Mercurial > repos > pjbriggs > rnachipintegrator

comparison run_planemo_tests.sh @ 0:0abe6bac47a6 draft

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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
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-1:000000000000 0:0abe6bac47a6
1 #!/bin/bash
2 #
3 # Install dependencies and set up environment for
4 # rnachipintegrator tool, then run tests using planemo
5 #
6 # Note that any arguments supplied to the script are
7 # passed directly to the "planemo test..." invocation
8 #
9 # e.g. --install_galaxy (to get planemo to create a
10 # Galaxy instance to run tests)
11 #
12 # --galaxy_root DIR (to run tests using existing
13 # Galaxy instance)
14 #
15 # List of dependencies
16 TOOL_DEPENDENCIES="rnachipintegrator/1.0.0
17 xlsxwriter/0.8.4"
18 # Where to find them
19 TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.rnachipintegrator
20 if [ ! -d $TOOL_DEPENDENCIES_DIR ] ; then
21 echo WARNING $TOOL_DEPENDENCIES_DIR not found >&2
22 echo Creating tool dependencies dir
23 mkdir -p $TOOL_DEPENDENCIES_DIR
24 echo Installing tool dependencies
25 $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR
26 fi
27 # Load dependencies
28 for dep in $TOOL_DEPENDENCIES ; do
29 env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh
30 if [ -e $env_file ] ; then
31 . $env_file
32 else
33 echo ERROR no env.sh file found for $dep >&2
34 exit 1
35 fi
36 done
37 # Run the planemo tests
38 planemo test $@ \
39 $(dirname $0)/rnachipintegrator_wrapper.xml \
40 $(dirname $0)/rnachipintegrator_canonical_genes.xml \
41 $(dirname $0)/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml
42 ##
43 #