annotate test-data.sh @ 13:31bc4129f589 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:32:01 +0000
parents f918cb7aefd5
children
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1 #!/usr/bin/env bash
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2
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3 VERSION=2.6
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4 FILETYPES="filetypes.txt"
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5 CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2"
11
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7 # import the magic
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8 . ./generate-foo.sh
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10 # install conda
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11 if [ -z "$tmp" ]; then
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 tmp=$(mktemp -d)
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13 created="yes"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 export OPENMSGIT="$tmp/OpenMS$VERSION.0-git"
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17 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"
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18 export OPENMSENV="$tmp/OpenMS$VERSION-env"
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19 export CTDCONVERTER="$tmp/CTDConverter"
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f918cb7aefd5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
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21 if [[ -z "$1" ]]; then
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22 autotests="/dev/null"
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23 else
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24 autotests="$1"
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25 fi
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65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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27 if type conda > /dev/null; then
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 true
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 else
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30 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
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32 source "$tmp/miniconda/bin/activate"
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 eval "$(conda shell.bash hook)"
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65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 ###############################################################################
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38 ## get
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39 ## - conda environment (for executing the binaries) and
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 ## - the git clone of OpenMS (for generating the tests)
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41 ###############################################################################
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42
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 echo "Clone OpenMS $VERSION sources"
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44 if [[ ! -d $OPENMSGIT ]]; then
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 cd $OPENMSGIT
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 git submodule init
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48 git submodule update
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 cd -
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50 else
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51 cd $OPENMSGIT
13
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52 git pull origin release/$VERSION.0
11
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53 cd -
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54 fi
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55
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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56 echo "Create OpenMS $VERSION conda env"
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57 # TODO currently add lxml (needed by CTDConverter)
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58 # TODO for some reason a to recent openjdk is used
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59 if conda env list | grep "$OPENMSENV"; then
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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60 true
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61 else
13
31bc4129f589 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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62 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml
11
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63 # chmod -R u-w $OPENMSENV
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64 fi
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65 ###############################################################################
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66 ## get the
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67 ## - conda package (for easy access and listing of the OpenMS binaries),
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68 ###############################################################################
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69 echo "Download OpenMS $VERSION package $CONDAPKG"
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70
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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71 if [[ ! -d $OPENMSPKG ]]; then
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72 mkdir $OPENMSPKG
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73 wget -q -P $OPENMSPKG/ "$CONDAPKG"
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74 tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
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75 rm $OPENMSPKG/"$(basename $CONDAPKG)"
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76 fi
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77
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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78 ###############################################################################
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79 ## Get python libaries for CTD -> Galaxy conversion
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80 ## TODO fix to main repo OR conda packkage if PRs are merged
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81 ###############################################################################
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82 echo "Clone CTDConverter"
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83 if [[ ! -d $CTDCONVERTER ]]; then
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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84 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
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85 git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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86 else
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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87 cd $CTDCONVERTER
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88 git pull origin topic/cdata
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89 cd -
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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90 fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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91
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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92 ###############################################################################
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93 ## copy all the test data files to test-data
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94 ## most of it (outputs) will be overwritten later, but its needed for
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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95 ## prepare_test_data
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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96 ###############################################################################
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97 echo "Get test data"
12
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98 find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete
f918cb7aefd5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
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99
11
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100 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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101 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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102 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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103 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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104 if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then
13
31bc4129f589 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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105 wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
31bc4129f589 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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106 mv MetaboliteSpectralDB.mzML test-data/
11
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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107 fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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108 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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109 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
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110
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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111 if [ ! -d test-data/pepnovo_models/ ]; then
13
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112 mkdir -p /tmp/pepnovo
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113 wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
31bc4129f589 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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114 unzip PepNovo.20120423.zip -d /tmp/pepnovo/
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115 mv /tmp/pepnovo/Models test-data/pepnovo_models/
31bc4129f589 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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116 rm PepNovo.20120423.zip
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117 rm -rf /tmp/pepnovo
11
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118 fi
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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119 ###############################################################################
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120 ## generate ctd files using the binaries in the conda package
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121 ###############################################################################
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122 echo "Create CTD files"
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123 conda activate $OPENMSENV
13
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124 rm -rf ctd
11
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125 mkdir -p ctd
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126
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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127 # TODO because of https://github.com/OpenMS/OpenMS/issues/4641
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128 # this needs to be done from within test-data
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129 cd test-data
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130 for i in $OPENMSPKG/bin/*
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131 do
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132 b=$(basename $i)
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133 echo $b
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134 $b -write_ctd ../ctd/
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135 sed -i -e 's/²/^2/' ../ctd/$b.ctd
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136 done
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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137 cd -
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138 ###############################################################################
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139 ## fix ini files: OpenMS test data contains ini files with outdated ini files.
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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140 ## e.g. variables might be in different nodes, outdated variables present, new
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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141 ## variables missing, ...
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142 ## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests)
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143 ## but it is for the generation of the tests
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144 ## see https://github.com/OpenMS/OpenMS/issues/4462
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145 ###############################################################################
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146 echo "Update test INI files"
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147 for ini in test-data/*ini
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148 do
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149 tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
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150 bin=$(which $tool)
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151 if [[ -z $bin ]]; then
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152 >&2 echo "missing binary to convert $ini"
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153 continue
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154 fi
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155 cp $ini $ini.backup
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156 $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
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157 if [[ "$?" -ne "0" ]]; then
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158 >&2 echo "could not convert $ini"
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159 fi
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160 done
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161
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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162 ###############################################################################
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163 ## create script to create results for the tests and run it
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164 ###############################################################################
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165 echo "Create test shell script"
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166
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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167 echo -n "" > prepare_test_data.sh
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168 echo 'export COMET_BINARY="comet"' >> prepare_test_data.sh
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169 echo 'export CRUX_BINARY="crux"' >> prepare_test_data.sh
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170 echo 'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"' >> prepare_test_data.sh
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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171 echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh
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172 echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh
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173
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174 echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh
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175 echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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176 echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh
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177 echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh
65be0674bb70 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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178 echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh
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179 echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh
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180 echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh
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181 echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh
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182 echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh
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183 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
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184 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
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185
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186 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh
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187
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188 # prepare_test_data > tmp_test_data.sh
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189 # # remove calls not needed for the tools listed in any .list file
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190 # echo LIST $LIST
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191 # if [ ! -z "$LIST" ]; then
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192 # REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
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193 # else
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194 # REX=".*"
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195 # fi
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196 # echo REX $REX
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197 # cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
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198 # rm tmp_test_data.sh
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199
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200 echo "Execute test shell script"
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201 chmod u+x prepare_test_data.sh
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202 cd ./test-data || exit
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203 ../prepare_test_data.sh
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204 cd - || exit
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205
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206
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207 ###############################################################################
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208 ## create/update test data for the manually generated tests
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209 ## - run convert once with the manual tests only and
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210 ## - update test-data (needs to run 2x)
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211 ###############################################################################
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212 echo "Execute test shell script for manually curated tests"
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213 chmod u+x prepare_test_data_manual.sh
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214
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215 cd ./test-data || exit
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216 ../prepare_test_data_manual.sh
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217 cd - || exit
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218
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219
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220 ###############################################################################
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221 ## auto generate tests
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222 ###############################################################################
12
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223 echo "Write test macros to $autotests"
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224 echo "<macros>" > "$autotests"
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225 for i in $(ls *xml |grep -v macros)
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226 do
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227 b=$(basename "$i" .xml)
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228 get_tests2 "$b" >> "$autotests"
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229 done
12
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230 echo "</macros>" >> "$autotests"
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231
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232 echo "Create test data links"
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233 link_tmp_files
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234
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235 # tests for tools using output_prefix parameters can not be auto generated
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236 # hence we output the tests for manual curation in macros_test.xml
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237 # and remove them from the autotests
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238 # -> OpenSwathFileSplitter IDRipper MzMLSplitter
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239 #
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240 # Furthermore we remove tests for tools without binaries in conda
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241 # -> MSFragger MaRaClusterAdapter NovorAdapter
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242 #
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243 # not able to specify composite test data
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244 # -> SpectraSTSearchAdapter
11
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245 if [[ ! -z "$1" ]]; then
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246 echo "" > macros_discarded_auto.xml
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247 for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
11
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248 do
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249 echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml
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250 xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml
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251 echo "</xml>" >> macros_discarded_auto.xml
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252 xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
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253 mv tmp macros_autotest.xml
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254 done
12
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255 >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
11
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256 fi
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257 conda deactivate
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258
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259 ## remove broken symlinks in test-data
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260 find test-data/ -xtype l -delete
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261
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262 # if [ ! -z "$created" ]; then
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263 # echo "Removing temporary directory"
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264 # rm -rf "$tmp"
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265 # fi