diff jbrowseArchiveCreator.py @ 32:7b955a58d8f2 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty

--- a/jbrowseArchiveCreator.py	Mon Oct 16 18:03:58 2017 -0400
+++ b/jbrowseArchiveCreator.py	Fri Oct 20 11:22:21 2017 -0400
@@ -39,10 +39,7 @@
     reference_genome = reader.getRefGenome()
     debug_mode = reader.getDebugMode()
     track_type = reader.getTrackType()
-    #jbrowse_path = reader.getJBrowsePath()
-    apollo_path = reader.getApolloPath()
-    apollo_host = reader.getApolloHost()
-    apollo_user = reader.getApolloUser()
+    
  
     #### Logging management ####
     # If we are in Debug mode, also print in stdout the debug dump
@@ -55,7 +52,7 @@
  
     # Create the Track Hub folder
     logging.info('#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n')
-    trackHub = TrackHub(reference_genome, apollo_user, outputFile, extra_files_path, toolDirectory, track_type, apollo_host, user_email) 
+    trackHub = TrackHub(reference_genome, outputFile, extra_files_path, toolDirectory, track_type) 
 
     # Create Ordered Dictionary to add the tracks in the tool form order
     logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n')