Mercurial > repos > iuc > jbrowse

changeset 28:d0743cb18ed8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d
author iuc
date Fri, 22 Feb 2019 03:20:59 -0500
parents 61ce21e36cb5
children 112eb40ba6cf
files jbrowse.py macros.xml
diffstat 2 files changed, 2 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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]
--- a/macros.xml	Wed Feb 20 11:50:21 2019 -0500
+++ b/macros.xml	Fri Feb 22 03:20:59 2019 -0500
@@ -14,7 +14,7 @@
     </requirements>
   </xml>
   <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-  <token name="@WRAPPER_VERSION@">galaxy1</token>
+  <token name="@WRAPPER_VERSION@">galaxy2</token>
   <token name="@ATTRIBUTION@"><![CDATA[
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