Mercurial > repos > galaxyp > openms_spectrafilterwindowmower
comparison generate.sh @ 9:45207485f1f1 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 12:43:33 +0000 |
parents | |
children | b28211400cc4 |
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8:3811d7efd2b7 | 9:45207485f1f1 |
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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 |