Mercurial > repos > galaxyp > openms_novoradapter

comparison generate.sh @ 0:562d46a2f8b6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:40:35 -0400
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children ea8f9d83f34f
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-1:000000000000 0:562d46a2f8b6
1 #!/usr/bin/env bash
2
3 # VERSION=2.3
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"
10 PROFILE="20.05"
11 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
12
13 export tmp=$(mktemp -d)
14
15 export CTDCONVERTER="$tmp/CTDConverter"
16
17 export PYTHONPATH="$(pwd)/CTDopts/"
18 ###############################################################################
19 ## reset old data
20 ###############################################################################
21 # rm $(ls *xml |grep -v macros)
22 # rm -rf ctd
23 # mkdir -p ctd
24 # echo "" > prepare_test_data.sh
25
26 ###############################################################################
27 ## generate tests
28 ## also creates
29 ## - conda environment (for executing the binaries) and
30 ## - the git clone of OpenMS (for generating the tests)
31 ## - ctd files
32 ###############################################################################
33 bash ./test-data.sh ./macros_autotest.xml
34
35 ###############################################################################
36 ## get the
37 ## - conda package (for easy access and listing of the OpenMS binaries),
38 ###############################################################################
39 # if [ ! -d $OPENMSPKG ]; then
40 # mkdir $OPENMSPKG/
41 # wget -P $OPENMSPKG/ "$CONDAPKG"
42 # tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/
43 # rm $OPENMSPKG/"$(basename $CONDAPKG)"
44 # fi
45
46 ###############################################################################
47 ## Get python libaries for CTD -> Galaxy conversion
48 ## TODO fix to main repo OR conda packkage if PRs are merged
49 ###############################################################################
50 # if [ ! -d CTDopts ]; then
51 # # git clone https://github.com/genericworkflownodes/CTDopts CTDopts
52 # git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts
53 # fi
54 if [ ! -d $CTDCONVERTER ]; then
55 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
56 git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
57 fi
58 # export PYTHONPATH=$(pwd)/CTDopts
59 ###############################################################################
60 ## conversion ctd->xml
61 ###############################################################################
62 source $(dirname $(which conda))/../etc/profile.d/conda.sh
63 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 $PROFILE > convert.out 2> convert.err
65 if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
66 conda deactivate
67
68 patch PepNovoAdapter.xml < PepNovoAdapter.patch
69 patch OMSSAAdapter.xml < OMSSAAdapter.patch
70
71 # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool
72
73 # for i in A-E F-H I-L M-N O-P Q-Z
74 # do
75 # planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json &
76 # done