Mercurial > repos > yating-l > jbrowse_hub
changeset 60:ed17bb465bde draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 8386544cbce1efb5e9dd1f805a2099b3e214363f-dirty
| author | yating-l |
|---|---|
| date | Fri, 07 Apr 2017 12:38:46 -0400 |
| parents | caf649fc310b |
| children | ea301a2d2229 |
| files | TrackHub.py jbrowse_hub.py jbrowse_hub.xml |
| diffstat | 3 files changed, 14 insertions(+), 3 deletions(-) [+] |
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--- a/TrackHub.py Fri Mar 31 17:11:11 2017 -0400 +++ b/TrackHub.py Fri Apr 07 12:38:46 2017 -0400 @@ -8,7 +8,7 @@ class TrackHub: - def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData): + def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData, jbrowse_host): self.input_files = inputFiles.tracks self.outfile = outputDirect self.outfolder = extra_files_path @@ -18,6 +18,7 @@ self.metaData = metaData self.raw = os.path.join(self.out_path, 'raw') self.json = os.path.join(self.out_path, 'json') + self.jbrowse_host = jbrowse_host try: if os.path.exists(self.json): shutil.rmtree(self.json) @@ -107,7 +108,8 @@ 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 = "http://192.168.56.11/JBrowse-1.12.1/index.html?data=%s" target="_blank">View JBrowse Hub</a></li>' + url = self.jbrowse_host + "/JBrowse-1.12.1/index.html?data=%s" + jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub</a></li>' % url filedir_abs = os.path.abspath(self.outfile) filedir = os.path.dirname(filedir_abs) filedir = os.path.join(filedir, self.outfolder)
--- a/jbrowse_hub.py Fri Mar 31 17:11:11 2017 -0400 +++ b/jbrowse_hub.py Fri Apr 07 12:38:46 2017 -0400 @@ -60,6 +60,9 @@ # Metadata json format parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs') + #JBrowse host + parser.add_argument('--jbrowse_host', help="JBrowse Host") + args = parser.parse_args() all_datatype_dictionary = dict() @@ -72,6 +75,7 @@ out_path = 'unknown.html' extra_files_path = '.' tool_directory = '.' + jbrowse_host = args.jbrowse_host if args.genome_name: genome = args.genome_name if args.out: @@ -148,7 +152,7 @@ #Convert tracks into gff3 format all_tracks.addToRaw(f, datatype) - jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path, inputs_data) + jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path, inputs_data, jbrowse_host) jbrowseHub.createHub() """
--- a/jbrowse_hub.xml Fri Mar 31 17:11:11 2017 -0400 +++ b/jbrowse_hub.xml Fri Apr 07 12:38:46 2017 -0400 @@ -19,6 +19,10 @@ --fasta '$reference' --genome_name '$genome_name' + #set galaxy_url = str($GALAXY_URL) + #set $jbrowse_url = galaxy_url.replace("8080", "80") + --jbrowse_host '$jbrowse_url' + ## json metadata recording from Remi's hub-archive-creator.xml #import json #set global data_parameter_dict = {} @@ -100,6 +104,7 @@ ]]></command> <inputs> + <param name="GALAXY_URL" type="baseurl" value="" /> <param name="reference" type="data" format="fasta" label="Reference Genome" /> <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" /> <repeat name="group" title="New group">