Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder
comparison data_manager/novocraft_index_builder.py @ 10:68b7023c6a2f draft
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 41c23255d958406b015574dd15b07d44175a2c1b
| author | sanbi-uwc |
|---|---|
| date | Sat, 05 Mar 2016 10:29:02 -0500 |
| parents | 56e8324519c4 |
| children | a9b725202132 |
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| 9:810d5013fdc2 | 10:68b7023c6a2f |
|---|---|
| 52 try: | 52 try: |
| 53 check_call(cmdline) | 53 check_call(cmdline) |
| 54 except CalledProcessError: | 54 except CalledProcessError: |
| 55 print("Error building RNA STAR index", file=sys.stderr) | 55 print("Error building RNA STAR index", file=sys.stderr) |
| 56 | 56 |
| 57 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=target_directory ) | 57 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=os.path.join(target_directory, index_filename) ) |
| 58 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) | 58 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) |
| 59 return ( index_filename ) | 59 return ( index_filename ) |
| 60 | 60 |
| 61 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): | 61 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): |
| 62 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | 62 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) |