Mercurial > repos > galaxyp > openms_mztabexporter

comparison test-data.sh @ 11:9bf4fbcf20c8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:59:30 +0000
parents c679f920716e
children 2735db4dd8d9
comparison
equal deleted inserted replaced
10:c679f920716e 11:9bf4fbcf20c8
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