view run_planemo_tests.sh @ 3:f8a9a5eaca8a draft

Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)

#!/bin/bash
#
# Install dependencies and set up environment for
# trimmomatic 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="trimmomatic/0.32"
# Where to find them
TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.trimmomatic
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)/trimmomatic.xml
##
#