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Merge branch 'master' into k8_recipe_update
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mencian authored Oct 1, 2024
2 parents 79cf483 + 547a8c9 commit ad519f5
Showing 21 changed files with 3,690 additions and 40 deletions.
4 changes: 2 additions & 2 deletions recipes/apscale/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
{% set name = "apscale" %}
{% set version = "2.0.2" %}
{% set version = "2.0.3" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/apscale-{{ version }}.tar.gz
sha256: 13d32ad87c1cf2d161bd577421e848006de8bcbb831aab15e5ecd3a5b6fc4563
sha256: 52cf592e1446c958b781e5a134a2945989b33008805f46a071c97d073d330f00

build:
entry_points:
7 changes: 6 additions & 1 deletion recipes/bambamc/build.sh
Original file line number Diff line number Diff line change
@@ -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
1,700 changes: 1,700 additions & 0 deletions recipes/bambamc/config.guess

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1,885 changes: 1,885 additions & 0 deletions recipes/bambamc/config.sub

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9 changes: 8 additions & 1 deletion recipes/bambamc/meta.yaml
Original file line number Diff line number Diff line change
@@ -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
3 changes: 2 additions & 1 deletion recipes/eukulele/meta.yaml
Original file line number Diff line number Diff line change
@@ -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 --use-pep517 -vvv"
run_exports:
@@ -41,6 +41,7 @@ requirements:
- sphinxcontrib-bibtex ==1.0.0
- blast
- diamond
- busco >=4.0.4

test:
commands:
4 changes: 2 additions & 2 deletions recipes/genmod/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
{% set name = "genmod" %}
{% set version = "3.8.2" %}
{% set version = "3.8.3" %}

package:
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
sha256: 72921cce29fd8d6b99eea76921a0a71d3846abcb92bcb02dafd24886ab9264a3
sha256: 97a411f3f014557cf57aed9cc18e55e097ab7c54b191eb7995c10dd97d4bdeaf

build:
number: 0
6 changes: 3 additions & 3 deletions recipes/genomic_address_service/meta.yaml
Original file line number Diff line number Diff line change
@@ -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") }}
4 changes: 2 additions & 2 deletions recipes/harpy/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{% set version = "1.8.1" %}
{% set sha256 = "e51ea8b7156fb628920d75d4bc517c11dae915e20f9cf5e51d29fe05267063a0" %}
{% set version = "1.8.2" %}
{% set sha256 = "b2459f6ed5514c406ce82b1303a242dcafc93e0c7aa7d1ac78273dee79b35654" %}

package:
name: harpy
4 changes: 2 additions & 2 deletions recipes/metabolabpy/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set name = "metabolabpy" %}
{% set version = "0.9.50" %}
{% set sha256 = "9fe9e080e72a7ed26d2ddaf32730a2b5a9edf752bef3aeb4b242b49b17813686" %}
{% set version = "0.9.51" %}
{% set sha256 = "808ecee750e3366191f0859049d8570805c2a7a309f0c8f524c040c423069a8c" %}

package:
name: {{ name|lower }}
49 changes: 49 additions & 0 deletions recipes/minimizers/meta.yaml
Original file line number Diff line number Diff line change
@@ -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
4 changes: 2 additions & 2 deletions recipes/nohuman/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
{% set version = "0.2.1" %}
{% 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: 0d9c647131077bfec327d3d8aeddb67cff1f0f93873543dbb97b4bac4948aed8
sha256: 3503a0e8b6fcbf92832fe4bfcfb3d5a071536a8ebe3230cac1ee4e053de3cf6a

build:
number: 0
9 changes: 5 additions & 4 deletions recipes/peptide-shaker/meta.yaml
Original file line number Diff line number Diff line change
@@ -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:
2 changes: 1 addition & 1 deletion recipes/peptide-shaker/peptide-shaker.py
Original file line number Diff line number Diff line change
@@ -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']
4 changes: 2 additions & 2 deletions recipes/psm-utils/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set name = "psm-utils" %}
{% set version = "1.1.0" %}
{% set sha256 = "b950ef8b4415b76c8d9b41023a93d65a3c66826524459e34c4faef1092a3f87f" %}
{% set version = "1.1.1" %}
{% set sha256 = "8926d8f5e2e05ac38d54d6ae5c89461568085b60d23414a907c820bc674a4a2b" %}

package:
name: {{ name|lower }}
4 changes: 2 additions & 2 deletions recipes/pyslow5/meta.yaml
Original file line number Diff line number Diff line change
@@ -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 }}
4 changes: 2 additions & 2 deletions recipes/pyteomics/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
{% set version = "4.7.3" %}
{% set version = "4.7.4" %}

package:
name: pyteomics
version: {{ version }}

source:
url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz
sha256: ae87f6ba02ee735b06ae56e1ac85a37051aa503e0c9dbfee650c8a7107d08f57
sha256: cd8a9b48ea3a3075bbbc3085880b5a4f76eb7359e3c71ee3948d9bb2aa48883b

build:
noarch: python
18 changes: 10 additions & 8 deletions recipes/searchgui/meta.yaml
Original file line number Diff line number Diff line change
@@ -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
2 changes: 1 addition & 1 deletion recipes/searchgui/searchgui.py
Original file line number Diff line number Diff line change
@@ -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']

4 changes: 2 additions & 2 deletions recipes/sizemeup/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
{% set name = "sizemeup" %}
{% set version = "1.1.1" %}
{% set version = "1.2.0" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://github.com/rpetit3/sizemeup/archive/v{{ version }}.tar.gz
sha256: 485b0d6bf712febf998db57d296c20a6d885a4d61ade67ee8ce0370dc5067d11
sha256: 521b31fc13ba5c440b45c107b3cc496001e77d928b7b6f7f5db373c95a1ad10b

build:
number: 0
4 changes: 2 additions & 2 deletions recipes/smalt/build.sh
Original file line number Diff line number Diff line change
@@ -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

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