2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5118cb9c05f7/ changeset: 5118cb9c05f7 user: jgoecks date: 2012-09-10 20:12:52 summary: Small fixes to make summary tree compatible with Circster. affected #: 2 files diff -r 6d3023815cd77ec3045bf81ff15af884b828c38d -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -93,8 +93,10 @@ starting_block = self.find_block( start, level ) ending_block = self.find_block( end, level ) for block in range( starting_block, ending_block + 1 ): + val = 0 if block in blocks[ level ]: - results.append( ( block * multiplier, blocks[ level ][ block ] ) ) + val = blocks[ level ][ block ] + results.append( ( block * multiplier, val ) ) return results return None diff -r 6d3023815cd77ec3045bf81ff15af884b828c38d -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -559,7 +559,7 @@ converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=3, detail_cutoff=0, draw_cutoff=0 ) } + track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) https://bitbucket.org/galaxy/galaxy-central/changeset/4e69bc5d9e1e/ changeset: 4e69bc5d9e1e user: jgoecks date: 2012-09-10 20:13:09 summary: Merge affected #: 3 files diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -186,6 +186,8 @@ self.os_conn_path = kwargs.get( 'os_conn_path', '/' ) self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 )) self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) + if self.distributed_object_store_config_file is not None: + self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,6 +19,7 @@ from galaxy.security.validate_user_input import validate_publicname from paste.httpexceptions import * from galaxy.exceptions import * +from galaxy.model import NoConverterException, ConverterDependencyException from Cheetah.Template import Template diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -90,6 +90,7 @@ config_dict = {} for key, value in config_parser.items('app:main'): config_dict[key] = value + config_dict['root_dir'] = galaxy_root self.config = galaxy.config.Configuration(**config_dict) 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.