diff jbrowse.py @ 34:9de82b4963e6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"

--- a/jbrowse.py	Fri Aug 30 03:36:39 2019 -0400
+++ b/jbrowse.py	Wed Sep 11 09:40:36 2019 -0400
@@ -654,7 +654,8 @@
         # Only index if not already done
         if not os.path.exists(dest):
             cmd = ['sort', '-k1,1', '-k2,2n', data]
-            self.subprocess_check_call(cmd, output=dest)
+            with open(dest, 'w') as handle:
+                self.subprocess_check_call(cmd, output=handle)
 
             self.subprocess_check_call(['bgzip', '-f', dest])
             self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz'])