Mercurial > repos > galaxyp > openms_consensusid
comparison test-data.sh @ 17:abffdfee3021 draft
"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 |