Mercurial > repos > galaxyp > openms_pepnovoadapter

comparison generate.sh @ 4:533859c7e75f draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:18:33 +0000
parents e570599ec9f2
children
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3:e570599ec9f2 4:533859c7e75f
1 #!/usr/bin/env bash
2
3 VERSION=2.6
4 FILETYPES="filetypes.txt"
5 PROFILE="20.05"
6 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
7
8 export tmp=$(mktemp -d)
9 export CTDCONVERTER="$tmp/CTDConverter"
10
11 ###############################################################################
12 ## reset old data
13 ###############################################################################
14 # rm $(ls *xml |grep -v macros)
15 # rm -rf ctd
16 # mkdir -p ctd
17 # echo "" > prepare_test_data.sh
18
19 ###############################################################################
20 ## generate tests
21 ## also creates
22 ## - conda environment (for executing the binaries) and
23 ## - the git clone of OpenMS (for generating the tests)
24 ## - ctd files
25 ###############################################################################
26 bash ./test-data.sh ./macros_autotest.xml
27
28 ###############################################################################
29 ## get the
30 ## - conda package (for easy access and listing of the OpenMS binaries),
31 ###############################################################################
32 # if [ ! -d $OPENMSPKG ]; then
33 # mkdir $OPENMSPKG/
34 # wget -P $OPENMSPKG/ "$CONDAPKG"
35 # tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/
36 # rm $OPENMSPKG/"$(basename $CONDAPKG)"
37 # fi
38
39 ###############################################################################
40 ## Get python libaries for CTD -> Galaxy conversion
41 ## TODO fix to main repo OR conda packkage if PRs are merged
42 ###############################################################################
43 # if [ ! -d CTDopts ]; then
44 # # git clone https://github.com/genericworkflownodes/CTDopts CTDopts
45 # git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts
46 # fi
47 if [ ! -d $CTDCONVERTER ]; then
48 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
49 git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
50 fi
51 # export PYTHONPATH=$(pwd)/CTDopts
52 ###############################################################################
53 ## conversion ctd->xml
54 ###############################################################################
55
56 find . -maxdepth 0 -name "[A-Z]*xml" -delete
57 source $(dirname $(which conda))/../etc/profile.d/conda.sh
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 $PROFILE > convert.out 2> convert.err
60 if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
61 conda deactivate
62
63 patch PepNovoAdapter.xml < PepNovoAdapter.patch
64 patch OMSSAAdapter.xml < OMSSAAdapter.patch
65
66 # https://github.com/OpenMS/OpenMS/pull/4984
67 sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
68 # https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976
69 patch -p0 <404-urls.patch
70
71 # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool
72
73 # for i in A-E F-H I-L M-N O-P Q-Z
74 # do
75 # planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json &
76 # done