From 32db8aac46d791a85c264896a0e9aea0181ee80c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Nov 2024 14:57:36 -0400 Subject: [PATCH 01/19] Update fgbio-minimal to 2.4.0 (#51866) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/fgbio-minimal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgbio-minimal/meta.yaml b/recipes/fgbio-minimal/meta.yaml index ec8d76b58f4d5..49f78563a49ec 100644 --- a/recipes/fgbio-minimal/meta.yaml +++ b/recipes/fgbio-minimal/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.3.0" %} +{% set version = "2.4.0" %} package: name: fgbio-minimal @@ -6,7 +6,7 @@ package: source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69 + sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937 build: noarch: generic From a959d05d9d4883b317d10166ab67eebbb6f0cf4b Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sat, 2 Nov 2024 19:00:24 +0000 Subject: [PATCH 02/19] Fix usearch path in lOTUs.cfg (#51870) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/lotus2/build.sh | 4 ++-- recipes/lotus2/meta.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/lotus2/build.sh b/recipes/lotus2/build.sh index 5b4edbec842fd..79c1bbc3500d4 100644 --- a/recipes/lotus2/build.sh +++ b/recipes/lotus2/build.sh @@ -1,10 +1,10 @@ #!/bin/sh SHARE_DIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -rm -rf bin/installs/ bin/LCA bin/rtk bin/sdm bin/vsearch configs/sdm_src/ +rm -rf bin/installs/ bin/lambda3* bin/LCA bin/rtk bin/sdm bin/vsearch # Configure LotuS2 cp configs/LotuS.cfg.def lOTUs.cfg -for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm vsearch; do +for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm usearch vsearch; do sed -i.bak -e "s|^$binary[[:space:]].*|$binary $PREFIX/bin/$binary|" lOTUs.cfg done for binary in cd-hit fasttree hmmsearch iqtree itsx makeBlastDB RDPjar; do diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml index bc46dd5be022e..2da7f320f44bf 100644 --- a/recipes/lotus2/meta.yaml +++ b/recipes/lotus2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x') }} From 208191896467f5e932b006190718532b60d465b3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Nov 2024 15:12:03 -0400 Subject: [PATCH 03/19] Update fgbio to 2.4.0 (#51869) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/fgbio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml index 496337cbe9149..04b43d63f15a4 100644 --- a/recipes/fgbio/meta.yaml +++ b/recipes/fgbio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.3.0" %} +{% set version = "2.4.0" %} package: name: fgbio @@ -6,7 +6,7 @@ package: source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69 + sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937 build: noarch: generic From da0cf96d7627ef371337570c3771417fe99c9263 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Nov 2024 15:17:16 -0400 Subject: [PATCH 04/19] Update fgsv to 0.2.1 (#51868) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/fgsv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgsv/meta.yaml b/recipes/fgsv/meta.yaml index 4d064dba5f553..5620d4693947c 100644 --- a/recipes/fgsv/meta.yaml +++ b/recipes/fgsv/meta.yaml @@ -1,5 +1,5 @@ -{% set version="0.2.0" %} -{% set sha256="c2f9536a677e7e99f251cada1338f611cea40477deca144f0c6928505755eb37" %} +{% set version="0.2.1" %} +{% set sha256="e3f15c7f1a97c009be65663405194faedf473c2636a3c3d742f463030caba860" %} package: From 230c74417e94c54f46e798c1ab2c261d1c3c499a Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Sun, 3 Nov 2024 03:21:17 +0800 Subject: [PATCH 05/19] Update csvtk to v0.31.0 (#51861) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/csvtk/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml index 86f0aee7a9418..93700fa5b0691 100644 --- a/recipes/csvtk/meta.yaml +++ b/recipes/csvtk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.30.0" %} +{% set version = "0.31.0" %} # This package should be migrated to conda-forge due to general utility # In that case it needs to be built from source package: @@ -6,19 +6,19 @@ package: version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('csvtk', max_pin='x.x') }} source: - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx and x86_64] - md5: c415255e265ba0cd547806fdbda05652 # [osx and x86_64] + md5: 5a23d000a1fc068360e1aeb439f3ae25 # [osx and x86_64] - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_arm64.tar.gz # [arm64] - md5: dd8a84c301d378ab7ff28c85d37fbefa # [arm64] + md5: 6aa24ce286910e83d95d28a21905f1d8 # [arm64] - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux and x86_64] - md5: 8f5877d4fbea89609d64bd2679956476 # [linux and x86_64] + md5: 09bc8c3288f028239c94d4c935ac7a6f # [linux and x86_64] - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_arm64.tar.gz # [aarch64] - md5: 2a6dd840291d23971ff538eaf3de00ec # [aarch64] + md5: f7a5b8839459d7d55685056331670eec # [aarch64] test: commands: From 4c3a2bc29d275e5891588c6252e458e9675c0e4a Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Sun, 3 Nov 2024 03:21:52 +0800 Subject: [PATCH 06/19] Update TaxonKit to v0.18.0 (#51862) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/taxonkit/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/taxonkit/meta.yaml b/recipes/taxonkit/meta.yaml index f1f47d02d7e8c..dd38d454a0249 100644 --- a/recipes/taxonkit/meta.yaml +++ b/recipes/taxonkit/meta.yaml @@ -1,23 +1,23 @@ -{% set version = "0.17.0" %} +{% set version = "0.18.0" %} package: name: taxonkit version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('taxonkit', max_pin='x.x') }} source: - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_amd64.tar.gz # [osx] - md5: 5c12cfac4939f966824eda8eb774cf9b # [osx] + md5: 2417d0b8a08210690498b98279c16ae0 # [osx] - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_arm64.tar.gz # [arm64] - md5: 4077cb27d588cd0c3ed174e80d9a54af # [arm64] + md5: 045a509947edf27345889db901291059 # [arm64] - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux and x86_64] - md5: bfedc8dbfc2db63460ed31843fc5f3c3 # [linux and x86_64] + md5: 5df8f74847a4b5968be787d78d6fc9a7 # [linux and x86_64] - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_arm64.tar.gz # [linux and aarch64] - md5: d0af9a15d225005705d8af63db6a970d # [linux and aarch64] + md5: 451aeaede731780d167b6771ca6d1f0e # [linux and aarch64] test: commands: From 3fbd6936933f5c52aba472987adc57d7486ade2d Mon Sep 17 00:00:00 2001 From: Xiyu Date: Sat, 2 Nov 2024 14:29:07 -0500 Subject: [PATCH 07/19] Add amplici package in bioconda (#51847) * add amplici * minor changes based on the suggestion * slightly change meta.yaml file * edit build.sh * update meta.yaml * add gfortran requirement * test v2.2 * update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/amplici/build.sh | 15 +++++++++++++ recipes/amplici/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 recipes/amplici/build.sh create mode 100644 recipes/amplici/meta.yaml diff --git a/recipes/amplici/build.sh b/recipes/amplici/build.sh new file mode 100644 index 0000000000000..3b7588794ae9a --- /dev/null +++ b/recipes/amplici/build.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + +cd src || exit 1 +cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_C_COMPILER="${CC}" \ + -DCMAKE_C_FLAGS="${CFLAGS}" \ + "${CONFIG_ARGS}" +cmake --build build --target install -j "${CPU_COUNT}" -v diff --git a/recipes/amplici/meta.yaml b/recipes/amplici/meta.yaml new file mode 100644 index 0000000000000..5949ed9ee80c6 --- /dev/null +++ b/recipes/amplici/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "2.2" %} + +package: + name: amplici + version: {{ version }} + +source: + url: https://github.com/DormanLab/AmpliCI/archive/refs/tags/v{{ version }}.tar.gz + sha256: 273362b5449ec29ff411d4c1aa5f89b1ec1eb361c8a9b69a4d89f4409fbdb70e + +build: + number: 0 + run_exports: + - {{ pin_subpackage("amplici", max_pin="x") }} + +requirements: + build: + - cmake + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('fortran') }} + host: + - zlib + +about: + home: https://github.com/DormanLab/AmpliCI + license: BSD 3-Clause + license_family: BSD + license_file: LICENSE + summary: "AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs." + dev_url: https://github.com/DormanLab/AmpliCI + +test: + commands: + - run_AmpliCI -h + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - xiyupeng + identifiers: + - biotools:amplici + - doi:10.1093/bioinformatics/btaa648 From 95bee8c1ef655a7440a0eba6e06adff979591f3c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Nov 2024 15:47:48 -0400 Subject: [PATCH 08/19] Update svision-pro to 2.1 (#51855) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/svision-pro/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/svision-pro/meta.yaml b/recipes/svision-pro/meta.yaml index 453d9406fca15..923e70cc358ee 100644 --- a/recipes/svision-pro/meta.yaml +++ b/recipes/svision-pro/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SVision-pro" %} -{% set version = "2.0" %} +{% set version = "2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/songbowang125/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 3892760ee421e1613f64cd7e61bd6876645e739fbf3198439e128fc9e50d1dd1 + sha256: c642bee23cfad1796929b97c93aff50d10ba25ac1b484b2a1bef210fcb75e151 build: number: 0 From f5934f60e08cc93cf8440e6b99e6af045178ce8f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Nov 2024 16:40:56 -0400 Subject: [PATCH 09/19] Update goldrush to 1.2.1 (#51872) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/goldrush/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml index f9a23e06eccd6..efce055df5c10 100644 --- a/recipes/goldrush/meta.yaml +++ b/recipes/goldrush/meta.yaml @@ -1,5 +1,5 @@ {% set name = "goldrush" %} -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bcgsc/goldrush/releases/download/{{ version }}/{{ name|lower }}-{{ version }}.tar.gz - sha256: 3f70860ed92b9313dbab16efed65ea7bc6080d78b4e18afc8cb910e086a7f0f7 + sha256: 0b8b91b0477510d341af1736539416f30f70f67af9bd84161ea51c4c4a0fcc39 build: skip: true # [py < 38 or win or py > 39] From 00d43e07e7f7318b005fa2533cbe477fc3deb8a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Nov 2024 16:41:10 -0400 Subject: [PATCH 10/19] Update nextstrain-cli to 8.5.4 (#51873) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update nextstrain-cli to 8.5.4 * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/nextstrain-cli/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index 88f19b53e3497..0dffea387c08a 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.5.3" %} +{% set version = "8.5.4" %} 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: 5401fd3f1b60479cb3b8c0519917fa5df43fdaddd6007e158888283a5c872428 + sha256: 3aa6c66d038d82de0c3bff2eb1b358599a9efc3f5f446eb523d3c9696aa72854 build: number: 0 @@ -21,7 +21,7 @@ requirements: host: - python >=3.8 - pip - + - setuptools run: - python >=3.8 - docutils From dc2e4c4c0e241b3e0bda17cfecc6427cee0096f3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Nov 2024 16:41:44 -0400 Subject: [PATCH 11/19] Update gsmap to 1.71.2 (#51854) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/gsmap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gsmap/meta.yaml b/recipes/gsmap/meta.yaml index f6100dbb4139b..97fc02a0dd18f 100644 --- a/recipes/gsmap/meta.yaml +++ b/recipes/gsmap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gsmap" %} -{% set version = "1.71.1" %} +{% set version = "1.71.2" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/gsMap/{{ name }}-{{ version }}.tar.gz" - sha256: f81debacf46d3e26614411d938a27345fcb42999a8ef2b740d134e910c2d0bcd + sha256: d058fb9c1e346b40cf3e6a1cf27fc6458acf3cdb29eb7d4dd74cb119ab0f88a9 build: noarch: python From 2ba9720b057a5c6b7a61cffefc91503b9440ace3 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Sat, 2 Nov 2024 21:42:04 +0100 Subject: [PATCH 12/19] Sentieon add ARM support (#51837) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Sentieon add ARM support Add ARM support to Sentieon recipe. * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/sentieon/meta.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/recipes/sentieon/meta.yaml b/recipes/sentieon/meta.yaml index be624c6675928..e2fee90b517d4 100644 --- a/recipes/sentieon/meta.yaml +++ b/recipes/sentieon/meta.yaml @@ -4,14 +4,14 @@ package: name: sentieon version: {{ version }} source: - - url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz # [linux64] - sha256: d51d1a192aa9fd3108f4baa5e1d0784ea80af6734fcc1a27a57e15779f43fcf1 # [linux64] - patches: # [linux64] + - url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz + sha256: d51d1a192aa9fd3108f4baa5e1d0784ea80af6734fcc1a27a57e15779f43fcf1 + patches: # Fix driver scripts so they resolves location including symlinks - - sentieon_symlinks.patch # [linux64] + - sentieon_symlinks.patch build: - number: 0 + number: 1 skip: True # [not linux64] binary_relocation: false run_exports: @@ -41,5 +41,6 @@ about: summary: Accelerated performance bioinformatics tools for mapping and variant calling extra: - skip-lints: - - should_be_noarch_generic # Supports Linux64 only + additional-platforms: + - linux-aarch64 + - osx-arm64 From bc6055397699a5401689b34deaabfa64fb6bfdd8 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Sun, 3 Nov 2024 11:02:03 +0800 Subject: [PATCH 13/19] Update SeqKit to v2.9.0 (#51860) --- recipes/seqkit/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 538a6f2093241..9994fb9779923 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.8.2" %} +{% set version = "2.9.0" %} package: name: seqkit @@ -6,19 +6,19 @@ package: source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: 03b13956b7e3ef1678db591a79eb68ed # [osx] + md5: 50fff73601f3094d664031e5c00674f5 # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_arm64.tar.gz # [arm64] - md5: 0b2716f39c3974a5c3e310bcbd4076eb # [arm64] + md5: cf1b7c4b74664f04d3cc361e9c5370a1 # [arm64] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] - md5: 67220b508f3f81c2c8697e6534eed440 # [linux] + md5: 83e359c186dee6b49cd4df362d0b6d5a # [linux] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_arm64.tar.gz # [aarch64] - md5: b83b021850c9447cfc8e0d5751b7be99 # [aarch64] + md5: 7a81adcd79553e10552456060c2b17ba # [aarch64] build: - number: 1 + number: 0 skip: False run_exports: - {{ pin_subpackage("seqkit", max_pin="x.x") }} From be644c5eb7fc0c7b3970cc86756144dc5cca11f7 Mon Sep 17 00:00:00 2001 From: Amirhossein <66441226+nilchia@users.noreply.github.com> Date: Sun, 3 Nov 2024 04:18:15 +0100 Subject: [PATCH 14/19] update version to 1.38.0 (#51877) --- recipes/bioconductor-protgenerics/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml index 99dbefecd9faf..ffe275e39ca5f 100644 --- a/recipes/bioconductor-protgenerics/meta.yaml +++ b/recipes/bioconductor-protgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "ProtGenerics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d55c00588169aa089bb457e2d94669a + md5: 7e7211a9fa758ca6f1b701c86e892895 build: number: 0 rpaths: From 4abf5661c4e04e38b10d2e3b27d3451ebcf64014 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Sat, 2 Nov 2024 21:34:56 -0700 Subject: [PATCH 15/19] Bump MUSCLE to 5.2 (#51881) Co-authored-by: Martin Grigorov --- recipes/muscle/build.sh | 19 +- recipes/muscle/meta.yaml | 10 +- recipes/muscle/support-linux-aarch64.patch | 14 +- recipes/muscle/vcxproj_make.py | 225 +++++++++++++++++++++ 4 files changed, 251 insertions(+), 17 deletions(-) create mode 100644 recipes/muscle/vcxproj_make.py diff --git a/recipes/muscle/build.sh b/recipes/muscle/build.sh index 6e358f5e2b44b..a6fb04c9c3860 100644 --- a/recipes/muscle/build.sh +++ b/recipes/muscle/build.sh @@ -1,9 +1,18 @@ #!/bin/bash +set -e -cd src/ -sed -i.bak -e 's/ -static//' Makefile +mkdir -p ${PREFIX}/bin +cd src || exit 1 +echo "0" > gitver.txt -make CXX=$CXX +cp ${RECIPE_DIR}/vcxproj_make.py . +chmod +x vcxproj_make.py +./vcxproj_make.py --openmp --cppcompiler ${CXX} -mkdir -p "$PREFIX"/bin -cp "$(uname)"/muscle "$PREFIX"/bin/muscle +# Verify binary exists and is executable +if [ ! -x ../bin/muscle ]; then + echo "Error: muscle binary not found" + exit 1 +fi + +cp ../bin/muscle ${PREFIX}/bin/muscle diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml index 9953f38bd5c3e..f52e85ac70a5e 100644 --- a/recipes/muscle/meta.yaml +++ b/recipes/muscle/meta.yaml @@ -1,18 +1,18 @@ {% set name = "muscle" %} -{% set version = "5.1.0" %} +{% set version = "5.2" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/rcedgar/muscle/archive/refs/tags/{{ version }}.tar.gz - sha256: 2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d + url: https://github.com/rcedgar/muscle/archive/refs/tags/v{{ version }}.tar.gz + sha256: 7aff1473241a36da94a88f37920a343fae91d2b6faae22e15c06591d1d0339b6 patches: - support-linux-aarch64.patch build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -30,7 +30,7 @@ about: home: https://github.com/rcedgar/muscle license: GPL-3.0-only license_file: LICENSE - summary: "MUSCLE: multiple sequence alignment with high accuracy and high throughput" + summary: Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences extra: additional-platforms: diff --git a/recipes/muscle/support-linux-aarch64.patch b/recipes/muscle/support-linux-aarch64.patch index 9308bf3333e2b..f9c8e2081e8b8 100644 --- a/recipes/muscle/support-linux-aarch64.patch +++ b/recipes/muscle/support-linux-aarch64.patch @@ -1,10 +1,10 @@ -diff --git i/src/myutils.h w/src/myutils.h -index 49d28ef..8e8167e 100644 ---- i/src/myutils.h -+++ w/src/myutils.h -@@ -11,7 +11,7 @@ - #define TRACK_ALLOC 0 - #define ALLOC_TOTALS 0 +diff --git a/src/myutils.h b/src/myutils.h +index a5d8a58..fbf6f9f 100644 +--- a/src/myutils.h ++++ b/src/myutils.h +@@ -10,7 +10,7 @@ + #include + #include "myalloc.h" -#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) +#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) || defined(__aarch64__) diff --git a/recipes/muscle/vcxproj_make.py b/recipes/muscle/vcxproj_make.py new file mode 100644 index 0000000000000..739663b29c933 --- /dev/null +++ b/recipes/muscle/vcxproj_make.py @@ -0,0 +1,225 @@ +#!/usr/bin/env python + +import argparse +import os +import sys + +Usage = ( + "Convert Visual Studio .vcxproj file in current directory to Makefile and run make." +) + +AP = argparse.ArgumentParser(description=Usage) + +# Value opts +AP.add_argument( + "--std", + required=False, + help="C++ standard option for GCC, e.g. c++11 or c++17 (default none)", +) +AP.add_argument( + "--cppcompiler", + required=False, + default="g++", + help="C++ compiler command name default g++)", +) +AP.add_argument( + "--ccompiler", + required=False, + default="gcc", + help="C++ compiler command name default gcc)", +) + +# Flag opts +AP.add_argument("--debug", required=False, action="store_true", help="Debug build") +AP.add_argument("--openmp", required=False, action="store_true", help="Requires OMP") +AP.add_argument( + "--pthread", required=False, action="store_true", help="Requires pthread" +) +AP.add_argument("--lrt", required=False, action="store_true", help="Requires lrt") +AP.add_argument( + "--symbols", + required=False, + action="store_true", + help="Debug symbols (default if --debug)", +) +AP.add_argument( + "--nostrip", + required=False, + action="store_true", + help="Don't strip symbols (default if --debug or --symbols)", +) + +Args = AP.parse_args() +debug = Args.debug +std = Args.std +cppcompiler = Args.cppcompiler +ccompiler = Args.ccompiler +nostrip = debug or Args.symbols +symbols = debug or Args.symbols + +ProjFileName = None +HdrNames = [] +for FileName in os.listdir("."): + if FileName.endswith(".vcxproj"): + ProjFileName = FileName + elif FileName.endswith(".h"): + HdrNames.append(FileName) +if ProjFileName is None: + sys.stderr.write("\nProject file not found in current directory\n") + sys.exit(1) + +binary = ProjFileName.replace(".vcxproj", "") +sys.stderr.write("binary=" + binary + "\n") + +compiler_opts = " -ffast-math -march=native" +linker_opts = " -ffast-math -march=native" + +if std: + compiler_opts += " --std=" + std + +if debug: + compiler_opts += " -O0 -DDEBUG" + linker_opts += " -O0" +else: + compiler_opts += " -O3 -DNDEBUG" + linker_opts += " -O3" + +if symbols: + compiler_opts += " -g3" + linker_opts += " -g3" + +if Args.openmp: + compiler_opts += " -fopenmp" + linker_opts += " -fopenmp" + +if Args.pthread: + compiler_opts += " -pthread" + linker_opts += " -lpthread" + +rc = os.system(r"rm -rf o/ ../bin/%s*" % binary) +if rc != 0: + sys.stderr.write("\n\nERROR -- failed to clean\n\n") + sys.exit(1) +sys.stderr.write("clean done.\n") + +OBJDIR = "o" +BINDIR = "../bin" + +Fields = ProjFileName.split("/") +n = len(Fields) +Name = Fields[n - 1] +Fields = Name.split(".") +binary = Fields[0] + +CXXNames = [] +CNames = [] +with open(ProjFileName) as File: + for Line in File: + Line = Line.strip() + Line = Line.replace('"', "") + Line = Line.replace(" ", "") + # + if Line.startswith("", "") + if FileName.endswith(".cpp"): + FileName = FileName.replace(".cpp", "") + CXXNames.append(FileName) + elif FileName.endswith(".c"): + FileName = FileName.replace(".c", "") + CNames.append(FileName) + +assert len(CXXNames) > 0 or len(CNames) > 0 + +with open("Makefile", "w") as f: + + def Out(s): + print(s, file=f) + + BINPATH = "$(BINDIR)/%s" % (binary) + + Out("######################################################") + Out("# Makefile is generated by " + sys.argv[0]) + Out("# Don't edit the Makefile -- update the python script") + Out("######################################################") + Out("") + Out("BINDIR := %s" % BINDIR) + Out("OBJDIR := %s" % OBJDIR) + Out("BINPATH := %s" % BINPATH) + + if CNames: + Out("") + Out("CC = " + ccompiler) + Out("CFLAGS := $(CFLAGS) " + compiler_opts) + + if CXXNames: + Out("") + Out("CXX = " + cppcompiler) + Out("CXXFLAGS := $(CFLAGS) " + compiler_opts) + + Out("") + Out("UNAME_S := $(shell uname -s)") + Out("LDFLAGS := $(LDFLAGS) " + linker_opts) + Out("ifeq ($(UNAME_S),Linux)") + Out(" LDFLAGS += -static") + Out("endif") + + Out("") + Out("HDRS = \\") + for Name in sorted(HdrNames): + Out(" %s \\" % Name) + + Out("") + Out("OBJS = \\") + for Name in CXXNames: + Out(" $(OBJDIR)/%s.o \\" % (Name)) + + for Name in CNames: + Out(" $(OBJDIR)/%s.o \\" % (Name)) + + Out("") + Out(".PHONY: clean") + + Out("") + Out("$(BINPATH) : $(BINDIR)/ $(OBJDIR)/ $(OBJS)") + + if len(CXXNames) > 0: + Cmd = "\t$(CXX) $(LDFLAGS) $(OBJS) -o $(BINPATH)" + else: + Cmd = "\t%(CC) $(LDFLAGS) $(OBJS) -o $(BINPATH)" + + if Args.lrt: + Cmd += " -lrt" + Out(Cmd) + + if not nostrip: + Out(" strip $(BINPATH)") + + Out("") + Out("$(OBJDIR)/ :") + Out(" mkdir -p $(OBJDIR)/") + + Out("") + Out("$(BINDIR)/ :") + Out(" mkdir -p $(BINDIR)/") + + if CNames: + Out("") + Out("$(OBJDIR)/%.o : %.c $(HDRS)") + Out(" $(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $<") + + if CXXNames: + Out("") + Out("$(OBJDIR)/%.o : %.cpp $(HDRS)") + Out(" $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<") + +sys.stderr.write("Makefile done.\n") + +rc = os.system("make") +if rc != 0: + sys.stderr.write("\n\nERROR -- make failed\n\n") + sys.exit(1) +sys.stderr.write("make done.\n") From 5bb866979804b7dd566fa446c4b2b109c8478ada Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 3 Nov 2024 02:42:56 -0500 Subject: [PATCH 16/19] Update rabbitqcplus to 2.3.0 (#51888) --- recipes/rabbitqcplus/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml index d85b61e5b355c..ba6390ac5ee70 100644 --- a/recipes/rabbitqcplus/meta.yaml +++ b/recipes/rabbitqcplus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.9" %} +{% set version = "2.3.0" %} package: name: rabbitqcplus @@ -6,10 +6,10 @@ package: source: url: https://github.com/RabbitBio/RabbitQCPlus/archive/refs/tags/{{ version }}.tar.gz - sha256: 076cb1e11046d5a41464f74d7df363e2ea337e2cf3ad8e8b0712c5c7df746466 + sha256: 9ce239d998582c50c373eefc8d5f83763439693fe348206107f27105a22d4aaf build: - number: 1 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage("rabbitqcplus", max_pin="x.x") }} From 92c334d737865661931512d141a70dad1cf835a9 Mon Sep 17 00:00:00 2001 From: Cormac Kinsella <27350062+CormacKinsella@users.noreply.github.com> Date: Sun, 3 Nov 2024 10:13:11 +0100 Subject: [PATCH 17/19] update vg to 1.60.0 (#51863) --- recipes/vg/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index 9ec0557e1bc67..4500b2e91bddb 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.59.0" %} +{% set version = "1.60.0" %} package: name: {{ name }} @@ -7,9 +7,9 @@ package: source: - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg # [linux and x86_64] - sha256: a2270237c8541867ac345ad924c1641881bc9fd60be157a6d3d29fa910aacfc2 # [linux and x86_64] + sha256: 8a014a89301fa3168b19adadfa23753dcfd4af3944493199028ec79c141da22e # [linux and x86_64] - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg-arm64 # [linux and aarch64] - sha256: e0df4e81e0c7b3ac1c7f3fc7a7bc8421416256bf2bc4a1ca2b87feebaf40d4d0 # [linux and aarch64] + sha256: b7700ac536cee961e0fe6bfd5cfd3b3f93844be47b45f21d67e0a0208fc01bc0 # [linux and aarch64] build: number: 0 From 0d6fa8c3466aa0ce5e3084e851e384f4b82c9f99 Mon Sep 17 00:00:00 2001 From: Parham Kazemi Date: Sun, 3 Nov 2024 05:33:31 -0800 Subject: [PATCH 18/19] Add ntStat (#51884) * Create meta.yaml * Create build.sh * Update meta.yaml --- ntstat/build.sh | 4 ++++ ntstat/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 ntstat/build.sh create mode 100644 ntstat/meta.yaml diff --git a/ntstat/build.sh b/ntstat/build.sh new file mode 100644 index 0000000000000..5b5b9d640ee41 --- /dev/null +++ b/ntstat/build.sh @@ -0,0 +1,4 @@ +#!/usr/bin/env bash + +meson setup --buildtype release --prefix=$PREFIX build +meson install -C build diff --git a/ntstat/meta.yaml b/ntstat/meta.yaml new file mode 100644 index 0000000000000..301e6426276d3 --- /dev/null +++ b/ntstat/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} + +package: + name: ntstat + version: {{ version }} + +source: + url: https://github.com/bcgsc/ntStat/archive/refs/tags/v{{ version }}.tar.gz + sha256: 262dc58ab6f781a6816a5d4fc129659c7fa2c3364871320eafb45bfa822fab6a + +build: + number: 0 + run_exports: + - {{ pin_subpackage('ntstat', max_pin="x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - meson + - meson-python + - cmake + host: + - python + - llvm-openmp # [osx] + - libgomp # [linux] + - btllib >=1.7.2 + - cpp-argparse + - cpp-tabulate + - indicators + - pybind11 + run: + - python + - ntcard + - matplotlib + - numpy + - scipy + - tabulate + +test: + commands: + - ntstat --version + - ntstat count --help + +about: + home: https://github.com/bcgsc/ntStat + license: GPL-3.0-or-later + license_file: LICENSE + summary: 'a toolkit for statistical analysis of k-mer frequency and depth' From f4f49181943e42535875300ad7d2baeccadf26b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Sun, 3 Nov 2024 14:37:31 +0100 Subject: [PATCH 19/19] Adding msa4u (#51864) * Adding msa4u * Add run_export * Update meta.yaml Clean up dependencies * Update meta.yaml * Fix home url --- recipes/msa4u/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 recipes/msa4u/meta.yaml diff --git a/recipes/msa4u/meta.yaml b/recipes/msa4u/meta.yaml new file mode 100644 index 0000000000000..a932f8d7df7a1 --- /dev/null +++ b/recipes/msa4u/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "msa4u" %} +{% set version = "0.4.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/msa4u-{{ version }}.tar.gz + sha256: 0471f334bbc1fbb8ea6c0974c39f9aed59030b32d3d790caf814c8f53c393c17 + +build: + run_exports: + - {{ pin_subpackage("msa4u", max_pin="x.x") }} + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + noarch: python + +requirements: + host: + - python + - pip + run: + - python + - biopython + - pandas + - reportlab + - configs + +test: + imports: + - msa4u + commands: + - msa4u --help + +about: + home: https://github.com/GCA-VH-lab/msa4u + summary: "A simple visualisation tool for Multiple Sequence Alignment." + license: WTFPL + license_file: LICENSE