Mercurial > repos > yating-l > jbrowsearchivecreator

comparison TrackHub.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
comparison
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30:2191bd0798a9 31:127037c49bc8
14 from util import subtools 14 from util import subtools
15 from util import santitizer 15 from util import santitizer
16 16
17 17
18 class TrackHub: 18 class TrackHub:
19 def __init__(self, inputFastaFile, apollo_user, outputFile, extra_files_path, tool_directory, trackType, apollo_host): 19 def __init__(self, inputFastaFile, apollo_user, outputFile, extra_files_path, tool_directory, trackType, apollo_host, user_email):
20 20
21 self.rootAssemblyHub = None 21 self.rootAssemblyHub = None
22 22
23 self.mySpecieFolderPath = None 23 self.mySpecieFolderPath = None
24 24
35 self.extra_files_path = extra_files_path 35 self.extra_files_path = extra_files_path
36 self.outputFile = outputFile 36 self.outputFile = outputFile
37 self.chromSizesFile = None 37 self.chromSizesFile = None
38 38
39 # Set up apollo 39 # Set up apollo
40 self.apollo = ApolloInstance(apollo_host) 40 self.apollo = ApolloInstance(apollo_host, tool_directory, user_email)
41 self.apollo_user = apollo_user 41 self.apollo_user = apollo_user
42 42
43 # Set all the missing variables of this class, and create physically the folders/files 43 # Set all the missing variables of this class, and create physically the folders/files
44 self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path) 44 self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
45 # Init the Datatype 45 # Init the Datatype