc-maskoutfa/include.patch b/recipes/ucsc-maskoutfa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maskoutfa/include.patch +++ b/recipes/ucsc-maskoutfa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maskoutfa/meta.yaml b/recipes/ucsc-maskoutfa/meta.yaml index 9edb65eb58987..fa8cc7eb1593a 100644 --- a/recipes/ucsc-maskoutfa/meta.yaml +++ b/recipes/ucsc-maskoutfa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maskoutfa" %} {% set program = "maskOutFa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Produce a masked .fa file given an unmasked .fa and" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mktime/build.sh b/recipes/ucsc-mktime/build.sh index ac60435474cef..736038679a3b1 100644 --- a/recipes/ucsc-mktime/build.sh +++ b/recipes/ucsc-mktime/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/timing/mktime && make) -cp bin/mktime "$PREFIX/bin" -chmod +x "$PREFIX/bin/mktime" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/timing/mktime && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mktime "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mktime" diff --git a/recipes/ucsc-mktime/include.patch b/recipes/ucsc-mktime/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mktime/include.patch +++ b/recipes/ucsc-mktime/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mktime/meta.yaml b/recipes/ucsc-mktime/meta.yaml index ff8b7b04ca583..e52b1b0b0c71b 100644 --- a/recipes/ucsc-mktime/meta.yaml +++ b/recipes/ucsc-mktime/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mktime" %} {% set program = "mktime" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert date string to unix timestamp" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mrnatogene/build.sh b/recipes/ucsc-mrnatogene/build.sh index 1f51dc89ac019..356d27d294304 100644 --- a/recipes/ucsc-mrnatogene/build.sh +++ b/recipes/ucsc-mrnatogene/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mrnaToGene && make) -cp bin/mrnaToGene "$PREFIX/bin" -chmod +x "$PREFIX/bin/mrnaToGene" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mrnaToGene && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mrnaToGene "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mrnaToGene" diff --git a/recipes/ucsc-mrnatogene/include.patch b/recipes/ucsc-mrnatogene/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mrnatogene/include.patch +++ b/recipes/ucsc-mrnatogene/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mrnatogene/meta.yaml b/recipes/ucsc-mrnatogene/meta.yaml index d20f36281b5ff..b867c1e781a84 100644 --- a/recipes/ucsc-mrnatogene/meta.yaml +++ b/recipes/ucsc-mrnatogene/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mrnatogene" %} {% set program = "mrnaToGene" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert PSL alignments of mRNAs to gene annotations" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-netchainsubset/build.sh b/recipes/ucsc-netchainsubset/build.sh index 8427193703407..59ab5b713497e 100644 --- a/recipes/ucsc-netchainsubset/build.sh +++ b/recipes/ucsc-netchainsubset/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netChainSubset && make) -cp bin/netChainSubset "$PREFIX/bin" -chmod +x "$PREFIX/bin/netChainSubset" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netChainSubset && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netChainSubset "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netChainSubset" diff --git a/recipes/ucsc-netchainsubset/include.patch b/recipes/ucsc-netchainsubset/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netchainsubset/include.patch +++ b/recipes/ucsc-netchainsubset/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netchainsubset/meta.yaml b/recipes/ucsc-netchainsubset/meta.yaml index d877f1327402a..2f921aa504a60 100644 --- a/recipes/ucsc-netchainsubset/meta.yaml +++ b/recipes/ucsc-netchainsubset/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netchainsubset" %} {% set program = "netChainSubset" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create chain file with subset of chains that appear in the net" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-netclass/build.sh b/recipes/ucsc-netclass/build.sh index 68e9b089f5bcb..cf06d9c6b23c1 100644 --- a/recipes/ucsc-netclass/build.sh +++ b/recipes/ucsc-netclass/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netClass && make) -cp bin/netClass "$PREFIX/bin" -chmod +x "$PREFIX/bin/netClass" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netClass && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netClass "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netClass" diff --git a/recipes/ucsc-netclass/include.patch b/recipes/ucsc-netclass/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netclass/include.patch +++ b/recipes/ucsc-netclass/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netclass/meta.yaml b/recipes/ucsc-netclass/meta.yaml index 48be742bee886..bd64db2ff8c0e 100644 --- a/recipes/ucsc-netclass/meta.yaml +++ b/recipes/ucsc-netclass/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netclass" %} {% set program = "netClass" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add classification info to net" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-netfilter/build.sh b/recipes/ucsc-netfilter/build.sh index be78f3e060ccc..69dd249c8e00d 100644 --- a/recipes/ucsc-netfilter/build.sh +++ b/recipes/ucsc-netfilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netFilter && make) -cp bin/netFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/netFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netFilter" diff --git a/recipes/ucsc-netfilter/include.patch b/recipes/ucsc-netfilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netfilter/include.patch +++ b/recipes/ucsc-netfilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netfilter/meta.yaml b/recipes/ucsc-netfilter/meta.yaml index 0561f41a51fc9..59415265530ab 100644 --- a/recipes/ucsc-netfilter/meta.yaml +++ b/recipes/ucsc-netfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netfilter" %} {% set program = "netFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter out parts of net. What passes" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-netsplit/build.sh b/recipes/ucsc-netsplit/build.sh index 75be84d8d69e7..5baa0ef4281d0 100644 --- a/recipes/ucsc-netsplit/build.sh +++ b/recipes/ucsc-netsplit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netSplit && make) -cp bin/netSplit "$PREFIX/bin" -chmod +x "$PREFIX/bin/netSplit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netSplit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netSplit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netSplit" diff --git a/recipes/ucsc-netsplit/include.patch b/recipes/ucsc-netsplit/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netsplit/include.patch +++ b/recipes/ucsc-netsplit/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netsplit/meta.yaml b/recipes/ucsc-netsplit/meta.yaml index 8c6739a77a8e9..feca545a7efbc 100644 --- a/recipes/ucsc-netsplit/meta.yaml +++ b/recipes/ucsc-netsplit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netsplit" %} {% set program = "netSplit" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split a genome net file into chromosome net files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-netsyntenic/build.sh b/recipes/ucsc-netsyntenic/build.sh index 2ac9ac5182941..5e8aebf053581 100644 --- a/recipes/ucsc-netsyntenic/build.sh +++ b/recipes/ucsc-netsyntenic/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netSyntenic && make) -cp bin/netSyntenic "$PREFIX/bin" -chmod +x "$PREFIX/bin/netSyntenic" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netSyntenic && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netSyntenic "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netSyntenic" diff --git a/recipes/ucsc-netsyntenic/include.patch b/recipes/ucsc-netsyntenic/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netsyntenic/include.patch +++ b/recipes/ucsc-netsyntenic/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netsyntenic/meta.yaml b/recipes/ucsc-netsyntenic/meta.yaml index 81b2bddddd265..87b26bea97f27 100644 --- a/recipes/ucsc-netsyntenic/meta.yaml +++ b/recipes/ucsc-netsyntenic/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netsyntenic" %} {% set program = "netSyntenic" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add synteny info to net." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-nettoaxt/build.sh b/recipes/ucsc-nettoaxt/build.sh index 733eca3ea04bf..73bdfb3fd65e8 100644 --- a/recipes/ucsc-nettoaxt/build.sh +++ b/recipes/ucsc-nettoaxt/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netToAxt && make) -cp bin/netToAxt "$PREFIX/bin" -chmod +x "$PREFIX/bin/netToAxt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netToAxt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netToAxt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netToAxt" diff --git a/recipes/ucsc-nettoaxt/include.patch b/recipes/ucsc-nettoaxt/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-nettoaxt/include.patch +++ b/recipes/ucsc-nettoaxt/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-nettoaxt/meta.yaml b/recipes/ucsc-nettoaxt/meta.yaml index 52f7b5123312b..aeef00d707002 100644 --- a/recipes/ucsc-nettoaxt/meta.yaml +++ b/recipes/ucsc-nettoaxt/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-nettoaxt" %} {% set program = "netToAxt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert net (and chain) to axt." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-nettobed/build.sh b/recipes/ucsc-nettobed/build.sh index ebd0e971bcab6..f24f2ee9b350d 100644 --- a/recipes/ucsc-nettobed/build.sh +++ b/recipes/ucsc-nettobed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netToBed && make) -cp bin/netToBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/netToBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netToBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netToBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netToBed" diff --git a/recipes/ucsc-nettobed/include.patch b/recipes/ucsc-nettobed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-nettobed/include.patch +++ b/recipes/ucsc-nettobed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-nettobed/meta.yaml b/recipes/ucsc-nettobed/meta.yaml index a1278573aba66..78ef0cc414f73 100644 --- a/recipes/ucsc-nettobed/meta.yaml +++ b/recipes/ucsc-nettobed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-nettobed" %} {% set program = "netToBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert target coverage of net to a bed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-newprog/build.sh b/recipes/ucsc-newprog/build.sh index c3ae494488a4a..8549421304b91 100644 --- a/recipes/ucsc-newprog/build.sh +++ b/recipes/ucsc-newprog/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/newProg && make) -cp bin/newProg "$PREFIX/bin" -chmod +x "$PREFIX/bin/newProg" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/newProg && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/newProg "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/newProg" diff --git a/recipes/ucsc-newprog/include.patch b/recipes/ucsc-newprog/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-newprog/include.patch +++ b/recipes/ucsc-newprog/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-newprog/meta.yaml b/recipes/ucsc-newprog/meta.yaml index 9d93bc10fe5fe..4f06ccbc16664 100644 --- a/recipes/ucsc-newprog/meta.yaml +++ b/recipes/ucsc-newprog/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-newprog" %} {% set program = "newProg" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "make a new C source skeleton." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-newpythonprog/build.sh b/recipes/ucsc-newpythonprog/build.sh index a049d1734108b..9b3d10a8a6f99 100644 --- a/recipes/ucsc-newpythonprog/build.sh +++ b/recipes/ucsc-newpythonprog/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/newPythonProg && make) -cp bin/newPythonProg "$PREFIX/bin" -chmod +x "$PREFIX/bin/newPythonProg" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/newPythonProg && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/newPythonProg "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/newPythonProg" diff --git a/recipes/ucsc-newpythonprog/include.patch b/recipes/ucsc-newpythonprog/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-newpythonprog/include.patch +++ b/recipes/ucsc-newpythonprog/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-newpythonprog/meta.yaml b/recipes/ucsc-newpythonprog/meta.yaml index 7f8c05c0c5380..361d9f8b5f4fd 100644 --- a/recipes/ucsc-newpythonprog/meta.yaml +++ b/recipes/ucsc-newpythonprog/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-newpythonprog" %} {% set program = "newPythonProg" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make a skeleton for a new python program" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-nibfrag/build.sh b/recipes/ucsc-nibfrag/build.sh index 088a651a09043..bb08f993f9b15 100644 --- a/recipes/ucsc-nibfrag/build.sh +++ b/recipes/ucsc-nibfrag/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/nibFrag && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -x bin/nibFrag "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/nibFrag" +cp bin/nibFrag "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/nibFrag" diff --git a/recipes/ucsc-nibfrag/meta.yaml b/recipes/ucsc-nibfrag/meta.yaml index 17bb497cfb5d5..d62bed526b13b 100644 --- a/recipes/ucsc-nibfrag/meta.yaml +++ b/recipes/ucsc-nibfrag/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-nibfrag" %} {% set program = "nibFrag" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract part of a nib file as .fa (all bases/gaps lower case by default)" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-nibsize/build.sh b/recipes/ucsc-nibsize/build.sh index e2caa29987ced..7a2721a2626ba 100644 --- a/recipes/ucsc-nibsize/build.sh +++ b/recipes/ucsc-nibsize/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/nibSize && make) -cp bin/nibSize "$PREFIX/bin" -chmod +x "$PREFIX/bin/nibSize" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/nibSize && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/nibSize "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/nibSize" diff --git a/recipes/ucsc-nibsize/include.patch b/recipes/ucsc-nibsize/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-nibsize/include.patch +++ b/recipes/ucsc-nibsize/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-nibsize/meta.yaml b/recipes/ucsc-nibsize/meta.yaml index 79d338775cab0..c137ff3bace8e 100644 --- a/recipes/ucsc-nibsize/meta.yaml +++ b/recipes/ucsc-nibsize/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-nibsize" %} {% set program = "nibSize" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "print size of nibs" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-oligomatch/build.sh b/recipes/ucsc-oligomatch/build.sh index a88ccff20a470..3d72e4bab8926 100644 --- a/recipes/ucsc-oligomatch/build.sh +++ b/recipes/ucsc-oligomatch/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/utils/oligoMatch && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/oligoMatch "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/oligoMatch" +cp bin/oligoMatch "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/oligoMatch" diff --git a/recipes/ucsc-oligomatch/meta.yaml b/recipes/ucsc-oligomatch/meta.yaml index e3e152c54dd21..f34d627ba9455 100644 --- a/recipes/ucsc-oligomatch/meta.yaml +++ b/recipes/ucsc-oligomatch/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-oligomatch" %} {% set program = "oligoMatch" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "find perfect matches in sequence." dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-overlapselect/build.sh b/recipes/ucsc-overlapselect/build.sh index cc2603b122258..142a3f3814a7c 100644 --- a/recipes/ucsc-overlapselect/build.sh +++ b/recipes/ucsc-overlapselect/build.sh @@ -1,15 +1,22 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -export LIBRARY_PATH=$PREFIX/lib -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/stringify && make) -(cd kent/src/hg/utils/overlapSelect && make) -cp bin/overlapSelect "$PREFIX/bin" -chmod +x "$PREFIX/bin/overlapSelect" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/overlapSelect && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/overlapSelect "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/overlapSelect" diff --git a/recipes/ucsc-overlapselect/include.patch b/recipes/ucsc-overlapselect/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-overlapselect/include.patch +++ b/recipes/ucsc-overlapselect/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-overlapselect/meta.yaml b/recipes/ucsc-overlapselect/meta.yaml index c56ff504055c6..00978ce2ec5d1 100644 --- a/recipes/ucsc-overlapselect/meta.yaml +++ b/recipes/ucsc-overlapselect/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-overlapselect" %} {% set program = "overlapSelect" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,24 +27,24 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Select records based on overlapping chromosome ranges. The ranges are specified in the selectFile, with each block specifying a range. @@ -50,3 +52,11 @@ Records are copied from the inFile to outFile based on the selection criteria. Selection is based on blocks or exons rather than entire range. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-para/build.sh b/recipes/ucsc-para/build.sh index 6fd859b06df5a..42637fdceedef 100644 --- a/recipes/ucsc-para/build.sh +++ b/recipes/ucsc-para/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/para "$PREFIX/bin" -chmod +x "$PREFIX/bin/para" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/para "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/para" diff --git a/recipes/ucsc-para/include.patch b/recipes/ucsc-para/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-para/include.patch +++ b/recipes/ucsc-para/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-para/meta.yaml b/recipes/ucsc-para/meta.yaml index ce4365c52b3fd..51ddc57dd7308 100644 --- a/recipes/ucsc-para/meta.yaml +++ b/recipes/ucsc-para/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-para" %} {% set program = "para" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parafetch/build.sh b/recipes/ucsc-parafetch/build.sh index 4ca0a8d0b0c96..4b721d3254311 100644 --- a/recipes/ucsc-parafetch/build.sh +++ b/recipes/ucsc-parafetch/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/paraFetch && make) -cp bin/paraFetch "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraFetch" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/paraFetch && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/paraFetch "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraFetch" diff --git a/recipes/ucsc-parafetch/include.patch b/recipes/ucsc-parafetch/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parafetch/include.patch +++ b/recipes/ucsc-parafetch/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parafetch/meta.yaml b/recipes/ucsc-parafetch/meta.yaml index f87780cd44f5a..027e9eb2c2a9f 100644 --- a/recipes/ucsc-parafetch/meta.yaml +++ b/recipes/ucsc-parafetch/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parafetch" %} {% set program = "paraFetch" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "try to fetch url with multiple connections" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parahub/build.sh b/recipes/ucsc-parahub/build.sh index b07637d49880f..b3179ffe3b0ea 100644 --- a/recipes/ucsc-parahub/build.sh +++ b/recipes/ucsc-parahub/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraHub "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraHub" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraHub "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraHub" diff --git a/recipes/ucsc-parahub/include.patch b/recipes/ucsc-parahub/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parahub/include.patch +++ b/recipes/ucsc-parahub/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parahub/meta.yaml b/recipes/ucsc-parahub/meta.yaml index 1c6a1f5c685f9..5643cd381a146 100644 --- a/recipes/ucsc-parahub/meta.yaml +++ b/recipes/ucsc-parahub/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parahub" %} {% set program = "paraHub" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "parasol hub server version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parahubstop/build.sh b/recipes/ucsc-parahubstop/build.sh index b6d59daed3d1b..4928c38160983 100644 --- a/recipes/ucsc-parahubstop/build.sh +++ b/recipes/ucsc-parahubstop/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraHubStop "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraHubStop" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraHubStop "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraHubStop" diff --git a/recipes/ucsc-parahubstop/include.patch b/recipes/ucsc-parahubstop/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parahubstop/include.patch +++ b/recipes/ucsc-parahubstop/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parahubstop/meta.yaml b/recipes/ucsc-parahubstop/meta.yaml index 3db97dd0e5048..58351f6cdbfed 100644 --- a/recipes/ucsc-parahubstop/meta.yaml +++ b/recipes/ucsc-parahubstop/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parahubstop" %} {% set program = "paraHubStop" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paranode/build.sh b/recipes/ucsc-paranode/build.sh index 9f0598370b27c..4264150ac6964 100644 --- a/recipes/ucsc-paranode/build.sh +++ b/recipes/ucsc-paranode/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraNode "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraNode" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraNode "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraNode" diff --git a/recipes/ucsc-paranode/include.patch b/recipes/ucsc-paranode/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paranode/include.patch +++ b/recipes/ucsc-paranode/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paranode/meta.yaml b/recipes/ucsc-paranode/meta.yaml index ac3724fcebfc6..bebf62ba576af 100644 --- a/recipes/ucsc-paranode/meta.yaml +++ b/recipes/ucsc-paranode/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paranode" %} {% set program = "paraNode" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paranodestart/build.sh b/recipes/ucsc-paranodestart/build.sh index 12c13b8de1cc0..bcd025dda9cfd 100644 --- a/recipes/ucsc-paranodestart/build.sh +++ b/recipes/ucsc-paranodestart/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraNodeStart "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraNodeStart" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraNodeStart "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraNodeStart" diff --git a/recipes/ucsc-paranodestart/include.patch b/recipes/ucsc-paranodestart/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paranodestart/include.patch +++ b/recipes/ucsc-paranodestart/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paranodestart/meta.yaml b/recipes/ucsc-paranodestart/meta.yaml index 616f68ffa2dc6..fc403349abe12 100644 --- a/recipes/ucsc-paranodestart/meta.yaml +++ b/recipes/ucsc-paranodestart/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paranodestart" %} {% set program = "paraNodeStart" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paranodestatus/build.sh b/recipes/ucsc-paranodestatus/build.sh index 1bcf47aaa7b35..511f3623d3dff 100644 --- a/recipes/ucsc-paranodestatus/build.sh +++ b/recipes/ucsc-paranodestatus/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraNodeStatus "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraNodeStatus" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraNodeStatus "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraNodeStatus" diff --git a/recipes/ucsc-paranodestatus/include.patch b/recipes/ucsc-paranodestatus/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paranodestatus/include.patch +++ b/recipes/ucsc-paranodestatus/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paranodestatus/meta.yaml b/recipes/ucsc-paranodestatus/meta.yaml index de880fd0e1e19..8f02ac48eb5c0 100644 --- a/recipes/ucsc-paranodestatus/meta.yaml +++ b/recipes/ucsc-paranodestatus/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paranodestatus" %} {% set program = "paraNodeStatus" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paranodestop/build.sh b/recipes/ucsc-paranodestop/build.sh index 70ee91dcb5ccb..3bf8a31b65e09 100644 --- a/recipes/ucsc-paranodestop/build.sh +++ b/recipes/ucsc-paranodestop/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraNodeStop "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraNodeStop" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraNodeStop "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraNodeStop" diff --git a/recipes/ucsc-paranodestop/include.patch b/recipes/ucsc-paranodestop/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paranodestop/include.patch +++ b/recipes/ucsc-paranodestop/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paranodestop/meta.yaml b/recipes/ucsc-paranodestop/meta.yaml index 4cd1915969163..f7128debc7d61 100644 --- a/recipes/ucsc-paranodestop/meta.yaml +++ b/recipes/ucsc-paranodestop/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paranodestop" %} {% set program = "paraNodeStop" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,24 +27,33 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Shut down parasol node daemons on a list of machines " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parasol/build.sh b/recipes/ucsc-parasol/build.sh index 71cb7156a637c..0c8cf86fdf1eb 100644 --- a/recipes/ucsc-parasol/build.sh +++ b/recipes/ucsc-parasol/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/parasol "$PREFIX/bin" -chmod +x "$PREFIX/bin/parasol" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/parasol "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/parasol" diff --git a/recipes/ucsc-parasol/include.patch b/recipes/ucsc-parasol/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parasol/include.patch +++ b/recipes/ucsc-parasol/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parasol/meta.yaml b/recipes/ucsc-parasol/meta.yaml index 312af4a41ac72..0b01fffa4b53f 100644 --- a/recipes/ucsc-parasol/meta.yaml +++ b/recipes/ucsc-parasol/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parasol" %} {% set program = "parasol" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,27 +27,36 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Parasol is the name given to the overall system for managing jobs on a computer cluster and to this specific command. This command is intended primarily for system administrators. The 'para' command is the primary command for users. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parasync/build.sh b/recipes/ucsc-parasync/build.sh index 471e37fc9c924..5d4414af87ee1 100644 --- a/recipes/ucsc-parasync/build.sh +++ b/recipes/ucsc-parasync/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/paraSync && make) -cp bin/paraSync "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraSync" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/paraSync && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/paraSync "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraSync" diff --git a/recipes/ucsc-parasync/include.patch b/recipes/ucsc-parasync/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parasync/include.patch +++ b/recipes/ucsc-parasync/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parasync/meta.yaml b/recipes/ucsc-parasync/meta.yaml index cd3b79f2d8324..ef74648b0d782 100644 --- a/recipes/ucsc-parasync/meta.yaml +++ b/recipes/ucsc-parasync/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parasync" %} {% set program = "paraSync" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "uses paraFetch to recursively mirror url to given path" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paratestjob/build.sh b/recipes/ucsc-paratestjob/build.sh index 3578cd03ac885..23d28f563e267 100644 --- a/recipes/ucsc-paratestjob/build.sh +++ b/recipes/ucsc-paratestjob/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraTestJob "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraTestJob" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraTestJob "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraTestJob" diff --git a/recipes/ucsc-paratestjob/include.patch b/recipes/ucsc-paratestjob/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paratestjob/include.patch +++ b/recipes/ucsc-paratestjob/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paratestjob/meta.yaml b/recipes/ucsc-paratestjob/meta.yaml index ab5b4396c8617..edbd7f5781f3d 100644 --- a/recipes/ucsc-paratestjob/meta.yaml +++ b/recipes/ucsc-paratestjob/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paratestjob" %} {% set program = "paraTestJob" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-positionaltblcheck/build.sh b/recipes/ucsc-positionaltblcheck/build.sh index 2aac0fb259542..4a2db6d3472b3 100644 --- a/recipes/ucsc-positionaltblcheck/build.sh +++ b/recipes/ucsc-positionaltblcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/positionalTblCheck && make) -cp bin/positionalTblCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/positionalTblCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/positionalTblCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/positionalTblCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/positionalTblCheck" diff --git a/recipes/ucsc-positionaltblcheck/include.patch b/recipes/ucsc-positionaltblcheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-positionaltblcheck/include.patch +++ b/recipes/ucsc-positionaltblcheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-positionaltblcheck/meta.yaml b/recipes/ucsc-positionaltblcheck/meta.yaml index 022176abef7e4..d71f3a86bf615 100644 --- a/recipes/ucsc-positionaltblcheck/meta.yaml +++ b/recipes/ucsc-positionaltblcheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-positionaltblcheck" %} {% set program = "positionalTblCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "check that positional tables are sorted" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-pslcat/build.sh b/recipes/ucsc-pslcat/build.sh index 8f0d19f7c40f9..ef4ae6bb97d3d 100644 --- a/recipes/ucsc-pslcat/build.sh +++ b/recipes/ucsc-pslcat/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslCat && make) -cp bin/pslCat "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslCat" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslCat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslCat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslCat" diff --git a/recipes/ucsc-pslcat/include.patch b/recipes/ucsc-pslcat/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslcat/include.patch +++ b/recipes/ucsc-pslcat/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslcat/meta.yaml b/recipes/ucsc-pslcat/meta.yaml index 21c04084ea807..84be38fe0d48b 100644 --- a/recipes/ucsc-pslcat/meta.yaml +++ b/recipes/ucsc-pslcat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslcat" %} {% set program = "pslCat" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "concatenate psl files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslcdnafilter/build.sh b/recipes/ucsc-pslcdnafilter/build.sh index 05a21275d4c6d..6f9c17e7cba0b 100644 --- a/recipes/ucsc-pslcdnafilter/build.sh +++ b/recipes/ucsc-pslcdnafilter/build.sh @@ -1,14 +1,22 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/stringify && make) -(cd kent/src/hg/pslCDnaFilter && make) -cp bin/pslCDnaFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslCDnaFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslCDnaFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslCDnaFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslCDnaFilter" diff --git a/recipes/ucsc-pslcdnafilter/include.patch b/recipes/ucsc-pslcdnafilter/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslcdnafilter/include.patch +++ b/recipes/ucsc-pslcdnafilter/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml index 8807ae5634842..58d533a67e4ff 100644 --- a/recipes/ucsc-pslcdnafilter/meta.yaml +++ b/recipes/ucsc-pslcdnafilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslcdnafilter" %} {% set program = "pslCDnaFilter" %} -{% set version = "445" %} -{% set sha256 = "c7abb5db6a5e16a79aefcee849d2b59dbc71ee112ca1e41fea0afb25229cf56c" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,39 +14,48 @@ source: - "include.patch" build: - skip: True # [osx] - number: 1 + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-pslcheck/build.sh b/recipes/ucsc-pslcheck/build.sh index 9b8ba14c30a7e..bea130066fb3d 100644 --- a/recipes/ucsc-pslcheck/build.sh +++ b/recipes/ucsc-pslcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslCheck && make) -cp bin/pslCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslCheck" diff --git a/recipes/ucsc-pslcheck/include.patch b/recipes/ucsc-pslcheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslcheck/include.patch +++ b/recipes/ucsc-pslcheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslcheck/meta.yaml b/recipes/ucsc-pslcheck/meta.yaml index bdb230d6bd710..58ac61563cab6 100644 --- a/recipes/ucsc-pslcheck/meta.yaml +++ b/recipes/ucsc-pslcheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslcheck" %} {% set program = "pslCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "validate PSL files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-psldropoverlap/build.sh b/recipes/ucsc-psldropoverlap/build.sh index 3d6c3a2acdf28..8056852ba266e 100644 --- a/recipes/ucsc-psldropoverlap/build.sh +++ b/recipes/ucsc-psldropoverlap/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslDropOverlap && make) -cp bin/pslDropOverlap "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslDropOverlap" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslDropOverlap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslDropOverlap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslDropOverlap" diff --git a/recipes/ucsc-psldropoverlap/include.patch b/recipes/ucsc-psldropoverlap/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-psldropoverlap/include.patch +++ b/recipes/ucsc-psldropoverlap/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-psldropoverlap/meta.yaml b/recipes/ucsc-psldropoverlap/meta.yaml index 69fc9e7fd456d..6e34ccd565410 100644 --- a/recipes/ucsc-psldropoverlap/meta.yaml +++ b/recipes/ucsc-psldropoverlap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psldropoverlap" %} {% set program = "pslDropOverlap" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "deletes all overlapping self alignments. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslfilter/build.sh b/recipes/ucsc-pslfilter/build.sh index 45a8bda3a2219..cf8b855b41b42 100644 --- a/recipes/ucsc-pslfilter/build.sh +++ b/recipes/ucsc-pslfilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslFilter && make) -cp bin/pslFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslFilter" diff --git a/recipes/ucsc-pslfilter/include.patch b/recipes/ucsc-pslfilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslfilter/include.patch +++ b/recipes/ucsc-pslfilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslfilter/meta.yaml b/recipes/ucsc-pslfilter/meta.yaml index 73d97517cbbee..3069b7da5417d 100644 --- a/recipes/ucsc-pslfilter/meta.yaml +++ b/recipes/ucsc-pslfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslfilter" %} {% set program = "pslFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "filter out psl file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslhisto/build.sh b/recipes/ucsc-pslhisto/build.sh index 238e2991da267..0e8b1fe8c5bf1 100644 --- a/recipes/ucsc-pslhisto/build.sh +++ b/recipes/ucsc-pslhisto/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslHisto && make) -cp bin/pslHisto "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslHisto" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslHisto && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslHisto "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslHisto" diff --git a/recipes/ucsc-pslhisto/include.patch b/recipes/ucsc-pslhisto/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslhisto/include.patch +++ b/recipes/ucsc-pslhisto/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslhisto/meta.yaml b/recipes/ucsc-pslhisto/meta.yaml index 4c2c365449d80..3f78d33a190b3 100644 --- a/recipes/ucsc-pslhisto/meta.yaml +++ b/recipes/ucsc-pslhisto/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslhisto" %} {% set program = "pslHisto" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,25 +27,34 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Collect counts on PSL alignments for making histograms. These then be analyzed with R, textHistogram, etc. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslliftsubrangeblat/build.sh b/recipes/ucsc-pslliftsubrangeblat/build.sh index 0e33ea9346038..a814a887df9b0 100644 --- a/recipes/ucsc-pslliftsubrangeblat/build.sh +++ b/recipes/ucsc-pslliftsubrangeblat/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/pslLiftSubrangeBlat && make) -cp bin/pslLiftSubrangeBlat "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslLiftSubrangeBlat" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/pslLiftSubrangeBlat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslLiftSubrangeBlat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslLiftSubrangeBlat" diff --git a/recipes/ucsc-pslliftsubrangeblat/include.patch b/recipes/ucsc-pslliftsubrangeblat/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslliftsubrangeblat/include.patch +++ b/recipes/ucsc-pslliftsubrangeblat/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslliftsubrangeblat/meta.yaml b/recipes/ucsc-pslliftsubrangeblat/meta.yaml index fecad941cbb28..79dce984359ef 100644 --- a/recipes/ucsc-pslliftsubrangeblat/meta.yaml +++ b/recipes/ucsc-pslliftsubrangeblat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslliftsubrangeblat" %} {% set program = "pslLiftSubrangeBlat" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "lift PSLs from blat subrange alignments" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-pslmap/build.sh b/recipes/ucsc-pslmap/build.sh index a50ee2333c360..dc5c2fd9f25d7 100644 --- a/recipes/ucsc-pslmap/build.sh +++ b/recipes/ucsc-pslmap/build.sh @@ -1,14 +1,22 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/stringify && make) -(cd kent/src/hg/utils/pslMap && make) -cp bin/pslMap "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslMap" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslMap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslMap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslMap" diff --git a/recipes/ucsc-pslmap/include.patch b/recipes/ucsc-pslmap/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslmap/include.patch +++ b/recipes/ucsc-pslmap/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslmap/meta.yaml b/recipes/ucsc-pslmap/meta.yaml index 2c144a480b637..df0c23ae1a8c3 100644 --- a/recipes/ucsc-pslmap/meta.yaml +++ b/recipes/ucsc-pslmap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslmap" %} {% set program = "pslMap" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "map PSLs alignments to new targets using alignments of" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslmappostchain/build.sh b/recipes/ucsc-pslmappostchain/build.sh index 54453ecba698c..5eadb4481a518 100644 --- a/recipes/ucsc-pslmappostchain/build.sh +++ b/recipes/ucsc-pslmappostchain/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/pslMapPostChain && make) -cp bin/pslMapPostChain "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslMapPostChain" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslMapPostChain && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslMapPostChain "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslMapPostChain" diff --git a/recipes/ucsc-pslmappostchain/include.patch b/recipes/ucsc-pslmappostchain/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslmappostchain/include.patch +++ b/recipes/ucsc-pslmappostchain/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslmappostchain/meta.yaml b/recipes/ucsc-pslmappostchain/meta.yaml index b2906a3216d1f..7c51187e06db4 100644 --- a/recipes/ucsc-pslmappostchain/meta.yaml +++ b/recipes/ucsc-pslmappostchain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslmappostchain" %} {% set program = "pslMapPostChain" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,27 +27,36 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Post genomic pslMap (TransMap) chaining. This takes transcripts that have been mapped via genomic chains adds back in blocks that didn't get include in genomic chains due to complex rearrangements or other issues. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslmrnacover/build.sh b/recipes/ucsc-pslmrnacover/build.sh index 356e0e2e3bc36..9cff5cb571c0e 100644 --- a/recipes/ucsc-pslmrnacover/build.sh +++ b/recipes/ucsc-pslmrnacover/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/pslMrnaCover && make) -cp bin/pslMrnaCover "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslMrnaCover" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/pslMrnaCover && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslMrnaCover "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslMrnaCover" diff --git a/recipes/ucsc-pslmrnacover/include.patch b/recipes/ucsc-pslmrnacover/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslmrnacover/include.patch +++ b/recipes/ucsc-pslmrnacover/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslmrnacover/meta.yaml b/recipes/ucsc-pslmrnacover/meta.yaml index 8a19d625c6e28..a50e026a5250b 100644 --- a/recipes/ucsc-pslmrnacover/meta.yaml +++ b/recipes/ucsc-pslmrnacover/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslmrnacover" %} {% set program = "pslMrnaCover" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make histogram of coverage percentage of mRNA in psl." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslpairs/build.sh b/recipes/ucsc-pslpairs/build.sh index e16513ef01203..6cd14191ba17c 100644 --- a/recipes/ucsc-pslpairs/build.sh +++ b/recipes/ucsc-pslpairs/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslPairs && make) -cp bin/pslPairs "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslPairs" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslPairs && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslPairs "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslPairs" diff --git a/recipes/ucsc-pslpairs/include.patch b/recipes/ucsc-pslpairs/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslpairs/include.patch +++ b/recipes/ucsc-pslpairs/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslpairs/meta.yaml b/recipes/ucsc-pslpairs/meta.yaml index 6f627277f1e4a..73161b3ec6fb7 100644 --- a/recipes/ucsc-pslpairs/meta.yaml +++ b/recipes/ucsc-pslpairs/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslpairs" %} {% set program = "pslPairs" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "join paired ends in psl alignments" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslpartition/build.sh b/recipes/ucsc-pslpartition/build.sh index 3a4209e4f50cf..291e7d801ec0b 100644 --- a/recipes/ucsc-pslpartition/build.sh +++ b/recipes/ucsc-pslpartition/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslPartition && make) -cp bin/pslPartition "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslPartition" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslPartition && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslPartition "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslPartition" diff --git a/recipes/ucsc-pslpartition/include.patch b/recipes/ucsc-pslpartition/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslpartition/include.patch +++ b/recipes/ucsc-pslpartition/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslpartition/meta.yaml b/recipes/ucsc-pslpartition/meta.yaml index 11df1060d2279..377e85b51ecf5 100644 --- a/recipes/ucsc-pslpartition/meta.yaml +++ b/recipes/ucsc-pslpartition/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslpartition" %} {% set program = "pslPartition" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "split PSL files into non-overlapping sets" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslpostarget/build.sh b/recipes/ucsc-pslpostarget/build.sh index a69900e05adbd..fb27dca9ad942 100644 --- a/recipes/ucsc-pslpostarget/build.sh +++ b/recipes/ucsc-pslpostarget/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/pslPosTarget && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslPosTarget "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslPosTarget" +cp bin/pslPosTarget "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslPosTarget" diff --git a/recipes/ucsc-pslpostarget/meta.yaml b/recipes/ucsc-pslpostarget/meta.yaml index 7dfaf50fd3ce5..8172abd6a6979 100644 --- a/recipes/ucsc-pslpostarget/meta.yaml +++ b/recipes/ucsc-pslpostarget/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslpostarget" %} {% set program = "pslPosTarget" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "flip psl strands so target is positive and implicit" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-pslpretty/build.sh b/recipes/ucsc-pslpretty/build.sh index 89c3ce9725e23..f4d1451c7c558 100644 --- a/recipes/ucsc-pslpretty/build.sh +++ b/recipes/ucsc-pslpretty/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslPretty && make) -cp bin/pslPretty "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslPretty" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslPretty && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslPretty "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslPretty" diff --git a/recipes/ucsc-pslpretty/include.patch b/recipes/ucsc-pslpretty/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslpretty/include.patch +++ b/recipes/ucsc-pslpretty/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslpretty/meta.yaml b/recipes/ucsc-pslpretty/meta.yaml index 9810dafca6c09..e2db3fedad559 100644 --- a/recipes/ucsc-pslpretty/meta.yaml +++ b/recipes/ucsc-pslpretty/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslpretty" %} {% set program = "pslPretty" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert PSL to human-readable output" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslrc/build.sh b/recipes/ucsc-pslrc/build.sh index 03b0eed50d4cd..6ca282e519ca1 100644 --- a/recipes/ucsc-pslrc/build.sh +++ b/recipes/ucsc-pslrc/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/pslRc && make) -cp bin/pslRc "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslRc" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslRc && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslRc "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslRc" diff --git a/recipes/ucsc-pslrc/include.patch b/recipes/ucsc-pslrc/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslrc/include.patch +++ b/recipes/ucsc-pslrc/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslrc/meta.yaml b/recipes/ucsc-pslrc/meta.yaml index a42ca7ee23c4d..3ac6f82f47dfe 100644 --- a/recipes/ucsc-pslrc/meta.yaml +++ b/recipes/ucsc-pslrc/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslrc" %} {% set program = "pslRc" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "reverse-complement psl" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslrecalcmatch/build.sh b/recipes/ucsc-pslrecalcmatch/build.sh index 8627cd251a72a..17f174080a9f0 100644 --- a/recipes/ucsc-pslrecalcmatch/build.sh +++ b/recipes/ucsc-pslrecalcmatch/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslRecalcMatch && make) -cp bin/pslRecalcMatch "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslRecalcMatch" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslRecalcMatch && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslRecalcMatch "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslRecalcMatch" diff --git a/recipes/ucsc-pslrecalcmatch/include.patch b/recipes/ucsc-pslrecalcmatch/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslrecalcmatch/include.patch +++ b/recipes/ucsc-pslrecalcmatch/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslrecalcmatch/meta.yaml b/recipes/ucsc-pslrecalcmatch/meta.yaml index 346d395661228..3a6b62e0f316b 100644 --- a/recipes/ucsc-pslrecalcmatch/meta.yaml +++ b/recipes/ucsc-pslrecalcmatch/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslrecalcmatch" %} {% set program = "pslRecalcMatch" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Recalculate match,mismatch,repMatch columns in psl file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslreps/build.sh b/recipes/ucsc-pslreps/build.sh index adbe151df2566..fa9e34309baed 100644 --- a/recipes/ucsc-pslreps/build.sh +++ b/recipes/ucsc-pslreps/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslReps && make) -cp bin/pslReps "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslReps" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslReps && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslReps "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslReps" diff --git a/recipes/ucsc-pslreps/include.patch b/recipes/ucsc-pslreps/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslreps/include.patch +++ b/recipes/ucsc-pslreps/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslreps/meta.yaml b/recipes/ucsc-pslreps/meta.yaml index 450be1b4a1e2c..a6430c181ea3c 100644 --- a/recipes/ucsc-pslreps/meta.yaml +++ b/recipes/ucsc-pslreps/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslreps" %} {% set program = "pslReps" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Analyze repeats and generate genome-wide best alignments from a" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslscore/build.sh b/recipes/ucsc-pslscore/build.sh index 1a0fa041d5306..874a7d983f790 100644 --- a/recipes/ucsc-pslscore/build.sh +++ b/recipes/ucsc-pslscore/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/pslScore && make) -cp bin/pslScore "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslScore" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslScore && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslScore "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslScore" diff --git a/recipes/ucsc-pslscore/include.patch b/recipes/ucsc-pslscore/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslscore/include.patch +++ b/recipes/ucsc-pslscore/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslscore/meta.yaml b/recipes/ucsc-pslscore/meta.yaml index 5be496a84abbb..1476a30e87a17 100644 --- a/recipes/ucsc-pslscore/meta.yaml +++ b/recipes/ucsc-pslscore/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslscore" %} {% set program = "pslScore" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "calculate web blat score from psl files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslselect/build.sh b/recipes/ucsc-pslselect/build.sh index 661a81177c6c2..c9df1304a0391 100644 --- a/recipes/ucsc-pslselect/build.sh +++ b/recipes/ucsc-pslselect/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslSelect && make) -cp bin/pslSelect "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslSelect" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslSelect && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslSelect "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslSelect" diff --git a/recipes/ucsc-pslselect/include.patch b/recipes/ucsc-pslselect/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslselect/include.patch +++ b/recipes/ucsc-pslselect/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslselect/meta.yaml b/recipes/ucsc-pslselect/meta.yaml index 94e42706a0ac7..58d456a600295 100644 --- a/recipes/ucsc-pslselect/meta.yaml +++ b/recipes/ucsc-pslselect/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslselect" %} {% set program = "pslSelect" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "select records from a PSL file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslsomerecords/build.sh b/recipes/ucsc-pslsomerecords/build.sh index c7390660855d1..ad88b60584d55 100644 --- a/recipes/ucsc-pslsomerecords/build.sh +++ b/recipes/ucsc-pslsomerecords/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslSomeRecords && make) -cp bin/pslSomeRecords "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslSomeRecords" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslSomeRecords && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslSomeRecords "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslSomeRecords" diff --git a/recipes/ucsc-pslsomerecords/include.patch b/recipes/ucsc-pslsomerecords/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslsomerecords/include.patch +++ b/recipes/ucsc-pslsomerecords/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslsomerecords/meta.yaml b/recipes/ucsc-pslsomerecords/meta.yaml index 1bc820c6a1f16..5af9a55a1dad2 100644 --- a/recipes/ucsc-pslsomerecords/meta.yaml +++ b/recipes/ucsc-pslsomerecords/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslsomerecords" %} {% set program = "pslSomeRecords" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract multiple psl records" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslsort/build.sh b/recipes/ucsc-pslsort/build.sh index b18c33998499e..046c3d78cb35f 100644 --- a/recipes/ucsc-pslsort/build.sh +++ b/recipes/ucsc-pslsort/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslSort "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslSort" +cp bin/pslSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslSort" diff --git a/recipes/ucsc-pslsort/meta.yaml b/recipes/ucsc-pslsort/meta.yaml index 79c34e14b5ec6..5e7ae26baeb3f 100644 --- a/recipes/ucsc-pslsort/meta.yaml +++ b/recipes/ucsc-pslsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslsort" %} {% set program = "pslSort" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Merge and sort psCluster .psl output files" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-pslstats/build.sh b/recipes/ucsc-pslstats/build.sh index e010d560bb0c1..5955bcc8bc430 100644 --- a/recipes/ucsc-pslstats/build.sh +++ b/recipes/ucsc-pslstats/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslStats && make) -cp bin/pslStats "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslStats" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslStats && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslStats "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslStats" diff --git a/recipes/ucsc-pslstats/include.patch b/recipes/ucsc-pslstats/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslstats/include.patch +++ b/recipes/ucsc-pslstats/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslstats/meta.yaml b/recipes/ucsc-pslstats/meta.yaml index 9a3e3b0f48491..df4dcdf568dde 100644 --- a/recipes/ucsc-pslstats/meta.yaml +++ b/recipes/ucsc-pslstats/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslstats" %} {% set program = "pslStats" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "collect statistics from a psl file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslswap/build.sh b/recipes/ucsc-pslswap/build.sh index 0b4455e51c576..e1bbe56df4c19 100644 --- a/recipes/ucsc-pslswap/build.sh +++ b/recipes/ucsc-pslswap/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslSwap && make) -cp bin/pslSwap "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslSwap" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslSwap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslSwap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslSwap" diff --git a/recipes/ucsc-pslswap/include.patch b/recipes/ucsc-pslswap/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslswap/include.patch +++ b/recipes/ucsc-pslswap/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslswap/meta.yaml b/recipes/ucsc-pslswap/meta.yaml index 3d086d16daa16..034f5d8fb55c0 100644 --- a/recipes/ucsc-pslswap/meta.yaml +++ b/recipes/ucsc-pslswap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslswap" %} {% set program = "pslSwap" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,24 +27,33 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Swap target and query in psls " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-psltobed/build.sh b/recipes/ucsc-psltobed/build.sh index aad6779233d63..7280bbec84dfc 100644 --- a/recipes/ucsc-psltobed/build.sh +++ b/recipes/ucsc-psltobed/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslToBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslToBed "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslToBed" +cp bin/pslToBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslToBed" diff --git a/recipes/ucsc-psltobed/meta.yaml b/recipes/ucsc-psltobed/meta.yaml index b80b18d71a5c4..470ba825d07d8 100644 --- a/recipes/ucsc-psltobed/meta.yaml +++ b/recipes/ucsc-psltobed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psltobed" %} {% set program = "pslToBed" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,8 +43,8 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " transform a psl format file to a bed format file. " @@ -52,5 +52,8 @@ transform a psl format file to a bed format file. doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-psltobigpsl/build.sh b/recipes/ucsc-psltobigpsl/build.sh index 3e1f3486afb2c..905ffabb5bda3 100644 --- a/recipes/ucsc-psltobigpsl/build.sh +++ b/recipes/ucsc-psltobigpsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/pslToBigPsl && make) -cp bin/pslToBigPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslToBigPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/pslToBigPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslToBigPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslToBigPsl" diff --git a/recipes/ucsc-psltobigpsl/include.patch b/recipes/ucsc-psltobigpsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-psltobigpsl/include.patch +++ b/recipes/ucsc-psltobigpsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-psltobigpsl/meta.yaml b/recipes/ucsc-psltobigpsl/meta.yaml index 2682f3653cd23..79c71bdbe2174 100644 --- a/recipes/ucsc-psltobigpsl/meta.yaml +++ b/recipes/ucsc-psltobigpsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psltobigpsl" %} {% set program = "pslToBigPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 5 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "converts psl to bigPsl input (bed format with extra fields)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-psltochain/build.sh b/recipes/ucsc-psltochain/build.sh index 4d4568b0f1411..ef1f2a4b3cbc2 100644 --- a/recipes/ucsc-psltochain/build.sh +++ b/recipes/ucsc-psltochain/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslToChain && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslToChain "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslToChain" +cp bin/pslToChain "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslToChain" diff --git a/recipes/ucsc-psltochain/meta.yaml b/recipes/ucsc-psltochain/meta.yaml index c851e92f46935..87146c0c41407 100644 --- a/recipes/ucsc-psltochain/meta.yaml +++ b/recipes/ucsc-psltochain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psltochain" %} {% set program = "pslToChain" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert psl records to chain records " dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-psltopslx/build.sh b/recipes/ucsc-psltopslx/build.sh index 5dbb6b7a422ec..922799ae7f212 100644 --- a/recipes/ucsc-psltopslx/build.sh +++ b/recipes/ucsc-psltopslx/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/pslToPslx && make) -cp bin/pslToPslx "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslToPslx" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslToPslx && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslToPslx "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslToPslx" diff --git a/recipes/ucsc-psltopslx/include.patch b/recipes/ucsc-psltopslx/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-psltopslx/include.patch +++ b/recipes/ucsc-psltopslx/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-psltopslx/meta.yaml b/recipes/ucsc-psltopslx/meta.yaml index 77454025bf7f0..cefae969c7fcd 100644 --- a/recipes/ucsc-psltopslx/meta.yaml +++ b/recipes/ucsc-psltopslx/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psltopslx" %} {% set program = "pslToPslx" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from psl to pslx format, which includes sequences" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslxtofa/build.sh b/recipes/ucsc-pslxtofa/build.sh index 863aec4ce315e..1f69a506672c3 100644 --- a/recipes/ucsc-pslxtofa/build.sh +++ b/recipes/ucsc-pslxtofa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslxToFa && make) -cp bin/pslxToFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslxToFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslxToFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslxToFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslxToFa" diff --git a/recipes/ucsc-pslxtofa/include.patch b/recipes/ucsc-pslxtofa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslxtofa/include.patch +++ b/recipes/ucsc-pslxtofa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslxtofa/meta.yaml b/recipes/ucsc-pslxtofa/meta.yaml index 67df737ea1129..25bb9bac1eb2d 100644 --- a/recipes/ucsc-pslxtofa/meta.yaml +++ b/recipes/ucsc-pslxtofa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslxtofa" %} {% set program = "pslxToFa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert pslx (with sequence) to fasta file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-qacagplift/build.sh b/recipes/ucsc-qacagplift/build.sh index 1bc5422348f6d..c964a8d70f369 100644 --- a/recipes/ucsc-qacagplift/build.sh +++ b/recipes/ucsc-qacagplift/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/qacAgpLift && make) -cp bin/qacAgpLift "$PREFIX/bin" -chmod +x "$PREFIX/bin/qacAgpLift" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/qacAgpLift && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/qacAgpLift "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/qacAgpLift" diff --git a/recipes/ucsc-qacagplift/include.patch b/recipes/ucsc-qacagplift/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-qacagplift/include.patch +++ b/recipes/ucsc-qacagplift/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-qacagplift/meta.yaml b/recipes/ucsc-qacagplift/meta.yaml index eac8a25f5ecf4..d801311aa1b38 100644 --- a/recipes/ucsc-qacagplift/meta.yaml +++ b/recipes/ucsc-qacagplift/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-qacagplift" %} {% set program = "qacAgpLift" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Use AGP to combine per-scaffold qac into per-chrom qac." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-qactoqa/build.sh b/recipes/ucsc-qactoqa/build.sh index e48a8804dd3e7..9eaa54e5d80b4 100644 --- a/recipes/ucsc-qactoqa/build.sh +++ b/recipes/ucsc-qactoqa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/qacToQa && make) -cp bin/qacToQa "$PREFIX/bin" -chmod +x "$PREFIX/bin/qacToQa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/qacToQa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/qacToQa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/qacToQa" diff --git a/recipes/ucsc-qactoqa/include.patch b/recipes/ucsc-qactoqa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-qactoqa/include.patch +++ b/recipes/ucsc-qactoqa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-qactoqa/meta.yaml b/recipes/ucsc-qactoqa/meta.yaml index 0fbf3dbd9b67e..510d12750220f 100644 --- a/recipes/ucsc-qactoqa/meta.yaml +++ b/recipes/ucsc-qactoqa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-qactoqa" %} {% set program = "qacToQa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert from compressed to uncompressed" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-qactowig/build.sh b/recipes/ucsc-qactowig/build.sh index 246d8ae2ab1e3..d39a37b27c18b 100644 --- a/recipes/ucsc-qactowig/build.sh +++ b/recipes/ucsc-qactowig/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/qacToWig && make) -cp bin/qacToWig "$PREFIX/bin" -chmod +x "$PREFIX/bin/qacToWig" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/qacToWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/qacToWig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/qacToWig" diff --git a/recipes/ucsc-qactowig/include.patch b/recipes/ucsc-qactowig/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-qactowig/include.patch +++ b/recipes/ucsc-qactowig/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-qactowig/meta.yaml b/recipes/ucsc-qactowig/meta.yaml index 70e06d45e11c1..86bbbe0154949 100644 --- a/recipes/ucsc-qactowig/meta.yaml +++ b/recipes/ucsc-qactowig/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-qactowig" %} {% set program = "qacToWig" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert from compressed quality score format to wiggle format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-qatoqac/build.sh b/recipes/ucsc-qatoqac/build.sh index 0211aa66be612..413392663e72b 100644 --- a/recipes/ucsc-qatoqac/build.sh +++ b/recipes/ucsc-qatoqac/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/qaToQac && make) -cp bin/qaToQac "$PREFIX/bin" -chmod +x "$PREFIX/bin/qaToQac" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/qaToQac && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/qaToQac "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/qaToQac" diff --git a/recipes/ucsc-qatoqac/include.patch b/recipes/ucsc-qatoqac/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-qatoqac/include.patch +++ b/recipes/ucsc-qatoqac/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-qatoqac/meta.yaml b/recipes/ucsc-qatoqac/meta.yaml index 5b77b89af8a07..2cdd1b678e576 100644 --- a/recipes/ucsc-qatoqac/meta.yaml +++ b/recipes/ucsc-qatoqac/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-qatoqac" %} {% set program = "qaToQac" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert from uncompressed to compressed" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-randomlines/build.sh b/recipes/ucsc-randomlines/build.sh index e180d45f77b14..ea6b63b0d2966 100644 --- a/recipes/ucsc-randomlines/build.sh +++ b/recipes/ucsc-randomlines/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/randomLines && make) -cp bin/randomLines "$PREFIX/bin" -chmod +x "$PREFIX/bin/randomLines" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/randomLines && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/randomLines "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/randomLines" diff --git a/recipes/ucsc-randomlines/include.patch b/recipes/ucsc-randomlines/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-randomlines/include.patch +++ b/recipes/ucsc-randomlines/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-randomlines/meta.yaml b/recipes/ucsc-randomlines/meta.yaml index b3923f83b759d..b186f57343ca7 100644 --- a/recipes/ucsc-randomlines/meta.yaml +++ b/recipes/ucsc-randomlines/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-randomlines" %} {% set program = "randomLines" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Pick out random lines from file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-rasqlquery/build.sh b/recipes/ucsc-rasqlquery/build.sh index 8973924b1eb3e..82a20c81779f9 100644 --- a/recipes/ucsc-rasqlquery/build.sh +++ b/recipes/ucsc-rasqlquery/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/raSqlQuery && make) -cp bin/raSqlQuery "$PREFIX/bin" -chmod +x "$PREFIX/bin/raSqlQuery" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/raSqlQuery && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/raSqlQuery "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/raSqlQuery" diff --git a/recipes/ucsc-rasqlquery/include.patch b/recipes/ucsc-rasqlquery/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-rasqlquery/include.patch +++ b/recipes/ucsc-rasqlquery/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-rasqlquery/meta.yaml b/recipes/ucsc-rasqlquery/meta.yaml index b61951542b664..8b9fca2d654b4 100644 --- a/recipes/ucsc-rasqlquery/meta.yaml +++ b/recipes/ucsc-rasqlquery/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-rasqlquery" %} {% set program = "raSqlQuery" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Do a SQL-like query on a RA file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-ratolines/build.sh b/recipes/ucsc-ratolines/build.sh index f7bda7baaa8f9..aee4cda65ffba 100644 --- a/recipes/ucsc-ratolines/build.sh +++ b/recipes/ucsc-ratolines/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/raToLines && make) -cp bin/raToLines "$PREFIX/bin" -chmod +x "$PREFIX/bin/raToLines" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/raToLines && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/raToLines "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/raToLines" diff --git a/recipes/ucsc-ratolines/include.patch b/recipes/ucsc-ratolines/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-ratolines/include.patch +++ b/recipes/ucsc-ratolines/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ratolines/meta.yaml b/recipes/ucsc-ratolines/meta.yaml index b7e5b58948156..2b95786fa9a09 100644 --- a/recipes/ucsc-ratolines/meta.yaml +++ b/recipes/ucsc-ratolines/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ratolines" %} {% set program = "raToLines" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Output .ra file stanzas as single lines, with pipe-separated fields." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-ratotab/build.sh b/recipes/ucsc-ratotab/build.sh index 376e0b2cb6681..6ef3bb6dbe25c 100644 --- a/recipes/ucsc-ratotab/build.sh +++ b/recipes/ucsc-ratotab/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/raToTab && make) -cp bin/raToTab "$PREFIX/bin" -chmod +x "$PREFIX/bin/raToTab" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/raToTab && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/raToTab "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/raToTab" diff --git a/recipes/ucsc-ratotab/include.patch b/recipes/ucsc-ratotab/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-ratotab/include.patch +++ b/recipes/ucsc-ratotab/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ratotab/meta.yaml b/recipes/ucsc-ratotab/meta.yaml index 2e41461139f83..a0318e0be1bf6 100644 --- a/recipes/ucsc-ratotab/meta.yaml +++ b/recipes/ucsc-ratotab/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ratotab" %} {% set program = "raToTab" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert ra file to table." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-rmfadups/build.sh b/recipes/ucsc-rmfadups/build.sh index b7cedf268cbd0..74f2d3bec2e33 100644 --- a/recipes/ucsc-rmfadups/build.sh +++ b/recipes/ucsc-rmfadups/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/rmFaDups && make) -cp bin/rmFaDups "$PREFIX/bin" -chmod +x "$PREFIX/bin/rmFaDups" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/rmFaDups && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/rmFaDups "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/rmFaDups" diff --git a/recipes/ucsc-rmfadups/include.patch b/recipes/ucsc-rmfadups/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-rmfadups/include.patch +++ b/recipes/ucsc-rmfadups/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-rmfadups/meta.yaml b/recipes/ucsc-rmfadups/meta.yaml index 6c578746a3630..3219c579197fb 100644 --- a/recipes/ucsc-rmfadups/meta.yaml +++ b/recipes/ucsc-rmfadups/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-rmfadups" %} {% set program = "rmFaDups" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "remove duplicate records in FA file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-rowstocols/build.sh b/recipes/ucsc-rowstocols/build.sh index f4c4bb2ade3fd..233ebf5926753 100644 --- a/recipes/ucsc-rowstocols/build.sh +++ b/recipes/ucsc-rowstocols/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/rowsToCols && make) -cp bin/rowsToCols "$PREFIX/bin" -chmod +x "$PREFIX/bin/rowsToCols" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/rowsToCols && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/rowsToCols "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/rowsToCols" diff --git a/recipes/ucsc-rowstocols/include.patch b/recipes/ucsc-rowstocols/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-rowstocols/include.patch +++ b/recipes/ucsc-rowstocols/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-rowstocols/meta.yaml b/recipes/ucsc-rowstocols/meta.yaml index 5996bb1425ee0..3b9bf1fc1db8b 100644 --- a/recipes/ucsc-rowstocols/meta.yaml +++ b/recipes/ucsc-rowstocols/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-rowstocols" %} {% set program = "rowsToCols" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert rows to columns and vice versa in a text file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-spacedtotab/build.sh b/recipes/ucsc-spacedtotab/build.sh index 6327bb4f36c3e..1a1c572360a7e 100644 --- a/recipes/ucsc-spacedtotab/build.sh +++ b/recipes/ucsc-spacedtotab/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/spacedToTab && make) -cp bin/spacedToTab "$PREFIX/bin" -chmod +x "$PREFIX/bin/spacedToTab" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/spacedToTab && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/spacedToTab "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/spacedToTab" diff --git a/recipes/ucsc-spacedtotab/include.patch b/recipes/ucsc-spacedtotab/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-spacedtotab/include.patch +++ b/recipes/ucsc-spacedtotab/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-spacedtotab/meta.yaml b/recipes/ucsc-spacedtotab/meta.yaml index d14f6086ea2dc..1f7c293aafb21 100644 --- a/recipes/ucsc-spacedtotab/meta.yaml +++ b/recipes/ucsc-spacedtotab/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-spacedtotab" %} {% set program = "spacedToTab" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert fixed width space separated fields to tab separated" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-splitfile/build.sh b/recipes/ucsc-splitfile/build.sh index e4cbfae5d5da6..0b085f08fe8bd 100644 --- a/recipes/ucsc-splitfile/build.sh +++ b/recipes/ucsc-splitfile/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/splitFile && make) -cp bin/splitFile "$PREFIX/bin" -chmod +x "$PREFIX/bin/splitFile" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/splitFile && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/splitFile "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/splitFile" diff --git a/recipes/ucsc-splitfile/include.patch b/recipes/ucsc-splitfile/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-splitfile/include.patch +++ b/recipes/ucsc-splitfile/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-splitfile/meta.yaml b/recipes/ucsc-splitfile/meta.yaml index d7462e408fdb9..e893afcb87139 100644 --- a/recipes/ucsc-splitfile/meta.yaml +++ b/recipes/ucsc-splitfile/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-splitfile" %} {% set program = "splitFile" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split up a file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-splitfilebycolumn/build.sh b/recipes/ucsc-splitfilebycolumn/build.sh index b15b6afb70873..7b1ed691f5fc8 100644 --- a/recipes/ucsc-splitfilebycolumn/build.sh +++ b/recipes/ucsc-splitfilebycolumn/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/splitFileByColumn && make) -cp bin/splitFileByColumn "$PREFIX/bin" -chmod +x "$PREFIX/bin/splitFileByColumn" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/splitFileByColumn && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/splitFileByColumn "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/splitFileByColumn" diff --git a/recipes/ucsc-splitfilebycolumn/include.patch b/recipes/ucsc-splitfilebycolumn/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-splitfilebycolumn/include.patch +++ b/recipes/ucsc-splitfilebycolumn/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-splitfilebycolumn/meta.yaml b/recipes/ucsc-splitfilebycolumn/meta.yaml index aebb3eae685cb..4bab401fc02c4 100644 --- a/recipes/ucsc-splitfilebycolumn/meta.yaml +++ b/recipes/ucsc-splitfilebycolumn/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-splitfilebycolumn" %} {% set program = "splitFileByColumn" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split text input into files named by column value" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-sqltoxml/build.sh b/recipes/ucsc-sqltoxml/build.sh index 825908cd3ff6b..2e84672942070 100644 --- a/recipes/ucsc-sqltoxml/build.sh +++ b/recipes/ucsc-sqltoxml/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/sqlToXml && make) -cp bin/sqlToXml "$PREFIX/bin" -chmod +x "$PREFIX/bin/sqlToXml" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/sqlToXml && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/sqlToXml "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/sqlToXml" diff --git a/recipes/ucsc-sqltoxml/include.patch b/recipes/ucsc-sqltoxml/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-sqltoxml/include.patch +++ b/recipes/ucsc-sqltoxml/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-sqltoxml/meta.yaml b/recipes/ucsc-sqltoxml/meta.yaml index 3556ed5c11082..690ca5a345e3b 100644 --- a/recipes/ucsc-sqltoxml/meta.yaml +++ b/recipes/ucsc-sqltoxml/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-sqltoxml" %} {% set program = "sqlToXml" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "dump out all or part of a relational database to XML, guided" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-stringify/build.sh b/recipes/ucsc-stringify/build.sh index 8a122223b89ca..431d016c0f80d 100644 --- a/recipes/ucsc-stringify/build.sh +++ b/recipes/ucsc-stringify/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/stringify "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/stringify" +cp bin/stringify "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/stringify" diff --git a/recipes/ucsc-stringify/meta.yaml b/recipes/ucsc-stringify/meta.yaml index b11c925f68302..32b2c0585670b 100644 --- a/recipes/ucsc-stringify/meta.yaml +++ b/recipes/ucsc-stringify/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-stringify" %} {% set program = "stringify" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -17,7 +17,7 @@ build: skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage(package, max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert file to C strings" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-subchar/build.sh b/recipes/ucsc-subchar/build.sh index e32711c636962..0e64313706326 100644 --- a/recipes/ucsc-subchar/build.sh +++ b/recipes/ucsc-subchar/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/subChar && make) -cp bin/subChar "$PREFIX/bin" -chmod +x "$PREFIX/bin/subChar" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/subChar && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/subChar "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/subChar" diff --git a/recipes/ucsc-subchar/include.patch b/recipes/ucsc-subchar/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-subchar/include.patch +++ b/recipes/ucsc-subchar/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-subchar/meta.yaml b/recipes/ucsc-subchar/meta.yaml index 7c31204869979..58f2a5ab8d6c0 100644 --- a/recipes/ucsc-subchar/meta.yaml +++ b/recipes/ucsc-subchar/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-subchar" %} {% set program = "subChar" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Substitute one character for another throughout a file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-subcolumn/build.sh b/recipes/ucsc-subcolumn/build.sh index 3373060867eb0..4e7e3c1492639 100644 --- a/recipes/ucsc-subcolumn/build.sh +++ b/recipes/ucsc-subcolumn/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/subColumn && make) -cp bin/subColumn "$PREFIX/bin" -chmod +x "$PREFIX/bin/subColumn" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/subColumn && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/subColumn "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/subColumn" diff --git a/recipes/ucsc-subcolumn/include.patch b/recipes/ucsc-subcolumn/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-subcolumn/include.patch +++ b/recipes/ucsc-subcolumn/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-subcolumn/meta.yaml b/recipes/ucsc-subcolumn/meta.yaml index 8a5c7293c3be4..f481ad2ca4aba 100644 --- a/recipes/ucsc-subcolumn/meta.yaml +++ b/recipes/ucsc-subcolumn/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-subcolumn" %} {% set program = "subColumn" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Substitute one column in a tab-separated file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-taillines/build.sh b/recipes/ucsc-taillines/build.sh index 1d3d8478855c2..31b3b4954aa6c 100644 --- a/recipes/ucsc-taillines/build.sh +++ b/recipes/ucsc-taillines/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/tailLines && make) -cp bin/tailLines "$PREFIX/bin" -chmod +x "$PREFIX/bin/tailLines" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/tailLines && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/tailLines "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/tailLines" diff --git a/recipes/ucsc-taillines/include.patch b/recipes/ucsc-taillines/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-taillines/include.patch +++ b/recipes/ucsc-taillines/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-taillines/meta.yaml b/recipes/ucsc-taillines/meta.yaml index 610642e21c3f4..5b2df04b6411d 100644 --- a/recipes/ucsc-taillines/meta.yaml +++ b/recipes/ucsc-taillines/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-taillines" %} {% set program = "tailLines" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "add tail to each line of file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-tdbquery/build.sh b/recipes/ucsc-tdbquery/build.sh index 2a385dd48fddb..0111e2ceb8681 100644 --- a/recipes/ucsc-tdbquery/build.sh +++ b/recipes/ucsc-tdbquery/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/tdbQuery && make) -cp bin/tdbQuery "$PREFIX/bin" -chmod +x "$PREFIX/bin/tdbQuery" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/tdbQuery && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/tdbQuery "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/tdbQuery" diff --git a/recipes/ucsc-tdbquery/include.patch b/recipes/ucsc-tdbquery/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-tdbquery/include.patch +++ b/recipes/ucsc-tdbquery/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-tdbquery/meta.yaml b/recipes/ucsc-tdbquery/meta.yaml index 3d46b7ee704a2..212fa54971621 100644 --- a/recipes/ucsc-tdbquery/meta.yaml +++ b/recipes/ucsc-tdbquery/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-tdbquery" %} {% set program = "tdbQuery" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Query the trackDb system using SQL syntax." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-texthistogram/build.sh b/recipes/ucsc-texthistogram/build.sh index 0b14714882311..4b83a0c70f4e6 100644 --- a/recipes/ucsc-texthistogram/build.sh +++ b/recipes/ucsc-texthistogram/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/textHistogram && make) -cp bin/textHistogram "$PREFIX/bin" -chmod +x "$PREFIX/bin/textHistogram" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/textHistogram && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/textHistogram "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/textHistogram" diff --git a/recipes/ucsc-texthistogram/include.patch b/recipes/ucsc-texthistogram/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-texthistogram/include.patch +++ b/recipes/ucsc-texthistogram/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-texthistogram/meta.yaml b/recipes/ucsc-texthistogram/meta.yaml index 087acaeef8301..756b419e8949d 100644 --- a/recipes/ucsc-texthistogram/meta.yaml +++ b/recipes/ucsc-texthistogram/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-texthistogram" %} {% set program = "textHistogram" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make a histogram in ascii" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-ticktodate/build.sh b/recipes/ucsc-ticktodate/build.sh index 1fb966c199fe3..576694c3ec6fe 100644 --- a/recipes/ucsc-ticktodate/build.sh +++ b/recipes/ucsc-ticktodate/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/tickToDate && make) -cp bin/tickToDate "$PREFIX/bin" -chmod +x "$PREFIX/bin/tickToDate" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/tickToDate && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/tickToDate "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/tickToDate" diff --git a/recipes/ucsc-ticktodate/include.patch b/recipes/ucsc-ticktodate/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-ticktodate/include.patch +++ b/recipes/ucsc-ticktodate/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ticktodate/meta.yaml b/recipes/ucsc-ticktodate/meta.yaml index 0e2ca23327479..ac0059144d920 100644 --- a/recipes/ucsc-ticktodate/meta.yaml +++ b/recipes/ucsc-ticktodate/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ticktodate" %} {% set program = "tickToDate" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert seconds since 1970 to time and date" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-tolower/build.sh b/recipes/ucsc-tolower/build.sh index c59cd1a12634d..1208c312db8dd 100644 --- a/recipes/ucsc-tolower/build.sh +++ b/recipes/ucsc-tolower/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/toLower && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/toLower "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/toLower" +cp bin/toLower "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/toLower" diff --git a/recipes/ucsc-tolower/meta.yaml b/recipes/ucsc-tolower/meta.yaml index 076b34215d2e8..332473fb2342b 100644 --- a/recipes/ucsc-tolower/meta.yaml +++ b/recipes/ucsc-tolower/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-tolower" %} {% set program = "toLower" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -19,7 +19,6 @@ build: run_exports: - {{ pin_subpackage(package, max_pin=None) }} - requirements: build: - make @@ -44,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert upper case to lower case in file. Leave other chars alone" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-toupper/build.sh b/recipes/ucsc-toupper/build.sh index d7cbdb9fffac3..ce555e0c80bf6 100644 --- a/recipes/ucsc-toupper/build.sh +++ b/recipes/ucsc-toupper/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/toUpper && make) -cp bin/toUpper "$PREFIX/bin" -chmod +x "$PREFIX/bin/toUpper" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/toUpper && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/toUpper "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/toUpper" diff --git a/recipes/ucsc-toupper/include.patch b/recipes/ucsc-toupper/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-toupper/include.patch +++ b/recipes/ucsc-toupper/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-toupper/meta.yaml b/recipes/ucsc-toupper/meta.yaml index 15c9ce22d1447..321ceb63c29a7 100644 --- a/recipes/ucsc-toupper/meta.yaml +++ b/recipes/ucsc-toupper/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-toupper" %} {% set program = "toUpper" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert lower case to upper case in file. Leave other chars alone" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-transmappsltogenepred/build.sh b/recipes/ucsc-transmappsltogenepred/build.sh index 9dd5385bb891c..5e65bc273c9cc 100644 --- a/recipes/ucsc-transmappsltogenepred/build.sh +++ b/recipes/ucsc-transmappsltogenepred/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/transMapPslToGenePred && make) -cp bin/transMapPslToGenePred "$PREFIX/bin" -chmod +x "$PREFIX/bin/transMapPslToGenePred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/transMapPslToGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/transMapPslToGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/transMapPslToGenePred" diff --git a/recipes/ucsc-transmappsltogenepred/include.patch b/recipes/ucsc-transmappsltogenepred/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-transmappsltogenepred/include.patch +++ b/recipes/ucsc-transmappsltogenepred/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-transmappsltogenepred/meta.yaml b/recipes/ucsc-transmappsltogenepred/meta.yaml index 79d57d1cd27f4..293cafa31d030 100644 --- a/recipes/ucsc-transmappsltogenepred/meta.yaml +++ b/recipes/ucsc-transmappsltogenepred/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-transmappsltogenepred" %} {% set program = "transMapPslToGenePred" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert PSL alignments of mRNAs to gene annotations." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-trfbig/build.sh b/recipes/ucsc-trfbig/build.sh index fa7537a9dec25..cdc8a63b351a6 100644 --- a/recipes/ucsc-trfbig/build.sh +++ b/recipes/ucsc-trfbig/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/trfBig && make) -cp bin/trfBig "$PREFIX/bin" -chmod +x "$PREFIX/bin/trfBig" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/trfBig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/trfBig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/trfBig" diff --git a/recipes/ucsc-trfbig/include.patch b/recipes/ucsc-trfbig/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-trfbig/include.patch +++ b/recipes/ucsc-trfbig/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-trfbig/meta.yaml b/recipes/ucsc-trfbig/meta.yaml index 828d2326d10e3..0025de973200c 100644 --- a/recipes/ucsc-trfbig/meta.yaml +++ b/recipes/ucsc-trfbig/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-trfbig" %} {% set program = "trfBig" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Mask tandem repeats on a big sequence file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-twobitdup/build.sh b/recipes/ucsc-twobitdup/build.sh index 245b2d099cb46..634c386a90d8d 100644 --- a/recipes/ucsc-twobitdup/build.sh +++ b/recipes/ucsc-twobitdup/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/twoBitDup && make) -cp bin/twoBitDup "$PREFIX/bin" -chmod +x "$PREFIX/bin/twoBitDup" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/twoBitDup && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/twoBitDup "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/twoBitDup" diff --git a/recipes/ucsc-twobitdup/include.patch b/recipes/ucsc-twobitdup/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-twobitdup/include.patch +++ b/recipes/ucsc-twobitdup/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-twobitdup/meta.yaml b/recipes/ucsc-twobitdup/meta.yaml index ceb58f9e80f56..18ea0f188ccfd 100644 --- a/recipes/ucsc-twobitdup/meta.yaml +++ b/recipes/ucsc-twobitdup/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitdup" %} {% set program = "twoBitDup" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "check to see if a twobit file has any identical sequences in it" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-twobitinfo/build.sh b/recipes/ucsc-twobitinfo/build.sh index 5921bddf59576..510984dbad870 100644 --- a/recipes/ucsc-twobitinfo/build.sh +++ b/recipes/ucsc-twobitinfo/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/twoBitInfo && make) -cp bin/twoBitInfo "$PREFIX/bin" -chmod +x "$PREFIX/bin/twoBitInfo" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/twoBitInfo && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/twoBitInfo "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/twoBitInfo" diff --git a/recipes/ucsc-twobitinfo/include.patch b/recipes/ucsc-twobitinfo/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-twobitinfo/include.patch +++ b/recipes/ucsc-twobitinfo/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml index 32559085469d0..f02d59ed3bbbe 100644 --- a/recipes/ucsc-twobitinfo/meta.yaml +++ b/recipes/ucsc-twobitinfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitinfo" %} {% set program = "twoBitInfo" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -12,14 +12,10 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" - - htmshell.patch build: - skip: True # [osx] - number: 1 - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -27,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "get information about sequences in a .2bit file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-twobitmask/build.sh b/recipes/ucsc-twobitmask/build.sh index 5368b1069ee35..04192302896ce 100644 --- a/recipes/ucsc-twobitmask/build.sh +++ b/recipes/ucsc-twobitmask/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/twoBitMask && make) -cp bin/twoBitMask "$PREFIX/bin" -chmod +x "$PREFIX/bin/twoBitMask" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/twoBitMask && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/twoBitMask "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/twoBitMask" diff --git a/recipes/ucsc-twobitmask/include.patch b/recipes/ucsc-twobitmask/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-twobitmask/include.patch +++ b/recipes/ucsc-twobitmask/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-twobitmask/meta.yaml b/recipes/ucsc-twobitmask/meta.yaml index b4712f7ebff1e..cfef8cf9866cd 100644 --- a/recipes/ucsc-twobitmask/meta.yaml +++ b/recipes/ucsc-twobitmask/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitmask" %} {% set program = "twoBitMask" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "apply masking to a .2bit file, creating a new .2bit file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-twobittofa/build.sh b/recipes/ucsc-twobittofa/build.sh index 8f25dc11367ae..1db3e3360894c 100644 --- a/recipes/ucsc-twobittofa/build.sh +++ b/recipes/ucsc-twobittofa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/utils/twoBitToFa && make -j ${CPU_COUNT}) -cp bin/twoBitToFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/twoBitToFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/twoBitToFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/twoBitToFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/twoBitToFa" diff --git a/recipes/ucsc-twobittofa/include.patch b/recipes/ucsc-twobittofa/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-twobittofa/include.patch +++ b/recipes/ucsc-twobittofa/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-twobittofa/meta.yaml b/recipes/ucsc-twobittofa/meta.yaml index 9469bbbab5f7e..6c74d0cff77f5 100644 --- a/recipes/ucsc-twobittofa/meta.yaml +++ b/recipes/ucsc-twobittofa/meta.yaml @@ -1,57 +1,57 @@ {% set package = "ucsc-twobittofa" %} {% set program = "twoBitToFa" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - skip: True # [osx] - number: 1 - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - - {{ pin_subpackage("ucsc-twobittofa", max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert all or part of .2bit file to fasta" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-validatefiles/build.sh b/recipes/ucsc-validatefiles/build.sh index d7fc914c34542..59fd038fccaa6 100644 --- a/recipes/ucsc-validatefiles/build.sh +++ b/recipes/ucsc-validatefiles/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/encode3/validateFiles && make) -cp bin/validateFiles "$PREFIX/bin" -chmod +x "$PREFIX/bin/validateFiles" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/encode3/validateFiles && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/validateFiles "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/validateFiles" diff --git a/recipes/ucsc-validatefiles/include.patch b/recipes/ucsc-validatefiles/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-validatefiles/include.patch +++ b/recipes/ucsc-validatefiles/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-validatefiles/meta.yaml b/recipes/ucsc-validatefiles/meta.yaml index 834d239050a73..67e9b60320e72 100644 --- a/recipes/ucsc-validatefiles/meta.yaml +++ b/recipes/ucsc-validatefiles/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-validatefiles" %} {% set program = "validateFiles" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Validates the format of different genomic files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-validatemanifest/build.sh b/recipes/ucsc-validatemanifest/build.sh index e727b91ce0514..f92f057e59eaf 100644 --- a/recipes/ucsc-validatemanifest/build.sh +++ b/recipes/ucsc-validatemanifest/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/encode3/validateManifest && make) -cp bin/validateManifest "$PREFIX/bin" -chmod +x "$PREFIX/bin/validateManifest" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/encode3/validateManifest && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/validateManifest "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/validateManifest" diff --git a/recipes/ucsc-validatemanifest/include.patch b/recipes/ucsc-validatemanifest/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-validatemanifest/include.patch +++ b/recipes/ucsc-validatemanifest/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-validatemanifest/meta.yaml b/recipes/ucsc-validatemanifest/meta.yaml index a80b36a6feb4d..a3b17fc4ab953 100644 --- a/recipes/ucsc-validatemanifest/meta.yaml +++ b/recipes/ucsc-validatemanifest/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-validatemanifest" %} {% set program = "validateManifest" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Validates the ENCODE3 manifest.txt file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-websync/build.sh b/recipes/ucsc-websync/build.sh index f39703618a8ac..eebbd4ce9a700 100644 --- a/recipes/ucsc-websync/build.sh +++ b/recipes/ucsc-websync/build.sh @@ -1,4 +1,7 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -cp kent/src/utils/webSync "$PREFIX/bin" -chmod +x "$PREFIX/bin/webSync" + +set -xe + +mkdir -p "${PREFIX}/bin" +cp kent/src/utils/webSync "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/webSync" diff --git a/recipes/ucsc-websync/include.patch b/recipes/ucsc-websync/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-websync/include.patch +++ b/recipes/ucsc-websync/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-websync/meta.yaml b/recipes/ucsc-websync/meta.yaml index c4bcd00e92eb8..91c8888cce901 100644 --- a/recipes/ucsc-websync/meta.yaml +++ b/recipes/ucsc-websync/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-websync" %} {% set program = "webSync" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,16 +15,25 @@ source: build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: + - {{ compiler('c') }} host: + - libpng + - libuuid + - mysql-connector-c + - libopenssl-static + - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - python - zlib @@ -37,3 +46,12 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "download from https server, using files.txt on their end to get the list of files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-wigcorrelate/build.sh b/recipes/ucsc-wigcorrelate/build.sh index dadcd1bb5bb53..716aad0dea677 100644 --- a/recipes/ucsc-wigcorrelate/build.sh +++ b/recipes/ucsc-wigcorrelate/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/wigCorrelate && make) -cp bin/wigCorrelate "$PREFIX/bin" -chmod +x "$PREFIX/bin/wigCorrelate" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/wigCorrelate && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/wigCorrelate "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/wigCorrelate" diff --git a/recipes/ucsc-wigcorrelate/include.patch b/recipes/ucsc-wigcorrelate/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-wigcorrelate/include.patch +++ b/recipes/ucsc-wigcorrelate/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-wigcorrelate/meta.yaml b/recipes/ucsc-wigcorrelate/meta.yaml index 691ade53701fd..dfa59e07f8970 100644 --- a/recipes/ucsc-wigcorrelate/meta.yaml +++ b/recipes/ucsc-wigcorrelate/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-wigcorrelate" %} {% set program = "wigCorrelate" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Produce a table that correlates all pairs of wigs." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-wigtobigwig/build.sh b/recipes/ucsc-wigtobigwig/build.sh index f150228de66bc..113f9a2031ecb 100644 --- a/recipes/ucsc-wigtobigwig/build.sh +++ b/recipes/ucsc-wigtobigwig/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/wigToBigWig && make) -cp bin/wigToBigWig "$PREFIX/bin" -chmod +x "$PREFIX/bin/wigToBigWig" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/wigToBigWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/wigToBigWig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/wigToBigWig" diff --git a/recipes/ucsc-wigtobigwig/include.patch b/recipes/ucsc-wigtobigwig/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-wigtobigwig/include.patch +++ b/recipes/ucsc-wigtobigwig/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-wigtobigwig/meta.yaml b/recipes/ucsc-wigtobigwig/meta.yaml index c21b3a9bb7d40..ac2226d78ed5d 100644 --- a/recipes/ucsc-wigtobigwig/meta.yaml +++ b/recipes/ucsc-wigtobigwig/meta.yaml @@ -1,57 +1,57 @@ {% set package = "ucsc-wigtobigwig" %} {% set program = "wigToBigWig" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 2 - skip: True # [osx] + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} - ignore_run_exports: - - libpng - - libuuid requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert ascii format wig file (in fixedStep, variableStep)" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Convert ascii format wig file (in fixedStep, variableStep" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-wordline/build.sh b/recipes/ucsc-wordline/build.sh index 2986588d188dc..f9483c43c25ce 100644 --- a/recipes/ucsc-wordline/build.sh +++ b/recipes/ucsc-wordline/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/wordLine && make) -cp bin/wordLine "$PREFIX/bin" -chmod +x "$PREFIX/bin/wordLine" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/wordLine && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/wordLine "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/wordLine" diff --git a/recipes/ucsc-wordline/include.patch b/recipes/ucsc-wordline/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-wordline/include.patch +++ b/recipes/ucsc-wordline/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-wordline/meta.yaml b/recipes/ucsc-wordline/meta.yaml index 340ea0ab85173..a4f886851f2d7 100644 --- a/recipes/ucsc-wordline/meta.yaml +++ b/recipes/ucsc-wordline/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-wordline" %} {% set program = "wordLine" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "chop up words by white space and output them with one" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-xmlcat/build.sh b/recipes/ucsc-xmlcat/build.sh index 0c43ba87a8e5e..8809a785168a9 100644 --- a/recipes/ucsc-xmlcat/build.sh +++ b/recipes/ucsc-xmlcat/build.sh @@ -1,21 +1,21 @@ #!/bin/bash set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/xmlCat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/xmlCat "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/xmlCat" +cp bin/xmlCat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/xmlCat" diff --git a/recipes/ucsc-xmlcat/meta.yaml b/recipes/ucsc-xmlcat/meta.yaml index f7728bd133b59..fdfb1b545ec90 100644 --- a/recipes/ucsc-xmlcat/meta.yaml +++ b/recipes/ucsc-xmlcat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-xmlcat" %} {% set program = "xmlCat" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Concatenate xml files together, stuffing all records inside a single outer tag. " dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-xmltosql/build.sh b/recipes/ucsc-xmltosql/build.sh index 9c0109eec1bf3..da748dca33f72 100644 --- a/recipes/ucsc-xmltosql/build.sh +++ b/recipes/ucsc-xmltosql/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/xmlToSql && make) -cp bin/xmlToSql "$PREFIX/bin" -chmod +x "$PREFIX/bin/xmlToSql" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/xmlToSql && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/xmlToSql "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/xmlToSql" diff --git a/recipes/ucsc-xmltosql/include.patch b/recipes/ucsc-xmltosql/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-xmltosql/include.patch +++ b/recipes/ucsc-xmltosql/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-xmltosql/meta.yaml b/recipes/ucsc-xmltosql/meta.yaml index e73be12d74a2d..d66247fc304ce 100644 --- a/recipes/ucsc-xmltosql/meta.yaml +++ b/recipes/ucsc-xmltosql/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-xmltosql" %} {% set program = "xmlToSql" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert XML dump into a fairly normalized relational database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/unicycler/meta.yaml b/recipes/unicycler/meta.yaml index 8b0db344689bb..5e1fa962a312d 100644 --- a/recipes/unicycler/meta.yaml +++ b/recipes/unicycler/meta.yaml @@ -13,8 +13,7 @@ source: - misc.py.patch build: - number: 1 - skip: True # [py < 39] + number: 2 entry_points: - unicycler = unicycler.unicycler:main script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir @@ -42,13 +41,13 @@ test: - "COLUMNS=80 unicycler -h" about: - home: https://github.com/rrwick/Unicycler - license: GPL-3.0-or-later + home: "https://github.com/rrwick/Unicycler" + license: "GPL-3.0-or-later" license_family: GPL3 license_file: LICENSE summary: "Hybrid assembly pipeline for bacterial genomes." - dev_url: https://github.com/rrwick/Unicycler - doc_url: https://github.com/rrwick/Unicycler/wiki + dev_url: "https://github.com/rrwick/Unicycler" + doc_url: "https://github.com/rrwick/Unicycler/wiki" extra: identifiers: diff --git a/recipes/usalign/build.sh b/recipes/usalign/build.sh new file mode 100644 index 0000000000000..e7c2ff701f28e --- /dev/null +++ b/recipes/usalign/build.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +set -exo pipefail + +readonly PROGRAMS=( + qTMclust + USalign + TMalign + TMscore + MMalign + se + pdb2xyz + xyz_sfetch + pdb2fasta + pdb2ss + NWalign + HwRMSD + cif2pdb + pdbAtomName + addChainID +) + +make -j${CPU_COUNT} CC="${CXX}" LDFLAGS="-lm" + +install -d "${PREFIX}/bin" +install -m 755 "${PROGRAMS[@]}" "${PREFIX}/bin/" diff --git a/recipes/usalign/meta.yaml b/recipes/usalign/meta.yaml new file mode 100644 index 0000000000000..b3e5a789aa3d8 --- /dev/null +++ b/recipes/usalign/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "US-align" %} +{% set version = "2024.07.30" %} + +package: + name: {{ name|lower|replace("-", "") }} + version: {{ version }} + +source: + url: https://github.com/eunos-1128/{{ name|lower|replace("-", "") }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 21b510507e9258c1a2e03c6d32680282981a54e27778a3f3f739861ca7c7b38a + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower|replace("-", ""), max_pin=None) }} + +requirements: + build: + - {{ compiler("c") }} + - {{ compiler("cxx") }} + - make + +test: + commands: + - USalign -h + +about: + home: https://zhanggroup.org/{{ name }} + dev_url: https://github.com/pylelab/{{ name|replace("-", "") }} + doc_url: https://zhanggroup.org/{{ name }}/help + summary: "Universal structure alignment of monomeric, complex proteins and nucleic acids" + description: | + US-align (Universal Structural alignment) is a unified protocol + to compare 3D structures of different macromolecules (proteins, RNAs and DNAs) + in different forms (monomers, oligomers and heterocomplexes) + for both pairwise and multiple structure alignments. + The core alogrithm of US-align is extended from TM-align and generates optimal structural alignments + by maximizing TM-score of compared strucures through heuristic dynamic programming iterations. + Large-scale benchmark tests showed that US-align can generate more accurate structural alignments + with significantly reduced CPU time, compared to the state-of-the-art methods developed + for specific structural alignment tasks. + TM-score has values in (0,1] with 1 indicating an identical structure match, + where a TM-score ≥0.5 (or 0.45) means the structures share the same global topology for proteins (or RNAs). + license: UNKNOWN + license_family: OTHER + license_file: LICENSE + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - eunos-1128 diff --git a/recipes/varfish-server-worker/build.sh b/recipes/varfish-server-worker/build.sh index 403679dd60ea7..701401e625188 100644 --- a/recipes/varfish-server-worker/build.sh +++ b/recipes/varfish-server-worker/build.sh @@ -1,10 +1,6 @@ #!/bin/bash -e -# TODO: Remove the following export when pinning is updated and we use -# {{ compiler('rust') }} in the recipe. -export \ - CARGO_NET_GIT_FETCH_WITH_CLI=true \ - CARGO_HOME="${BUILD_PREFIX}/.cargo" +set -xe export BINDGEN_EXTRA_CLANG_ARGS="${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" diff --git a/recipes/varfish-server-worker/meta.yaml b/recipes/varfish-server-worker/meta.yaml index 607e7a5b58f63..e7c4ceb6229c5 100644 --- a/recipes/varfish-server-worker/meta.yaml +++ b/recipes/varfish-server-worker/meta.yaml @@ -1,24 +1,24 @@ -{% set version = "0.12.0" %} +{% set version = "0.13.0" %} package: name: varfish-server-worker version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("varfish-server-worker", max_pin="x.x") }} source: url: https://github.com/varfish-org/varfish-server-worker/archive/refs/tags/v{{ version }}.tar.gz - sha256: da36b0cb9138adb4c30d1957f1d7d0e577fc49fc4b8bbad90fdd4d7f0f1e3b38 + sha256: 2a593575ae37bd1c9f934e45b378024912108d2391cccba1b9120c4685c2362a requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - rust >=1.30 + - {{ compiler('rust') }} - clangdev - pkg-config - protobuf @@ -43,5 +43,7 @@ about: Rust-based tool for the heavy lifting in varfish-server. extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - holtgrewe diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index a7b36a5733c75..571d69adc5e48 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varlociraptor" %} -{% set version = "8.4.9" %} +{% set version = "8.4.11" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: f55476d87dabf3e4a6792b42b91beb06ec1b7c5812aca937765f15b13bc6222d + sha256: 1785d13aee5f37381042bf280bcc1bd4f0306d5f94d22b9ec85b8d76a56ff70a build: number: 0 diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index f058276c11216..ef8d005799c0f 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 5c9fe4f1c458812808a1d08ce2e6f5166b5bc5f136f15bdcde99a496f05fd07b + sha256: 335707c71b1c834f0f548001bc18485b2dd6e93368434137607ecaec58f66ff5 build: entry_points: diff --git a/recipes/vcf-validator/build.sh b/recipes/vcf-validator/build.sh index acd838e4eac4f..7a7491a9e1988 100644 --- a/recipes/vcf-validator/build.sh +++ b/recipes/vcf-validator/build.sh @@ -1,11 +1,6 @@ mkdir -p ${PREFIX}/bin -# Check if linux or osx -if [ -z ${OSX_ARCH+x} ]; then - mv vcf_validator_linux ${PREFIX}/bin/vcf_validator - mv vcf_assembly_checker_linux ${PREFIX}/bin/vcf_assembly_checker -else - mv vcf_validator_macos ${PREFIX}/bin/vcf_validator - mv vcf_assembly_checker_macos ${PREFIX}/bin/vcf_assembly_checker -fi + +mv vcf_validator* ${PREFIX}/bin/vcf_validator +mv vcf_assembly_checker* ${PREFIX}/bin/vcf_assembly_checker chmod 755 ${PREFIX}/bin/vcf_assembly_checker ${PREFIX}/bin/vcf_validator diff --git a/recipes/vcf-validator/meta.yaml b/recipes/vcf-validator/meta.yaml index 252a24c4013d0..03877f075b8f4 100644 --- a/recipes/vcf-validator/meta.yaml +++ b/recipes/vcf-validator/meta.yaml @@ -1,19 +1,19 @@ {% set name = "vcf-validator" %} -{% set version = "0.9.6" %} +{% set version = "0.9.7" %} package: name: {{ name }} version: {{ version }} source: - - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_linux # [linux] - sha256: 33fc99334e77a90e99415daebfa877a9bc0375a3d7c18809082ace64d8373cdd # [linux] - - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_linux # [linux] - sha256: 7913a6b3f12fdf5a66c98026ef144be4f8964f981f80eca4b509e06e6b8282ab # [linux] - - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_macos # [osx] - sha256: 68f50e38323260dcd77e236c27872e1a0eb5c6407736baf003cbc755c87bab94 # [osx] - - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_macos # [osx] - sha256: afb7383468fa08d597fc8f7588918dbcdafc8d6d41eb7d33d37ae71a30860cb7 # [osx] + - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_linux # [linux] + sha256: 49aef4841cd7d0913ba12020465830b834ccfe20f2094222c8c41511f6c801ac # [linux] + - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_linux # [linux] + sha256: a9a00303c05c1fb5a33a5bd1f5c74fb5d8097f92a1f3ee815e19c137c0e26f13 # [linux] + - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_macos_x64 # [osx and x86] + sha256: 0b97a34fac6cf23951ffc33cdfb7b0602a89b4d5390564c8d816cb83019a3ffc # [osx and x86] + - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_macos_x64 # [osx and x86] + sha256: 1b5404a4239da9f5e5e39bece975e4eea55d87c486121a076226829b79477bc3 # [osx and x86] build: script: diff --git a/recipes/vcflib/0006-wfa2-lib.patch b/recipes/vcflib/0006-wfa2-lib.patch new file mode 100644 index 0000000000000..392b1a17c2d31 --- /dev/null +++ b/recipes/vcflib/0006-wfa2-lib.patch @@ -0,0 +1,32 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 40dedb3..b738d28 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -380,10 +380,7 @@ if(WFA_GITMODULE) + else(WFA_GITMODULE) + include_directories($ENV{CMAKE_PREFIX_PATH}/include/wfa2lib) + set(WFA_INCLUDE_DIRS ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib) +- find_library(WFALIB wfa2 wfa) # distro search for shared lib +- if(NOT WFALIB) +- message(STATUS "ERROR: Can not find libfwa! Make sure it is installed or use the git submodule instead") +- endif() ++ find_library(WFALIB wfa2 wfa REQUIRED) # distro search for shared lib + endif(WFA_GITMODULE) + + include_directories(${WFA_INCLUDE_DIRS}) +@@ -454,6 +451,7 @@ if (NOT BUILD_ONLY_LIB) + add_executable(${BIN} src/${BIN}.cpp) + add_dependencies(${BIN} vcflib) + target_link_libraries(${BIN} PUBLIC ${vcflib_LIBS} vcflib) ++ target_link_libraries(${BIN} PUBLIC ${vcflib_LIBS} ${WFALIB}) + endforeach(BIN ${BINS}) + # These binaries include WFALIB + target_link_libraries(vcfallelicprimitives PUBLIC ${WFALIB}) +@@ -602,6 +600,6 @@ endif (PANDOC) + + install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) + +-install(FILES ${INCLUDES} DESTINATION include) ++install(FILES ${INCLUDES} DESTINATION include/vcflib) + + install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1) diff --git a/recipes/vcflib/build.sh b/recipes/vcflib/build.sh index ac929087a86e7..d4948a04001c5 100644 --- a/recipes/vcflib/build.sh +++ b/recipes/vcflib/build.sh @@ -4,20 +4,23 @@ set -ex OS=$(uname) ARCH=$(uname -m) -if [ "${OS}" == "Darwin" ]; then +if [[ "${OS}" == "Darwin" && "${ARCH}" == "x86_64" ]]; then echo $(pwd)/zig-macos-x86_64-* export PATH="$(pwd)/zig-macos-x86_64-0.10.1:${PATH}" +elif [[ "${OS}" == "Darwin" && "${ARCH}" == "arm64" ]]; then + echo $(pwd)/zig-macos-aarch64-* + export PATH="$(pwd)/zig-macos-aarch64-0.10.1:${PATH}" else echo $(pwd)/zig-linux-${ARCH}-* export PATH="$(pwd)/zig-linux-${ARCH}-0.10.1:${PATH}" fi -export INCLUDES="-I${PREFIX}/include -I. -Ihtslib -Itabixpp -I\$(INC_DIR)" -export LIBPATH="-L${PREFIX}/lib -L. -Lhtslib -Ltabixpp" +export INCLUDES="-I${PREFIX}/include -I. -Ihtslib -Itabixpp -Iwfa2 -I\$(INC_DIR)" +export LIBPATH="-L${PREFIX}/lib -L. -Lhtslib -Ltabixpp -Lwfa2" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -lhts -ltabixpp -lpthread -lz -lm -llzma -lbz2 -fopenmp -lwfa2" -export CXXFLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64" +export CXXFLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64 -I${PREFIX}/include" -sed -i.bak 's/CFFFLAGS:= -O3/CFFFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -std=c++0x/' contrib/smithwaterman/Makefile +sed -i.bak 's/CFFFLAGS:= -O3/CFFFLAGS=-O3 -D_FILE_OFFSET_BITS=64/' contrib/smithwaterman/Makefile sed -i.bak 's/CFLAGS/CXXFLAGS/g' contrib/smithwaterman/Makefile sed -i.bak 's/$=3 - perl - htslib - tabixpp + - wfa2-lib - eigen - jsoncpp - - wfa2-lib + - wget test: requires: @@ -66,18 +74,47 @@ test: - "vcfuniq test.vcf" about: - home: https://github.com/vcflib/vcflib + home: "https://github.com/vcflib/vcflib" license: MIT license_family: MIT license_file: LICENSE - summary: Command-line tools for manipulating VCF files + summary: "Command-line tools for manipulating VCF files." + dev_url: "https://github.com/vcflib/vcflib" + doc_url: "https://github.com/vcflib/vcflib/blob/v{{ version }}/README.md" extra: + skip-lints: + # uses submodules + - uses_vcs_url additional-platforms: - linux-aarch64 + #zig osx-arm64 error: error(link): undefined reference to symbol 'dyld_stub_binder' + #- osx-arm64 recipe-maintainers: - jpuritz identifiers: - biotools:vcflib - doi:10.1371/journal.pcbi.1009123 - usegalaxy-eu:vcfsort + - usegalaxy-eu:vcfallelicprimitives + - usegalaxy-eu:vcfbreakcreatemulti + - usegalaxy-eu:vcffilter2 + - usegalaxy-eu:vcfcheck + - usegalaxy-eu:vcfcombine + - usegalaxy-eu:vcfaddinfo + - usegalaxy-eu:vcf2tsv + - usegalaxy-eu:vcfleftalign + - usegalaxy-eu:vcfhethom + - usegalaxy-eu:vcfrandomsample + - usegalaxy-eu:vcfbedintersect + - usegalaxy-eu:vcfgenotypes + - usegalaxy-eu:vcffixup + - usegalaxy-eu:vcfgeno2haplo + - usegalaxy-eu:vcfvcfintersect + - usegalaxy-eu:vcfanno + - usegalaxy-eu:vcfannotate + - usegalaxy-eu:vcfcommonsamples + - usegalaxy-eu:vcfflatten2 + - usegalaxy-eu:vcfdistance + - usegalaxy-eu:vcfannotategenotypes + - usegalaxy-eu:vcfselectsamples diff --git a/recipes/vcflib/pkg-config.patch b/recipes/vcflib/pkg-config.patch index ae58978242cc2..3001b66884c21 100644 --- a/recipes/vcflib/pkg-config.patch +++ b/recipes/vcflib/pkg-config.patch @@ -1,18 +1,18 @@ Author: Andreas Tille modified for bioconda by Jon Puritz -Description: Add pkg-config file to simplify building of freebayes +Description: Add pkg-config file to simplify building of freebayes. Forwarded: not-needed --- a/dev/null +++ b/libvcflib/libvcflib.pc @@ -0,0 +1,12 @@ -+prefix=/usr ++prefix=${PREFIX} +exec_prefix=${prefix} +libdir=${exec_prefix}/lib -+includedir=${prefix}/include/vcflib ++includedir=${prefix}/include + +Name: libvcflib +Version: 1.0 +Requires: +Description: C++ library for parsing and manipulating VCF files +Libs: -L${libdir} -lvcflib -+Cflags: -I${includedir} ++Cflags: -I${includedir}/vcflib + diff --git a/recipes/vcfsim/meta.yaml b/recipes/vcfsim/meta.yaml index 00ad1f01fbe82..27dbb82d06a37 100644 --- a/recipes/vcfsim/meta.yaml +++ b/recipes/vcfsim/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcfsim" %} -{% set version = "1.0.12.alpha" %} +{% set version = "1.0.16.alpha" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Pie115/VCFSimulator-SamukLab/archive/{{ version }}.tar.gz - sha256: 58ff93f1652f71a5559d0e1b1660c11ecc391ecf32a82bc761aa3837f5c26e94 + sha256: 385640fdee385c6710ba7bda68cedd28f665f3b0d950d400662f3d5aa374ccfa build: noarch: python diff --git a/recipes/vclean/meta.yaml b/recipes/vclean/meta.yaml index d70333f25020c..7f4824bbecb8d 100644 --- a/recipes/vclean/meta.yaml +++ b/recipes/vclean/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vclean" %} -{% set version = "0.0.2" %} +{% set version = "0.1.5" %} package: name: {{ name|lower }} @@ -7,28 +7,28 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/vclean-{{ version }}.tar.gz - sha256: 3624ccf7b8160af1584cc7fa99b7036fb81818a1941b9fd31729ce85c48cce73 + sha256: 29b2c380ca7de17f4cb17e5653706ec375869faf998e1cc3d8da72b04d116921 build: entry_points: - vclean = vclean.cli:cli noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 run_exports: - - {{ pin_subpackage("vclean", max_pin="x") }} + - {{ pin_subpackage("vclean", max_pin="x.x") }} requirements: host: - - python >=3.9 + - python ==3.9.0 - flit-core >=3.2,<4 - pip run: - - python >=3.9 + - python ==3.9.0 - pandas - numpy - matplotlib-base - - seaborn + - seaborn-base - scikit-learn - lightgbm - biopython @@ -46,7 +46,9 @@ about: summary: 'vClean: Assessing the contamination of viral genomes' home: https://github.com/TsumaR/vclean license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE + dev_url: https://github.com/TsumaR/vclean extra: recipe-maintainers: diff --git a/recipes/vcontact3/meta.yaml b/recipes/vcontact3/meta.yaml index 7fe1af8435c22..908e3e0868885 100644 --- a/recipes/vcontact3/meta.yaml +++ b/recipes/vcontact3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcontact3" %} -{% set version = "3.0.0.b38" %} +{% set version = "3.0.0.b65" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://bitbucket.org/MAVERICLab/vcontact3/get/{{ version }}.tar.gz" - sha256: fc56f0c3ae4d3016287e4ab9ad86847b089e7c8eca78fa393fe8eba965c182fc + sha256: 2f1bab1b332a2ece1f4eabceaaa431baa0c45c769efa725bc5a709dcb093f7f7 build: number: 0 @@ -48,6 +48,7 @@ requirements: - markupsafe >=2.0.1 - mmseqs2 >=15.6f452 - bioinfokit >=2.1.3 + - networkit >=11.0 test: commands: @@ -59,4 +60,4 @@ about: license_file: LICENSE license_family: GPL summary: Viral Contig Automatic Clustering and Taxonomy - doc_url: https://bitbucket.org/MAVERICLab/vcontact3/src/master/README.md \ No newline at end of file + doc_url: https://bitbucket.org/MAVERICLab/vcontact3/src/master/README.md diff --git a/recipes/vembrane/meta.yaml b/recipes/vembrane/meta.yaml index 5b3851289ab76..0c4003b0d066e 100644 --- a/recipes/vembrane/meta.yaml +++ b/recipes/vembrane/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.5" %} +{% set version = "1.0.7" %} package: name: vembrane @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/v/vembrane/vembrane-{{ version }}.tar.gz - sha256: c0afc7dc69dd32ac95c45ba679b5751c2d63170e4876dbc0ce860d44f6b6c18e + sha256: 4e94ff702662d2b2cd3043525500c250661a51a39dec69ca4ef94d17ceb51892 build: number: 0 diff --git a/recipes/verkko/build.sh b/recipes/verkko/build.sh index c03607f1ff961..72be8124e90ef 100644 --- a/recipes/verkko/build.sh +++ b/recipes/verkko/build.sh @@ -1,6 +1,8 @@ #!/bin/bash set -ex +mkdir -p "$PREFIX/bin" + # taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh if [ "$(uname)" == "Darwin" ]; then @@ -10,10 +12,17 @@ if [ "$(uname)" == "Darwin" ]; then mkdir -p $HOME/.cargo/registry/index/ fi +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" + +# on osx we remove the built-in boost and make sure todepend on the system boost pushd src +if [ "$(uname)" == "Darwin" ]; then + rm -rf ./canu/src/utgcns/libboost/ +fi make clean && make -j$CPU_COUNT popd -mkdir -p "$PREFIX/bin" cp -rf bin/* $PREFIX/bin/ cp -rf lib/* $PREFIX/lib/ diff --git a/recipes/verkko/meta.yaml b/recipes/verkko/meta.yaml index 460a299b91ba7..bc812c97aaa3a 100644 --- a/recipes/verkko/meta.yaml +++ b/recipes/verkko/meta.yaml @@ -1,5 +1,5 @@ {% set name = "verkko" %} -{% set version = "2.1" %} +{% set version = "2.2.1" %} package: name: {{ name|lower }} @@ -7,11 +7,9 @@ package: source: url: https://github.com/marbl/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: e989710a43cc6f721938f6393d20c8a674b110cd74a7c27f23f4d06a9dd78e9f - + sha256: 4ab40961352cac22eebfb37606c82bb5a589f9361c36430e7278227e62db3860 patches: - - version.patch - - osx_availability.patch # [osx] + - osx_availability.patch # [osx] build: number: 0 @@ -21,22 +19,27 @@ build: requirements: build: - make - - llvm-openmp # [osx] - - libgomp # [linux] - {{ compiler('cxx') }} - rust >=1.74 host: + - boost-cpp >=1.56 #[osx] - llvm-openmp # [osx] - - libgomp # [linux] + - libgomp # [linux] - gsl - zlib + - htslib run: - - python >=3.7 + - python >=3.9 + - boost-cpp >=1.56 #[osx] + - llvm-openmp # [osx] + - libgomp # [linux] + - pulp <=2.7.0 - perl >=5.6 - seqtk - parasail-python >=1.3.3 - networkx >=2.6.3 - biopython + - pysam - snakemake-minimal >=7.8.0,<8.0 - graphaligner >=1.0.19 - findutils >=4.6.0 @@ -53,12 +56,12 @@ test: - verkko --version about: - home: https://github.com/marbl/verkko + home: "https://github.com/marbl/verkko" license: CC0 license_file: README.licenses - summary: "A hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads." + summary: "A hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate (HiFi, ONT Duplex, ONT HERRO) and long (ONT UL) reads." dev_url: "https://github.com/marbl/verkko" - doc_url: "https://github.com/marbl/verkko/blob/master/README.md" + doc_url: "https://github.com/marbl/verkko/blob/v{{ version }}/README.md" extra: identifiers: diff --git a/recipes/verkko/osx_availability.patch b/recipes/verkko/osx_availability.patch index 22bdc376bf98c..69344ea5b476f 100644 --- a/recipes/verkko/osx_availability.patch +++ b/recipes/verkko/osx_availability.patch @@ -50,18 +50,3 @@ index 0bc9ee7..0f53de7 100644 VERSION := Branch $(shell git rev-parse --abbrev-ref HEAD) commit $(shell git rev-parse HEAD) $(shell git show -s --format=%ci) -diff --git a/src/verkko.sh b/src/verkko.sh -index 1744b4a..6016aea 100755 ---- a/src/verkko.sh -+++ b/src/verkko.sh -@@ -1324,8 +1324,8 @@ if [ "x$withhic" = "xTrue" -o "x$withporec" = "xTrue" ] ; then - fi - cp -p emptyfile ${newoutd}/emptyfile - cd $newoutd -- sed -i 's/runRukkiHIC/cnspath/g' snakemake.sh -- sed -i 's/HiC_rdnascaff/cnspath/g' snakemake.sh -+ sed -i.bak 's/runRukkiHIC/cnspath/g' snakemake.sh -+ sed -i.bak 's/HiC_rdnascaff/cnspath/g' snakemake.sh - ./snakemake.sh - cp *.fasta ../../ - cp *.layout ../../ diff --git a/recipes/verkko/run_test.sh b/recipes/verkko/run_test.sh index 95ed12e451477..abf76882b8363 100644 --- a/recipes/verkko/run_test.sh +++ b/recipes/verkko/run_test.sh @@ -40,7 +40,7 @@ if [ ! -s asm/assembly_circular.fasta ]; then exit 1 fi -verkko -d asm --hifi reference.fasta.gz $ONT --hic1 empty.fasta --hic2 empty.fasta +verkko -d asm --hifi reference.fasta.gz $ONT --porec reference.fasta.gz if [[ ! -s asm/assembly.unassigned.fasta || -s asm/assembly.haplotype1.fasta || -s asm/assembly.haplotype2.fasta ]]; then echo "Error: verkko hic assembly test failed!" diff --git a/recipes/verkko/version.patch b/recipes/verkko/version.patch deleted file mode 100644 index 65a9a043a84a7..0000000000000 --- a/recipes/verkko/version.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff --git a/src/Makefile b/src/Makefile -index 5f33ff4..25c2285 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -301,7 +301,7 @@ - $${OBJS}: SRC_CFLAGS := $${$${TGT}_CFLAGS} $${SRC_CFLAGS} - $${OBJS}: SRC_CXXFLAGS := $${$${TGT}_CXXFLAGS} $${SRC_CXXFLAGS} - $${OBJS}: SRC_DEFS := $$(addprefix -D,$${$${TGT}_DEFS} $${SRC_DEFS}) -- $${OBJS}: SRC_INCDIRS := $$(addprefix -I,\ -+ $${OBJS}: SRC_INCDIRS := $$(addprefix -iquote,\ - $${$${TGT}_INCDIRS} $${SRC_INCDIRS}) - endif - -@@ -389,7 +389,7 @@ - ALL_TGTS := - DEFS := - DIR_STACK := --INCDIRS := -+INCDIRS := utgcns/libboost - TGT_STACK := - - # Discover our OS and architecture. These were previously used to set -@@ -703,7 +703,7 @@ - - # Perform post-processing on global variables as needed. - DEFS := $(addprefix -D,${DEFS}) --INCDIRS := $(addprefix -I,$(call CANONICAL_PATH,${INCDIRS})) --VERSION := verkko release v2.1 -+INCDIRS := $(addprefix -isystem,$(call CANONICAL_PATH,${INCDIRS})) -+VERSION := bioconda $(PKG_NAME) bioconda $(PKG_VERSION) - - # Define the "all" target (which simply builds all user-defined targets) as the - # default goal. diff --git a/recipes/veryfasttree/build.sh b/recipes/veryfasttree/build.sh index 85c77f01983a1..8cf6516043503 100644 --- a/recipes/veryfasttree/build.sh +++ b/recipes/veryfasttree/build.sh @@ -1,5 +1,40 @@ #!/bin/bash -cmake -DUSE_NATIVE=OFF -USE_AVX2=ON . -make + mkdir -p $PREFIX/bin -cp VeryFastTree $PREFIX/bin/VeryFastTree + +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I{PREFIX}/include" + +OS=$(uname) +ARCH=$(uname -m) + +if [[ "${OS}" == "Darwin" && "${ARCH}" == "x86_64" ]]; then + export SIMD_LEVEL="-DUSE_SEE4=ON" +elif [[ "${OS}" == "Linux" && "${ARCH}" == "x86_64" ]]; then + export SIMD_LEVEL="-DUSE_AVX2=ON" +elif [[ "${OS}" == "Linux" && "${ARCH}" == "aarch64" ]]; then + export SIMD_LEVEL="-DUSE_SEE2=OFF" +else + export SIMD_LEVEL="" +fi + +if [[ "$(uname)" == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" + export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" +else + export CONFIG_ARGS="" +fi + +cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DUSE_NATIVE=OFF \ + "${CONFIG_ARGS}" \ + "${SIMD_LEVEL}" + +cmake --build build --target install -j "${CPU_COUNT}" -v + +chmod 0755 ${PREFIX}/bin/VeryFastTree diff --git a/recipes/veryfasttree/meta.yaml b/recipes/veryfasttree/meta.yaml index 34bdf32369805..1f3718f2aba7f 100644 --- a/recipes/veryfasttree/meta.yaml +++ b/recipes/veryfasttree/meta.yaml @@ -1,6 +1,6 @@ {% set name = "veryFastTree" %} -{% set version = "4.0.03" %} -{% set sha256 = "40c6b2f94d7d94f0a58b4736174c091f1131c83a8a090c0776c1789f3c13ef8a" %} +{% set version = "4.0.4" %} +{% set sha256 = "27c779164f4fa0c75897a6e95b35f820a2a10e7c244b8923c575e0ea46f15f6b" %} package: name: {{ name|lower }} @@ -12,36 +12,45 @@ source: build: number: 0 - skip: True # [osx] run_exports: - {{ pin_subpackage('veryfasttree', max_pin="x") }} requirements: build: - {{ compiler('cxx') }} - - libgomp - cmake - make host: - - libgomp + - libgomp # [linux] + - llvm-openmp # [osx] run: - - libgomp + - libgomp # [linux] + - llvm-openmp # [osx] test: commands: - VeryFastTree --help about: - home: https://github.com/citiususc/veryfasttree - license: GPL-3.0-only + home: "https://github.com/citiususc/veryfasttree" + license: "GPL-3.0-only" + license_family: GPL3 license_file: LICENSE - summary: VeryFastTree -- speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies + summary: "VeryFastTree -- speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies." description: | VeryFastTree is a highly-tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments. - dev_url: https://github.com/citiususc/veryfasttree + dev_url: "https://github.com/citiususc/veryfasttree" + doc_url: "https://github.com/citiususc/veryfasttree/blob/v{{ version }}/README.md" extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 recipe-maintainers: - cesarpomar - jcpichel + identifiers: + - doi:10.1093/bioinformatics/btaa582 + - doi:10.1093/gigascience/giae055 + - biotools:veryfasttree diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index d901ef21a8cb6..9ec0557e1bc67 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.56.0" %} +{% set version = "1.59.0" %} package: name: {{ name }} @@ -7,12 +7,12 @@ package: source: - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg # [linux and x86_64] - sha256: 8b82e300a386d6bf34d0d1025a7dc806b2b95bb57bd063226fc3984e920710e4 # [linux and x86_64] + sha256: a2270237c8541867ac345ad924c1641881bc9fd60be157a6d3d29fa910aacfc2 # [linux and x86_64] - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg-arm64 # [linux and aarch64] - sha256: 35693928a3aa049809fd906088f54594940e2de20e8b396cffe2b6b6b73a9e7a # [linux and aarch64] + sha256: e0df4e81e0c7b3ac1c7f3fc7a7bc8421416256bf2bc4a1ca2b87feebaf40d4d0 # [linux and aarch64] build: - number: 1 + number: 0 skip: true # [osx] script: - mkdir -p ${PREFIX}/bin diff --git a/recipes/viroconstrictor/meta.yaml b/recipes/viroconstrictor/meta.yaml index 2bbfb5a0c5666..d3bce9d30f325 100644 --- a/recipes/viroconstrictor/meta.yaml +++ b/recipes/viroconstrictor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ViroConstrictor" %} -{% set version = "1.4.3" %} +{% set version = "1.4.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/RIVM-bioinformatics/ViroConstrictor/archive/v{{ version }}.tar.gz - sha256: 43e7e6b29745367f3eabaef4ea736dfb25e2797fbe0e532b10f8594f71fc5883 + sha256: 1c218fe88d13187e6f77827489644958e21adc7f753048c9ec1076a465edb92d build: noarch: python @@ -17,7 +17,7 @@ build: - viroConstrictor = ViroConstrictor.__main__:main - Viroconstrictor = ViroConstrictor.__main__:main script: {{ PYTHON }} -m pip install . --no-deps -vvv - number: 0 + number: 1 run_exports: - {{ pin_subpackage('viroconstrictor', max_pin="x") }} @@ -40,7 +40,7 @@ requirements: - snakemake >=7.15.2, < 8 - aminoextract ==0.3.1 - conda - - mamba + - mamba >=1.5.0, <2.0.0 test: imports: @@ -63,5 +63,6 @@ about: extra: recipe-maintainers: - florianzwagemaker - - KHajji + - raaijmag + - wolthuisr - ids-bioinformatics diff --git a/recipes/vitap/meta.yaml b/recipes/vitap/meta.yaml new file mode 100644 index 0000000000000..7b8d4f94b6d99 --- /dev/null +++ b/recipes/vitap/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "vitap" %} +{% set version = "1.5" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/DrKaiyangZheng/VITAP/archive/refs/tags/v.{{ version }}.tar.gz + sha256: 4384925f0f6f53f08eb2a16cabc3ea325efd39a7e76139803668744b030b1d9a + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('vitap', max_pin='x') }} + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + +requirements: + host: + - pip + - python + - setuptools-markdown + run: + - python >=3.9 + - networkx >=3.1 + - scipy >=1.10 + - pandas >=1.5 + - numpy >=1.25 + - biopython >=1.78 + - tqdm >=4.65 + - diamond >=0.9 + - entrez-direct =16.2 + - seqkit >=2.5.1 + - prodigal-gv >=2.6 + +test: + commands: + - VITAP upd -h + - VITAP assignment -h + +about: + home: https://github.com/DrKaiyangZheng/VITAP/ + license: GPL-3.0-only + license_file: LICENSE + license_family: GPL + summary: Viral Taxonomic Assignment Pipeline + doc_url: https://github.com/DrKaiyangZheng/VITAP/blob/main/README.md + description: Viral Taxonomic Assignment Pipeline (VITAP) is a cutting-edge tool designed to address the growing need for accurate and comprehensive classification of DNA and RNA viral sequences. By integrating alignment-based techniques with graph theory, VITAP achieves high precision in classifying viral sequences, including those as short as 1000 base pairs, down to the genus level. diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 7cee8874d5bbb..f3b2d947ad235 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.28.1" %} -{% set sha256 = "4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c" %} +{% set version = "2.29.0" %} +{% set sha256 = "2c5bd0d9b3c2ec8eecd1af06ae11611138d87fdfecfa423ae791d52dccd27e63" %} package: name: vsearch @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('vsearch', max_pin="x") }} diff --git a/recipes/vsnp3/meta.yaml b/recipes/vsnp3/meta.yaml index 28ed73458bf68..d816791c62ea2 100644 --- a/recipes/vsnp3/meta.yaml +++ b/recipes/vsnp3/meta.yaml @@ -1,7 +1,7 @@ {% set user = "USDA-VS" %} {% set name = "vsnp3" %} -{% set version = "3.23" %} -{% set sha256 = "2ec038783ca43a3014dac3756efd460abea26d8c2edca8a41a65915c036388d9" %} +{% set version = "3.26" %} +{% set sha256 = "7d83019dd8537d686f66d17610722d636d2e918aed563db175fc4f3d3e9807f0" %} package: @@ -20,7 +20,7 @@ source: requirements: run: - - python >=3.8,<3.10 + - python >=3.8,<3.12 - bcftools - biopython >=1.79 - bwa diff --git a/recipes/wally/build.sh b/recipes/wally/build.sh index 0ed542795a662..c41da757c0afd 100644 --- a/recipes/wally/build.sh +++ b/recipes/wally/build.sh @@ -1,5 +1,3 @@ #!/bin/sh -make all CXX=$CXX CXXFLAGS="-D__STDC_FORMAT_MACROS -I${PREFIX}/include -L${PREFIX}/lib" -mkdir -p $PREFIX/bin -cp src/wally $PREFIX/bin +CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS -I${PREFIX}/include -L${PREFIX}/lib" make -j${CPU_COUNT} CXX="${CXX}" prefix="${PREFIX}" install diff --git a/recipes/wally/build_failure.linux-64.yaml b/recipes/wally/build_failure.linux-64.yaml deleted file mode 100644 index c65f87709d7fd..0000000000000 --- a/recipes/wally/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d48576ae8fde1a2e33ae3eb308cf274506b9c7e8cb9287b6ead7d7532ee0e9d8 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/conda/conda-bld/src_cache - Downloading source to cache: v0.5.8_ddd3376ad4.tar.gz - Downloading https://github.com/tobiasrausch/wally/archive/v0.5.8.tar.gz - Success - Extracting download - source tree in: /opt/conda/conda-bld/wally_1717808847579/work - export PREFIX=/opt/conda/conda-bld/wally_1717808847579/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/conda/conda-bld/wally_1717808847579/_build_env - export SRC_DIR=/opt/conda/conda-bld/wally_1717808847579/work - INFO: activate-binutils_linux-64.sh made the following environmental changes: - ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line - AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar - AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as - CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt - ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit - GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof - LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld - LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold - NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm - OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy - OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump - RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib - READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf - SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size - STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings - STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip - INFO: activate-gcc_linux-64.sh made the following environmental changes: - BUILD=x86_64-conda-linux-gnu - CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wally-0.5.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr - CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot - CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu - CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu - CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp - CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include - DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wally-0.5.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include - GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc - GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar - GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm - GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib - HOST=x86_64-conda-linux-gnu - LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu - build_alias=x86_64-conda-linux-gnu - host_alias=x86_64-conda-linux-gnu - -BUILD=x86_64-conda_cos6-linux-gnu - -CONDA_BUILD_SYSROOT= - INFO: activate-gxx_linux-64.sh made the following environmental changes: - CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wally-0.5.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wally-0.5.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g - if [ -r src/htslib/Makefile ]; then cd src/htslib && autoreconf -i && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && make && make lib-static && cd ../../ && touch .htslib; fi - if [ -f src/opencv/CMakeLists.txt ]; then cd src/opencv/ && mkdir build && cd build/ && cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=$SRC_DIR/src/ocv -D BUILD_SHARED_LIBS="ON" -DOPENCV_GENERATE_PKGCONFIG=ON -D BUILD_ZLIB=ON -D BUILD_PNG=ON -D BUILD_OPENJPEG=ON -D WITH_OPENEXR=OFF -D WITH_JPEG=OFF -D WITH_JASPER=OFF -D WITH_TIFF=OFF -D WITH_WEBP=OFF -D WITH_OPENCL=OFF -D WITH_GTK="ON" -D WITH_FFMPEG=OFF -D WITH_1394=OFF -D WITH_IPP=OFF -D BUILD_TESTS=OFF -D BUILD_PERF_TESTS=OFF -D BUILD_opencv_apps=OFF .. && make -j 4 && make install && cd ../ && rm -rf build/ && cd ../../ && touch .opencv; fi - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -D__STDC_FORMAT_MACROS -I$PREFIX/include -L$PREFIX/lib -I$PREFIX/include/opencv4 src/wally.cpp -o src/wally -L$PREFIX/lib -lopencv_gapi -lopencv_stitching -lopencv_alphamat -lopencv_aruco -lopencv_bgsegm -lopencv_bioinspired -lopencv_ccalib -lopencv_cvv -lopencv_dnn_objdetect -lopencv_dnn_superres -lopencv_dpm -lopencv_face -lopencv_freetype -lopencv_fuzzy -lopencv_hdf -lopencv_hfs -lopencv_img_hash -lopencv_intensity_transform -lopencv_line_descriptor -lopencv_mcc -lopencv_quality -lopencv_rapid -lopencv_reg -lopencv_rgbd -lopencv_saliency -lopencv_signal -lopencv_stereo -lopencv_structured_light -lopencv_phase_unwrapping -lopencv_superres -lopencv_optflow -lopencv_surface_matching -lopencv_tracking -lopencv_highgui -lopencv_datasets -lopencv_text -lopencv_plot -lopencv_videostab -lopencv_videoio -lopencv_wechat_qrcode -lopencv_xfeatures2d -lopencv_shape -lopencv_ml -lopencv_ximgproc -lopencv_video -lopencv_xobjdetect -lopencv_objdetect -lopencv_calib3d -lopencv_imgcodecs -lopencv_features2d -lopencv_dnn -lopencv_flann -lopencv_xphoto -lopencv_photo -lopencv_imgproc -lopencv_core -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/src/htslib/ -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -pthread -lhts -lz -llzma -lbz2 -Wl,-rpath,$SRC_DIR/src/htslib/ -Wl,-rpath,$SRC_DIR/src/ocv/lib/ -Wl,-rpath,$SRC_DIR/src/ocv/lib64/ - In file included from src/region.h:29, - from src/wally.cpp:13: - src/util.h:114:37: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 114 | struct SortMappings : public std::binary_function - | ^~~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/wally_1717808847579/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/string:48, - from /opt/conda/conda-bld/wally_1717808847579/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/locale_classes.h:40, - from /opt/conda/conda-bld/wally_1717808847579/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/ios_base.h:41, - from /opt/conda/conda-bld/wally_1717808847579/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/ios:42, - from /opt/conda/conda-bld/wally_1717808847579/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/ostream:38, - from /opt/conda/conda-bld/wally_1717808847579/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/iostream:39, - from src/wally.cpp:3: - /opt/conda/conda-bld/wally_1717808847579/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ - In file included from src/wally.cpp:15: - src/dotplot.h: In function 'int wallysworld::dotplotRun(TConfigStruct&)': - src/dotplot.h:500:74: error: 'boost::filesystem::copy_option' has not been declared - 500 | boost::filesystem::copy_file(c.file, c.seqfile, boost::filesystem::copy_option::overwrite_if_exists); - | ^~~~~~~~~~~ - make: *** [Makefile:67: src/wally] Error 1 - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/wally_1717808847579/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/wally/build_failure.osx-64.yaml b/recipes/wally/build_failure.osx-64.yaml deleted file mode 100644 index c79f6688d6ab9..0000000000000 --- a/recipes/wally/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d48576ae8fde1a2e33ae3eb308cf274506b9c7e8cb9287b6ead7d7532ee0e9d8 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - ~~~~~^~~~~~~~~~~~~~~ - __binary_function - /opt/mambaforge/envs/bioconda/conda-bld/wally_1717635453488/_build_env/bin/../include/c/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here - using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>; - ^ - In file included from src/wally.cpp:15: - src/dotplot.h:500:74: error: no member named 'copy_option' in namespace 'boost::filesystem'; did you mean 'copy_options'? - boost::filesystem::copy_file(c.file, c.seqfile, boost::filesystem::copy_option::overwrite_if_exists); - ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ - copy_options - /opt/mambaforge/envs/bioconda/conda-bld/wally_1717635453488/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/boost/filesystem/operations.hpp:44:12: note: 'copy_options' declared here - enum class copy_options : unsigned int - ^ - In file included from src/wally.cpp:15: - src/dotplot.h:500:87: error: no member named 'overwrite_if_exists' in 'boost::filesystem::copy_options'; did you mean 'overwrite_existing'? - boost::filesystem::copy_file(c.file, c.seqfile, boost::filesystem::copy_option::overwrite_if_exists); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ - overwrite_existing - /opt/mambaforge/envs/bioconda/conda-bld/wally_1717635453488/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/boost/filesystem/operations.hpp:50:5: note: 'overwrite_existing' declared here - overwrite_existing = 1u << 1u, // Overwrite existing file - ^ - In file included from src/wally.cpp:18: - In file included from src/gfa.h:36: - src/gfadraw.h:103:10: error: no member named 'random_shuffle' in namespace 'std' - std::random_shuffle(sf.begin(), sf.end()); - ~~~~~^ - 5 errors generated. - make: *** [Makefile:67: src/wally] Error 1 - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/wally_1717635453488/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/wally_1717635453488/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/wally_1717635453488/_build_env - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/wally_1717635453488/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - api.build( - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wally-0.5.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/wally_1717635453488/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wally-0.5.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wally-0.5.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wally-0.5.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - if [ -r src/htslib/Makefile ]; then cd src/htslib && autoreconf -i && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && make && make lib-static && cd ../../ && touch .htslib; fi - if [ -f src/opencv/CMakeLists.txt ]; then cd src/opencv/ && mkdir build && cd build/ && cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=$SRC_DIR/src/ocv -D BUILD_SHARED_LIBS="ON" -DOPENCV_GENERATE_PKGCONFIG=ON -D BUILD_ZLIB=ON -D BUILD_PNG=ON -D BUILD_OPENJPEG=ON -D WITH_OPENEXR=OFF -D WITH_JPEG=OFF -D WITH_JASPER=OFF -D WITH_TIFF=OFF -D WITH_WEBP=OFF -D WITH_OPENCL=OFF -D WITH_GTK="ON" -D WITH_FFMPEG=OFF -D WITH_1394=OFF -D WITH_IPP=OFF -D BUILD_TESTS=OFF -D BUILD_PERF_TESTS=OFF -D BUILD_opencv_apps=OFF .. && make -j 4 && make install && cd ../ && rm -rf build/ && cd ../../ && touch .opencv; fi - x86_64-apple-darwin13.4.0-clang -D__STDC_FORMAT_MACROS -I$PREFIX/include -L$PREFIX/lib -I$PREFIX/include/opencv4 src/wally.cpp -o src/wally -L$PREFIX/lib -lopencv_gapi -lopencv_stitching -lopencv_alphamat -lopencv_aruco -lopencv_bgsegm -lopencv_bioinspired -lopencv_ccalib -lopencv_dnn_objdetect -lopencv_dnn_superres -lopencv_dpm -lopencv_face -lopencv_freetype -lopencv_fuzzy -lopencv_hdf -lopencv_hfs -lopencv_img_hash -lopencv_intensity_transform -lopencv_line_descriptor -lopencv_mcc -lopencv_quality -lopencv_rapid -lopencv_reg -lopencv_rgbd -lopencv_saliency -lopencv_stereo -lopencv_structured_light -lopencv_phase_unwrapping -lopencv_superres -lopencv_optflow -lopencv_surface_matching -lopencv_tracking -lopencv_highgui -lopencv_datasets -lopencv_text -lopencv_plot -lopencv_videostab -lopencv_videoio -lopencv_wechat_qrcode -lopencv_xfeatures2d -lopencv_shape -lopencv_ml -lopencv_ximgproc -lopencv_video -lopencv_xobjdetect -lopencv_objdetect -lopencv_calib3d -lopencv_imgcodecs -lopencv_features2d -lopencv_dnn -lopencv_flann -lopencv_xphoto -lopencv_photo -lopencv_imgproc -lopencv_core -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/src/htslib/ -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -pthread -lhts -lz -llzma -lbz2 -Wl,-rpath,$SRC_DIR/src/htslib/ -Wl,-rpath,$SRC_DIR/src/ocv/lib/ -Wl,-rpath,$SRC_DIR/src/ocv/lib64/ -# Last 100 lines of the build log. diff --git a/recipes/wally/meta.yaml b/recipes/wally/meta.yaml index 035f146190cf1..26a0beaba7985 100644 --- a/recipes/wally/meta.yaml +++ b/recipes/wally/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.5.8" %} -{% set sha256 = "ddd3376ad4dc3a37ccdafd813a9f6824fd3d78f35b440be7f810471b250facbd" %} +{% set version = "0.6.1" %} +{% set sha256 = "8c83808b112996cef6557cd0f26d4de9b96722ce7cb1c2fa482c8af32ef1c422" %} package: name: wally @@ -10,29 +10,25 @@ source: sha256: '{{ sha256 }}' build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage("wally", max_pin="x.x") }} requirements: build: - - {{ compiler('cxx') }} - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - {{ cdt('libxext') }} # [linux] - - xorg-libxfixes # [linux] - make - - pkg-config # [osx] + - {{ compiler('cxx') }} host: - zlib - bzip2 + - libdeflate - boost-cpp - libopencv >=4.5.3 - htslib run: - zlib - bzip2 + - libdeflate - boost-cpp - libopencv >=4.5.3 - htslib @@ -41,13 +37,13 @@ test: commands: - wally --help -extra: - container: - extended-base: True - about: home: https://github.com/tobiasrausch/wally license: BSD-3-Clause license_family: BSD license_file: LICENSE summary: Visualization of aligned sequencing reads and genomic variants. + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/wfa2-lib/build.sh b/recipes/wfa2-lib/build.sh index ae970ee6f6ad4..70bd4b1b6e752 100644 --- a/recipes/wfa2-lib/build.sh +++ b/recipes/wfa2-lib/build.sh @@ -1,9 +1,11 @@ #!/bin/bash set -ex -export C_INCLUDE_PATH="${PREFIX}/include" +export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" case $(uname -m) in aarch64 | arm64) @@ -14,13 +16,22 @@ case $(uname -m) in ;; esac +if [[ "$(uname)" == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + cmake -S . -B build \ -DCMAKE_CXX_COMPILER="${CXX}" \ -DCMAKE_C_COMPILER="${CC}" \ - -DCMAKE_CXX_FLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64 -I${PREFIX}/include ${LDFLAGS}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DCMAKE_C_FLAGS="${CFLAGS}" \ -DEXTRA_FLAGS="${EXTRA_FLAGS}" \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ - -DOPENMP=TRUE + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_INSTALL_LIBDIR="${PREFIX}/lib" \ + -DOPENMP=TRUE "${CONFIG_ARGS}" -cmake --build build/ --target install -j ${CPU_COUNT} -v +cmake --build build/ --target install -j "${CPU_COUNT}" -v diff --git a/recipes/wfa2-lib/meta.yaml b/recipes/wfa2-lib/meta.yaml index 1ae790fdcb1e4..3be8971631094 100644 --- a/recipes/wfa2-lib/meta.yaml +++ b/recipes/wfa2-lib/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -20,8 +20,8 @@ requirements: - {{ compiler('cxx') }} - make - cmake - host: - pkg-config + host: - rhash # [osx] - libgomp # [linux] - llvm-openmp # [osx] @@ -36,7 +36,7 @@ about: license: MIT license_family: MIT license_file: LICENSE - summary: "Wavefront alignment algorithm library v2" + summary: "Wavefront alignment algorithm library v2." dev_url: "https://github.com/smarco/WFA2-lib" doc_url: "https://github.com/smarco/WFA2-lib/blob/v{{ version }}/README.md" diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index cc440afd74bf9..980acc916dbe1 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "wfmash" %} -{% set version = "0.18.0" %} +{% set version = "0.21.0" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/waveygang/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 8a86254dec1fa972cf4f15aa8eb2a21a8c241c1d28df4bcc8c6b10cce77cd510 + sha256: fc1482c0098f36bb5fe4730ad4504ed7c8037c902e7fa3339b33d18e338e2f6d build: skip: True # [osx] diff --git a/recipes/whatshap/build_failure.linux-64.yaml b/recipes/whatshap/build_failure.linux-64.yaml deleted file mode 100644 index 0c20579f0ddd7..0000000000000 --- a/recipes/whatshap/build_failure.linux-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 9b572de4ff8373a2d807ddec40dc17bf503ae9bc41ed9e9afa694c1b3fc643d8 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue -log: |2- - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("zstandard"), MatchSpec("xopen==1.7.0=py312h7900ff3_3")} - Encountered problems while solving: - - package xopen-1.7.0-py312h7900ff3_3 requires zstandard, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - [32mpysam >=0.18 [0m is installable with the potential options - [32mpysam 0.22.1[0m would require - [32mlibcurl >=8.8.0,<9.0a0 [0m, which requires - [32mzstd >=1.5.6,<1.6.0a0 [0m, which can be installed; - [32mpysam [0.18.0|0.19.0|0.19.1|0.20.0][0m would require - [32mpython_abi 2.7.* *_cp27mu[0m, which can be installed; - [32mpysam [0.18.0|0.19.0|0.19.1|0.20.0|0.21.0][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mpysam [0.18.0|0.19.0|0.19.1|0.20.0|0.21.0][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mpysam [0.18.0|0.19.0|...|0.22.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam [0.18.0|0.19.0|...|0.22.1][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam [0.19.1|0.20.0|0.21.0|0.22.0|0.22.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32mpysam 0.22.1[0m would require - [32mpython_abi 3.11.* *_cp311[0m, which can be installed; - [31mpython_abi 3.12.* *_cp312[0m is not installable because it conflicts with any installable versions previously reported; - [32mxopen >=1.2.0 [0m is installable with the potential options - [32mxopen 1.2.0[0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mxopen [1.2.0|1.2.1|...|1.6.0][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mxopen [1.2.0|1.2.1|...|1.6.0][0m would require - [32mpython_abi 3.7 *_pypy37_pp73[0m, which can be installed; - [32mxopen [1.2.0|1.2.1|...|2.0.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mxopen [1.2.0|1.2.1|...|2.0.1][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mxopen [1.2.1|1.3.0|...|2.0.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32mxopen [1.6.0|1.7.0|1.8.0|1.9.0|2.0.1][0m would require - [32mpython_abi 3.11.* *_cp311[0m, which can be installed; - [32mxopen [1.7.0|1.8.0|1.9.0|2.0.1][0m would require - [32mzstandard[0m with the potential options - [32mzstandard [0.10.2|0.11.0|...|0.8.1][0m would require - [32mpython_abi * *_cp27mu[0m, which can be installed; - [32mzstandard [0.10.2|0.11.0|...|0.8.1][0m would require - [32mpython_abi * *_cp36m[0m, which can be installed; - [32mzstandard [0.10.2|0.11.0|0.11.1|0.12.0|0.13.0][0m would require - [32mpython_abi * *_cp37m[0m, which can be installed; - [32mzstandard [0.12.0|0.13.0][0m would require - [32mpython_abi * *_cp38[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|0.15.1|0.15.2][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|0.15.1|0.15.2][0m would require - [32mpython_abi 3.6 *_pypy36_pp73[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|...|0.18.0][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|...|0.22.0][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|...|0.22.0][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mzstandard [0.14.1|0.15.1|0.15.2|0.16.0|0.17.0][0m would require - [32mpython_abi 3.7 *_pypy37_pp73[0m, which can be installed; - [32mzstandard [0.16.0|0.17.0|...|0.22.0][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32mzstandard [0.17.0|0.18.0|0.19.0][0m would require - [32mpython_abi 3.8 *_pypy38_pp73[0m, which can be installed; - [32mzstandard [0.17.0|0.18.0|0.19.0|0.21.0|0.22.0][0m would require - [32mpython_abi 3.9 *_pypy39_pp73[0m, which can be installed; - [32mzstandard [0.18.0|0.19.0|0.21.0|0.22.0][0m would require - [32mpython_abi 3.11.* *_cp311[0m, which can be installed; - [32mzstandard 0.8.1[0m would require - [32mpython_abi * *_cp35m[0m, which can be installed; - [31mzstandard [0.21.0|0.22.0][0m would require - [31mzstd >=1.5.5,<1.5.6.0a0 [0m, which conflicts with any installable versions previously reported; - [32mxopen 1.7.0[0m would require - [32mpython_abi 3.8 *_pypy38_pp73[0m, which can be installed; - [32mxopen [1.7.0|1.8.0|1.9.0|2.0.1][0m would require - [32mpython_abi 3.9 *_pypy39_pp73[0m, which can be installed. -# Last 100 lines of the build log. diff --git a/recipes/whatshap/build_failure.linux-aarch64.yaml b/recipes/whatshap/build_failure.linux-aarch64.yaml deleted file mode 100644 index 286d834638539..0000000000000 --- a/recipes/whatshap/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 9b572de4ff8373a2d807ddec40dc17bf503ae9bc41ed9e9afa694c1b3fc643d8 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue -log: |2- - - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("xopen==1.7.0=py312h8025657_3"), MatchSpec("zstandard")} - Encountered problems while solving: - - package xopen-1.7.0-py312h8025657_3 requires zstandard, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - [32mpysam >=0.18 [0m is installable with the potential options - [32mpysam 0.22.1[0m would require - [32mlibcurl >=8.8.0,<9.0a0 [0m, which requires - [32mzstd >=1.5.6,<1.6.0a0 [0m, which can be installed; - [32mpysam [0.22.0|0.22.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32mpysam [0.22.0|0.22.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam [0.22.0|0.22.1][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam 0.22.1[0m would require - [32mpython_abi 3.11.* *_cp311[0m, which can be installed; - [31mpython_abi 3.12.* *_cp312[0m is not installable because it conflicts with any installable versions previously reported; - [32mxopen >=1.2.0 [0m is installable with the potential options - [32mxopen [1.7.0|1.8.0|1.9.0|2.0.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32mxopen [1.7.0|1.8.0|1.9.0|2.0.1][0m would require - [32mpython_abi 3.11.* *_cp311[0m, which can be installed; - [32mxopen [1.7.0|1.8.0|1.9.0|2.0.1][0m would require - [32mzstandard[0m with the potential options - [32mzstandard [0.12.0|0.13.0][0m would require - [32mpython_abi * *_cp36m[0m, which can be installed; - [32mzstandard [0.12.0|0.13.0][0m would require - [32mpython_abi * *_cp37m[0m, which can be installed; - [32mzstandard [0.12.0|0.13.0][0m would require - [32mpython_abi * *_cp38[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|0.15.1|0.15.2][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|0.15.1|0.15.2][0m would require - [32mpython_abi 3.6 *_pypy36_pp73[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|...|0.18.0][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|...|0.22.0][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mzstandard [0.14.0|0.14.1|...|0.22.0][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mzstandard [0.14.1|0.15.1|0.15.2|0.16.0|0.17.0][0m would require - [32mpython_abi 3.7 *_pypy37_pp73[0m, which can be installed; - [32mzstandard [0.16.0|0.17.0|...|0.22.0][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32mzstandard [0.17.0|0.18.0|0.19.0][0m would require - [32mpython_abi 3.8 *_pypy38_pp73[0m, which can be installed; - [32mzstandard [0.17.0|0.18.0|0.19.0|0.21.0|0.22.0][0m would require - [32mpython_abi 3.9 *_pypy39_pp73[0m, which can be installed; - [32mzstandard [0.18.0|0.19.0|0.21.0|0.22.0][0m would require - [32mpython_abi 3.11.* *_cp311[0m, which can be installed; - [31mzstandard [0.21.0|0.22.0][0m would require - [31mzstd >=1.5.5,<1.5.6.0a0 [0m, which conflicts with any installable versions previously reported; - [32mxopen [1.7.0|1.8.0|1.9.0|2.0.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mxopen [1.7.0|1.8.0|1.9.0][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mxopen [1.7.0|1.8.0|1.9.0][0m would require - [32mpython_abi 3.9 *_pypy39_pp73[0m, which can be installed. -# Last 100 lines of the build log. diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index bf85a3c4c3e1f..60ae860a8702e 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -1,16 +1,19 @@ +{% set name = "whatshap" %} +{% set version = "2.3" %} + package: - name: whatshap - version: "2.3" + name: {{ name }} + version: {{ version }} source: url: https://files.pythonhosted.org/packages/37/99/7f156642064fe65aabbe6fa044a485e2aae6437dd545a9d539c06c1535dd/whatshap-2.3.tar.gz sha256: 1f7ac47b18784b213492e4b92dddc63132d371b2f353660462536bcadc15e62e build: - number: 1 - # Unexplicable CI failure, feel free to try to make this work again - skip: true # [osx] - script: python -m pip install --no-deps --ignore-installed . + number: 2 + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv run_exports: - {{ pin_subpackage('whatshap', max_pin="x") }} @@ -21,13 +24,12 @@ requirements: - python - pip - cython - - setuptools - setuptools-scm run: - python - pysam >=0.18 - pyfaidx >=0.5.5.2 - - networkx >=2.4 + - networkx - biopython >=1.73 - scipy - xopen >=1.2.0 @@ -40,16 +42,21 @@ test: imports: - whatshap commands: - - whatshap --help > /dev/null + - "whatshap --help > /dev/null" about: - home: https://whatshap.readthedocs.io/ - license: MIT License - summary: 'phase genomic variants using DNA sequencing reads (haplotype assembly)' + home: "https://whatshap.readthedocs.io" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Phase genomic variants using DNA sequencing reads (haplotype assembly)." + dev_url: "https://github.com/whatshap/whatshap" + doc_url: "https://whatshap.readthedocs.io" extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - biotools:whatshap - doi:10.1089/cmb.2014.0157 diff --git a/recipes/wisecondorx/meta.yaml b/recipes/wisecondorx/meta.yaml index c32c17e5562fa..94a801e6d7d16 100644 --- a/recipes/wisecondorx/meta.yaml +++ b/recipes/wisecondorx/meta.yaml @@ -1,11 +1,11 @@ -{% set version="1.2.7" %} +{% set version="1.2.9" %} package: name: wisecondorx version: {{ version }} source: url: https://github.com/CenterForMedicalGeneticsGhent/wisecondorX/archive/v{{ version }}.tar.gz - sha256: 4597377e664afd5b4d78f92061d854186bbaba92ba9951f034e9e7ce4c2d1c29 + sha256: 345faaf81822d6532d278ca9819059c1a2860e0856432b054d3bed076c95326c build: number: 0 @@ -19,15 +19,16 @@ requirements: - python >=3.6 - setuptools run: + - pandas - python >=3.6 - - pysam - - scipy - - scikit-learn - - numpy - - r-jsonlite >=1.5 + - pysam ==0.22 + - scipy ==1.13 + - scikit-learn ==1.4 + - numpy ==1.26 + - r-jsonlite ==1.8.8 - r-png - - bioconductor-dnacopy - - matplotlib-base + - bioconductor-dnacopy ==1.76 + - matplotlib-base ==3.8.4 test: imports: diff --git a/recipes/xclone/meta.yaml b/recipes/xclone/meta.yaml new file mode 100644 index 0000000000000..9d503c1eb1603 --- /dev/null +++ b/recipes/xclone/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "xclone" %} +{% set version = "0.3.8" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/xclone-{{ version }}.tar.gz + sha256: 67fbf73ece48f41e2ae4531f2554c80ff62472066cb18b11045f7f41307a9115 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('xclone', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - poetry-core + - pip + run: + - python >=3.9 + - numpy >=1.26.4,<2.0.0 + - pandas >=2.2.2,<3.0.0 + - scipy >=1.13.1,<2.0.0 + - matplotlib-base >=3.9.0,<4.0.0 + - anndata >=0.10.7,<0.11.0 + - statsmodels >=0.14.2,<0.15.0 + - scanpy >=1.10.1,<2.0.0 + - h5py >=3.11.0,<4.0.0 + - palettable >=3.3.3,<4.0.0 + - requests >=2.32.3,<3.0.0 + - importlib-metadata >=7.1.0,<8.0.0 + - squidpy >=1.5.0,<2.0.0 + +test: + imports: + - xclone + +about: + home: "https://github.com/single-cell-genetics/XClone" + summary: "Inference of clonal Copy Number Alterations in single cells." + license: "Apache-2.0" + license_family: APACHE + license_file: LICENSE + dev_url: "https://github.com/single-cell-genetics/XClone" + doc_url: "https://xclone-cnv.readthedocs.io/en/latest" diff --git a/recipes/xengsort/meta.yaml b/recipes/xengsort/meta.yaml index 64fbad850f790..81ad38b3bace4 100644 --- a/recipes/xengsort/meta.yaml +++ b/recipes/xengsort/meta.yaml @@ -1,5 +1,5 @@ {% set name = "xengsort" %} -{% set version = "2.0.5" %} +{% set version = "2.0.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 243567ee3bdb7111ca7294c5979c2cd9ab5e76fdeefd30b7e27a177c839b33c9 + sha256: 22ca92e0548effb263f843a2233381f4a6d3073c2931ee0ec0cdbbddb625cf17 build: number: 0 @@ -16,14 +16,14 @@ build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" requirements: host: - pip - - python ==3.11 + - python >=3.12 run: - - python ==3.11 + - python >=3.12 - numpy >=1.22 - numba >=0.56 - zarr @@ -45,6 +45,7 @@ about: license_file: LICENSE license_family: MIT summary: "A fast xenograft read sorter based on space-efficient k-mer hashing" + dev_url: https://gitlab.com/genomeinformatics/xengsort extra: identifiers: diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml index 660b5f47c822d..c38a49f2cc743 100644 --- a/recipes/yacht/meta.yaml +++ b/recipes/yacht/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.2" %} +{% set version = "1.2.3" %} package: name: yacht @@ -6,7 +6,7 @@ package: source: url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz - sha256: a5c97eecac7aee24e5850f29537cfe5f0b3647ac2766b7876321d369e8bdf514 + sha256: 93adb23ad4f143d48c9f0ea661fe2283ff42e9c51e073a05460596ecabc65214 build: number: 0 @@ -28,10 +28,14 @@ requirements: - tqdm - biom-format - numpy + - setuptools + - requests run: - python >3.6 - sourmash >=4.8.3,<5 + - rust - scipy + - requests - numpy - pandas - scikit-learn @@ -39,12 +43,15 @@ requirements: - pytest - pytest-cov - loguru + - maturin >=1,<2 - tqdm - biom-format - pytaxonkit - openpyxl + - ruff - sourmash_plugin_branchwater + test: commands: - yacht --help @@ -75,3 +82,4 @@ extra: - ShaopengLiu1 - raquellewei - mohsenht + diff --git a/recipes/yahs/Makefile.patch b/recipes/yahs/Makefile.patch index 347d4e9d7231d..263e6bffe6e59 100644 --- a/recipes/yahs/Makefile.patch +++ b/recipes/yahs/Makefile.patch @@ -1,10 +1,10 @@ diff --git a/Makefile b/Makefile -index 2174509..f7b8646 100644 +index 1cb880c..1c2283f 100644 --- a/Makefile +++ b/Makefile @@ -1,4 +1,4 @@ --CFLAGS= -g -O0 -Wall -fno-strict-aliasing -+CFLAGS += -g -O0 -Wall -fno-strict-aliasing +-CFLAGS= -O3 -Wall -fno-strict-aliasing ++CFLAGS += -O3 -Wall -fno-strict-aliasing CPPFLAGS= INCLUDES= OBJS= diff --git a/recipes/yahs/build.sh b/recipes/yahs/build.sh index 113e16a0a7912..f8fed6a93fb1c 100644 --- a/recipes/yahs/build.sh +++ b/recipes/yahs/build.sh @@ -1,6 +1,12 @@ +#!/bin/bash + mkdir -p ${PREFIX}/bin -export CFLAGS="-I$PREFIX/include -L$PREFIX/lib" -make + +export CFLAGS="${CFLAGS} -O3 -I$PREFIX/include -L$PREFIX/lib" + +make -j"${CPU_COUNT}" CC="${CC}" CFLAGS="${CFLAGS}" + +chmod 0755 yahs agp_to_fasta juicer mv yahs ${PREFIX}/bin mv agp_to_fasta ${PREFIX}/bin mv juicer ${PREFIX}/bin diff --git a/recipes/yahs/meta.yaml b/recipes/yahs/meta.yaml index d7a37d8ed4e11..b4cc5e55f410f 100644 --- a/recipes/yahs/meta.yaml +++ b/recipes/yahs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2a.2" %} +{% set version = "1.2.2" %} package: name: yahs @@ -6,18 +6,20 @@ package: source: url: https://github.com/c-zhou/yahs/archive/refs/tags/v{{ version }}.tar.gz - sha256: c94e62d00f6c8cc1339e2d55845b9b2729fc74831352798d60ba3ff47a09b7a3 + sha256: 9ee37f72ee9f62015fe92029d0fa97eec90963ddf15a2f4b760b45ee2e0014aa patches: - Makefile.patch build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('yahs', max_pin="x") }} requirements: build: - {{ compiler('c') }} - host: - make + host: - zlib test: @@ -29,5 +31,12 @@ test: about: home: https://github.com/c-zhou/yahs license: MIT + license_family: MIT license_file: LICENSE - summary: YaHS, yet another Hi-C scaffolding tool. + summary: "YaHS, yet another Hi-C scaffolding tool." + dev_url: https://github.com/c-zhou/yahs + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/yak/build.sh b/recipes/yak/build.sh index c5001f0f716ee..f5b7e2bdc2652 100644 --- a/recipes/yak/build.sh +++ b/recipes/yak/build.sh @@ -1,6 +1,12 @@ -#!/bin/bash +#!/bin/bash -ex -mkdir -p $PREFIX/bin +mkdir -p ${PREFIX}/bin -make INCLUDES="-I$PREFIX/include" CFLAGS="-g -Wall -O2 -L$PREFIX/lib" -cp yak $PREFIX/bin +#install_name_tool error fix +if [[ "$(uname)" == Darwin ]]; then + export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib -headerpad_max_install_names" +fi + +make INCLUDES="-I${PREFIX}/include" CFLAGS="${CFLAGS} -g -Wall -O3 -L${PREFIX}/lib" +cp -rf yak ${PREFIX}/bin +chmod 755 ${PREFIX}/bin/yak diff --git a/recipes/yak/meta.yaml b/recipes/yak/meta.yaml index a4147c53a2141..f44283997a96a 100644 --- a/recipes/yak/meta.yaml +++ b/recipes/yak/meta.yaml @@ -7,9 +7,13 @@ package: source: url: https://github.com/lh3/yak/archive/v{{ version }}.tar.gz sha256: a4237af25005eb8e7e721519c62d6bbcf203bf0a572506af63c3f6ecb6b11836 + patches: + - yak.patch build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage('yak', max_pin="x.x") }} requirements: build: @@ -17,14 +21,21 @@ requirements: - {{ compiler('c') }} host: - zlib - run: - - zlib test: commands: - yak 2>&1 | grep 'Usage' about: - home: https://github.com/lh3/yak + home: "https://github.com/lh3/yak" license: MIT - summary: 'Yet another k-mer analyzer' + license_family: MIT + license_file: LICENSE.txt + summary: 'Yet another k-mer analyzer.' + dev_url: "https://github.com/lh3/yak" + doc_url: "https://github.com/lh3/yak/blob/v{{ version }}/README.md" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/yak/yak.patch b/recipes/yak/yak.patch new file mode 100644 index 0000000000000..6343f0d11db87 --- /dev/null +++ b/recipes/yak/yak.patch @@ -0,0 +1,760 @@ +diff --git a/LICENSE.txt b/LICENSE.txt +new file mode 100644 +index 0000000..d7ac24e +--- /dev/null ++++ b/LICENSE.txt +@@ -0,0 +1,23 @@ ++The MIT License ++ ++Copyright (c) 2019- Dana-Farber Cancer Institute ++ ++Permission is hereby granted, free of charge, to any person obtaining ++a copy of this software and associated documentation files (the ++"Software"), to deal in the Software without restriction, including ++without limitation the rights to use, copy, modify, merge, publish, ++distribute, sublicense, and/or sell copies of the Software, and to ++permit persons to whom the Software is furnished to do so, subject to ++the following conditions: ++ ++The above copyright notice and this permission notice shall be ++included in all copies or substantial portions of the Software. ++ ++THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, ++EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF ++MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND ++NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS ++BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ++ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN ++CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE ++SOFTWARE. +diff --git a/Makefile b/Makefile +index 41c92f7..540b080 100644 +--- a/Makefile ++++ b/Makefile +@@ -2,7 +2,7 @@ CFLAGS= -g -Wall -O2 + CPPFLAGS= + INCLUDES= + OBJS= kthread.o bbf.o htab.o bseq.o misc.o sys.o 6gjdn.o \ +- count.o qv.o triobin.o trioeval.o inspect.o ++ count.o qv.o triobin.o trioeval.o inspect.o chkerr.o sexchr.o + PROG= yak + LIBS= -lm -lz -lpthread + +@@ -32,6 +32,7 @@ depend: + + bbf.o: yak.h + bseq.o: bseq.h kseq.h ++chkerr.o: kthread.h ketopt.h bseq.h yak-priv.h yak.h + count.o: kthread.h yak-priv.h yak.h kseq.h + htab.o: kthread.h yak-priv.h yak.h khashl.h + inspect.o: ketopt.h yak-priv.h yak.h +@@ -39,6 +40,7 @@ kthread.o: kthread.h + main.o: ketopt.h yak-priv.h yak.h + misc.o: yak-priv.h yak.h + qv.o: kthread.h yak-priv.h yak.h bseq.h ++sexchr.o: kthread.h ketopt.h bseq.h yak-priv.h yak.h + sys.o: yak-priv.h yak.h + triobin.o: kthread.h ketopt.h bseq.h yak-priv.h yak.h + trioeval.o: kthread.h ketopt.h bseq.h yak-priv.h yak.h +diff --git a/README.md b/README.md +index a467de7..f0c3c99 100644 +--- a/README.md ++++ b/README.md +@@ -26,8 +26,12 @@ cd yak && make + + # print k-mer histogram + ./yak inspect sr.yak > sr.hist +-# print k-mers (warning: large output) +-./yak inspect -p sr.yak > sr.kmers ++ ++# partition chrX/Y in human de novo assembly ++wget -O- 'https://zenodo.org/record/7882299/files/human-chrXY-yak.tar?download=1' | tar tf - ++./yak sexchr -K2g -t16 chrY-no-par.yak chrX-no-par.yak par.yak hap1.fa hap2.fa > cnt.txt ++./groupxy.pl cnt.txt|awk '$4==1'|cut -f2|seqtk subseq -l80 <(cat hap1.fa hap2.fa) - > new-hap1.fa ++./groupxy.pl cnt.txt|awk '$4==2'|cut -f2|seqtk subseq -l80 <(cat hap1.fa hap2.fa) - > new-hap2.fa + ``` + + ## Introduction +diff --git a/chkerr.c b/chkerr.c +new file mode 100644 +index 0000000..ed777f0 +--- /dev/null ++++ b/chkerr.c +@@ -0,0 +1,133 @@ ++#include ++#include ++#include ++#include "kthread.h" ++#include "ketopt.h" ++#include "bseq.h" ++#include "yak-priv.h" ++ ++typedef struct { ++ int k, n_threads, min_cnt, min_streak; ++ int64_t chunk_size; ++ bseq_file_t *fp; ++ const yak_ch_t *ch; ++} ce_shared_t; ++ ++typedef struct { ++ int n_seq; ++ ce_shared_t *aux; ++ bseq1_t *seq; ++} ce_step_t; ++ ++static void te_worker(void *_data, long k, int tid) ++{ ++ ce_step_t *t = (ce_step_t*)_data; ++ ce_shared_t *aux = t->aux; ++ bseq1_t *s = &t->seq[k]; ++ uint64_t x[4], mask; ++ int i, l, last, streak, shift; ++ if (aux->ch->k < 32) { ++ mask = (1ULL<<2*aux->ch->k) - 1; ++ shift = 2 * (aux->ch->k - 1); ++ } else { ++ mask = (1ULL<ch->k) - 1; ++ shift = aux->ch->k - 1; ++ } ++ last = -1, streak = 0; ++ for (i = l = 0, x[0] = x[1] = x[2] = x[3] = 0; i < s->l_seq; ++i) { ++ int cnt, c = seq_nt4_table[(uint8_t)s->seq[i]]; ++ if (c < 4) { ++ if (aux->ch->k < 32) { ++ x[0] = (x[0] << 2 | c) & mask; ++ x[1] = x[1] >> 2 | (uint64_t)(3 - c) << shift; ++ } else { ++ x[0] = (x[0] << 1 | (c&1)) & mask; ++ x[1] = (x[1] << 1 | (c>>1)) & mask; ++ x[2] = x[2] >> 1 | (uint64_t)(1 - (c&1)) << shift; ++ x[3] = x[3] >> 1 | (uint64_t)(1 - (c>>1)) << shift; ++ } ++ if (++l >= aux->k) { ++ uint64_t y; ++ if (aux->ch->k < 32) ++ y = yak_hash64(x[0] < x[1]? x[0] : x[1], mask); ++ else ++ y = yak_hash_long(x); ++ cnt = yak_ch_get(aux->ch, y); ++ if (cnt < aux->min_cnt) { ++ if (i != last + 1) { ++ if (streak > aux->min_streak) ++ printf("%s\t%d\t%d\t%d\n", s->name, last + 1 - aux->k - (streak - 1), last + 1, streak); ++ streak = 1; ++ } else ++streak; ++ last = i; ++ } ++ } ++ } else l = 0, x[0] = x[1] = x[2] = x[3] = 0; ++ } ++ if (streak > aux->min_streak) ++ printf("%s\t%d\t%d\t%d\n", s->name, last + 1 - aux->k - (streak - 1), last + 1, streak); ++} ++ ++static void *ce_pipeline(void *shared, int step, void *_data) ++{ ++ ce_shared_t *aux = (ce_shared_t*)shared; ++ if (step == 0) { ++ ce_step_t *s; ++ s = (ce_step_t*)calloc(1, sizeof(ce_step_t)); ++ s->seq = bseq_read(aux->fp, aux->chunk_size, 0, &s->n_seq); ++ s->aux = aux; ++ if (s->n_seq) { ++ fprintf(stderr, "[M::%s] read %d sequences\n", __func__, s->n_seq); ++ return s; ++ } else free(s); ++ } else if (step == 1) { ++ int i; ++ ce_step_t *s = (ce_step_t*)_data; ++ kt_for(aux->n_threads, te_worker, s, s->n_seq); ++ for (i = 0; i < s->n_seq; ++i) { ++ free(s->seq[i].name); free(s->seq[i].seq); free(s->seq[i].qual); ++ free(s->seq[i].comment); ++ } ++ free(s->seq); free(s); ++ } ++ return 0; ++} ++ ++int main_chkerr(int argc, char *argv[]) ++{ ++ ketopt_t o = KETOPT_INIT; ++ int c; ++ yak_ch_t *ch; ++ ce_shared_t aux; ++ ++ memset(&aux, 0, sizeof(ce_shared_t)); ++ aux.chunk_size = 1000000000; ++ aux.n_threads = 8, aux.min_cnt = 3, aux.min_streak = 5; ++ while ((c = ketopt(&o, argc, argv, 1, "t:c:s:", 0)) >= 0) { ++ if (c == 't') aux.n_threads = atoi(o.arg); ++ else if (c == 'c') aux.min_cnt = atoi(o.arg); ++ else if (c == 's') aux.min_streak = atoi(o.arg); ++ } ++ if (argc - o.ind < 2) { ++ fprintf(stderr, "Usage: yak chkerr [options] \n"); ++ fprintf(stderr, "Options:\n"); ++ fprintf(stderr, " -t INT number of threads [%d]\n", aux.n_threads); ++ fprintf(stderr, " -c INT min k-mer count [%d]\n", aux.min_cnt); ++ fprintf(stderr, " -s INT min k-mer streak [%d]\n", aux.min_streak); ++ return 1; ++ } ++ ++ ch = yak_ch_restore(argv[o.ind]); ++ ++ aux.k = ch->k; ++ aux.fp = bseq_open(argv[o.ind+1]); ++ if (aux.fp == 0) { ++ fprintf(stderr, "ERROR: fail to open file '%s'\n", argv[o.ind+1]); ++ exit(1); ++ } ++ aux.ch = ch; ++ kt_pipeline(2, ce_pipeline, &aux, 2); ++ bseq_close(aux.fp); ++ yak_ch_destroy(ch); ++ return 0; ++} +diff --git a/groupxy.pl b/groupxy.pl +new file mode 100755 +index 0000000..55a41f9 +--- /dev/null ++++ b/groupxy.pl +@@ -0,0 +1,48 @@ ++#!/usr/bin/perl ++ ++use strict; ++use warnings; ++use Getopt::Std; ++ ++my %opts = (s=>.7, c=>.3, r=>.9); ++getopts('s:c:r:', \%opts); ++die("Usage: sexchr.pl [-s $opts{s}] [-c $opts{c}] [-r $opts{r}] in.sexchr\n") if @ARGV == 0; ++ ++# read data ++my @a = (); ++while (<>) { ++ chomp; ++ my @t = split("\t"); ++ next if $t[0] ne 'S'; ++ push(@a, \@t); ++} ++ ++# assign sex chromosome for individual contigs ++my @c = (0, 0, 0, 0); ++for (@a) { ++ next if $_->[5] < $_->[4] * $opts{s}; ++ next if $_->[6] + $_->[7] < $_->[5] * $opts{c}; ++ $_->[3] = $_->[6] > ($_->[6] + $_->[7]) * $opts{r}? 3 : $_->[7] > ($_->[6] + $_->[7]) * $opts{r}? 4 : 0; ++ next if $_->[3] == 0; ++ my $hap = $_->[2] - 1; ++ $c[$hap<<1|0] += $_->[6]; ++ $c[$hap<<1|1] += $_->[7]; ++} ++ ++# determine which partition correspond to sexchr1 or sexchr2 ++my $max_chr = $c[0] + $c[2] > $c[1] + $c[3]? 0 : 1; ++my $type = ($c[0<<1|$max_chr] > $c[1<<1|$max_chr]? 0 : 1) ^ $max_chr; ++ ++# update partition ++for (@a) { ++ if ($_->[3] >= 3) { ++ $_->[3] -= 2; ++ } else { ++ $_->[3] = $type == 0? $_->[2] : 3 - $_->[2]; ++ } ++} ++ ++# print out ++for (@a) { ++ print join("\t", @$_), "\n"; ++} +diff --git a/htab.c b/htab.c +index 5075e54..1112816 100644 +--- a/htab.c ++++ b/htab.c +@@ -228,6 +228,10 @@ yak_ch_t *yak_ch_restore_core(yak_ch_t *ch0, const char *fn, int mode, ...) + mid_cnt = va_arg(ap, int); + if (ch0 == 0 && mode == YAK_LOAD_TRIOBIN2) + mode_err = 1; ++ } else if (mode == YAK_LOAD_SEXCHR1 || mode == YAK_LOAD_SEXCHR2 || mode == YAK_LOAD_SEXCHR3) { ++ assert(YAK_COUNTER_BITS >= 3); ++ if (ch0 == 0 && (mode == YAK_LOAD_SEXCHR2 || mode == YAK_LOAD_SEXCHR3)) ++ mode_err = 1; + } else mode_err = 1; + va_end(ap); + if (mode_err) return 0; +@@ -251,7 +255,7 @@ yak_ch_t *yak_ch_restore_core(yak_ch_t *ch0, const char *fn, int mode, ...) + for (i = 0; i < 1<pre; ++i) { + yak_ht_t *h = ch->h[i].h; + fread(t, 4, 2, fp); +- if (ch0 == 0) yak_ht_resize(h, t[0]); ++ yak_ht_resize(h, t[0]); + for (j = 0; j < t[1]; ++j) { + uint64_t key; + fread(&key, 8, 1, fp); +@@ -272,6 +276,14 @@ yak_ch_t *yak_ch_restore_core(yak_ch_t *ch0, const char *fn, int mode, ...) + if (absent) ++n_new; + else kh_key(h, k) = kh_key(h, k) | x; + } ++ } else if (mode == YAK_LOAD_SEXCHR1 || mode == YAK_LOAD_SEXCHR2 || mode == YAK_LOAD_SEXCHR3) { ++ int shift = mode == YAK_LOAD_SEXCHR1? 0 : mode == YAK_LOAD_SEXCHR2? 1 : 2, x = 1<= 0) { + if (c == 'k') opt.k = atoi(o.arg); + else if (c == 'p') opt.pre = atoi(o.arg); +- else if (c == 'K') opt.chunk_size = atoi(o.arg); ++ else if (c == 'K') opt.chunk_size = mm_parse_num(o.arg); + else if (c == 't') opt.n_thread = atoi(o.arg); + else if (c == 'b') opt.bf_shift = atoi(o.arg); + else if (c == 'H') opt.bf_n_hash = mm_parse_num(o.arg); +@@ -84,12 +73,13 @@ int main_qv(int argc, char *argv[]) + yak_qstat_t qs; + + yak_qopt_init(&opt); +- while ((c = ketopt(&o, argc, argv, 1, "K:t:l:f:pe:", 0)) >= 0) { ++ while ((c = ketopt(&o, argc, argv, 1, "K:t:l:f:pe:E", 0)) >= 0) { + if (c == 'K') opt.chunk_size = mm_parse_num(o.arg); + else if (c == 'l') opt.min_len = mm_parse_num(o.arg); + else if (c == 'f') opt.min_frac = atof(o.arg); + else if (c == 't') opt.n_threads = atoi(o.arg); + else if (c == 'p') opt.print_each = 1; ++ else if (c == 'E') opt.print_err_kmer = 1; + else if (c == 'e') opt.fpr = atof(o.arg); + } + if (argc - o.ind < 2) { +@@ -99,6 +89,7 @@ int main_qv(int argc, char *argv[]) + fprintf(stderr, " -f FLOAT min k-mer fraction [%g]\n", opt.min_frac); + fprintf(stderr, " -e FLOAT false positive rate [%g]\n", opt.fpr); + fprintf(stderr, " -p print QV for each sequence\n"); ++ fprintf(stderr, " -E print the positions of wrong k-mers\n"); + fprintf(stderr, " -t INT number of threads [%d]\n", opt.n_threads); + fprintf(stderr, " -K NUM batch size [1g]\n"); + return 1; +@@ -131,6 +122,8 @@ int main(int argc, char *argv[]) + extern int main_triobin(int argc, char *argv[]); + extern int main_trioeval(int argc, char *argv[]); + extern int main_inspect(int argc, char *argv[]); ++ extern int main_chkerr(int argc, char *argv[]); ++ extern int main_sexchr(int argc, char *argv[]); + int ret = 0, i; + yak_reset_realtime(); + if (argc == 1) { +@@ -141,6 +134,8 @@ int main(int argc, char *argv[]) + fprintf(stderr, " triobin trio binning\n"); + fprintf(stderr, " trioeval evaluate phasing accuracy with trio\n"); + fprintf(stderr, " inspect k-mer hash tables\n"); ++ fprintf(stderr, " chkerr check errors\n"); ++ fprintf(stderr, " sexchr count sex-chromosome-specific k-mers\n"); + fprintf(stderr, " version print version number\n"); + return 1; + } +@@ -149,6 +144,8 @@ int main(int argc, char *argv[]) + else if (strcmp(argv[1], "triobin") == 0) ret = main_triobin(argc-1, argv+1); + else if (strcmp(argv[1], "trioeval") == 0) ret = main_trioeval(argc-1, argv+1); + else if (strcmp(argv[1], "inspect") == 0) ret = main_inspect(argc-1, argv+1); ++ else if (strcmp(argv[1], "chkerr") == 0) ret = main_chkerr(argc-1, argv+1); ++ else if (strcmp(argv[1], "sexchr") == 0) ret = main_sexchr(argc-1, argv+1); + else if (strcmp(argv[1], "version") == 0) { + puts(YAKS_VERSION); + return 0; +diff --git a/qv.c b/qv.c +index 6fdf73b..12e25a0 100644 +--- a/qv.c ++++ b/qv.c +@@ -59,6 +59,9 @@ static void worker_qv(void *_data, long k, int tid) + t = yak_ch_get(qs->ch, y); + if (t < 0) t = 0; + if (t > 0) ++non0; ++ else if (qs->opt->print_err_kmer) { ++ printf("EK\t%s\t%d\n", s->name, i + 1 - qs->k); ++ } + b->s[tot++] = (uint64_t)i<<32 | t; + } + } else l = 0, x[0] = x[1] = 0; +@@ -229,8 +232,13 @@ int yak_qv_solve(const int64_t *hist, const int64_t *cnt, int kmer, double fpr, + // compute adjusted qv + for (c = 0, adj_sum = 0.0; c < n_cnt; ++c) + adj_sum += qs->adj_cnt[c]; +- assert(adj_sum <= (double)qs->tot); +- qs->err = qs->tot - adj_sum; +- qs->qv = -4.3429448190325175 * log(log(qs->tot / adj_sum) / kmer); ++ if (adj_sum <= (double)qs->tot) { ++ qs->err = qs->tot - adj_sum; ++ qs->qv = -4.3429448190325175 * log(log(qs->tot / adj_sum) / kmer); ++ } else { ++ fprintf(stderr, "WARNING: failed to estimate the calibrated QV\n"); ++ qs->err = 0; ++ qs->qv = qs->qv_raw; ++ } + return 0; + } +diff --git a/sexchr.c b/sexchr.c +new file mode 100644 +index 0000000..acf80e9 +--- /dev/null ++++ b/sexchr.c +@@ -0,0 +1,140 @@ ++#include ++#include ++#include ++#include "kthread.h" ++#include "ketopt.h" ++#include "bseq.h" ++#include "yak-priv.h" ++ ++#ifndef kroundup32 ++#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) ++#endif ++ ++static long sc_chunk_size = 1000000000L; ++ ++typedef struct { ++ int k, n_threads, hap; ++ bseq_file_t *fp; ++ const yak_ch_t *ch; ++ uint32_t m_info, n_info; ++} sc_shared_t; ++ ++typedef struct { ++ int n_seq; ++ sc_shared_t *aux; ++ bseq1_t *seq; ++} sc_step_t; ++ ++static void sc_worker(void *_data, long k, int tid) ++{ ++ sc_step_t *t = (sc_step_t*)_data; ++ sc_shared_t *aux = t->aux; ++ bseq1_t *s = &t->seq[k]; ++ uint64_t x[4], mask; ++ long n_k = 0, n_sexchr = 0, n_sex1 = 0, n_sex2 = 0; ++ int i, l, shift; ++ if (aux->ch->k < 32) { ++ mask = (1ULL<<2*aux->ch->k) - 1; ++ shift = 2 * (aux->ch->k - 1); ++ } else { ++ mask = (1ULL<ch->k) - 1; ++ shift = aux->ch->k - 1; ++ } ++ for (i = l = 0, x[0] = x[1] = x[2] = x[3] = 0; i < s->l_seq; ++i) { ++ int flag, c = seq_nt4_table[(uint8_t)s->seq[i]]; ++ if (c < 4) { ++ if (aux->ch->k < 32) { ++ x[0] = (x[0] << 2 | c) & mask; ++ x[1] = x[1] >> 2 | (uint64_t)(3 - c) << shift; ++ } else { ++ x[0] = (x[0] << 1 | (c&1)) & mask; ++ x[1] = (x[1] << 1 | (c>>1)) & mask; ++ x[2] = x[2] >> 1 | (uint64_t)(1 - (c&1)) << shift; ++ x[3] = x[3] >> 1 | (uint64_t)(1 - (c>>1)) << shift; ++ } ++ if (++l >= aux->k) { ++ uint64_t y; ++ if (aux->ch->k < 32) ++ y = yak_hash64(x[0] < x[1]? x[0] : x[1], mask); ++ else ++ y = yak_hash_long(x); ++ ++n_k; ++ flag = yak_ch_get(aux->ch, y); ++ if (flag > 0) { ++ ++n_sexchr; ++ if (flag == 1) ++n_sex1; ++ if (flag == 2) ++n_sex2; ++ } ++ } ++ } else l = 0, x[0] = x[1] = x[2] = x[3] = 0; ++ } ++ printf("S\t%s\t%d\t0\t%ld\t%ld\t%ld\t%ld\n", s->name, aux->hap, n_k, n_sexchr, n_sex1, n_sex2); ++} ++ ++static void *sc_pipeline(void *shared, int step, void *_data) ++{ ++ sc_shared_t *aux = (sc_shared_t*)shared; ++ if (step == 0) { ++ sc_step_t *s; ++ s = (sc_step_t*)calloc(1, sizeof(sc_step_t)); ++ s->seq = bseq_read(aux->fp, sc_chunk_size, 0, &s->n_seq); ++ s->aux = aux; ++ if (s->n_seq) { ++ fprintf(stderr, "[M::%s] read %d sequences\n", __func__, s->n_seq); ++ return s; ++ } else free(s); ++ } else if (step == 1) { ++ int i; ++ sc_step_t *s = (sc_step_t*)_data; ++ kt_for(aux->n_threads, sc_worker, s, s->n_seq); ++ for (i = 0; i < s->n_seq; ++i) { ++ free(s->seq[i].name); free(s->seq[i].seq); free(s->seq[i].qual); free(s->seq[i].comment); ++ } ++ free(s->seq); free(s); ++ } ++ return 0; ++} ++ ++int main_sexchr(int argc, char *argv[]) ++{ ++ ketopt_t o = KETOPT_INIT; ++ int i, c; ++ yak_ch_t *ch; ++ sc_shared_t aux; ++ ++ memset(&aux, 0, sizeof(sc_shared_t)); ++ aux.n_threads = 8; ++ while ((c = ketopt(&o, argc, argv, 1, "t:K:", 0)) >= 0) { ++ if (c == 't') aux.n_threads = atoi(o.arg); ++ else if (c == 'K') sc_chunk_size = mm_parse_num(o.arg); ++ } ++ if (argc - o.ind < 5) { ++ fprintf(stderr, "Usage: yak sexchr [options] \n"); ++ fprintf(stderr, "Options:\n"); ++ fprintf(stderr, " -t INT number of threads [%d]\n", aux.n_threads); ++ fprintf(stderr, " -K NUM chunk size [1g]\n"); ++ return 1; ++ } ++ ++ ch = yak_ch_restore_core(0, argv[o.ind], YAK_LOAD_SEXCHR1); ++ ch = yak_ch_restore_core(ch, argv[o.ind + 1], YAK_LOAD_SEXCHR2); ++ ch = yak_ch_restore_core(ch, argv[o.ind + 2], YAK_LOAD_SEXCHR3); ++ ++ printf("C\tS seqName originalHap 0 #k-mer #sexchr #sex1-specifc #sex2-specific\n"); ++ printf("C\n"); ++ ++ aux.k = ch->k; ++ aux.ch = ch; ++ for (i = 1; i <= 2; ++i) { ++ aux.hap = i; ++ aux.fp = bseq_open(argv[o.ind+i+2]); ++ if (aux.fp == 0) { ++ fprintf(stderr, "ERROR: fail to open file '%s'\n", argv[o.ind+i+2]); ++ exit(1); ++ } ++ kt_pipeline(2, sc_pipeline, &aux, 2); ++ bseq_close(aux.fp); ++ } ++ yak_ch_destroy(ch); ++ return 0; ++} +diff --git a/trioeval.c b/trioeval.c +index 02c6622..dbdde34 100644 +--- a/trioeval.c ++++ b/trioeval.c +@@ -10,7 +10,7 @@ + #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) + #endif + +-#define CHUNK_SIZE 200000000 ++#define CHUNK_SIZE 1000000000 + + typedef struct { + int nk, c[4], d[2]; +@@ -22,11 +22,12 @@ typedef struct { + } te_buf_t; + + typedef struct { +- int k, n_threads, min_n; ++ int k, n_threads, min_n, print_err, print_frag; + bseq_file_t *fp; + const yak_ch_t *ch; + te_buf_t *buf; + int64_t n_pair, n_site, n_switch, n_err; ++ int64_t n_par[2]; + } te_shared_t; + + typedef struct { +@@ -44,6 +45,7 @@ static void te_worker(void *_data, long k, int tid) + te_buf_t *b = &aux->buf[tid]; + uint64_t x[4], mask; + int i, l, shift, last; ++ int f_st, f_en, f_type, f_cnt; + if (aux->ch->k < 32) { + mask = (1ULL<<2*aux->ch->k) - 1; + shift = 2 * (aux->ch->k - 1); +@@ -86,20 +88,32 @@ static void te_worker(void *_data, long k, int tid) + } + } else l = 0, x[0] = x[1] = x[2] = x[3] = 0; + } ++ f_type = f_st = f_en = f_cnt = 0; + for (l = 0, i = 1, last = 0; i <= s->l_seq; ++i) { +- if (i == s->l_seq || b->s[i] != b->s[l]) { ++ if (i == s->l_seq || b->s[i] != b->s[l]) { // found a streak + if (b->s[l] > 0 && i - l >= aux->min_n) { // skip singletons + int n = (i - l + aux->k - 1) / aux->k; + int c = b->s[l] - 1; + t->cnt[k].c[c << 1 | c] += n - 1; + t->cnt[k].d[c] += n; +- if (last > 0) ++ if (last > 0) { + ++t->cnt[k].c[(last - 1) << 1 | c]; ++ if (aux->print_err && last - 1 != c) ++ printf("E\t%s\t%d\t%d\t%d\n", s->name, i, last, c+1); ++ } ++ if (f_type != b->s[l]) { ++ if (f_type > 0 && aux->print_frag) ++ printf("F\t%s\t%d\t%d\t%d\t%d\n", s->name, f_type, f_st, f_en, f_cnt); ++ f_type = b->s[l], f_st = l + 1 - aux->ch->k, f_cnt = 0; ++ } ++ ++f_cnt, f_en = i + 1; + last = b->s[l]; + } + l = i; + } + } ++ if (f_type > 0 && aux->print_frag) ++ printf("F\t%s\t%d\t%d\t%d\t%d\n", s->name, f_type, f_st, f_en, f_cnt); + } + + static void *te_pipeline(void *shared, int step, void *_data) +@@ -121,13 +135,15 @@ static void *te_pipeline(void *shared, int step, void *_data) + kt_for(aux->n_threads, te_worker, s, s->n_seq); + for (i = 0; i < s->n_seq; ++i) { + int *c = s->cnt[i].c, *d = s->cnt[i].d; ++ aux->n_par[0] += d[0]; ++ aux->n_par[1] += d[1]; + if (d[0] + d[1] >= 2) { + aux->n_pair += c[0] + c[1] + c[2] + c[3]; + aux->n_switch += c[1] + c[2]; + aux->n_site += d[0] + d[1]; + aux->n_err += d[0] < d[1]? d[0] : d[1]; + } +- printf("S\t%s\t%d\t%d\t%d\t%d\t%d\t%d\n", s->seq[i].name, d[0], d[1], c[0], c[1], c[2], c[3]); ++ printf("S\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", s->seq[i].name, d[0], d[1], c[0], c[1], c[2], c[3], s->seq[i].l_seq); + free(s->seq[i].name); free(s->seq[i].seq); free(s->seq[i].qual); free(s->seq[i].comment); + } + free(s->seq); free(s->cnt); free(s); +@@ -144,12 +160,14 @@ int main_trioeval(int argc, char *argv[]) + te_shared_t aux; + + memset(&aux, 0, sizeof(te_shared_t)); +- aux.n_threads = 8, aux.min_n = 2; +- while ((c = ketopt(&o, argc, argv, 1, "c:d:t:n:", 0)) >= 0) { ++ aux.n_threads = 8, aux.min_n = 2, aux.print_frag = 1; ++ while ((c = ketopt(&o, argc, argv, 1, "c:d:t:n:eF", 0)) >= 0) { + if (c == 'c') min_cnt = atoi(o.arg); + else if (c == 'd') mid_cnt = atoi(o.arg); + else if (c == 't') aux.n_threads = atoi(o.arg); + else if (c == 'n') aux.min_n = atoi(o.arg); ++ else if (c == 'e') aux.print_err = 1; ++ else if (c == 'F') aux.print_frag = 0; + } + if (argc - o.ind < 2) { + fprintf(stderr, "Usage: yak trioeval [options] \n"); +@@ -158,6 +176,7 @@ int main_trioeval(int argc, char *argv[]) + fprintf(stderr, " -d INT mid occurrence [%d]\n", mid_cnt); + fprintf(stderr, " -n INT min streak [%d]\n", aux.min_n); + fprintf(stderr, " -t INT number of threads [%d]\n", aux.n_threads); ++ fprintf(stderr, " -e print error positions (out of order)\n"); + return 1; + } + +@@ -173,6 +192,12 @@ int main_trioeval(int argc, char *argv[]) + fprintf(stderr, "ERROR: fail to open file '%s'\n", argv[o.ind+2]); + exit(1); + } ++ printf("C\tS seqName #patKmer #matKmer #pat-pat #pat-mat #mat-pat #mat-mat seqLen\n"); ++ printf("C\tF seqName type startPos endPos count\n"); ++ printf("C\tW #switchErr denominator switchErrRate\n"); ++ printf("C\tH #hammingErr denominator hammingErrRate\n"); ++ printf("C\tN #totPatKmer #totMatKmer errRate\n"); ++ printf("C\n"); + aux.ch = ch; + aux.buf = (te_buf_t*)calloc(aux.n_threads, sizeof(te_buf_t)); + kt_pipeline(2, te_pipeline, &aux, 2); +@@ -181,6 +206,7 @@ int main_trioeval(int argc, char *argv[]) + for (i = 0; i < aux.n_threads; ++i) free(aux.buf[i].s); + printf("W\t%ld\t%ld\t%.6f\n", (long)aux.n_switch, (long)aux.n_pair, (double)aux.n_switch/aux.n_pair); + printf("H\t%ld\t%ld\t%.6f\n", (long)aux.n_err, (long)aux.n_site, (double)aux.n_err/aux.n_site); ++ printf("N\t%ld\t%ld\t%.6f\n", (long)aux.n_par[0], (long)aux.n_par[1], (double)(aux.n_par[0] < aux.n_par[1]? aux.n_par[0] : aux.n_par[1]) / (aux.n_par[0] + aux.n_par[1])); + free(aux.buf); + return 0; + } +diff --git a/yak-priv.h b/yak-priv.h +index f6a3af7..ee7569b 100644 +--- a/yak-priv.h ++++ b/yak-priv.h +@@ -1,6 +1,7 @@ + #ifndef YAK_PRIV_H + #define YAK_PRIV_H + ++#include + #include "yak.h" + + #define CALLOC(ptr, len) ((ptr) = (__typeof__(ptr))calloc((len), sizeof(*(ptr)))) +@@ -42,4 +43,15 @@ void yak_reset_realtime(void); + double yak_realtime(void); + long yak_peakrss(void); + ++static inline int64_t mm_parse_num(const char *str) ++{ ++ double x; ++ char *p; ++ x = strtod(str, &p); ++ if (*p == 'G' || *p == 'g') x *= 1e9; ++ else if (*p == 'M' || *p == 'm') x *= 1e6; ++ else if (*p == 'K' || *p == 'k') x *= 1e3; ++ return (int64_t)(x + .499); ++} ++ + #endif +diff --git a/yak.h b/yak.h +index e71dacc..ab3d8ed 100644 +--- a/yak.h ++++ b/yak.h +@@ -1,7 +1,7 @@ + #ifndef YAK_H + #define YAK_H + +-#define YAKS_VERSION "0.1-r56" ++#define YAKS_VERSION "0.1-r69-dirty" + + #include + +@@ -16,6 +16,9 @@ + #define YAK_LOAD_ALL 1 + #define YAK_LOAD_TRIOBIN1 2 + #define YAK_LOAD_TRIOBIN2 3 ++#define YAK_LOAD_SEXCHR1 4 ++#define YAK_LOAD_SEXCHR2 5 ++#define YAK_LOAD_SEXCHR3 6 + + #define YAK_MAGIC "YAK\2" + +@@ -28,7 +31,7 @@ typedef struct { + } yak_copt_t; + + typedef struct { +- int32_t print_each; ++ int32_t print_each, print_err_kmer; + int32_t min_len; + int32_t n_threads; + double min_frac; diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml index 007604596b270..cdfd987fa4d37 100644 --- a/recipes/zdb/meta.yaml +++ b/recipes/zdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.2" %} +{% set version = "1.3.3" %} package: name: zdb @@ -11,8 +11,8 @@ build: - {{ pin_subpackage('zdb', max_pin="x.x") }} source: - url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.3.2.tar.gz - sha256: bd2f4e132376f78e6fe0a28f9be003dd35a0b0d86d2880a39e5a25d9778e0d3e + url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.3.3.tar.gz + sha256: 9f5e29d3730740c2e60fb275db709916ef54d3a2c3e4cf54ae448e9add14bb49 requirements: run: diff --git a/recipes/zga/meta.yaml b/recipes/zga/meta.yaml index 6470f6afbd465..884a3fb5ec221 100644 --- a/recipes/zga/meta.yaml +++ b/recipes/zga/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zga" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: "{{ name|lower }}" @@ -7,23 +7,24 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f0ecaefd7d535a69aabf2ddeee9408a45773baa3779abfebe3621d0a505778d2 + sha256: dd159db1cb4c0afcfb9bd47d9b4bd804e6b479507c49e77c38247abd1c8a4ca4 build: noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} number: 0 entry_points: - zga = zga.zga:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" requirements: host: - - biopython - pip - - python >=3.6 + - python >=3.8 run: - biopython - - python >=3.6 + - python >=3.8 - fastp - bbmap - mash >=2 @@ -33,7 +34,7 @@ requirements: - checkm-genome >=1.1.0 - blast - samtools >=1.9 - - dfast >=1.2.12 + - bakta - nxtrim - racon - minimap2 @@ -46,7 +47,7 @@ test: about: home: "https://github.com/laxeye/zga" - license: BSD + license: BSD-3-Clause license_family: BSD summary: "Prokaryotic genome assembly and annotation pipeline" dev_url: https://github.com/laxeye/zga/ diff --git a/recipes/zga/post-link.sh b/recipes/zga/post-link.sh deleted file mode 100755 index f8442f0b17fd1..0000000000000 --- a/recipes/zga/post-link.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -dfast_file_downloader.py --protein dfast --cdd Cog --hmm TIGR diff --git a/scripts/bioconductor/missingCranPackages.py b/scripts/bioconductor/missingCranPackages.py index e0bd60d6bdde0..28bcd2317a01d 100755 --- a/scripts/bioconductor/missingCranPackages.py +++ b/scripts/bioconductor/missingCranPackages.py @@ -1,55 +1,164 @@ #!/usr/bin/env python import argparse +from itertools import chain import networkx as nx -from datetime import datetime, timedelta import requests -from bioconda_utils import utils, graph +from bioconda_utils import utils def getRepoData(): res = set() - for subdir in ["linux-64", "noarch", "osx-64"]: + for subdir in ["linux-64", "noarch", "osx-64", "linux-aarch64", "osx-arm64"]: for channel in ["conda-forge", "bioconda"]: r = requests.get(f"https://conda.anaconda.org/{channel}/{subdir}/repodata.json") - js = r.json()['packages'] - for k, v in r.json()['packages'].items(): - if k.startswith('r-'): - res.add(v['name']) + for k, v in chain(r.json()["packages"].items(), r.json()["packages.conda"].items()): + if k.startswith("r-"): + res.add(v["name"]) return res -def printMissingCRAN(config_path, recipe_folder): - config = utils.load_config(config_path) - recipes = utils.get_recipes(recipe_folder) +def getDag(js): + dag = nx.DiGraph() + for k, v in js["_feedstock_status"].items(): + dag.add_node(k) + children = v["immediate_children"] + dag.add_edges_from((k, dep) for dep in set(children)) + return dag + + +def getCondaForgeMigrationStatus(migration_id): + r = requests.get(f"https://raw.githubusercontent.com/regro/cf-graph-countyfair/master/status/migration_json/{migration_id}.json") + js = r.json() + depDag = getDag(js) + res = { + "in-pr": dict(), + "bot-error": dict(), + "not-solvable": dict(), + "awaiting-parents": dict(), + "dag": depDag, + } + for recipe in js["in-pr"]: + res["in-pr"][recipe] = f"`{recipe}`: In PR {js['_feedstock_status'][recipe]['pr_url']}" + for recipe in js["bot-error"]: + status = js["_feedstock_status"][recipe]["pre_pr_migrator_status"] + segment = status.split("\n") + res["bot-error"][recipe] = f"`{recipe}`: {segment[0] + ' ' + segment[1]}" + for recipe in js["not-solvable"]: + status = js["_feedstock_status"][recipe]["pre_pr_migrator_status"] + segment1 = status.split("\n")[0] + segment2 = status.split(":")[3].split("\n")[0] + res["not-solvable"][recipe] = f"`{recipe}`: {segment1 + ' ' + segment2}" + for recipe in js["awaiting-parents"]: + res["awaiting-parents"][recipe] = f"`{recipe}`: Awaiting parents" + return res - repo = getRepoData() +def printMissingCRAN(recipe_folder, migration_id, format): # Construct a set of all dependencies (ignoring versions) + recipes = utils.get_recipes(recipe_folder) dependencies = set() for r in recipes: if "bioconductor" not in r: continue d = utils.load_meta_fast(r)[0] # a dictionary with keys requirements, build, etc. - if d['requirements']['run'] is None: + if d["requirements"]["run"] is None: continue - for dep in d['requirements']['run']: - if dep.startswith('r-'): - dependencies.add(dep.split(' ')[0]) + for dep in d["requirements"]["run"]: + if dep.startswith("r-"): + dependencies.add(dep.split(" ")[0]) + + CHECKBOX = "- [ ]" + # Find packages waiting for a migration + if migration_id: + cf = getCondaForgeMigrationStatus(migration_id) + dag = cf["dag"] + # Update dependencies based on DAG from conda-forge migration data + awaiting_parents = set.intersection(dependencies, set(cf["awaiting-parents"].keys())) + for recipe in awaiting_parents: + dependencies = set.union(dependencies, nx.algorithms.ancestors(dag, recipe)) + # Now that we expanded dependencies, get the new list of awaiting parents + awaiting_parents = set.intersection(dependencies, set(cf["awaiting-parents"].keys())) + in_pr = set.intersection(dependencies, set(cf["in-pr"].keys())) + bot_error = set.intersection(dependencies, set(cf["bot-error"].keys())) + not_solvable = set.intersection(dependencies, set(cf["not-solvable"].keys())) + if format == "markdown": + print( + "## Awaiting migration of {} packages ##".format( + len(in_pr) + len(bot_error) + len(not_solvable) + len(awaiting_parents) + ) + ) + print("### In PR ({} packages) ###".format(len(in_pr))) + for recipe in in_pr: + print(CHECKBOX, cf["in-pr"][recipe]) + print("### Bot Error ({} packages) ###".format(len(bot_error))) + for recipe in bot_error: + print(CHECKBOX, cf["bot-error"][recipe]) + print("### Not Solvable ({} packages) ###".format(len(not_solvable))) + for recipe in not_solvable: + print(CHECKBOX, cf["not-solvable"][recipe]) + print("### Awaiting Parents ({} packages) ###".format(len(awaiting_parents))) + for recipe in awaiting_parents: + print( + CHECKBOX, + cf["awaiting-parents"][recipe], + "(", + ", ".join([r for r in nx.algorithms.ancestors(dag, recipe) if r in set.union(in_pr, bot_error, not_solvable, awaiting_parents)]), + ")", + ) + else: + print("In PR:") + for recipe in in_pr: + print(recipe) + print("Bot Error:") + for recipe in bot_error: + print(recipe) + print("Not Solvable:") + for recipe in not_solvable: + print(recipe) + print("Awaiting Parents:") + for recipe in awaiting_parents: + print(recipe) + + # Find missing packages + repo = getRepoData() missing = dependencies - repo - print("Missing {} packages!".format(len(missing))) - for m in missing: - print(m) + if format == "markdown": + print("## Missing {} packages ##".format(len(missing))) + for recipe in missing: + print(CHECKBOX, recipe) + else: + print("Missing:") + for recipe in missing: + print(recipe) def main(): - parser = argparse.ArgumentParser(description="""Print a list of missing CRAN dependencies for Bioconductor packages.""") - parser.add_argument("config_path", default="config.yml", help="Location of config.yml (default: %(default)s", nargs='?') - parser.add_argument("recipe_folder", default="recipes", help="Location of the recipes folder (default: %(default)s)", nargs='?') + parser = argparse.ArgumentParser( + description="""Print a list of missing CRAN dependencies for Bioconductor packages.""" + ) + parser.add_argument( + "recipe_folder", + default="recipes", + help="Location of the recipes folder (default: %(default)s)", + nargs="?", + ) + parser.add_argument( + "--migration_id", + help="See conda-forge status page. If populated, will report packages held up in a conda-forge migration (default: None)", + nargs="?", + ) + parser.add_argument( + "--format", + dest="format", + default="plain", + help="Format of results: ['plain', 'markdown'] (default: %(default)s)", + nargs="?", + ) args = parser.parse_args() - printMissingCRAN(args.config_path, args.recipe_folder) + printMissingCRAN(args.recipe_folder, args.migration_id, args.format) -if __name__ == '__main__': +if __name__ == "__main__": main() diff --git a/scripts/check-for-additional-platforms.sh b/scripts/check-for-additional-platforms.sh index d088794f14422..844a09652c04d 100755 --- a/scripts/check-for-additional-platforms.sh +++ b/scripts/check-for-additional-platforms.sh @@ -1,5 +1,7 @@ #!/bin/bash +# Do not set -x, this script outputs a value with echo + # Check to see if any changed recipes have specified the key # extra:additional-platforms, and if so, if they match the platform of the # currently-running machine. @@ -18,7 +20,7 @@ wget https://github.com/mikefarah/yq/releases/latest/download/yq_${yq_platform}_ chmod +x ${HOME}/bin/yq # Find recipes changed from this merge -files=`git diff --name-only --diff-filter AMR ${git_range} | grep -E 'meta.yaml$' ` +files=`git diff --name-only --diff-filter AMR ${git_range} | grep -v 'template' | grep -E 'meta.yaml$' ` build=0 for file in $files; do @@ -32,6 +34,9 @@ for file in $files; do parsing_status=$? if [ $parsing_status -gt 0 ]; then echo "An error occurred while reading/parsing ${file}" + echo "==================== ${file} START ===========================" + cat $file + echo "==================== ${file} END =============================" exit $parsing_status fi diff --git a/scripts/ucsc/create-ucsc-packages.py b/scripts/ucsc/create-ucsc-packages.py index f07ea3be2f92e..d9a3520fe573b 100755 --- a/scripts/ucsc/create-ucsc-packages.py +++ b/scripts/ucsc/create-ucsc-packages.py @@ -13,7 +13,6 @@ # e.g.,# "addCols - Sum columns in a text file." re_summary = re.compile(r'^(?P\w.*?) - (?P.*)$') - def parse_footer(fn): """ Parse the downloaded FOOTER file, which contains a header for each program @@ -54,13 +53,13 @@ def parse_footer(fn): # # version: 332 # sha256: 8c2663c7bd302a77cdf52b2e9e85e2cd -ucsc_config = yaml.load(open('ucsc_config.yaml')) +ucsc_config = yaml.safe_load(open('ucsc_config.yaml')) VERSION = ucsc_config['version'] SHA256 = ucsc_config['sha256'] # Download tarball if it doesn't exist. Always download FOOTER. tarball = ( - 'http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{0}.src.tgz' + 'http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{0}.src.tgz' .format(VERSION)) if not os.path.exists(os.path.basename(tarball)): f = urllib.request.urlopen(tarball) @@ -198,6 +197,72 @@ def program_subdir(program, names): 'gfServer', ] +# A list of programs which have problems to build on linux-aarch64 +SKIP_AARCH64 = [ + 'pslCDnaFilter', # https://github.com/bioconda/bioconda-recipes/pull/49297 + 'pslCheck', # https://github.com/bioconda/bioconda-recipes/pull/50193 + 'bedCoverage', + 'bedExtendRanges', + 'bedItemOverlapCount', + 'bedToGenePred', + 'checkCoverageGaps', + 'checkTableCoords', + 'chromGraphFromBin', + 'chromGraphToBin', + 'dbTrash', + 'estOrient', + 'featureBits', + 'gapToLift', + 'genePredCheck', + 'genePredFilter', + 'genePredHisto', + 'genePredSingleCover', + 'genePredToBed', + 'genePredToBigGenePred', + 'genePredToFakePsl', + 'genePredToGtf', + 'genePredToMafFrames', + 'genePredToProt', + 'getRna', + 'getRnaPred', + 'gff3ToGenePred', + 'gtfToGenePred', + 'hgFindSpec', + 'hgGcPercent', + 'hgLoadBed', + 'hgLoadChain', + 'hgLoadMaf', + 'hgLoadNet', + 'hgLoadOut', + 'hgLoadOutJoined', + 'hgLoadWiggle', + 'hgSpeciesRna', + 'hgTrackDb', + 'hubCheck', + 'hubPublicCheck', + 'ldHgGene', + 'liftOver', + 'liftUp', + 'mafCoverage', + 'mafFetch', + 'mafFrag', + 'mafFrags', + 'mafGene', + 'mafSplitPos', + 'mafToSnpBed', + 'makeTableList', + 'mrnaToGene', + 'netClass', + 'overlapSelect', + 'positionalTblCheck', + 'pslLiftSubrangeBlat', + 'pslToBigPsl', + 'raSqlQuery', + 'tdbQuery', + 'transMapPslToGenePred', + 'validateFiles' +] + # Some programs need to be built differently. It seems that a subset of # programs need the "stringify" binary build as well. Or, in the case of # fetchChromSizes, it's simply a script that needs to be copied. @@ -294,6 +359,7 @@ def program_subdir(program, names): summary=description, version=VERSION, sha256=SHA256, + linux_aarch64='' if program in SKIP_AARCH64 else 'additional-platforms:\n - linux-aarch64\n', ) ) diff --git a/scripts/ucsc/include.patch b/scripts/ucsc/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/scripts/ucsc/include.patch +++ b/scripts/ucsc/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/scripts/ucsc/template-build-cp-short.sh b/scripts/ucsc/template-build-cp-short.sh index d47bb19e9f7d9..f51f7ee2c9c55 100644 --- a/scripts/ucsc/template-build-cp-short.sh +++ b/scripts/ucsc/template-build-cp-short.sh @@ -1,4 +1,7 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -cp kent/src/utils/{program} "$PREFIX/bin" -chmod +x "$PREFIX/bin/{program}" + +set -xe + +mkdir -p "${{PREFIX}}/bin" +cp kent/src/utils/{program} "${{PREFIX}}/bin" +chmod 0755 "${{PREFIX}}/bin/{program}" diff --git a/scripts/ucsc/template-build-cp.sh b/scripts/ucsc/template-build-cp.sh index 73f3a75e23add..937159593f973 100644 --- a/scripts/ucsc/template-build-cp.sh +++ b/scripts/ucsc/template-build-cp.sh @@ -1,4 +1,7 @@ #!/bin/bash + +set -xe + mkdir -p "$PREFIX/bin" -cp {program_source_dir}/{program} "$PREFIX/bin" -chmod +x "$PREFIX/bin/{program}" +cp {program_source_dir}/{program} "${{PREFIX}}/bin" +chmod 0755 "${{PREFIX}}/bin/{program}" diff --git a/scripts/ucsc/template-build-fetchChromSizes.sh b/scripts/ucsc/template-build-fetchChromSizes.sh index 502e537cac181..487e643544ef8 100644 --- a/scripts/ucsc/template-build-fetchChromSizes.sh +++ b/scripts/ucsc/template-build-fetchChromSizes.sh @@ -1,4 +1,6 @@ #!/bin/bash -cp kent/src/utils/userApps/fetchChromSizes $PREFIX/bin -chmod +x $PREFIX/bin/fetchChromSizes +set -xe + +cp kent/src/utils/userApps/fetchChromSizes ${{PREFIX}}/bin +chmod 0755 ${{PREFIX}}/bin/fetchChromSizes diff --git a/scripts/ucsc/template-build-no-bin.sh b/scripts/ucsc/template-build-no-bin.sh index 24469788935d2..9e597e406cf4d 100644 --- a/scripts/ucsc/template-build-no-bin.sh +++ b/scripts/ucsc/template-build-no-bin.sh @@ -1,12 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${{PREFIX}}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${{PREFIX}}/include" +export LIBRARY_PATH="${{PREFIX}}/lib" +export LDFLAGS="${{LDFLAGS} -L${{PREFIX}}/lib" +export CFLAGS="${{CFLAGS}} -O3 ${{LDFLAGS}}" +export CXXFLAGS="${{CXXFLAGS}} -I${{PREFIX}}/include ${{LDFLAGS}}" export BINDIR=$(pwd)/bin -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd {program_source_dir} && make) -cp {program_source_dir}/{program} "$PREFIX/bin" -chmod +x "$PREFIX/bin/{program}" +export L="${{LDFLAGS}}" +mkdir -p "${{BINDIR}}" +(cd kent/src/lib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/htslib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/jkOwnLib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd {program_source_dir} && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +cp {program_source_dir}/{program} "${{PREFIX}}/bin" +chmod 0755 "${{PREFIX}}/bin/{program}" diff --git a/scripts/ucsc/template-build-parasol.sh b/scripts/ucsc/template-build-parasol.sh index 5614488afa6a1..253f747ebad66 100644 --- a/scripts/ucsc/template-build-parasol.sh +++ b/scripts/ucsc/template-build-parasol.sh @@ -1,12 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${{PREFIX}}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${{PREFIX}}/include" +export LIBRARY_PATH="${{PREFIX}}/lib" +export LDFLAGS="${{LDFLAGS}} -L${{PREFIX}}/lib" +export CFLAGS="${{CFLAGS}} -O3 ${{LDFLAGS}}" +export CXXFLAGS="${{CXXFLAGS}} -I${{PREFIX}}/include ${{LDFLAGS}}" export BINDIR=$(pwd)/bin -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/{program} "$PREFIX/bin" -chmod +x "$PREFIX/bin/{program}" +export L="${{LDFLAGS}}" +mkdir -p "${{BINDIR}}" +(cd kent/src/lib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/htslib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/jkOwnLib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/parasol && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +cp kent/src/parasol/bin/{program} "${{PREFIX}}/bin" +chmod 0755 "${{PREFIX}}/bin/{program}" diff --git a/scripts/ucsc/template-build-with-stringify.sh b/scripts/ucsc/template-build-with-stringify.sh index 225c22fe8fda1..c61d710eaa8f1 100644 --- a/scripts/ucsc/template-build-with-stringify.sh +++ b/scripts/ucsc/template-build-with-stringify.sh @@ -1,13 +1,22 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${{PREFIX}}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${{PREFIX}}/include" +export LIBRARY_PATH="${{PREFIX}}/lib" +export LDFLAGS="${{LDFLAGS}} -L${{PREFIX}}/lib" +export CFLAGS="${{CFLAGS}} -O3 ${{LDFLAGS}}" +export CXXFLAGS="${{CXXFLAGS}} -I${{PREFIX}}/include ${{LDFLAGS}}" export BINDIR=$(pwd)/bin -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/stringify && make) -(cd {program_source_dir} && make) -cp bin/{program} "$PREFIX/bin" -chmod +x "$PREFIX/bin/{program}" +export L="${{LDFLAGS}}" +mkdir -p "${{BINDIR}}" +(cd kent/src/lib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/htslib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/jkOwnLib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/utils/stringify && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd {program_source_dir} && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +cp bin/{program} "${{PREFIX}}/bin" +chmod 0755 "${{PREFIX}}/bin/{program}" diff --git a/scripts/ucsc/template-build.sh b/scripts/ucsc/template-build.sh index e5f98c64a3a1c..f2f5d27f6e621 100644 --- a/scripts/ucsc/template-build.sh +++ b/scripts/ucsc/template-build.sh @@ -1,12 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${{PREFIX}}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd {program_source_dir} && make) -cp bin/{program} "$PREFIX/bin" -chmod +x "$PREFIX/bin/{program}" +export INCLUDE_PATH="${{PREFIX}}/include" +export LIBRARY_PATH="${{PREFIX}}/lib" +export LDFLAGS="${{LDFLAGS}} -L${{PREFIX}}/lib" +export CFLAGS="${{CFLAGS}} -O3 ${{LDFLAGS}}" +export CXXFLAGS="${{CXXFLAGS}} -I${{PREFIX}}/include ${{LDFLAGS}}" +export L="${{LDFLAGS}}" +mkdir -p "${{BINDIR}}" +(cd kent/src/lib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/htslib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/jkOwnLib && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +(cd {program_source_dir} && make CC="${{CC}}" CXX="${{CXX}}" CFLAGS="${{CFLAGS}}" CXXFLAGS="${{CXXFLAGS}}" -j "${{CPU_COUNT}}") +cp bin/{program} "${{PREFIX}}/bin" +chmod 0755 "${{PREFIX}}/bin/{program}" diff --git a/scripts/ucsc/template-meta-with-python.yaml b/scripts/ucsc/template-meta-with-python.yaml index e232fd400c642..2094dd74c6821 100644 --- a/scripts/ucsc/template-meta-with-python.yaml +++ b/scripts/ucsc/template-meta-with-python.yaml @@ -8,13 +8,16 @@ package: version: "{{{{ version }}}}" source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{{{ version }}}}.src.tgz" + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{{{ version }}}}.src.tgz" sha256: "{{{{ sha256 }}}}" patches: - "include.patch" build: + skip: True # [osx] number: 0 + run_exports: + - {{{{ pin_subpackage(package, max_pin=None) }}}} requirements: build: @@ -23,14 +26,14 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - python - zlib @@ -43,3 +46,11 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "{summary}" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + {linux_aarch64} \ No newline at end of file diff --git a/scripts/ucsc/template-meta.yaml b/scripts/ucsc/template-meta.yaml index 74498a6983ed3..8408f645ef084 100644 --- a/scripts/ucsc/template-meta.yaml +++ b/scripts/ucsc/template-meta.yaml @@ -8,37 +8,49 @@ package: version: "{{{{ version }}}}" source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{{{ version }}}}.src.tgz" + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{{{ version }}}}.src.tgz" sha256: "{{{{ sha256 }}}}" patches: - "include.patch" build: + skip: True # [osx] number: 0 + run_exports: + - {{{{ pin_subpackage(package, max_pin=None) }}}} requirements: build: + - make - {{{{ compiler('c') }}}} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{{{ program }}}} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${{PREFIX}}/bin/{{{{ program }}}} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "{summary}" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + {linux_aarch64} \ No newline at end of file diff --git a/scripts/ucsc/ucsc_config.yaml b/scripts/ucsc/ucsc_config.yaml index 0111932c1c44f..96df218c9e5ca 100644 --- a/scripts/ucsc/ucsc_config.yaml +++ b/scripts/ucsc/ucsc_config.yaml @@ -1,2 +1,2 @@ -version: 377 -sha256: 932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676 +version: 469 +sha256: 3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963