Mercurial > repos > pjbriggs > trimmomatic
annotate trimmomatic.sh @ 0:3358c3d30143 draft
Uploaded initial version.
| author | pjbriggs |
|---|---|
| date | Mon, 01 Dec 2014 10:40:07 -0500 |
| parents | |
| children |
| rev | line source |
|---|---|
| 0 | 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 # |