Mercurial > repos > galaxyp > openms_openpepxllf
comparison generate.sh @ 6:e574d3f268f6 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
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date | Tue, 13 Oct 2020 20:10:48 +0000 |
parents | a8c028751a74 |
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5:a8c028751a74 | 6:e574d3f268f6 |
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1 #!/usr/bin/env bash | 1 #!/usr/bin/env bash |
2 | 2 |
3 # VERSION=2.3 | 3 VERSION=2.6 |
4 # CONDAPKG=https://anaconda.org/bioconda/openms/2.3.0/download/linux-64/openms-2.3.0-py27h932d754_3.tar.bz2 | |
5 # VERSION=2.4 | |
6 # CONDAPKG=https://anaconda.org/bioconda/openms/2.4.0/download/linux-64/openms-2.4.0-py27h574aadf_1.tar.bz2 | |
7 | |
8 VERSION=2.5 | |
9 FILETYPES="filetypes.txt" | 4 FILETYPES="filetypes.txt" |
10 PROFILE="20.05" | 5 PROFILE="20.05" |
11 ## 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/|$//'| sed 's/|/\\|/g') |
12 | 7 |
13 export tmp=$(mktemp -d) | 8 export tmp=$(mktemp -d) |
14 | |
15 export CTDCONVERTER="$tmp/CTDConverter" | 9 export CTDCONVERTER="$tmp/CTDConverter" |
16 | 10 |
17 export PYTHONPATH="$(pwd)/CTDopts/" | |
18 ############################################################################### | 11 ############################################################################### |
19 ## reset old data | 12 ## reset old data |
20 ############################################################################### | 13 ############################################################################### |
21 # rm $(ls *xml |grep -v macros) | 14 # rm $(ls *xml |grep -v macros) |
22 # rm -rf ctd | 15 # rm -rf ctd |
57 fi | 50 fi |
58 # export PYTHONPATH=$(pwd)/CTDopts | 51 # export PYTHONPATH=$(pwd)/CTDopts |
59 ############################################################################### | 52 ############################################################################### |
60 ## conversion ctd->xml | 53 ## conversion ctd->xml |
61 ############################################################################### | 54 ############################################################################### |
55 | |
56 find . -maxdepth 0 -name "[A-Z]*xml" -delete | |
62 source $(dirname $(which conda))/../etc/profile.d/conda.sh | 57 source $(dirname $(which conda))/../etc/profile.d/conda.sh |
63 conda activate $tmp/OpenMS$VERSION-env | 58 conda activate $tmp/OpenMS$VERSION-env |
64 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 $PROFILE > convert.out 2> convert.err |
65 if [[ "$?" -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 |
66 conda deactivate | 61 conda deactivate |
67 | 62 |
68 patch PepNovoAdapter.xml < PepNovoAdapter.patch | 63 patch PepNovoAdapter.xml < PepNovoAdapter.patch |
69 patch OMSSAAdapter.xml < OMSSAAdapter.patch | 64 patch OMSSAAdapter.xml < OMSSAAdapter.patch |
65 | |
66 # 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 | |
68 # https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976 | |
70 patch -p0 <404-urls.patch | 69 patch -p0 <404-urls.patch |
71 | 70 |
72 # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool | 71 # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool |
73 | 72 |
74 # for i in A-E F-H I-L M-N O-P Q-Z | 73 # for i in A-E F-H I-L M-N O-P Q-Z |