Mercurial > repos > galaxyp > openms_msstatsconverter

comparison generate.sh @ 4:99c6cad61de6 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
author galaxyp
date Sun, 13 Dec 2020 15:44:06 +0000
parents fd97539098b3
children
comparison
equal deleted inserted replaced
3:64b10f17c9c0 4:99c6cad61de6
4 FILETYPES="filetypes.txt" 4 FILETYPES="filetypes.txt"
5 PROFILE="20.05" 5 PROFILE="20.05"
6 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g') 6 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
7 7
8 export tmp=$(mktemp -d) 8 export tmp=$(mktemp -d)
9
9 export CTDCONVERTER="$tmp/CTDConverter" 10 export CTDCONVERTER="$tmp/CTDConverter"
10
11 ############################################################################### 11 ###############################################################################
12 ## reset old data 12 ## reset old data
13 ############################################################################### 13 ###############################################################################
14 # rm $(ls *xml |grep -v macros) 14 # rm $(ls *xml |grep -v macros)
15 # rm -rf ctd 15 # rm -rf ctd
54 ############################################################################### 54 ###############################################################################
55 55
56 find . -maxdepth 0 -name "[A-Z]*xml" -delete 56 find . -maxdepth 0 -name "[A-Z]*xml" -delete
57 source $(dirname $(which conda))/../etc/profile.d/conda.sh 57 source $(dirname $(which conda))/../etc/profile.d/conda.sh
58 conda activate $tmp/OpenMS$VERSION-env 58 conda activate $tmp/OpenMS$VERSION-env
59 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 59 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 $PROFILE --bump-file bump.json > convert.out 2> convert.err
60 if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi 60 if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
61 conda deactivate 61 conda deactivate
62 62
63 patch PepNovoAdapter.xml < PepNovoAdapter.patch 63 patch PepNovoAdapter.xml < PepNovoAdapter.patch
64 patch OMSSAAdapter.xml < OMSSAAdapter.patch 64 patch OMSSAAdapter.xml < OMSSAAdapter.patch
65 # this should not be necessary from 2.7 https://github.com/OpenMS/OpenMS/pull/5087
66 patch PSMFeatureExtractor.xml < PSMFeatureExtractor.patch
65 67
66 # https://github.com/OpenMS/OpenMS/pull/4984 68 # https://github.com/OpenMS/OpenMS/pull/4984
67 sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml 69 sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
68 # https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976 70 # https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976
69 patch -p0 <404-urls.patch 71 patch -p0 <404-urls.patch