view trimmomatic.sh @ 0:3358c3d30143 draft

Uploaded initial version.
author pjbriggs
date Mon, 01 Dec 2014 10:40:07 -0500
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#!/bin/sh
#
# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
echo Arguments:
for i in $@ ; do
    echo "*" $i
done
java $@ 2>&1 | tee trimmomatic.log
status=$?
echo "Exit status: $status"
# Check for successful completion
if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
    echo "Trimmomatic did not finish successfully" >&2
    exit 1
fi
exit $status
##
#