Mercurial > repos > galaxyp > openms_spectrafilterparentpeakmower
view test-data.sh @ 12:d2de797154f7 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author | galaxyp |
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date | Fri, 06 Nov 2020 19:59:38 +0000 |
parents | 75492ef0bff5 |
children | 5694ec584f4c |
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#!/usr/bin/env bash VERSION=2.6 FILETYPES="filetypes.txt" 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 # install conda if [ -z "$tmp" ]; then tmp=$(mktemp -d) created="yes" fi export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" export OPENMSENV="$tmp/OpenMS$VERSION-env" export CTDCONVERTER="$tmp/CTDConverter" if [[ -z "$1" ]]; then autotests="/dev/null" else autotests="$1" fi if type conda > /dev/null; then true else wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" source "$tmp/miniconda/bin/activate" fi eval "$(conda shell.bash hook)" ############################################################################### ## get ## - conda environment (for executing the binaries) and ## - the git clone of OpenMS (for generating the tests) ############################################################################### echo "Clone OpenMS $VERSION sources" if [[ ! -d $OPENMSGIT ]]; then git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT cd $OPENMSGIT git submodule init git submodule update cd - else cd $OPENMSGIT git pull origin release/$VERSION.0 cd - fi echo "Create OpenMS $VERSION conda env" # TODO currently add lxml (needed by CTDConverter) # TODO for some reason a to recent openjdk is used if conda env list | grep "$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 ctdopts=1.4 lxml # chmod -R u-w $OPENMSENV fi ############################################################################### ## get the ## - conda package (for easy access and listing of the OpenMS binaries), ############################################################################### echo "Download OpenMS $VERSION package $CONDAPKG" if [[ ! -d $OPENMSPKG ]]; then mkdir $OPENMSPKG wget -q -P $OPENMSPKG/ "$CONDAPKG" tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ rm $OPENMSPKG/"$(basename $CONDAPKG)" fi ############################################################################### ## Get python libaries for CTD -> Galaxy conversion ## TODO fix to main repo OR conda packkage if PRs are merged ############################################################################### echo "Clone CTDConverter" if [[ ! -d $CTDCONVERTER ]]; then #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER else cd $CTDCONVERTER git pull origin topic/cdata cd - fi ############################################################################### ## copy all the test data files to test-data ## most of it (outputs) will be overwritten later, but its needed for ## prepare_test_data ############################################################################### echo "Get test data" find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then 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 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 # this needs to be done from within test-data cd test-data for i in $OPENMSPKG/bin/* do b=$(basename $i) echo $b $b -write_ctd ../ctd/ sed -i -e 's/²/^2/' ../ctd/$b.ctd done cd - ############################################################################### ## fix ini files: OpenMS test data contains ini files with outdated ini files. ## e.g. variables might be in different nodes, outdated variables present, new ## variables missing, ... ## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests) ## but it is for the generation of the tests ## see https://github.com/OpenMS/OpenMS/issues/4462 ############################################################################### echo "Update test INI files" for ini in test-data/*ini do tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') bin=$(which $tool) if [[ -z $bin ]]; then >&2 echo "missing binary to convert $ini" continue fi cp $ini $ini.backup $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr if [[ "$?" -ne "0" ]]; then >&2 echo "could not convert $ini" fi done ############################################################################### ## create script to create results for the tests and run it ############################################################################### echo "Create test shell script" echo -n "" > prepare_test_data.sh echo 'export COMET_BINARY="comet"' >> prepare_test_data.sh echo 'export CRUX_BINARY="crux"' >> prepare_test_data.sh echo 'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"' >> prepare_test_data.sh echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh echo 'export OMSSA_BINARY="$(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="'"$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 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh # prepare_test_data > tmp_test_data.sh # # remove calls not needed for the tools listed in any .list file # echo LIST $LIST # if [ ! -z "$LIST" ]; then # REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') # else # REX=".*" # fi # echo REX $REX # cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh # rm tmp_test_data.sh echo "Execute test shell script" chmod u+x prepare_test_data.sh cd ./test-data || exit ../prepare_test_data.sh cd - || exit ############################################################################### ## create/update test data for the manually generated tests ## - run convert once with the manual tests only and ## - update test-data (needs to run 2x) ############################################################################### echo "Execute test shell script for manually curated tests" chmod u+x prepare_test_data_manual.sh cd ./test-data || exit ../prepare_test_data_manual.sh cd - || exit ############################################################################### ## auto generate tests ############################################################################### echo "Write test macros to $autotests" echo "<macros>" > "$autotests" for i in $(ls *xml |grep -v macros) do b=$(basename "$i" .xml) get_tests2 "$b" >> "$autotests" done echo "</macros>" >> "$autotests" echo "Create test data links" link_tmp_files # tests for tools using output_prefix parameters can not be auto generated # hence we output the tests for manual curation in macros_test.xml # and remove them from the autotests # -> OpenSwathFileSplitter IDRipper MzMLSplitter # # Furthermore we remove tests for tools without binaries in conda # -> MSFragger MaRaClusterAdapter NovorAdapter # # not able to specify composite test data # -> SpectraSTSearchAdapter if [[ ! -z "$1" ]]; then echo "" > macros_discarded_auto.xml for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter do echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml echo "</xml>" >> macros_discarded_auto.xml xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp mv tmp macros_autotest.xml done >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" fi conda deactivate ## remove broken symlinks in test-data find test-data/ -xtype l -delete # if [ ! -z "$created" ]; then # echo "Removing temporary directory" # rm -rf "$tmp" # fi