# HG changeset patch
# User yating-l
# Date 1489527689 14400
# Node ID 55c62db0291735a27edc537c146720c7c6387fbc
# Parent  a051609fc8b43434b5537d08ecc071b6465f5e0f
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty

diff -r a051609fc8b4 -r 55c62db02917 TrackHub.py
--- a/TrackHub.py	Tue Mar 14 17:03:13 2017 -0400
+++ b/TrackHub.py	Tue Mar 14 17:41:29 2017 -0400
@@ -60,7 +60,7 @@
             bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
             bam_track['label'] = track['fileName']
             bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
-            bam_track['baiUrlTemplate'] = os.path.join('../raw', track['fileName'])
+            #bam_track['baiUrlTemplate'] = os.path.join('../raw', track['fileName'])
             utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
             print "add bam track\n"
         elif track['dataType'] == 'bigwig':
diff -r a051609fc8b4 -r 55c62db02917 jbrowse_hub.xml
--- a/jbrowse_hub.xml	Tue Mar 14 17:03:13 2017 -0400
+++ b/jbrowse_hub.xml	Tue Mar 14 17:41:29 2017 -0400
@@ -26,9 +26,7 @@
             #end if
             #if $f.formatChoice.format_select == 'bam'
                 --bam $f.formatChoice.BAM
-            #end if
-            #if $f.formatChoice.format_select == 'bai'
-                --bai $f.formatChoice.BAI
+                --bai $f.formatChoice.BAM.metadata.bam_index
             #end if
             #if $f.formatChoice.format_select == 'gff3_transcript'
                 --gff3_transcript $f.formatChoice.GFF3_transcript