Mercurial > repos > galaxyp > openms_cometadapter
diff generate.sh @ 5:704cace078c4 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3cafa1cc1ea87eb7a0dc0e7aae013780c3565178"
| author | galaxyp |
|---|---|
| date | Sat, 05 Dec 2020 19:51:29 +0000 |
| parents | bf9bd980f729 |
| children |
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--- a/generate.sh Fri Nov 06 19:19:46 2020 +0000 +++ b/generate.sh Sat Dec 05 19:51:29 2020 +0000 @@ -6,8 +6,8 @@ ## 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 ############################################################################### @@ -56,12 +56,14 @@ 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 +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 $PROFILE --bump-file bump.json > convert.out 2> convert.err if [[ "$?" -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 +# this should not be necessary from 2.7 https://github.com/OpenMS/OpenMS/pull/5087 +patch PSMFeatureExtractor.xml < PSMFeatureExtractor.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