Mercurial > repos > yating-l > jbrowse_hub
changeset 53:1e4806330e51 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit a505d6c97db9d044761b5ce92be4a39cb84eda29-dirty
| author | yating-l |
|---|---|
| date | Fri, 31 Mar 2017 11:54:09 -0400 |
| parents | 6fec27968f86 |
| children | 9c45b81bc4e6 |
| files | TrackHub.py |
| diffstat | 1 files changed, 18 insertions(+), 6 deletions(-) [+] |
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--- a/TrackHub.py Thu Mar 30 18:03:43 2017 -0400 +++ b/TrackHub.py Fri Mar 31 11:54:09 2017 -0400 @@ -32,8 +32,8 @@ for input_file in self.input_files: self.addTrack(input_file) self.indexName() - self.makeArchive() - self.outHtml() + slink = self.makeArchive() + self.outHtml(slink) print "Success!\n" def prepareRefseq(self): @@ -72,7 +72,18 @@ def makeArchive(self): shutil.make_archive(self.out_path, 'zip', self.out_path) - data_folder = '/var/www/html/JBrowse-1.12.1/jbrowse_hub' + source = os.path.abspath(self.out_path) + slink = source.replace('/', '_') + slink = os.path.join('/home/galaxy/galaxy/static/JBrowse-1.12.1/data', slink) + try: + if os.path.islink(slink): + os.unlink(slink) + except OSError as oserror: + print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror) + os.symlink(source, slink) + return slink + ''' + data_folder = '/gonramp/static/JBrowse-1.12.1/jbrowse_hub' try: if os.path.exists(data_folder): if os.path.isdir(data_folder): @@ -84,14 +95,15 @@ shutil.copytree(self.out_path, data_folder) subprocess.call(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub']) shutil.rmtree(self.out_path) + ''' #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 #run it locally. May need modify - def outHtml(self): + def outHtml(self, slink): with open(self.outfile, 'w') as htmlfile: htmlstr = 'The JBrowse Hub is created: <br>' zipfiles = '<li><a href = "%s">Download</a></li>' - jbrowse_hub = '<li><a href = ":80/JBrowse-1.12.1/index.html?data=jbrowse_hub/json" target="_blank">View JBrowse Hub</a></li>' + jbrowse_hub = '<li><a href = "/gonramp/static/JBrowse-1.12.1/index.html?data="%s" target="_blank">View JBrowse Hub</a></li>' filedir_abs = os.path.abspath(self.outfile) filedir = os.path.dirname(filedir_abs) filedir = os.path.join(filedir, self.outfolder) @@ -101,7 +113,7 @@ relative_directory = os.path.relpath(root, filedir) relative_file_path = os.path.join(relative_directory, file) htmlstr += zipfiles % relative_file_path - htmlstr += jbrowse_hub + htmlstr += jbrowse_hub % slink htmlfile.write(htmlstr) def createTrackList(self):