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changeset 28:4e70455b49e6 draft

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Uploaded
author zzhou
date Mon, 26 Nov 2012 11:31:41 -0500
parents 299357d4f801
children 215f9e9855e6
files bamedit.py
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/bamedit.py	Mon Nov 26 11:27:08 2012 -0500
+++ b/bamedit.py	Mon Nov 26 11:31:41 2012 -0500
@@ -19,10 +19,10 @@
 		cmdline = "samtools merge  %s %s %s %s" % ( options['bamout'], options['input1'], options['input2'], options['input3'] )
     elif (options['action'] == "split"):
 	#cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] )
-	cmdline = "bash $SCRIPT_PATH/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] )
+	cmdline = "bash $SCRIPT_PATH//split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] )
     elif (options['action'] == "pileup"):
 	#cmdline = "perl /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )
-	cmdline = "perl $SCRIPT_PATH/pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )
+	cmdline = "perl $SCRIPT_PATH//pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )
     elif (options['action'] == "filter"):
 	cmdline = "samtools view -q %s %s -bo %s" % ( options['quality'], options['input1'], options['bamout'] )