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Add sipros #50631
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Add sipros #50631
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23b5849
add sipros
bernt-matthias 80579fb
add skip and norach
bernt-matthias 83ea3d8
try skip noarch test
bernt-matthias 2c3e85f
another try
bernt-matthias ff7e354
try without skip
bernt-matthias 0b14aa7
try should_be_noarch_generic
bernt-matthias c30aeda
fix name in pin_subpackage
bernt-matthias 0ec5fec
fix chmod call
bernt-matthias c321c08
add license
bernt-matthias 1ff8e7e
add shell script to call exe via mono
bernt-matthias f1432ba
changes as suggested by author
bernt-matthias 53d4e43
try to fix pinnings
bernt-matthias ebdc239
do not use ~=
bernt-matthias 6d38e97
unpin r-base
bernt-matthias 76b5d13
unpin bioconductor-biostrings
bernt-matthias 375cc0c
unpin numpy
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MIT License | ||
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Copyright (c) 2023 Phase Technician XYZ | ||
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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: | ||
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The above copyright notice and this permission notice shall be included in all | ||
copies or substantial portions of the Software. | ||
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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. | ||
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Code written for the MSToolkit uses the Apache License, Version 2.0. All 3rd | ||
party software included in the MSToolkit library retains its original license. |
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#!/usr/bin/env bash | ||
SOURCE="${BASH_SOURCE[0]}" | ||
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink | ||
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" | ||
SOURCE="$(readlink "$SOURCE")" | ||
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located | ||
done | ||
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" | ||
mono $DIR/Raxport.exe $@ |
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set -e | ||
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mkdir -p "$PREFIX/bin" | ||
chmod u+x bin/* | ||
cp -r bin/* "$PREFIX/bin" | ||
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cp -r EnsembleScripts "$PREFIX" | ||
cp -r V4Scripts "$PREFIX" | ||
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cp -r configTemplates "$PREFIX" | ||
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cp $RECIPE_DIR/Raxport.sh "$PREFIX/bin/Raxport" | ||
chmod +x "$PREFIX/bin/Raxport" | ||
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ln -s "$PREFIX"/EnsembleScripts/sipros_psm_tabulating.py "$PREFIX"/bin/sipros_psm_tabulating.py | ||
ln -s "$PREFIX"/V4Scripts/sipros_peptides_filtering.py "$PREFIX"/bin/sipros_peptides_filtering.py |
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{% set name = "sipros" %} | ||
{% set version = "4.01" %} | ||
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package: | ||
name: {{ name|lower }} | ||
version: {{ version }} | ||
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source: | ||
url: https://github.com/thepanlab/Sipros4/releases/download/{{ version }}/siprosRelease.zip | ||
sha256: 10030671b94a8a2ab354396178f35c30a8e8e0c633864533690c1ff285906c9c | ||
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build: | ||
noarch: generic | ||
number: 0 | ||
run_exports: | ||
- {{ pin_subpackage('sipros', max_pin="x") }} | ||
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requirements: | ||
host: | ||
- python <3 | ||
- numpy | ||
- scikit-learn ==0.20.3 | ||
- mono | ||
- r-base | ||
- r-stringr ==1.5 | ||
- r-tidyr ==1.3 | ||
- bioconductor-biostrings | ||
run: | ||
- python <3 | ||
- numpy | ||
- scikit-learn ==0.20.3 | ||
- mono | ||
- r-base | ||
- r-stringr ==1.5 | ||
- r-tidyr ==1.3 | ||
- bioconductor-biostrings | ||
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test: | ||
commands: | ||
- configGenerator -h | ||
- SiprosEnsembleOMP --help | ||
- SiprosV4OMP --help | ||
- Raxport -h | ||
- python $CONDA_PREFIX/EnsembleScripts/sipros_psm_tabulating.py -v | ||
- python $CONDA_PREFIX/V4Scripts/sipros_peptides_filtering.py -v | ||
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about: | ||
home: https://github.com/thepanlab/Sipros4 | ||
license: MIT | ||
# currently include in the recipe folder because from the release (https://github.com/thepanlab/Sipros4/issues/3) | ||
license_file: LICENSE | ||
summary: "Tools for stable isotopic mass spectrometry-based metaproteomics" | ||
description: | | ||
"Tools for stable isotopic mass spectrometry-based metaproteomics research developed by Sipros team. These include Raxport, SiprosV4, SiprosEnsemble and some python / R scripts." | ||
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extra: | ||
recipe-maintainers: | ||
- bernt-matthias | ||
- yi-xiong | ||
skip-lints: | ||
- should_be_noarch_generic | ||
- should_not_be_noarch_source | ||
identifiers: | ||
- biotools:sipros | ||
- doi:10.1186/s40168-024-01866-1 |
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noarch ?
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Thanks for the feedback.
I tried
noarch: generic
here -- without success.But in my intuition
noarch
makes no sense, because the package ships binaries which will only work on linux (in addition to some auxiliary python and R scripts).There was a problem hiding this comment.
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In that case you need to add: