diff jbrowse.py @ 28:d0743cb18ed8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d

--- a/jbrowse.py	Wed Feb 20 11:50:21 2019 -0500
+++ b/jbrowse.py	Fri Feb 22 03:20:59 2019 -0500
@@ -614,10 +614,7 @@
 
         if not os.path.exists(dest):
             # Only index if not already done
-            cmd = "grep ^\"#\" '%s' > '%s'" % (data, dest)
-            self.subprocess_popen(cmd)
-
-            cmd = "grep -v ^\"#\" '%s' | grep -v \"^$\" | grep \"\t\" | sort -k1,1 -k4,4n >> '%s'" % (data, dest)
+            cmd = "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" % (data, dest)
             self.subprocess_popen(cmd)
 
             cmd = ['bgzip', '-f', dest]