Mercurial > repos > yating-l > jbrowsearchivecreator
comparison TrackHub.py @ 33:07cc5384dd61 draft
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 74a020b6b0a2fa7ff5670d7f154de838dee51dfd
| author | yating-l |
|---|---|
| date | Wed, 25 Oct 2017 12:43:23 -0400 |
| parents | 7b955a58d8f2 |
| children | d17f629f5486 |
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| 32:7b955a58d8f2 | 33:07cc5384dd61 |
|---|---|
| 119 output_encoding='utf-8', encoding_errors='replace') | 119 output_encoding='utf-8', encoding_errors='replace') |
| 120 htmlTemplate = mylookup.get_template("display.txt") | 120 htmlTemplate = mylookup.get_template("display.txt") |
| 121 | 121 |
| 122 with open(self.outputFile, 'w') as htmlfile: | 122 with open(self.outputFile, 'w') as htmlfile: |
| 123 htmlMakoRendered = htmlTemplate.render( | 123 htmlMakoRendered = htmlTemplate.render( |
| 124 genome_name = self.genome_name, | 124 species_folder = os.path.relpath(self.mySpecieFolderPath, self.extra_files_path), |
| 125 trackList = os.path.relpath(self.trackList, self.extra_files_path) | 125 trackList = os.path.relpath(self.trackList, self.extra_files_path) |
| 126 ) | 126 ) |
| 127 htmlfile.write(htmlMakoRendered) | 127 htmlfile.write(htmlMakoRendered) |
| 128 #with open(self.outputFile, 'w') as htmlfile: | 128 #with open(self.outputFile, 'w') as htmlfile: |
| 129 # htmlstr = 'The new Organism "%s" is created on Apollo: <br>' % self.genome_name | 129 # htmlstr = 'The new Organism "%s" is created on Apollo: <br>' % self.genome_name |
| 130 # jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name | 130 # jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name |
| 131 # htmlstr += jbrowse_hub | 131 # htmlstr += jbrowse_hub |
| 132 # htmlfile.write(htmlstr) | 132 # htmlfile.write(htmlstr) |
| 133 | |
| 133 | 134 |
| 134 | 135 |
| 135 def __createAssemblyHub__(self, extra_files_path): | 136 def __createAssemblyHub__(self, extra_files_path): |
| 136 # Get all necessaries infos first | 137 # Get all necessaries infos first |
| 137 # 2bit file creation from input fasta | 138 # 2bit file creation from input fasta |