Mercurial > repos > galaxyp > openms_spectrastsearchadapter
comparison test-data.sh @ 10:27ddea86fe90 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 19:50:42 +0000 |
| parents | 7e2e9379aec7 |
| children | 4d189842ebfc |
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| 9:7e2e9379aec7 | 10:27ddea86fe90 |
|---|---|
| 1 #!/usr/bin/env bash | 1 #!/usr/bin/env bash |
| 2 | 2 |
| 3 VERSION=2.5 | 3 VERSION=2.6 |
| 4 FILETYPES="filetypes.txt" | 4 FILETYPES="filetypes.txt" |
| 5 CONDAPKG="https://anaconda.org/bioconda/openms/2.5.0/download/linux-64/openms-2.5.0-h463af6b_1.tar.bz2" | 5 CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2" |
| 6 | 6 |
| 7 # import the magic | 7 # import the magic |
| 8 . ./generate-foo.sh | 8 . ./generate-foo.sh |
| 9 | 9 |
| 10 # install conda | 10 # install conda |
| 47 git submodule init | 47 git submodule init |
| 48 git submodule update | 48 git submodule update |
| 49 cd - | 49 cd - |
| 50 else | 50 else |
| 51 cd $OPENMSGIT | 51 cd $OPENMSGIT |
| 52 git pull origin release/$VERSION.0 | 52 git pull origin release/$VERSION.0 |
| 53 cd - | 53 cd - |
| 54 fi | 54 fi |
| 55 | 55 |
| 56 echo "Create OpenMS $VERSION conda env" | 56 echo "Create OpenMS $VERSION conda env" |
| 57 # TODO currently add lxml (needed by CTDConverter) | 57 # TODO currently add lxml (needed by CTDConverter) |
| 58 # TODO for some reason a to recent openjdk is used | 58 # TODO for some reason a to recent openjdk is used |
| 59 if conda env list | grep "$OPENMSENV"; then | 59 if conda env list | grep "$OPENMSENV"; then |
| 60 true | 60 true |
| 61 else | 61 else |
| 62 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 | 62 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 |
| 63 # chmod -R u-w $OPENMSENV | 63 # chmod -R u-w $OPENMSENV |
| 64 fi | 64 fi |
| 65 ############################################################################### | 65 ############################################################################### |
| 66 ## get the | 66 ## get the |
| 67 ## - conda package (for easy access and listing of the OpenMS binaries), | 67 ## - conda package (for easy access and listing of the OpenMS binaries), |
| 86 else | 86 else |
| 87 cd $CTDCONVERTER | 87 cd $CTDCONVERTER |
| 88 git pull origin topic/cdata | 88 git pull origin topic/cdata |
| 89 cd - | 89 cd - |
| 90 fi | 90 fi |
| 91 # export PYTHONPATH=$(pwd)/CTDopts | |
| 92 | 91 |
| 93 ############################################################################### | 92 ############################################################################### |
| 94 ## copy all the test data files to test-data | 93 ## copy all the test data files to test-data |
| 95 ## most of it (outputs) will be overwritten later, but its needed for | 94 ## most of it (outputs) will be overwritten later, but its needed for |
| 96 ## prepare_test_data | 95 ## prepare_test_data |
| 101 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ | 100 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ |
| 102 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ | 101 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ |
| 103 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ | 102 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ |
| 104 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ | 103 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ |
| 105 if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then | 104 if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then |
| 106 wget -q https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML && mv MetaboliteSpectralDB.mzML test-data/ | 105 wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML |
| 106 mv MetaboliteSpectralDB.mzML test-data/ | |
| 107 fi | 107 fi |
| 108 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt | 108 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt |
| 109 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv | 109 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv |
| 110 | 110 |
| 111 if [ ! -d test-data/pepnovo_models/ ]; then | 111 if [ ! -d test-data/pepnovo_models/ ]; then |
| 112 wget http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip | 112 mkdir -p /tmp/pepnovo |
| 113 unzip -e PepNovo.20120423.zip -d /tmp/ | 113 wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip |
| 114 mv /tmp/Models test-data/pepnovo_models/ | 114 unzip PepNovo.20120423.zip -d /tmp/pepnovo/ |
| 115 mv /tmp/pepnovo/Models test-data/pepnovo_models/ | |
| 116 rm PepNovo.20120423.zip | |
| 117 rm -rf /tmp/pepnovo | |
| 115 fi | 118 fi |
| 116 ############################################################################### | 119 ############################################################################### |
| 117 ## generate ctd files using the binaries in the conda package | 120 ## generate ctd files using the binaries in the conda package |
| 118 ############################################################################### | 121 ############################################################################### |
| 119 echo "Create CTD files" | 122 echo "Create CTD files" |
| 120 conda activate $OPENMSENV | 123 conda activate $OPENMSENV |
| 124 rm -rf ctd | |
| 121 mkdir -p ctd | 125 mkdir -p ctd |
| 122 | 126 |
| 123 # TODO because of https://github.com/OpenMS/OpenMS/issues/4641 | 127 # TODO because of https://github.com/OpenMS/OpenMS/issues/4641 |
| 124 # this needs to be done from within test-data | 128 # this needs to be done from within test-data |
| 125 cd test-data | 129 cd test-data |
| 173 echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh | 177 echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh |
| 174 echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh | 178 echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh |
| 175 echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh | 179 echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh |
| 176 echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh | 180 echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh |
| 177 echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh | 181 echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh |
| 178 echo 'export SPECTRAST_BINARY="spectrast"' >> prepare_test_data.sh | 182 echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh |
| 179 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh | 183 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh |
| 180 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh | 184 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh |
| 181 | 185 |
| 182 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh | 186 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh |
| 183 | 187 |