-
Notifications
You must be signed in to change notification settings - Fork 3.3k
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* add sipros * revise the error * fix python2 error * Update recipes/sipros/build.sh Co-authored-by: M Bernt <m.bernt@ufz.de> * symlink the python scripts * Update recipes/sipros/copyConfigTemplate.sh Co-authored-by: M Bernt <m.bernt@ufz.de> --------- Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com> Co-authored-by: M Bernt <m.bernt@ufz.de>
- Loading branch information
1 parent
6139482
commit 6942d4d
Showing
5 changed files
with
155 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,24 @@ | ||
MIT License | ||
|
||
Copyright (c) 2023 Phase Technician XYZ | ||
|
||
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. | ||
|
||
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. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,9 @@ | ||
#!/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 "$DIR/Raxport.exe" "$@" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,35 @@ | ||
#!/usr/bin/env bash | ||
|
||
set -e | ||
|
||
mkdir -p "$PREFIX/bin" | ||
chmod u+x bin/* | ||
cp -r bin/* "$PREFIX/bin" | ||
|
||
cp -r EnsembleScripts "$PREFIX" | ||
|
||
cp -r V4Scripts "$PREFIX" | ||
|
||
cp -r configTemplates "$PREFIX" | ||
|
||
for script in sipros_prepare_protein_database.py sipros_psm_tabulating.py sipros_ensemble_filtering.py sipros_peptides_assembling.py; do | ||
baseName=$(basename $script .py) | ||
sed -i '1i#!/usr/bin/env python\n' "$PREFIX/EnsembleScripts/$script" | ||
ln -s "$PREFIX/EnsembleScripts/$script" "$PREFIX/bin/EnsembleScripts_$baseName" | ||
done | ||
|
||
for script in sipros_peptides_filtering.py sipros_peptides_assembling.py ClusterSip.py; do | ||
baseName=$(basename $script .py) | ||
sed -i '1i#!/usr/bin/env python\n' "$PREFIX/V4Scripts/$script" | ||
ln -s "$PREFIX/V4Scripts/$script" "$PREFIX/bin/V4Scripts_$baseName" | ||
done | ||
|
||
for script in refineProteinFDR.R getSpectraCountInEachFT.R makeDBforLabelSearch.R getLabelPCTinEachFT.R; do | ||
baseName=$(basename $script .R) | ||
sed -i '1i#!/usr/bin/env Rscript\n' "$PREFIX/V4Scripts/$script" | ||
ln -s "$PREFIX/V4Scripts/$script" "$PREFIX/bin/V4Scripts_$baseName" | ||
done | ||
|
||
cp "$RECIPE_DIR"/Raxport.sh "$PREFIX/bin/Raxport" | ||
cp "$RECIPE_DIR"/copyConfigTemplate.sh "$PREFIX/bin/copyConfigTemplate" | ||
chmod u+x $PREFIX/bin/* |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,30 @@ | ||
#!/usr/bin/env bash | ||
|
||
if [ -z "$2" ]; then | ||
OUTPUT_PATH="." | ||
else | ||
OUTPUT_PATH=$2 | ||
fi | ||
|
||
if [ -z "$CONDA_PREFIX" ]; then | ||
echo "Error: CONDA_PREFIX is not set. Are you running this in a Conda environment?" | ||
exit 1 | ||
fi | ||
|
||
TEMPLATE_DIR="$CONDA_PREFIX/configTemplates" | ||
|
||
if [ "$1" == "-Regular" ]; then | ||
TEMPLATE="$TEMPLATE_DIR/SiprosEnsembleConfig.cfg" | ||
elif [ "$1" == "-SIP" ]; then | ||
TEMPLATE="$TEMPLATE_DIR/SiprosV4Config.cfg" | ||
else | ||
echo "Usage: copyConfigTemplate {-Regular|-SIP} <output_path>" | ||
exit 1 | ||
fi | ||
|
||
if [ ! -f "$TEMPLATE" ]; then | ||
echo "Error: Template file $TEMPLATE not found" | ||
exit 1 | ||
fi | ||
|
||
cp -v "$TEMPLATE" "$OUTPUT_PATH" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,57 @@ | ||
{% set name = "sipros" %} | ||
{% set version = "4.01" %} | ||
|
||
package: | ||
name: {{ name|lower }} | ||
version: {{ version }} | ||
|
||
source: | ||
url: https://github.com/thepanlab/Sipros4/releases/download/{{ version }}/siprosRelease.zip | ||
sha256: 10030671b94a8a2ab354396178f35c30a8e8e0c633864533690c1ff285906c9c | ||
|
||
build: | ||
noarch: generic | ||
number: 0 | ||
skip: False | ||
run_exports: | ||
- {{ pin_subpackage('sipros', max_pin="x") }} | ||
|
||
requirements: | ||
run: | ||
- bioconductor-biostrings | ||
- mono | ||
- numpy =1.16 | ||
- python =2.7 | ||
- r-base | ||
- r-stringr | ||
- r-tidyr | ||
- scikit-learn =0.20.3 | ||
|
||
test: | ||
commands: | ||
- configGenerator -h | ||
- SiprosEnsembleOMP --help | ||
- SiprosV4OMP --help | ||
- Raxport -h | ||
- EnsembleScripts_sipros_psm_tabulating -v | ||
- V4Scripts_sipros_peptides_filtering -v | ||
- V4Scripts_getSpectraCountInEachFT -help | ||
- V4Scripts_refineProteinFDR -help | ||
- copyConfigTemplate -SIP | ||
|
||
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." | ||
extra: | ||
recipe-maintainers: | ||
- bernt-matthias | ||
- yi-xiong | ||
identifiers: | ||
- biotools:sipros | ||
- doi:10.1186/s40168-024-01866-1 |