Mercurial > repos > pjbriggs > trimmomatic
comparison run_planemo_tests.sh @ 3:f8a9a5eaca8a draft
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
author | pjbriggs |
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date | Wed, 23 Sep 2015 08:59:23 -0400 |
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2:a60283899c6d | 3:f8a9a5eaca8a |
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1 #!/bin/bash | |
2 # | |
3 # Install dependencies and set up environment for | |
4 # trimmomatic 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="trimmomatic/0.32" | |
17 # Where to find them | |
18 TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.trimmomatic | |
19 if [ ! -d $TOOL_DEPENDENCIES_DIR ] ; then | |
20 echo WARNING $TOOL_DEPENDENCIES_DIR not found >&2 | |
21 echo Creating tool dependencies dir | |
22 mkdir -p $TOOL_DEPENDENCIES_DIR | |
23 echo Installing tool dependencies | |
24 $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR | |
25 fi | |
26 # Load dependencies | |
27 for dep in $TOOL_DEPENDENCIES ; do | |
28 env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh | |
29 if [ -e $env_file ] ; then | |
30 . $env_file | |
31 else | |
32 echo ERROR no env.sh file found for $dep >&2 | |
33 exit 1 | |
34 fi | |
35 done | |
36 # Run the planemo tests | |
37 planemo test $@ $(dirname $0)/trimmomatic.xml | |
38 ## | |
39 # |