Mercurial > repos > pjbriggs > trimmomatic

comparison trimmomatic.sh @ 0:3358c3d30143 draft

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Uploaded initial version.
author pjbriggs
date Mon, 01 Dec 2014 10:40:07 -0500
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1 #!/bin/sh
2 #
3 # Shell wrapper to run Trimmomatic jar file as a Galaxy tool
4 echo Arguments:
5 for i in $@ ; do
6 echo "*" $i
7 done
8 java $@ 2>&1 | tee trimmomatic.log
9 status=$?
10 echo "Exit status: $status"
11 # Check for successful completion
12 if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then
13 echo "Trimmomatic did not finish successfully" >&2
14 exit 1
15 fi
16 exit $status
17 ##
18 #