Mercurial > repos > pjbriggs > rnachipintegrator
diff 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 |
|---|---|
| date | Wed, 24 Feb 2016 09:25:18 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_planemo_tests.sh Wed Feb 24 09:25:18 2016 -0500 @@ -0,0 +1,43 @@ +#!/bin/bash +# +# Install dependencies and set up environment for +# rnachipintegrator tool, then run tests using planemo +# +# Note that any arguments supplied to the script are +# passed directly to the "planemo test..." invocation +# +# e.g. --install_galaxy (to get planemo to create a +# Galaxy instance to run tests) +# +# --galaxy_root DIR (to run tests using existing +# Galaxy instance) +# +# List of dependencies +TOOL_DEPENDENCIES="rnachipintegrator/1.0.0 + xlsxwriter/0.8.4" +# Where to find them +TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.rnachipintegrator +if [ ! -d $TOOL_DEPENDENCIES_DIR ] ; then + echo WARNING $TOOL_DEPENDENCIES_DIR not found >&2 + echo Creating tool dependencies dir + mkdir -p $TOOL_DEPENDENCIES_DIR + echo Installing tool dependencies + $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR +fi +# Load dependencies +for dep in $TOOL_DEPENDENCIES ; do + env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh + if [ -e $env_file ] ; then + . $env_file + else + echo ERROR no env.sh file found for $dep >&2 + exit 1 + fi +done +# Run the planemo tests +planemo test $@ \ + $(dirname $0)/rnachipintegrator_wrapper.xml \ + $(dirname $0)/rnachipintegrator_canonical_genes.xml \ + $(dirname $0)/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml +## +#