Mercurial > repos > sanbi-uwc > trimmomatic
diff trimmomatic_BASE_16831.sh @ 4:642a39a927c9 draft
planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
| author | sanbi-uwc |
|---|---|
| date | Mon, 23 Jan 2017 07:46:47 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trimmomatic_BASE_16831.sh Mon Jan 23 07:46:47 2017 -0500 @@ -0,0 +1,18 @@ +#!/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 +## +#