Mercurial > repos > pjbriggs > rnachipintegrator
annotate run_planemo_tests.sh @ 0:0abe6bac47a6 draft
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
| author | pjbriggs |
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| date | Wed, 24 Feb 2016 09:25:18 -0500 |
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| rev | line source |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
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1 #!/bin/bash |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
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2 # |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
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3 # Install dependencies and set up environment for |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
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4 # rnachipintegrator tool, then run tests using planemo |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
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changeset
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5 # |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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6 # Note that any arguments supplied to the script are |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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7 # passed directly to the "planemo test..." invocation |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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8 # |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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9 # e.g. --install_galaxy (to get planemo to create a |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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10 # Galaxy instance to run tests) |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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11 # |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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12 # --galaxy_root DIR (to run tests using existing |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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13 # Galaxy instance) |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
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14 # |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
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changeset
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15 # List of dependencies |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
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16 TOOL_DEPENDENCIES="rnachipintegrator/1.0.0 |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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17 xlsxwriter/0.8.4" |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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18 # Where to find them |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
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19 TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.rnachipintegrator |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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20 if [ ! -d $TOOL_DEPENDENCIES_DIR ] ; then |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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21 echo WARNING $TOOL_DEPENDENCIES_DIR not found >&2 |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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22 echo Creating tool dependencies dir |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
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23 mkdir -p $TOOL_DEPENDENCIES_DIR |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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24 echo Installing tool dependencies |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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25 $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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26 fi |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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27 # Load dependencies |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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28 for dep in $TOOL_DEPENDENCIES ; do |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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29 env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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30 if [ -e $env_file ] ; then |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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31 . $env_file |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
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32 else |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
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33 echo ERROR no env.sh file found for $dep >&2 |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
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34 exit 1 |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
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35 fi |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
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36 done |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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37 # Run the planemo tests |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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38 planemo test $@ \ |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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39 $(dirname $0)/rnachipintegrator_wrapper.xml \ |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
changeset
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40 $(dirname $0)/rnachipintegrator_canonical_genes.xml \ |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
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41 $(dirname $0)/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
diff
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42 ## |
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0abe6bac47a6
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
pjbriggs
parents:
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43 # |