1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8872e75d8d43/ changeset: 8872e75d8d43 user: jgoecks date: 2012-06-07 20:16:26 summary: Fix bugs in fetching reference genome data. affected #: 1 file
diff -r d238d7aabc016c01a4320908e67c561472713e73 -r 8872e75d8d4321c491ee43aca91d149362585ca6 lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -190,6 +190,7 @@ # Get/create genome object. # genome = None + twobit_file = None
# Look first in user's custom builds. if dbkey_user and 'dbkeys' in dbkey_user.preferences: @@ -199,11 +200,14 @@ if 'fasta' in dbkey_attributes: build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] ) len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name + converted_dataset = build_fasta.get_converted_dataset( trans, 'twobit' ) + if converted_dataset: + twobit_file = converted_dataset.file_name # Backwards compatibility: look for len file directly. elif 'len' in dbkey_attributes: len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name if len_file: - genome = Genome( dbkey, len_file=len_file ) + genome = Genome( dbkey, len_file=len_file, twobit_file=twobit_file )
# Look in system builds. @@ -256,9 +260,9 @@ # Get twobit file with reference data. # twobit_file_name = None - if dbkey in self.available_genomes: + if dbkey in self.genomes: # Built-in twobit. - twobit_file_name = self.available_genomes[dbkey] + twobit_file_name = self.genomes[dbkey].twobit_file else: user_keys = from_json_string( dbkey_user.preferences['dbkeys'] ) dbkey_attributes = user_keys[ dbkey ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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