Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowseArchiveCreator.py @ 32:7b955a58d8f2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty
author yating-l
date Fri, 20 Oct 2017 11:22:21 -0400
parents 127037c49bc8
children
comparison
equal deleted inserted replaced
31:127037c49bc8 32:7b955a58d8f2
37 #outputFile = reader.getOutputDir() 37 #outputFile = reader.getOutputDir()
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
43 apollo_path = reader.getApolloPath()
44 apollo_host = reader.getApolloHost()
45 apollo_user = reader.getApolloUser()
46 43
47 #### Logging management #### 44 #### Logging management ####
48 # If we are in Debug mode, also print in stdout the debug dump 45 # If we are in Debug mode, also print in stdout the debug dump
49 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path) 46 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
50 log.setup_logging() 47 log.setup_logging()
53 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args)) 50 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
54 #### END Logging management #### 51 #### END Logging management ####
55 52
56 # Create the Track Hub folder 53 # Create the Track Hub folder
57 logging.info('#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n') 54 logging.info('#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n')
58 trackHub = TrackHub(reference_genome, apollo_user, outputFile, extra_files_path, toolDirectory, track_type, apollo_host, user_email) 55 trackHub = TrackHub(reference_genome, outputFile, extra_files_path, toolDirectory, track_type)
59 56
60 # Create Ordered Dictionary to add the tracks in the tool form order 57 # Create Ordered Dictionary to add the tracks in the tool form order
61 logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n') 58 logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n')
62 all_datatype_dictionary = reader.getTracksData() 59 all_datatype_dictionary = reader.getTracksData()
63 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary) 60 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)