Mercurial > repos > galaxyp > openms_idextractor
view generate.sh @ 14:ef4ecc9d45fb 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 19:40:34 +0000 |
parents | 2a2fa2b57306 |
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#!/usr/bin/env bash VERSION=2.6 FILETYPES="filetypes.txt" PROFILE="20.05" ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g') export tmp=$(mktemp -d) export CTDCONVERTER="$tmp/CTDConverter" ############################################################################### ## reset old data ############################################################################### # rm $(ls *xml |grep -v macros) # rm -rf ctd # mkdir -p ctd # echo "" > prepare_test_data.sh ############################################################################### ## generate tests ## also creates ## - conda environment (for executing the binaries) and ## - the git clone of OpenMS (for generating the tests) ## - ctd files ############################################################################### bash ./test-data.sh ./macros_autotest.xml ############################################################################### ## get the ## - conda package (for easy access and listing of the OpenMS binaries), ############################################################################### # if [ ! -d $OPENMSPKG ]; then # mkdir $OPENMSPKG/ # wget -P $OPENMSPKG/ "$CONDAPKG" # tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/ # rm $OPENMSPKG/"$(basename $CONDAPKG)" # fi ############################################################################### ## Get python libaries for CTD -> Galaxy conversion ## TODO fix to main repo OR conda packkage if PRs are merged ############################################################################### # if [ ! -d CTDopts ]; then # # git clone https://github.com/genericworkflownodes/CTDopts CTDopts # git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts # fi 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 $CTDCONVERTER fi # export PYTHONPATH=$(pwd)/CTDopts ############################################################################### ## conversion ctd->xml ############################################################################### find . -maxdepth 0 -name "[A-Z]*xml" -delete source $(dirname $(which conda))/../etc/profile.d/conda.sh conda activate $tmp/OpenMS$VERSION-env python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_ --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi conda deactivate patch PepNovoAdapter.xml < PepNovoAdapter.patch patch OMSSAAdapter.xml < OMSSAAdapter.patch # https://github.com/OpenMS/OpenMS/pull/4984 sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml # https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976 patch -p0 <404-urls.patch # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool # for i in A-E F-H I-L M-N O-P Q-Z # do # planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json & # done