Mercurial > repos > biomonika > linkyx
changeset 25:ffe50d004cb4
samtools sort, echo path
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Thu, 11 Sep 2014 22:01:22 -0400 |
| parents | cf0d2b74769e |
| children | 0c7f60054ee3 |
| files | sort_bam.sh |
| diffstat | 1 files changed, 2 insertions(+), 0 deletions(-) [+] |
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--- a/sort_bam.sh Thu Sep 11 21:58:16 2014 -0400 +++ b/sort_bam.sh Thu Sep 11 22:01:22 2014 -0400 @@ -3,5 +3,7 @@ bam_file=$2; hash samtools 2>/dev/null || { echo "I require samtools in path but it's not installed. Aborting."; exit 1; } +echo $LINKYX_PATH +echo $SAMTOOLS samtools sort $bam_file $results 2>log.txt