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commit/galaxy-central: greg: Only load the tool panel if in Galaxy.
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/172e1713535c/ Changeset: 172e1713535c User: greg Date: 2014-05-20 23:13:26 Summary: Only load the tool panel if in Galaxy. Affected #: 1 file diff -r c5e14473dfb79328f077d81a6cafd9c8a07ffe23 -r 172e1713535c24cc6c07caa5f90494b68827b638 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -145,7 +145,7 @@ self.init_tools( config_filename ) except: log.exception( "Error loading tools defined in config %s", config_filename ) - if self.integrated_tool_panel_config_has_contents: + if self.app.name == 'galaxy' and self.integrated_tool_panel_config_has_contents: # Load self.tool_panel based on the order in self.integrated_tool_panel. self.load_tool_panel() if app.config.update_integrated_tool_panel: 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.

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commit/galaxy-central: jmchilton: Document install_database_connection in universe_wsgi.ini.
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c5e14473dfb7/ Changeset: c5e14473dfb7 User: jmchilton Date: 2014-05-20 23:07:43 Summary: Document install_database_connection in universe_wsgi.ini. Affected #: 1 file diff -r 622d4d3ed3bdb34edeca089a0775cdff86114798 -r c5e14473dfb79328f077d81a6cafd9c8a07ffe23 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -118,6 +118,14 @@ # 'galaxy.model.orm.logging_connection_proxy' #database_query_profiling_proxy = False +# By default, Galaxy will use the same database to track user data and +# tool shed install data. There are many situtations in which it is +# valuable to seperate these - for instance bootstrapping fresh Galaxy +# instances with pretested installs. The following optin can be used to +# separate the tool shed install database (all other options listed above +# but prefixed with install_ are also available). +#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + # -- Files and directories # Path where genome builds are stored. This defaults to tool-data/genome 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.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff42e7cdcd97/ Changeset: ff42e7cdcd97 Branch: next-stable User: jmchilton Date: 2014-05-20 22:31:14 Summary: Enable job metrics by default. They should work with all stock Galaxy runners now. Affected #: 1 file diff -r b814c23924470203ff3f37b28066a118e75bf348 -r ff42e7cdcd9716324c7b423135f24b44d327168c run.sh --- a/run.sh +++ b/run.sh @@ -19,6 +19,7 @@ data_manager_conf.xml.sample shed_data_manager_conf.xml.sample openid_conf.xml.sample + job_metrics_conf.xml.sample universe_wsgi.ini.sample tool-data/shared/ncbi/builds.txt.sample tool-data/shared/ensembl/builds.txt.sample https://bitbucket.org/galaxy/galaxy-central/commits/e49feb93943d/ Changeset: e49feb93943d Branch: next-stable User: jmchilton Date: 2014-05-20 22:31:14 Summary: Fix up job_conf.xml env element logging. Now works with all runners. Affected #: 1 file diff -r ff42e7cdcd9716324c7b423135f24b44d327168c -r e49feb93943da7c6a1ccb84d6dff4518742282a8 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -104,12 +104,11 @@ </destination><destination id="remote_cluster" runner="drmaa" tags="longjobs"/><destination id="java_cluster" runner="drmaa"> - <env id="_JAVA_OPTIONS">-Xmx=6GB</env><env id="ANOTHER_OPTION" raw="true">'5'</env> https://bitbucket.org/galaxy/galaxy-central/commits/622d4d3ed3bd/ Changeset: 622d4d3ed3bd User: jmchilton Date: 2014-05-20 22:31:43 Summary: Merge next-stable. Affected #: 2 files diff -r 70400d62e299e041b18e934788fc34ad7bfc2ddb -r 622d4d3ed3bdb34edeca089a0775cdff86114798 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -104,12 +104,11 @@ </destination><destination id="remote_cluster" runner="drmaa" tags="longjobs"/><destination id="java_cluster" runner="drmaa"> - <env id="_JAVA_OPTIONS">-Xmx=6GB</env><env id="ANOTHER_OPTION" raw="true">'5'</env> diff -r 70400d62e299e041b18e934788fc34ad7bfc2ddb -r 622d4d3ed3bdb34edeca089a0775cdff86114798 run.sh --- a/run.sh +++ b/run.sh @@ -19,6 +19,7 @@ data_manager_conf.xml.sample shed_data_manager_conf.xml.sample openid_conf.xml.sample + job_metrics_conf.xml.sample universe_wsgi.ini.sample tool-data/shared/ncbi/builds.txt.sample tool-data/shared/ensembl/builds.txt.sample 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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b814c2392447/ Changeset: b814c2392447 Branch: next-stable User: dannon Date: 2014-05-20 18:06:07 Summary: Clarify default option (no quotes) for amqp_internal_connection Affected #: 1 file diff -r 8b66d43bc2d1e2119baa7589b6721e360840948e -r b814c23924470203ff3f37b28066a118e75bf348 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -831,7 +831,7 @@ # will automatically create and use a separate sqlite database located in your # <galaxy>/database folder (indicated in the commented out line below). -#amqp_internal_connection = "sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE" +#amqp_internal_connection = sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE https://bitbucket.org/galaxy/galaxy-central/commits/70400d62e299/ Changeset: 70400d62e299 User: dannon Date: 2014-05-20 18:06:21 Summary: Merge next-stable. Affected #: 1 file diff -r 512424a01563a2427fc0ff6225fde2737edc6900 -r 70400d62e299e041b18e934788fc34ad7bfc2ddb universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -831,7 +831,7 @@ # will automatically create and use a separate sqlite database located in your # <galaxy>/database folder (indicated in the commented out line below). -#amqp_internal_connection = "sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE" +#amqp_internal_connection = sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE 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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8b66d43bc2d1/ Changeset: 8b66d43bc2d1 Branch: next-stable User: dannon Date: 2014-05-20 17:55:24 Summary: When using AMQP, if the AMQP server goes down this will now more nicely catch the Connection refused error in send_control_task Affected #: 1 file diff -r 2ed7d87b4ddda2f32eb9d6fc8c05d74667842fef -r 8b66d43bc2d1e2119baa7589b6721e360840948e lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -70,11 +70,16 @@ 'kwargs': kwargs} if noop_self: payload['noop'] = trans.app.config.server_name - c = Connection(trans.app.config.amqp_internal_connection) - with producers[c].acquire(block=True) as producer: - producer.publish(payload, exchange=galaxy.queues.galaxy_exchange, - declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config), - routing_key='control') + try: + c = Connection(trans.app.config.amqp_internal_connection) + with producers[c].acquire(block=True) as producer: + producer.publish(payload, exchange=galaxy.queues.galaxy_exchange, + declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config), + routing_key='control') + except Exception: + # This is likely connection refused. + # TODO Use the specific Exception above. + log.exception("Error sending control task: %s." % payload) # Tasks -- to be reorganized into a separate module as appropriate. This is https://bitbucket.org/galaxy/galaxy-central/commits/512424a01563/ Changeset: 512424a01563 User: dannon Date: 2014-05-20 17:55:54 Summary: Merge next-stable. Affected #: 1 file diff -r 37509e01ee5db4b0552537c77f3771b9671e5dae -r 512424a01563a2427fc0ff6225fde2737edc6900 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -70,11 +70,16 @@ 'kwargs': kwargs} if noop_self: payload['noop'] = trans.app.config.server_name - c = Connection(trans.app.config.amqp_internal_connection) - with producers[c].acquire(block=True) as producer: - producer.publish(payload, exchange=galaxy.queues.galaxy_exchange, - declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config), - routing_key='control') + try: + c = Connection(trans.app.config.amqp_internal_connection) + with producers[c].acquire(block=True) as producer: + producer.publish(payload, exchange=galaxy.queues.galaxy_exchange, + declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config), + routing_key='control') + except Exception: + # This is likely connection refused. + # TODO Use the specific Exception above. + log.exception("Error sending control task: %s." % payload) # Tasks -- to be reorganized into a separate module as appropriate. This is 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.

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commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/37509e01ee5d/ Changeset: 37509e01ee5d User: dan Date: 2014-05-20 16:32:31 Summary: merge next-stable Affected #: 2 files diff -r a968515e0a3128b39d2e5290d7d15559ae38ca44 -r 37509e01ee5db4b0552537c77f3771b9671e5dae lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -15,7 +15,7 @@ if self.config.database_connection: db_url = self.config.database_connection else: - db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Setup the database engine and ORM self.model = galaxy.model.mapping.init( self.config.file_path, db_url, diff -r a968515e0a3128b39d2e5290d7d15559ae38ca44 -r 37509e01ee5db4b0552537c77f3771b9671e5dae lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -19,7 +19,7 @@ self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) # Database related configuration - self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root ) + self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) self.database_engine_options = get_database_engine_options( kwargs ) # Where dataset files are stored 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.

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commit/galaxy-central: dan: Fix for reports app's default database/sqlite settings. Most of the reports app will still not work with sqlite however.
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2ed7d87b4ddd/ Changeset: 2ed7d87b4ddd Branch: next-stable User: dan Date: 2014-05-20 16:32:13 Summary: Fix for reports app's default database/sqlite settings. Most of the reports app will still not work with sqlite however. Affected #: 2 files diff -r f3948f90b9002ae47f0941b0e39cb63d122415a3 -r 2ed7d87b4ddda2f32eb9d6fc8c05d74667842fef lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -15,7 +15,7 @@ if self.config.database_connection: db_url = self.config.database_connection else: - db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Setup the database engine and ORM self.model = galaxy.model.mapping.init( self.config.file_path, db_url, diff -r f3948f90b9002ae47f0941b0e39cb63d122415a3 -r 2ed7d87b4ddda2f32eb9d6fc8c05d74667842fef lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -19,7 +19,7 @@ self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) # Database related configuration - self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root ) + self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) self.database_engine_options = get_database_engine_options( kwargs ) # Where dataset files are stored 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.

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commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a968515e0a31/ Changeset: a968515e0a31 User: dan Date: 2014-05-20 16:18:49 Summary: merge next-stable Affected #: 1 file diff -r 9fee549c5ef78f80e35fa5ca37c1861267bc12f8 -r a968515e0a3128b39d2e5290d7d15559ae38ca44 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -22,17 +22,16 @@ self._static_dbkeys[ key ] = value def get_genome_build_names( self, trans=None ): - #FIXME: how to deal with key duplicates? - #Load old builds.txt static keys - rval = ( self._static_dbkeys.items() ) - #load dbkeys from dbkey data table - dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) - if dbkey_table is not None: - for field_dict in dbkey_table.get_named_fields_list(): - rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) - #load user custom genome builds + # FIXME: how to deal with key duplicates? + rval = [] + # load user custom genome builds if trans is not None: if trans.history: + # This is a little bit Odd. We are adding every .len file in the current history to dbkey list, + # but this is previous behavior from trans.db_names, so we'll continue to do it. + # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering, + # so a len file will be listed twice (as the build name and again as dataset name), + # if custom dbkey creation/conversion occurred within the current history. datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: @@ -42,10 +41,17 @@ user_keys = from_json_string( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) + # Load old builds.txt static keys + rval.extend( self._static_dbkeys.items() ) + #load dbkeys from dbkey data table + dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) + if dbkey_table is not None: + for field_dict in dbkey_table.get_named_fields_list(): + rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) return rval def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True ): - #FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required + # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds @@ -75,7 +81,7 @@ dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None ) - #use configured len path + # use configured server len path if not chrom_info: # Default to built-in build. chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey ) 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.

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commit/galaxy-central: dan: To maintain previous behavior, list custom genome build names first.
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3948f90b900/ Changeset: f3948f90b900 Branch: next-stable User: dan Date: 2014-05-20 16:18:28 Summary: To maintain previous behavior, list custom genome build names first. Affected #: 1 file diff -r b3342bc20de522e5b98f9b97de69737b069d6d64 -r f3948f90b9002ae47f0941b0e39cb63d122415a3 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -22,17 +22,16 @@ self._static_dbkeys[ key ] = value def get_genome_build_names( self, trans=None ): - #FIXME: how to deal with key duplicates? - #Load old builds.txt static keys - rval = ( self._static_dbkeys.items() ) - #load dbkeys from dbkey data table - dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) - if dbkey_table is not None: - for field_dict in dbkey_table.get_named_fields_list(): - rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) - #load user custom genome builds + # FIXME: how to deal with key duplicates? + rval = [] + # load user custom genome builds if trans is not None: if trans.history: + # This is a little bit Odd. We are adding every .len file in the current history to dbkey list, + # but this is previous behavior from trans.db_names, so we'll continue to do it. + # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering, + # so a len file will be listed twice (as the build name and again as dataset name), + # if custom dbkey creation/conversion occurred within the current history. datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: @@ -42,10 +41,17 @@ user_keys = from_json_string( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) + # Load old builds.txt static keys + rval.extend( self._static_dbkeys.items() ) + #load dbkeys from dbkey data table + dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) + if dbkey_table is not None: + for field_dict in dbkey_table.get_named_fields_list(): + rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) return rval def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True ): - #FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required + # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds @@ -75,7 +81,7 @@ dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None ) - #use configured len path + # use configured server len path if not chrom_info: # Default to built-in build. chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey ) 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.

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commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9fee549c5ef7/ Changeset: 9fee549c5ef7 User: dan Date: 2014-05-20 16:01:53 Summary: merge next-stable Affected #: 2 files diff -r 11403745e7ceb0a6946af648dcd3ca24a638ca7e -r 9fee549c5ef78f80e35fa5ca37c1861267bc12f8 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,7 +193,7 @@ # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} - ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id!='CONVERTER_fasta_to_len' ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r 11403745e7ceb0a6946af648dcd3ca24a638ca7e -r 9fee549c5ef78f80e35fa5ca37c1861267bc12f8 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -44,19 +44,18 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, tool, trans=None ): + def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True ): + #FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds if trans: db_dataset = trans.db_dataset_for( dbkey ) if db_dataset: - #incoming[ "chromInfo" ] = db_dataset.file_name chrom_info = db_dataset.file_name else: - # -- Get chrom_info (len file) from either a custom or built-in build. -- + # Do Custom Build handling if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): - # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ] # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, @@ -64,17 +63,19 @@ # 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': + if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion: # Build is defined by fasta; get len file, which is obtained from converting fasta. 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 elif 'len' in custom_build_dict: # Build is defined by len file, so use it. chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name + # Check Data table if not chrom_info: dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None ) + #use configured len path if not chrom_info: # Default to built-in build. chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey ) 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.

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