Mercurial > repos > galaxyp > openms_idrtcalibration

annotate test-data.sh @ 14:7ff821b34ebc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:25:24 +0000
parents 28805cf9b024
children f7226e34dc70
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1 #!/usr/bin/env bash
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3 VERSION=2.8
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4 FILETYPES="aux/filetypes.txt"
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5 CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2"
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8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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7 # import the magic
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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8 . ./generate-foo.sh
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10 # install conda
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11 if [ -z "$tmp" ]; then
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12 tmp=$(mktemp -d)
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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13 created="yes"
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14 fi
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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8bd1fe67a9b1 "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"
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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17 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"
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18 export OPENMSENV="OpenMS$VERSION-env"
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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20 if [ -z "$CTDCONVERTER" ]; then
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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21 export CTDCONVERTER="$tmp/CTDConverter"
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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22 fi
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24 if [[ -z "$1" ]]; then
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25 autotests="/dev/null"
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26 else
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27 autotests="$1"
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28 fi
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8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 if type conda > /dev/null; then
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31 true
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32 else
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33 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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34 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
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35 source "$tmp/miniconda/bin/activate"
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36 fi
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37 eval "$(conda shell.bash hook)"
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8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 ###############################################################################
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41 ## get
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42 ## - conda environment (for executing the binaries) and
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 ## - the git clone of OpenMS (for generating the tests)
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 ###############################################################################
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46 echo "Clone OpenMS $VERSION sources"
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47 if [[ ! -d $OPENMSGIT ]]; then
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48 # TODO >2.8 reenable original release branch .. also in else branch
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49 # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917
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50 # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
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51 git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT
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52 cd $OPENMSGIT
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53 git submodule init
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54 git submodule update
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55 cd -
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56 else
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57 cd $OPENMSGIT
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58 git pull origin release/$VERSION.0-plus
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59 cd -
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60 fi
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62 echo "Create OpenMS $VERSION conda env"
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63 # TODO currently add lxml (needed by CTDConverter)
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64 # TODO for some reason a to recent openjdk is used
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65 if conda env list | grep "$OPENMSENV"; then
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66 true
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67 else
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68 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml
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69 # chmod -R u-w $OPENMSENV
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70 fi
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71 ###############################################################################
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72 ## get the
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73 ## - conda package (for easy access and listing of the OpenMS binaries),
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74 ###############################################################################
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75 echo "Download OpenMS $VERSION package $CONDAPKG"
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77 if [[ ! -d $OPENMSPKG ]]; then
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78 mkdir $OPENMSPKG
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79 wget -q -P $OPENMSPKG/ "$CONDAPKG"
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80 tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
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81 rm $OPENMSPKG/"$(basename $CONDAPKG)"
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82 fi
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84 ###############################################################################
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85 ## Get python libaries for CTD -> Galaxy conversion
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86 ## TODO fix to main repo OR conda packkage if PRs are merged
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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87 ###############################################################################
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88 echo "Clone CTDConverter"
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89 if [[ ! -d $CTDCONVERTER ]]; then
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90 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
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91 git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
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92 else
14
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93 cd $CTDCONVERTER
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94 git pull origin topic/fix-selects2
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95 cd -
10
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96 fi
14
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97 conda activate $OPENMSENV
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98 cd $CTDCONVERTER
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99 python -m pip install . --no-deps
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100 cd -
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101 conda deactivate
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102
14
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103
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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104 # ###############################################################################
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105 # ## copy all the test data files to test-data
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106 # ## most of it (outputs) will be overwritten later, but its needed for
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107 # ## prepare_test_data
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108 # ###############################################################################
10
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109 echo "Get test data"
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110 find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete
11
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111
10
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112 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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113 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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114 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
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115 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
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116 if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then
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117 wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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118 mv MetaboliteSpectralDB.mzML test-data/
10
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119 fi
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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120 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
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121 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
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122
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123 if [ ! -d test-data/pepnovo_models/ ]; then
14
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124 mkdir -p /tmp/pepnovo
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125 wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
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126 unzip PepNovo.20120423.zip -d /tmp/pepnovo/
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127 mv /tmp/pepnovo/Models test-data/pepnovo_models/
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128 rm PepNovo.20120423.zip
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129 rm -rf /tmp/pepnovo
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130 fi
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131 ###############################################################################
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132 ## generate ctd files using the binaries in the conda package
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133 ###############################################################################
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134 echo "Create CTD files"
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135 conda activate $OPENMSENV
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136 rm -rf ctd
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137 mkdir -p ctd
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138
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139 for i in $OPENMSPKG/bin/*
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140 do
14
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141 b=$(basename $i)
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142 echo $b
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143 $b -write_ctd ctd/
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144 sed -i -e 's/²/^2/' ctd/$b.ctd
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145 done
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146 ###############################################################################
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147 ## fix ini files: OpenMS test data contains ini files with outdated ini files.
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148 ## e.g. variables might be in different nodes, outdated variables present, new
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149 ## variables missing, ...
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150 ## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests)
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151 ## but it is for the generation of the tests
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152 ## see https://github.com/OpenMS/OpenMS/issues/4462
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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153 ###############################################################################
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154 echo "Update test INI files"
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155 for ini in test-data/*ini
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156 do
14
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157 tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
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158 bin=$(which $tool)
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159 if [[ -z $bin ]]; then
10
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160 >&2 echo "missing binary to convert $ini"
14
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161 continue
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162 fi
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163 cp $ini $ini.backup
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164 $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
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165 if [[ "$?" -ne "0" ]]; then
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166 >&2 echo "could not convert $ini"
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167 fi
10
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168 done
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169
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170 ###############################################################################
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171 ## create script to create results for the tests and run it
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172 ###############################################################################
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173 echo "Create test shell script"
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174
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175 echo -n "" > prepare_test_data.sh
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176 echo 'export COMET_BINARY="comet"' >> prepare_test_data.sh
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177 echo 'export CRUX_BINARY="crux"' >> prepare_test_data.sh
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178 echo 'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"' >> prepare_test_data.sh
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179 echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh
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180 echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh
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181
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182 echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh
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183 echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh
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184 echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh
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185 echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh
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186 echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh
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187 echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh
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188 echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh
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189 echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh
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190 echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh
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191 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
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192 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
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193
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194 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh
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195
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196 ## prepare_test_data > tmp_test_data.sh
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197 ## # remove calls not needed for the tools listed in any .list file
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198 ## echo LIST $LIST
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199 ## if [ ! -z "$LIST" ]; then
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200 ## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
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201 ## else
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202 ## REX=".*"
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203 ## fi
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204 ## echo REX $REX
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205 ## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
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206 ## rm tmp_test_data.sh
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207
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208 echo "Execute test shell script"
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209 chmod u+x prepare_test_data.sh
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210 cd ./test-data || exit
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211 ../prepare_test_data.sh
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212 cd - || exit
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213
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214
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215 # ###############################################################################
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216 # ## create/update test data for the manually generated tests
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217 # ## - run convert once with the manual tests only and
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218 # ## - update test-data (needs to run 2x)
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219 # ###############################################################################
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220 echo "Execute test shell script for manually curated tests"
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221 chmod u+x prepare_test_data_manual.sh
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222 cd ./test-data || exit
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223 ../prepare_test_data_manual.sh
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224 cd - || exit
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225
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226
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227 ###############################################################################
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228 ## auto generate tests
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229 ###############################################################################
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230
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231 echo "Write test macros to $autotests"
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232 echo "<macros>" > "$autotests"
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233
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234 for i in $(ls ctd/*ctd)
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235 do
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236 b=$(basename "$i" .ctd)
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237 get_tests2 "$b" >> "$autotests"
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238 done
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239 echo "</macros>" >> "$autotests"
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240
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241 # echo "Create test data links"
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242 # Breaks DecoyDatabase
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243 # link_tmp_files
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244
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245 # tests for tools using output_prefix parameters can not be auto generated
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246 # hence we output the tests for manual curation in macros_test.xml
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247 # and remove them from the autotests
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248 # -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator
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249 # TODO reevaluate in >2.8
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250 # - https://github.com/OpenMS/OpenMS/pull/5873
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251 # - https://github.com/OpenMS/OpenMS/pull/5912
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252 #
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253 # Furthermore we remove tests for tools without binaries in conda
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254 # -> MSFragger MaRaClusterAdapter NovorAdapter
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255 #
4215810bb49d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
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256 # not able to specify composite test data
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257 # -> SpectraSTSearchAdapter
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8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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258 if [[ ! -z "$1" ]]; then
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259 echo "" > macros_discarded_auto.xml
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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260 for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
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261 do
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262 echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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263 xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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264 echo "</xml>" >> macros_discarded_auto.xml
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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265 xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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266 mv tmp macros_autotest.xml
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267 done
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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268 >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
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8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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269 fi
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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270 conda deactivate
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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271
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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272 ## remove broken symlinks in test-data
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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273 find test-data/ -xtype l -delete
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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274
14
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275 if [ ! -z "$created" ]; then
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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276 echo "Removing temporary directory"
7ff821b34ebc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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277 rm -rf "$tmp"
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278 fi