# HG changeset patch
# User yating-l
# Date 1489525393 14400
# Node ID a051609fc8b43434b5537d08ecc071b6465f5e0f
# Parent  2a12d257f95d48689f39d6b2a279e3225aa76443
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty

diff -r 2a12d257f95d -r a051609fc8b4 TrackHub.py
--- a/TrackHub.py	Tue Mar 14 16:28:20 2017 -0400
+++ b/TrackHub.py	Tue Mar 14 17:03:13 2017 -0400
@@ -60,6 +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'])
             utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
             print "add bam track\n"
         elif track['dataType'] == 'bigwig':
@@ -69,12 +70,6 @@
             bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
             bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
             bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
-            bigwig_track['variance_band'] = True
-            bigwig_track['style'] = dict()
-            bigwig_track['style']['pos_color'] = '#FFA600'
-            bigwig_track['style']['neg_color'] = '#005EFF'
-            bigwig_track['style']['clip_marker_color'] = 'red'
-            bigwig_track['style']['height'] = 100
             utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
         else: 
             gff3_file = os.path.join(self.raw, track['fileName'])