Mercurial > repos > yating-l > jbrowsearchivecreator

comparison TrackHub.py @ 11:45b5cb50c29e draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 479fc6490e24ca0e5034ae6c3579882e97e095e6-dirty
author yating-l
date Wed, 31 May 2017 15:42:51 -0400
parents 91b3558fa73f
children cdc32923786d
comparison
equal deleted inserted replaced
10:91b3558fa73f 11:45b5cb50c29e
71 def indexName(self): 71 def indexName(self):
72 subprocess.call(['generate-names.pl', '-v', '--out', self.json]) 72 subprocess.call(['generate-names.pl', '-v', '--out', self.json])
73 print "finished name index \n" 73 print "finished name index \n"
74 74
75 def makeArchive(self): 75 def makeArchive(self):
76 #shutil.make_archive(self.out_path, 'zip', self.out_path)
77 os.chdir(os.path.dirname(self.out_path))
78 with zipfile.ZipFile(self.out_path + '.zip', 'w', zipfile.ZIP_DEFLATED, allowZip64=True) as zf:
79 for root, _, filenames in os.walk(os.path.basename(self.out_path)):
80 for name in filenames:
81 name = os.path.join(root, name)
82 name = os.path.normpath(name)
83 zf.write(name, name)
84 file_dir = os.path.abspath(self.outfile) 76 file_dir = os.path.abspath(self.outfile)
85 source_dir = os.path.dirname(file_dir) 77 source_dir = os.path.dirname(file_dir)
86 folder_name = os.path.basename(self.outfolder) 78 folder_name = os.path.basename(self.outfolder)
87 source_name = os.path.basename(self.out_path) 79 source_name = os.path.basename(self.out_path)
88 source = os.path.join(source_dir, folder_name, source_name) 80 source = os.path.join(source_dir, folder_name, source_name)
94 except OSError as oserror: 86 except OSError as oserror:
95 print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror) 87 print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror)
96 os.symlink(source, slink) 88 os.symlink(source, slink)
97 return slink 89 return slink
98 90
99 #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
100 #run it locally. May need modify
101 def outHtml(self, slink): 91 def outHtml(self, slink):
102 with open(self.outfile, 'w') as htmlfile: 92 with open(self.outfile, 'w') as htmlfile:
103 htmlstr = 'The JBrowse Hub is created: <br>' 93 htmlstr = 'The JBrowse Hub is created: <br>'
104 zipfiles = '<li><a href = "%s">Download</a></li>'
105 url = self.jbrowse_host + "/JBrowse-1.12.1/index.html?data=%s" 94 url = self.jbrowse_host + "/JBrowse-1.12.1/index.html?data=%s"
106 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub</a></li>' % url 95 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub</a></li>' % url
107 filedir_abs = os.path.abspath(self.outfile)
108 filedir = os.path.dirname(filedir_abs)
109 filedir = os.path.join(filedir, self.outfolder)
110 for root, dirs, files in os.walk(filedir):
111 for file in files:
112 if file.endswith('.zip'):
113 relative_directory = os.path.relpath(root, filedir)
114 relative_file_path = os.path.join(relative_directory, file)
115 htmlstr += zipfiles % relative_file_path
116 link_name = os.path.basename(slink) 96 link_name = os.path.basename(slink)
117 relative_path = os.path.join('data', link_name + '/json') 97 relative_path = os.path.join('data', link_name + '/json')
118 htmlstr += jbrowse_hub % relative_path 98 htmlstr += jbrowse_hub % relative_path
119 htmlfile.write(htmlstr) 99 htmlfile.write(htmlstr)
120 100