2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/88a08db3c733/ Changeset: 88a08db3c733 Branch: stable User: jgoecks Date: 2013-11-14 00:41:23 Summary: Implement a hack to avoid infinite recursion in custom builds. Affected #: 1 file diff -r 9bde6f2b9c59a29a35b85b7fe3c2e3bef3ae6a2e -r 88a08db3c73393ef4f64b0c2f50262d5aa03967b lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -206,12 +206,19 @@ db_datasets[ "chromInfo" ] = db_dataset incoming[ "chromInfo" ] = db_dataset.file_name else: - # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. + # -- Get chrom_info from either a custom or built-in build. -- + chrom_info = None if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] - if 'fasta' in custom_build_dict: + # HACK: the attempt to get chrom_info below will trigger the + # fasta-to-len converter if the dataset is not available or, + # which will in turn create a recursive loop when + # running the fasta-to-len tool. So, use a hack in the second + # condition below to avoid getting chrom_info when running the + # fasta-to-len converter. + if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len': build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] ) chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name https://bitbucket.org/galaxy/galaxy-central/commits/1c4bb73d630a/ Changeset: 1c4bb73d630a User: jgoecks Date: 2013-11-14 00:42:54 Summary: Merge stable branch to default. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.