Mercurial > repos > biomonika > linkyx

annotate sort_bam.sh @ 32:cf7cd22fc5d3 default tip

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author biomonika
date Tue, 10 Feb 2015 12:09:34 -0500
parents 0c7f60054ee3
children
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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; }
26
0c7f60054ee3 toolshed perl, newest commit, two occurencies - based on toolshed bioperl
biomonika <biomonika@psu.edu>
parents: 25
diff changeset
6 echo "LINKYX_PATH:" $LINKYX_PATH
0c7f60054ee3 toolshed perl, newest commit, two occurencies - based on toolshed bioperl
biomonika <biomonika@psu.edu>
parents: 25
diff changeset
7 echo "SAMTOOLS:" $SAMTOOLS
0c7f60054ee3 toolshed perl, newest commit, two occurencies - based on toolshed bioperl
biomonika <biomonika@psu.edu>
parents: 25
diff changeset
8 echo "PATH:" $PATH
20
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
9 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
10