Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowseArchiveCreator.py @ 31:127037c49bc8 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
author yating-l
date Mon, 16 Oct 2017 18:03:58 -0400
parents 31a41ce128cc
children 7b955a58d8f2
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30:2191bd0798a9 31:127037c49bc8
38 user_email = reader.getUserEmail() 38 user_email = reader.getUserEmail()
39 reference_genome = reader.getRefGenome() 39 reference_genome = reader.getRefGenome()
40 debug_mode = reader.getDebugMode() 40 debug_mode = reader.getDebugMode()
41 track_type = reader.getTrackType() 41 track_type = reader.getTrackType()
42 #jbrowse_path = reader.getJBrowsePath() 42 #jbrowse_path = reader.getJBrowsePath()
43 apollo_path = reader.getApolloPath()
43 apollo_host = reader.getApolloHost() 44 apollo_host = reader.getApolloHost()
44 apollo_user = reader.getApolloUser() 45 apollo_user = reader.getApolloUser()
45 46
46 #### Logging management #### 47 #### Logging management ####
47 # If we are in Debug mode, also print in stdout the debug dump 48 # If we are in Debug mode, also print in stdout the debug dump
52 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args)) 53 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
53 #### END Logging management #### 54 #### END Logging management ####
54 55
55 # Create the Track Hub folder 56 # Create the Track Hub folder
56 logging.info('#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n') 57 logging.info('#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n')
57 trackHub = TrackHub(reference_genome, apollo_user, outputFile, extra_files_path, toolDirectory, track_type, apollo_host) 58 trackHub = TrackHub(reference_genome, apollo_user, outputFile, extra_files_path, toolDirectory, track_type, apollo_host, user_email)
58 59
59 # Create Ordered Dictionary to add the tracks in the tool form order 60 # Create Ordered Dictionary to add the tracks in the tool form order
60 logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n') 61 logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n')
61 all_datatype_dictionary = reader.getTracksData() 62 all_datatype_dictionary = reader.getTracksData()
62 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary) 63 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)