Mercurial > repos > galaxyp > openms_consensusid

comparison test-data.sh @ 17:abffdfee3021 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author galaxyp
date Mon, 22 Feb 2021 10:46:10 +0000
parents feebe2054e40
children f4be248c3d47
comparison
equal deleted inserted replaced
16:01dbaf6a57e0 17:abffdfee3021
13 created="yes" 13 created="yes"
14 fi 14 fi
15 15
16 export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" 16 export OPENMSGIT="$tmp/OpenMS$VERSION.0-git"
17 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" 17 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"
18 export OPENMSENV="$tmp/OpenMS$VERSION-env" 18 export OPENMSENV="OpenMS$VERSION-env"
19 export CTDCONVERTER="$tmp/CTDConverter" 19
20 if [ -z "$CTDCONVERTER" ]; then
21 export CTDCONVERTER="$tmp/CTDConverter"
22 fi
20 23
21 if [[ -z "$1" ]]; then 24 if [[ -z "$1" ]]; then
22 autotests="/dev/null" 25 autotests="/dev/null"
23 else 26 else
24 autotests="$1" 27 autotests="$1"
57 # TODO currently add lxml (needed by CTDConverter) 60 # TODO currently add lxml (needed by CTDConverter)
58 # TODO for some reason a to recent openjdk is used 61 # TODO for some reason a to recent openjdk is used
59 if conda env list | grep "$OPENMSENV"; then 62 if conda env list | grep "$OPENMSENV"; then
60 true 63 true
61 else 64 else
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 65 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml
63 # chmod -R u-w $OPENMSENV 66 # chmod -R u-w $OPENMSENV
64 fi 67 fi
65 ############################################################################### 68 ###############################################################################
66 ## get the 69 ## get the
67 ## - conda package (for easy access and listing of the OpenMS binaries), 70 ## - conda package (for easy access and listing of the OpenMS binaries),
80 ## TODO fix to main repo OR conda packkage if PRs are merged 83 ## TODO fix to main repo OR conda packkage if PRs are merged
81 ############################################################################### 84 ###############################################################################
82 echo "Clone CTDConverter" 85 echo "Clone CTDConverter"
83 if [[ ! -d $CTDCONVERTER ]]; then 86 if [[ ! -d $CTDCONVERTER ]]; then
84 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter 87 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
85 git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER 88 git clone -b topic/fix-selects https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
86 else 89 else
87 cd $CTDCONVERTER 90 cd $CTDCONVERTER
88 git pull origin topic/cdata 91 git pull origin topic/fix-selects
89 cd - 92 cd -
90 fi 93 fi
91 94
92 ############################################################################### 95 ###############################################################################
93 ## copy all the test data files to test-data 96 ## copy all the test data files to test-data
183 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh 186 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
184 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh 187 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
185 188
186 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh 189 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh
187 190
188 # prepare_test_data > tmp_test_data.sh 191 ## prepare_test_data > tmp_test_data.sh
189 # # remove calls not needed for the tools listed in any .list file 192 ## # remove calls not needed for the tools listed in any .list file
190 # echo LIST $LIST 193 ## echo LIST $LIST
191 # if [ ! -z "$LIST" ]; then 194 ## if [ ! -z "$LIST" ]; then
192 # REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') 195 ## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
193 # else 196 ## else
194 # REX=".*" 197 ## REX=".*"
195 # fi 198 ## fi
196 # echo REX $REX 199 ## echo REX $REX
197 # cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh 200 ## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
198 # rm tmp_test_data.sh 201 ## rm tmp_test_data.sh
199 202
200 echo "Execute test shell script" 203 echo "Execute test shell script"
201 chmod u+x prepare_test_data.sh 204 chmod u+x prepare_test_data.sh
202 cd ./test-data || exit 205 cd ./test-data || exit
203 ../prepare_test_data.sh 206 ../prepare_test_data.sh