Mercurial > repos > biomonika > linkyx
annotate sort_bam.sh @ 7:90098d9cb691 default tip
workflows updated
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Fri, 20 Feb 2015 18:34:34 -0500 |
| parents | 0d8315be76b7 |
| children |
| rev | line source |
|---|---|
| 2 | 1 #!/bin/bash |
| 2 results=$1; | |
| 3 bam_file=$2; | |
| 4 | |
| 5 hash samtools 2>/dev/null || { echo "I require samtools in path but it's not installed. Aborting."; exit 1; } | |
| 6 echo "LINKYX_PATH:" $LINKYX_PATH | |
| 7 echo "SAMTOOLS:" $SAMTOOLS | |
| 8 echo "PATH:" $PATH | |
| 9 samtools sort $bam_file $results 2>log.txt | |
| 10 |