Mercurial > repos > galaxyp > openms_idrtcalibration

comparison generate.sh @ 12:28805cf9b024 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:15:58 +0000
parents 4215810bb49d
children
comparison
equal deleted inserted replaced
11:4215810bb49d 12:28805cf9b024
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