Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

annotate generate.sh @ 18:6daaa75ccb99 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
author galaxyp
date Sun, 13 Dec 2020 15:03:50 +0000
parents 6f6c1cb968a0
children 2ad1b4ec3e5e
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dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1 #!/usr/bin/env bash
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3 VERSION=2.6
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4 FILETYPES="filetypes.txt"
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5 PROFILE="20.05"
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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6 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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8 export tmp=$(mktemp -d)
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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9 export tmp="/tmp/openms-stuff"
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11 export CTDCONVERTER="$tmp/CTDConverter"
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12 ###############################################################################
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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13 ## reset old data
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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14 ###############################################################################
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 # rm $(ls *xml |grep -v macros)
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16 # rm -rf ctd
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17 # mkdir -p ctd
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18 # echo "" > prepare_test_data.sh
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dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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20 ###############################################################################
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 ## generate tests
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22 ## also creates
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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23 ## - conda environment (for executing the binaries) and
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24 ## - the git clone of OpenMS (for generating the tests)
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25 ## - ctd files
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26 ###############################################################################
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27 # bash ./test-data.sh ./macros_autotest.xml
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dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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29 ###############################################################################
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30 ## get the
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 ## - conda package (for easy access and listing of the OpenMS binaries),
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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32 ###############################################################################
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33 # if [ ! -d $OPENMSPKG ]; then
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34 # mkdir $OPENMSPKG/
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35 # wget -P $OPENMSPKG/ "$CONDAPKG"
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36 # tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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37 # rm $OPENMSPKG/"$(basename $CONDAPKG)"
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38 # fi
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dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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40 ###############################################################################
dd366d7a206e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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41 ## Get python libaries for CTD -> Galaxy conversion
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42 ## TODO fix to main repo OR conda packkage if PRs are merged
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43 ###############################################################################
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44 # if [ ! -d CTDopts ]; then
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45 # # git clone https://github.com/genericworkflownodes/CTDopts CTDopts
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46 # git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts
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47 # fi
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48 if [ ! -d $CTDCONVERTER ]; then
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49 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
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50 git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
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51 fi
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52 # export PYTHONPATH=$(pwd)/CTDopts
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53 ###############################################################################
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54 ## conversion ctd->xml
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55 ###############################################################################
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ae60d589fc0f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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57 find . -maxdepth 0 -name "[A-Z]*xml" -delete
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58 source $(dirname $(which conda))/../etc/profile.d/conda.sh
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59 conda activate $tmp/OpenMS$VERSION-env
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60 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 $PROFILE --bump-file bump.json > convert.out 2> convert.err
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61 if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
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62 conda deactivate
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64 patch PepNovoAdapter.xml < PepNovoAdapter.patch
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65 patch OMSSAAdapter.xml < OMSSAAdapter.patch
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66 # this should not be necessary from 2.7 https://github.com/OpenMS/OpenMS/pull/5087
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67 patch PSMFeatureExtractor.xml < PSMFeatureExtractor.patch
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ae60d589fc0f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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69 # https://github.com/OpenMS/OpenMS/pull/4984
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70 sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
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71 # https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976
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72 patch -p0 <404-urls.patch
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74 # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool
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75
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76 # for i in A-E F-H I-L M-N O-P Q-Z
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77 # do
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78 # planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json &
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79 # done