Mercurial > repos > galaxyp > openms_tofcalibration

annotate test-data.sh @ 9:40a101cabd0e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:59:26 +0000
parents
children 58bdbab5cc5e
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9
40a101cabd0e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 #!/usr/bin/env bash
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2
40a101cabd0e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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3 VERSION=2.5
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4 FILETYPES="filetypes.txt"
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5 CONDAPKG="https://anaconda.org/bioconda/openms/2.5.0/download/linux-64/openms-2.5.0-h463af6b_1.tar.bz2"
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6
40a101cabd0e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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7 # import the magic
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8 . ./generate-foo.sh
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9
40a101cabd0e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 # install conda
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11 if [ -z "$tmp" ]; then
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12 tmp=$(mktemp -d)
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13 created="yes"
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14 fi
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40a101cabd0e "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="$tmp/CTDConverter"
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21
40a101cabd0e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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22 if type conda > /dev/null; then
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23 true
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24 else
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25 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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26 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
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27 source "$tmp/miniconda/bin/activate"
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28 fi
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29 eval "$(conda shell.bash hook)"
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30
40a101cabd0e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 if [[ -z "$1" ]]; then
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32 autotests="/dev/null"
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33 else
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34 autotests="$1"
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35 fi
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36
40a101cabd0e "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
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40 ## - the git clone of OpenMS (for generating the tests)
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41 ###############################################################################
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42
40a101cabd0e "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 $OPENMSGIT ]]; then
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45 git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
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46 cd $OPENMSGIT
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47 git submodule init
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48 git submodule update
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49 cd -
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50 else
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51 cd $OPENMSGIT
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52 git pull origin release/$VERSION.0
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53 cd -
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54 fi
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55
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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
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60 true
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61 else
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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 openjdk=8.0.192 ctdopts=1.4 lxml
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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
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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
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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
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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
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86 else
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87 cd $CTDCONVERTER
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88 git pull origin topic/cdata
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89 cd -
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90 fi
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91 export PYTHONPATH=$(pwd)/CTDopts
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92
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93 ###############################################################################
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94 ## copy all the test data files to test-data
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95 ## most of it (outputs) will be overwritten later, but its needed for
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96 ## prepare_test_data
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97 ###############################################################################
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98 echo "Get test data"
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99 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
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100 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
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101 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
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102 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
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103 if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then
40a101cabd0e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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104 wget -q https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML && mv MetaboliteSpectralDB.mzML test-data/
40a101cabd0e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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105 fi
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106 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
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107 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
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108
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109 if [ ! -d test-data/pepnovo_models/ ]; then
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110 wget http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
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111 unzip -e PepNovo.20120423.zip -d /tmp/
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112 mv /tmp/Models test-data/pepnovo_models/
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113 fi
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114 ###############################################################################
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115 ## generate ctd files using the binaries in the conda package
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116 ###############################################################################
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117 echo "Create CTD files"
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118 conda activate $OPENMSENV
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119 mkdir -p ctd
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120
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121 # TODO because of https://github.com/OpenMS/OpenMS/issues/4641
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122 # this needs to be done from within test-data
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123 cd test-data
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124 for i in $OPENMSPKG/bin/*
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125 do
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126 b=$(basename $i)
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127 echo $b
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128 $b -write_ctd ../ctd/
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129 sed -i -e 's/²/^2/' ../ctd/$b.ctd
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130 done
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131 cd -
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132 ###############################################################################
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133 ## fix ini files: OpenMS test data contains ini files with outdated ini files.
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134 ## e.g. variables might be in different nodes, outdated variables present, new
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135 ## variables missing, ...
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136 ## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests)
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137 ## but it is for the generation of the tests
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138 ## see https://github.com/OpenMS/OpenMS/issues/4462
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139 ###############################################################################
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140 echo "Update test INI files"
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141 for ini in test-data/*ini
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142 do
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143 tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
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144 bin=$(which $tool)
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145 if [[ -z $bin ]]; then
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146 >&2 echo "missing binary to convert $ini"
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147 continue
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148 fi
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149 cp $ini $ini.backup
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150 $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
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151 if [[ "$?" -ne "0" ]]; then
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152 >&2 echo "could not convert $ini"
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153 fi
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154 done
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155
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156 ###############################################################################
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157 ## create script to create results for the tests and run it
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158 ###############################################################################
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159 echo "Create test shell script"
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160
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161 echo -n "" > prepare_test_data.sh
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162 echo 'export COMET_BINARY="comet"' >> prepare_test_data.sh
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163 echo 'export CRUX_BINARY="crux"' >> prepare_test_data.sh
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164 echo 'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"' >> prepare_test_data.sh
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165 echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh
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166 echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh
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167
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168 echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh
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169 echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh
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170 echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh
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171 echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh
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172 echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh
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173 echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh
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174 echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh
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175 echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh
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176 echo 'export SPECTRAST_BINARY="spectrast"' >> prepare_test_data.sh
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177 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
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178 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
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179
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180 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh
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181
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182 # prepare_test_data > tmp_test_data.sh
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183 # # remove calls not needed for the tools listed in any .list file
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184 # echo LIST $LIST
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185 # if [ ! -z "$LIST" ]; then
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186 # REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
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187 # else
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188 # REX=".*"
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189 # fi
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190 # echo REX $REX
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191 # cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
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192 # rm tmp_test_data.sh
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193
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194 echo "Execute test shell script"
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195 chmod u+x prepare_test_data.sh
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196 cd ./test-data || exit
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197 ../prepare_test_data.sh
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198 cd - || exit
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199
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200
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201 ###############################################################################
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202 ## create/update test data for the manually generated tests
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203 ## - run convert once with the manual tests only and
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204 ## - update test-data (needs to run 2x)
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205 ###############################################################################
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206 echo "Execute test shell script for manually curated tests"
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207 chmod u+x prepare_test_data_manual.sh
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208
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209 cd ./test-data || exit
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210 ../prepare_test_data_manual.sh
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211 cd - || exit
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212
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213
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214 # # # exit
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215
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216 ###############################################################################
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217 ## auto generate tests
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218 ###############################################################################
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219
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220 echo "Write test macros to "$autotests
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221 echo "<macros>" > $autotests
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222 for i in $(ls *xml |grep -v macros)
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223 do
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224 b=$(basename "$i" .xml)
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225 get_tests2 "$b" >> $autotests
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226 done
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227 echo "</macros>" >> $autotests
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228
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229 echo "Create test data links"
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230 link_tmp_files
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231
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232 # tests for tools using output_prefix parameters can not be auto generated
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233 # hence we output the tests for manual curation in macros_test.xml
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234 # and remove them from the autotests
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235 if [[ ! -z "$1" ]]; then
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236 echo "" > macros_discarded_auto.xml
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237 for i in OpenSwathFileSplitter IDRipper MzMLSplitter
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238 do
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239 echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml
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240 xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml
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241 echo "</xml>" >> macros_discarded_auto.xml
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242 xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
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243 mv tmp macros_autotest.xml
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244 done
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245 >&2 "discarded autogenerated macros for curation in macros_discarded_auto.xml"
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246 fi
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247 conda deactivate
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248
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249 ## remove broken symlinks in test-data
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250 find test-data/ -xtype l -delete
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251
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252 # if [ ! -z "$created" ]; then
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253 # echo "Removing temporary directory"
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254 # rm -rf "$tmp"
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255 # fi