Mercurial > repos > galaxyp > openms_nucleicacidsearchengine
diff generate.sh @ 0:fe6eddc2e756 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 27 Aug 2020 19:47:24 -0400 |
parents | |
children | 0b91652c7743 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate.sh Thu Aug 27 19:47:24 2020 -0400 @@ -0,0 +1,76 @@ +#!/usr/bin/env bash + +# VERSION=2.3 +# CONDAPKG=https://anaconda.org/bioconda/openms/2.3.0/download/linux-64/openms-2.3.0-py27h932d754_3.tar.bz2 +# VERSION=2.4 +# CONDAPKG=https://anaconda.org/bioconda/openms/2.4.0/download/linux-64/openms-2.4.0-py27h574aadf_1.tar.bz2 + +VERSION=2.5 +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="$tmp/CTDConverter" + +export PYTHONPATH="$(pwd)/CTDopts/" +############################################################################### +## 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 +############################################################################### +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$(cat convert.err)"; fi +conda deactivate + +patch PepNovoAdapter.xml < PepNovoAdapter.patch +patch OMSSAAdapter.xml < OMSSAAdapter.patch + +# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool + +# for i in A-E F-H I-L M-N O-P Q-Z +# do +# planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json & +# done