Mercurial > repos > galaxyp > openms_eicextractor
diff test-data.sh @ 13:0546885ddaf9 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:23:13 +0000 |
| parents | aeaadbf1d7ec |
| children | f253d41d9170 |
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--- a/test-data.sh Wed Sep 23 14:59:15 2020 +0000 +++ b/test-data.sh Tue Oct 13 20:23:13 2020 +0000 @@ -1,8 +1,8 @@ #!/usr/bin/env bash -VERSION=2.5 +VERSION=2.6 FILETYPES="filetypes.txt" -CONDAPKG="https://anaconda.org/bioconda/openms/2.5.0/download/linux-64/openms-2.5.0-h463af6b_1.tar.bz2" +CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2" # import the magic . ./generate-foo.sh @@ -49,7 +49,7 @@ cd - else cd $OPENMSGIT - git pull origin release/$VERSION.0 + git pull origin release/$VERSION.0 cd - fi @@ -59,7 +59,7 @@ if conda env list | grep "$OPENMSENV"; then true else - conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION openjdk=8.0.192 ctdopts=1.4 lxml + conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml # chmod -R u-w $OPENMSENV fi ############################################################################### @@ -88,7 +88,6 @@ git pull origin topic/cdata cd - fi -# export PYTHONPATH=$(pwd)/CTDopts ############################################################################### ## copy all the test data files to test-data @@ -103,21 +102,26 @@ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then - wget -q https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML && mv MetaboliteSpectralDB.mzML test-data/ + wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML + mv MetaboliteSpectralDB.mzML test-data/ fi ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv if [ ! -d test-data/pepnovo_models/ ]; then - wget http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip - unzip -e PepNovo.20120423.zip -d /tmp/ - mv /tmp/Models test-data/pepnovo_models/ + mkdir -p /tmp/pepnovo + wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip + unzip PepNovo.20120423.zip -d /tmp/pepnovo/ + mv /tmp/pepnovo/Models test-data/pepnovo_models/ + rm PepNovo.20120423.zip + rm -rf /tmp/pepnovo fi ############################################################################### ## generate ctd files using the binaries in the conda package ############################################################################### echo "Create CTD files" conda activate $OPENMSENV +rm -rf ctd mkdir -p ctd # TODO because of https://github.com/OpenMS/OpenMS/issues/4641 @@ -175,7 +179,7 @@ echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh -echo 'export SPECTRAST_BINARY="spectrast"' >> prepare_test_data.sh +echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh