Mercurial > repos > pjbriggs > trimmomatic
view trimmomatic.sh @ 4:14d05f2d511d draft
Version that supports Trimmomatic 0.36.
author | pjbriggs |
---|---|
date | Thu, 14 Jul 2016 09:17:38 -0400 |
parents | 3358c3d30143 |
children |
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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 ## #