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annotate sort_bam.sh @ 25:ffe50d004cb4

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samtools sort, echo path
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 22:01:22 -0400
parents cf0d2b74769e
children 0c7f60054ee3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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20
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
1 #!/bin/bash
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
2 results=$1;
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
3 bam_file=$2;
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
4
24
cf0d2b74769e samtools_sort_debug
biomonika <biomonika@psu.edu>
parents: 20
diff changeset
5 hash samtools 2>/dev/null || { echo "I require samtools in path but it's not installed. Aborting."; exit 1; }
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ffe50d004cb4 samtools sort, echo path
biomonika <biomonika@psu.edu>
parents: 24
diff changeset
6 echo $LINKYX_PATH
ffe50d004cb4 samtools sort, echo path
biomonika <biomonika@psu.edu>
parents: 24
diff changeset
7 echo $SAMTOOLS
20
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
8 samtools sort $bam_file $results 2>log.txt
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
9