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commit/galaxy-central: dan: Cleanup for dbkey handling.
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b3342bc20de5/ Changeset: b3342bc20de5 Branch: next-stable User: dan Date: 2014-05-20 16:01:28 Summary: Cleanup for dbkey handling. Affected #: 2 files diff -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 -r b3342bc20de522e5b98f9b97de69737b069d6d64 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 b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 -r b3342bc20de522e5b98f9b97de69737b069d6d64 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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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/b29ac7cfd60e/ Changeset: b29ac7cfd60e Branch: next-stable User: dannon Date: 2014-05-20 01:54:05 Summary: Additional anyjson requires (appeared to cause Toolshed issues for Greg) Affected #: 2 files diff -r faf07312a7daf640f5ecdddd531e90268404a4fd -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -9,6 +9,7 @@ import galaxy.queues from galaxy import eggs, util +eggs.require('anyjson') if sys.version_info < (2, 7, 0): # Kombu requires importlib and ordereddict to function under Python 2.6. eggs.require('importlib') diff -r faf07312a7daf640f5ecdddd531e90268404a4fd -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -8,6 +8,7 @@ from galaxy import eggs +eggs.require('anyjson') if sys.version_info < (2, 7, 0): # Kombu requires importlib and ordereddict to function in Python 2.6. eggs.require('importlib') https://bitbucket.org/galaxy/galaxy-central/commits/11403745e7ce/ Changeset: 11403745e7ce User: dannon Date: 2014-05-20 01:54:25 Summary: Merge next-stable Affected #: 2 files diff -r 4b3cfc947e1d151d61351d75397863760f1443f1 -r 11403745e7ceb0a6946af648dcd3ca24a638ca7e lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -9,6 +9,7 @@ import galaxy.queues from galaxy import eggs, util +eggs.require('anyjson') if sys.version_info < (2, 7, 0): # Kombu requires importlib and ordereddict to function under Python 2.6. eggs.require('importlib') diff -r 4b3cfc947e1d151d61351d75397863760f1443f1 -r 11403745e7ceb0a6946af648dcd3ca24a638ca7e lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -8,6 +8,7 @@ from galaxy import eggs +eggs.require('anyjson') if sys.version_info < (2, 7, 0): # Kombu requires importlib and ordereddict to function in Python 2.6. eggs.require('importlib') 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/faf07312a7da/ Changeset: faf07312a7da Branch: next-stable User: dannon Date: 2014-05-20 00:58:13 Summary: Kombu also requires ordereddict backport to support python2.6, more eggs. Affected #: 3 files diff -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 -r faf07312a7daf640f5ecdddd531e90268404a4fd eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -51,6 +51,7 @@ nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 +ordereddict = 1.1 paramiko = 1.11.1 Parsley = 1.1 Paste = 1.7.5.1 diff -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 -r faf07312a7daf640f5ecdddd531e90268404a4fd lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -10,8 +10,9 @@ import galaxy.queues from galaxy import eggs, util if sys.version_info < (2, 7, 0): - # Kombu requires importlib to function under Python 2.6. + # Kombu requires importlib and ordereddict to function under Python 2.6. eggs.require('importlib') + eggs.require('ordereddict') eggs.require('kombu') from kombu import Connection diff -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 -r faf07312a7daf640f5ecdddd531e90268404a4fd lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -9,8 +9,9 @@ from galaxy import eggs if sys.version_info < (2, 7, 0): - # Kombu requires importlib to function in Python 2.6. + # Kombu requires importlib and ordereddict to function in Python 2.6. eggs.require('importlib') + eggs.require('ordereddict') eggs.require('kombu') from kombu import Exchange, Queue https://bitbucket.org/galaxy/galaxy-central/commits/4b3cfc947e1d/ Changeset: 4b3cfc947e1d User: dannon Date: 2014-05-20 00:58:28 Summary: Merge from next-stable. Affected #: 3 files diff -r e170406ece79b72e991dd94345f5f1da9efd88a6 -r 4b3cfc947e1d151d61351d75397863760f1443f1 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -51,6 +51,7 @@ nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 +ordereddict = 1.1 paramiko = 1.11.1 Parsley = 1.1 Paste = 1.7.5.1 diff -r e170406ece79b72e991dd94345f5f1da9efd88a6 -r 4b3cfc947e1d151d61351d75397863760f1443f1 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -10,8 +10,9 @@ import galaxy.queues from galaxy import eggs, util if sys.version_info < (2, 7, 0): - # Kombu requires importlib to function under Python 2.6. + # Kombu requires importlib and ordereddict to function under Python 2.6. eggs.require('importlib') + eggs.require('ordereddict') eggs.require('kombu') from kombu import Connection diff -r e170406ece79b72e991dd94345f5f1da9efd88a6 -r 4b3cfc947e1d151d61351d75397863760f1443f1 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -9,8 +9,9 @@ from galaxy import eggs if sys.version_info < (2, 7, 0): - # Kombu requires importlib to function in Python 2.6. + # Kombu requires importlib and ordereddict to function in Python 2.6. eggs.require('importlib') + eggs.require('ordereddict') eggs.require('kombu') from kombu import Exchange, Queue 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/1ec7fa5ac5e3/ Changeset: 1ec7fa5ac5e3 Branch: next-stable User: dannon Date: 2014-05-20 00:11:52 Summary: Add conditional requirement of importlib for python 2.6/kombu. Affected #: 3 files diff -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -43,6 +43,7 @@ elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 +importlib = 1.0.3 kombu = 3.0.12 lrucache = 0.2 Mako = 0.4.1 diff -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -5,8 +5,13 @@ import logging import threading +import sys + import galaxy.queues from galaxy import eggs, util +if sys.version_info < (2, 7, 0): + # Kombu requires importlib to function under Python 2.6. + eggs.require('importlib') eggs.require('kombu') from kombu import Connection diff -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -4,9 +4,14 @@ """ +import sys + from galaxy import eggs -eggs.require("kombu") +if sys.version_info < (2, 7, 0): + # Kombu requires importlib to function in Python 2.6. + eggs.require('importlib') +eggs.require('kombu') from kombu import Exchange, Queue ALL_CONTROL = "control.*" https://bitbucket.org/galaxy/galaxy-central/commits/e170406ece79/ Changeset: e170406ece79 User: dannon Date: 2014-05-20 00:12:05 Summary: Merge next-stable Affected #: 3 files diff -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 -r e170406ece79b72e991dd94345f5f1da9efd88a6 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -43,6 +43,7 @@ elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 +importlib = 1.0.3 kombu = 3.0.12 lrucache = 0.2 Mako = 0.4.1 diff -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 -r e170406ece79b72e991dd94345f5f1da9efd88a6 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -5,8 +5,13 @@ import logging import threading +import sys + import galaxy.queues from galaxy import eggs, util +if sys.version_info < (2, 7, 0): + # Kombu requires importlib to function under Python 2.6. + eggs.require('importlib') eggs.require('kombu') from kombu import Connection diff -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 -r e170406ece79b72e991dd94345f5f1da9efd88a6 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -4,9 +4,14 @@ """ +import sys + from galaxy import eggs -eggs.require("kombu") +if sys.version_info < (2, 7, 0): + # Kombu requires importlib to function in Python 2.6. + eggs.require('importlib') +eggs.require('kombu') from kombu import Exchange, Queue ALL_CONTROL = "control.*" 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 19 May '14

19 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/70f062a9e200/ Changeset: 70f062a9e200 User: dannon Date: 2014-05-19 23:44:25 Summary: Merge from next-stable. Affected #: 1 file diff -r 05302ebc73772d383ef55781e7c59d7365258e5b -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -55,9 +55,9 @@ chrom_info = db_dataset.file_name else: # -- Get chrom_info (len file) from either a custom or built-in build. -- - if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): + 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' ] )[ input_dbkey ] + 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, # which will in turn create a recursive loop when https://bitbucket.org/galaxy/galaxy-central/commits/5c2c82003b8f/ Changeset: 5c2c82003b8f Branch: next-stable User: dannon Date: 2014-05-19 23:47:20 Summary: Fix get_chrom_info to take (and use) the tool in question. Affected #: 2 files diff -r d62fd7469c626064d8fe9792ea4584c57b5ed431 -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae 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, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r d62fd7469c626064d8fe9792ea4584c57b5ed431 -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -2,7 +2,7 @@ Functionality for dealing with dbkeys. """ #dbkeys read from disk using builds.txt -from galaxy.util import dbnames, galaxy_directory +from galaxy.util import dbnames from galaxy.util.json import from_json_string from galaxy.util.odict import odict import os.path @@ -44,7 +44,7 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, trans=None ): + def get_chrom_info( self, dbkey, tool, trans=None ): chrom_info = None db_dataset = None # Collect chromInfo from custom builds https://bitbucket.org/galaxy/galaxy-central/commits/3100a0f55b14/ Changeset: 3100a0f55b14 User: dannon Date: 2014-05-19 23:47:36 Summary: Merge next-stable. Affected #: 2 files diff -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 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, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -2,7 +2,7 @@ Functionality for dealing with dbkeys. """ #dbkeys read from disk using builds.txt -from galaxy.util import dbnames, galaxy_directory +from galaxy.util import dbnames from galaxy.util.json import from_json_string from galaxy.util.odict import odict import os.path @@ -44,7 +44,7 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, trans=None ): + def get_chrom_info( self, dbkey, tool, trans=None ): chrom_info = None db_dataset = None # Collect chromInfo from custom builds 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: dannon: Fix (kind of a guess as to the intended functionality) input_dbkey error.
by commits-noreply＠bitbucket.org 19 May '14

19 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d62fd7469c62/ Changeset: d62fd7469c62 Branch: next-stable User: dannon Date: 2014-05-19 23:42:05 Summary: Fix (kind of a guess as to the intended functionality) input_dbkey error. Affected #: 1 file diff -r e7bcba2bec53e16c8e11bb136da9f8aad9e430ba -r d62fd7469c626064d8fe9792ea4584c57b5ed431 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -55,9 +55,9 @@ chrom_info = db_dataset.file_name else: # -- Get chrom_info (len file) from either a custom or built-in build. -- - if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): + 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' ] )[ input_dbkey ] + 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, # which will in turn create a recursive loop when 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 19 May '14

19 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e7bcba2bec53/ Changeset: e7bcba2bec53 Branch: next-stable User: jmchilton Date: 2014-05-19 23:18:02 Summary: HACK: Fix circular dependency non-sense related to tools and dataset collections. https://gist.github.com/jmchilton/6e19d248002b1080e8ba. Affected #: 1 file diff -r c822084e6e5407c6ac80f999fa313808049e58f7 -r e7bcba2bec53e16c8e11bb136da9f8aad9e430ba lib/galaxy/tools/parameters/meta.py --- a/lib/galaxy/tools/parameters/meta.py +++ b/lib/galaxy/tools/parameters/meta.py @@ -2,8 +2,6 @@ from galaxy import model from galaxy import util from galaxy import exceptions -from galaxy.dataset_collections import matching -from galaxy.dataset_collections import subcollections import logging log = logging.getLogger( __name__ ) @@ -29,6 +27,7 @@ else: return permutations.input_classification.SINGLE, incoming[ input_key ] + from galaxy.dataset_collections import matching collections_to_match = matching.CollectionsToMatch() def collection_classifier( input_key ): @@ -52,6 +51,7 @@ hdc = trans.sa_session.query( model.HistoryDatasetCollectionAssociation ).get( hdc_id ) collections_to_match.add( input_key, hdc, subcollection_type=subcollection_type ) if subcollection_type is not None: + from galaxy.dataset_collections import subcollections subcollection_elements = subcollections.split_dataset_collection_instance( hdc, subcollection_type ) return permutations.input_classification.MATCHED, subcollection_elements else: https://bitbucket.org/galaxy/galaxy-central/commits/05302ebc7377/ Changeset: 05302ebc7377 User: jmchilton Date: 2014-05-19 23:18:31 Summary: Merge next-stable. Affected #: 1 file diff -r 35afd36f9014915c4c82f65b1c52a6636f48328e -r 05302ebc73772d383ef55781e7c59d7365258e5b lib/galaxy/tools/parameters/meta.py --- a/lib/galaxy/tools/parameters/meta.py +++ b/lib/galaxy/tools/parameters/meta.py @@ -2,8 +2,6 @@ from galaxy import model from galaxy import util from galaxy import exceptions -from galaxy.dataset_collections import matching -from galaxy.dataset_collections import subcollections import logging log = logging.getLogger( __name__ ) @@ -29,6 +27,7 @@ else: return permutations.input_classification.SINGLE, incoming[ input_key ] + from galaxy.dataset_collections import matching collections_to_match = matching.CollectionsToMatch() def collection_classifier( input_key ): @@ -52,6 +51,7 @@ hdc = trans.sa_session.query( model.HistoryDatasetCollectionAssociation ).get( hdc_id ) collections_to_match.add( input_key, hdc, subcollection_type=subcollection_type ) if subcollection_type is not None: + from galaxy.dataset_collections import subcollections subcollection_elements = subcollections.split_dataset_collection_instance( hdc, subcollection_type ) return permutations.input_classification.MATCHED, subcollection_elements else: 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: dannon: Merge from next-stable.
by commits-noreply＠bitbucket.org 19 May '14

19 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/35afd36f9014/ Changeset: 35afd36f9014 User: dannon Date: 2014-05-19 22:56:28 Summary: Merge from next-stable. Affected #: 7 files diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -18,6 +18,7 @@ from galaxy.tools.data_manager.manager import DataManagers from galaxy.jobs import metrics as job_metrics from galaxy.web.base import pluginframework +from galaxy.queue_worker import GalaxyQueueWorker import logging log = logging.getLogger( __name__ ) @@ -146,6 +147,10 @@ # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self ) self.model.engine.dispose() + self.control_worker = GalaxyQueueWorker(self, + galaxy.queues.control_queue_from_config(self.config), + galaxy.queue_worker.control_message_to_task) + self.control_worker.start() def shutdown( self ): self.job_manager.shutdown() diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -340,6 +340,17 @@ amqp_config = {} for k, v in amqp_config: self.amqp[k] = v + # Galaxy internal control queue configuration. + # If specified in universe, use it, otherwise we use whatever 'real' + # database is specified. Lastly, we create and use new sqlite database + # (to minimize locking) as a final option. + if 'amqp_internal_connection' in kwargs: + self.amqp_internal_connection = kwargs.get('amqp_internal_connection') + # TODO Get extra amqp args as necessary for ssl + elif 'database_connection' in kwargs: + self.amqp_internal_connection = "sqlalchemy+"+self.database_connection + else: + self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path( "database/control.sqlite", self.root ) self.biostar_url = kwargs.get( 'biostar_url', None ) self.biostar_key_name = kwargs.get( 'biostar_key_name', None ) self.biostar_key = kwargs.get( 'biostar_key', None ) diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/queue_worker.py --- /dev/null +++ b/lib/galaxy/queue_worker.py @@ -0,0 +1,94 @@ +""" +Galaxy control queue and worker. This is used to handle 'app' control like +reloading the toolbox, etc., across multiple processes. +""" + +import logging +import threading +import galaxy.queues +from galaxy import eggs, util +eggs.require('kombu') + +from kombu import Connection +from kombu.mixins import ConsumerMixin +from kombu.pools import producers + + +log = logging.getLogger(__name__) + + +class GalaxyQueueWorker(ConsumerMixin, threading.Thread): + """ + This is a flexible worker for galaxy's queues. Each process, web or + handler, will have one of these used for dispatching so called 'control' + tasks. + """ + def __init__(self, app, queue, task_mapping): + super(GalaxyQueueWorker, self).__init__() + log.info("Initalizing Galaxy Queue Worker on %s" % app.config.amqp_internal_connection) + self.connection = Connection(app.config.amqp_internal_connection) + self.app = app + # Eventually we may want different workers w/ their own queues and task + # mappings. Right now, there's only the one. + self.control_queue = queue + self.task_mapping = task_mapping + self.declare_queues = galaxy.queues.all_control_queues_for_declare(app.config) + # TODO we may want to purge the queue at the start to avoid executing + # stale 'reload_tool', etc messages. This can happen if, say, a web + # process goes down and messages get sent before it comes back up. + # Those messages will no longer be useful (in any current case) + + def get_consumers(self, Consumer, channel): + return [Consumer(queues=self.control_queue, + callbacks=[self.process_task])] + + def process_task(self, body, message): + if body['task'] in self.task_mapping: + if body.get('noop', None) != self.app.config.server_name: + try: + f = self.task_mapping[body['task']] + log.debug("Instance recieved '%s' task, executing now." % body['task']) + f(self.app, **body['kwargs']) + except Exception: + # this shouldn't ever throw an exception, but... + log.exception("Error running control task type: %s" % body['task']) + else: + log.warning("Recieved a malformed task message:\n%s" % body) + message.ack() + + +def send_control_task(trans, task, noop_self=False, kwargs={}): + log.info("Sending %s control task." % task) + payload = {'task': task, + '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') + + +# Tasks -- to be reorganized into a separate module as appropriate. This is +# just an example method. Ideally this gets pushed into atomic tasks, whether +# where they're currently invoked, or elsewhere. (potentially using a dispatch +# decorator). +def reload_tool(app, **kwargs): + params = util.Params(kwargs) + tool_id = params.get('tool_id', None) + log.debug("Executing reload tool task for %s" % tool_id) + if tool_id: + app.toolbox.reload_tool_by_id( tool_id ) + else: + log.error("Reload tool invoked without tool id.") + + +def reload_tool_data_tables(app, **kwargs): + params = util.Params(kwargs) + log.debug("Executing tool data table reload for %s" % params.get('table_names', 'all tables')) + table_names = app.tool_data_tables.reload_tables( table_names=params.get('table_name', None)) + log.debug("Finished data table reload for %s" % table_names) + +control_message_to_task = { 'reload_tool': reload_tool, + 'reload_tool_data_tables': reload_tool_data_tables} diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/queues.py --- /dev/null +++ b/lib/galaxy/queues.py @@ -0,0 +1,32 @@ +""" + +All message queues used by Galaxy + +""" + +from galaxy import eggs + +eggs.require("kombu") +from kombu import Exchange, Queue + +ALL_CONTROL = "control.*" +galaxy_exchange = Exchange('galaxy_core_exchange', type='topic') + + +def all_control_queues_for_declare(config): + """ + For in-memory routing (used by sqlalchemy-based transports), we need to be able to + build the entire routing table in producers. + + Refactor later to actually persist this somewhere instead of building it repeatedly. + """ + return [Queue('control.%s' % q, galaxy_exchange, routing_key='control') for q in config.server_names] + + +def control_queue_from_config(config): + """ + Returns a Queue instance with the correct name and routing key for this + galaxy process's config + """ + return Queue("control.%s" % config.server_name, galaxy_exchange, + routing_key='control') diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -5,6 +5,7 @@ from galaxy.util import inflector from galaxy.web.form_builder import CheckboxField from string import punctuation as PUNCTUATION +import galaxy.queue_worker log = logging.getLogger( __name__ ) @@ -62,8 +63,9 @@ toolbox = self.app.toolbox tool_id = None if params.get( 'reload_tool_button', False ): - tool_id = params.tool_id - message, status = toolbox.reload_tool_by_id( tool_id ) + tool_id = params.get('tool_id', None) + galaxy.queue_worker.send_control_task(trans, 'reload_tool', noop_self=True, kwargs={'tool_id': tool_id} ) + message, status = trans.app.toolbox.reload_tool_by_id( tool_id) return trans.fill_template( '/admin/reload_tool.mako', tool_id=tool_id, toolbox=toolbox, diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -1,6 +1,7 @@ +import galaxy.queue_worker from galaxy import web +from galaxy.util.json import from_json_string from galaxy.web.base.controller import BaseUIController -from galaxy.util.json import from_json_string import pkg_resources; pkg_resources.require( "Paste" ) @@ -90,6 +91,9 @@ table_name = table_name.split( "," ) # Reload the tool data tables table_names = self.app.tool_data_tables.reload_tables( table_names=table_name ) + galaxy.queue_worker.send_control_task(trans, 'reload_tool_data_tables', + noop_self=True, + kwargs={'table_name': table_name} ) redirect_url = None if table_names: status = 'done' diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -821,7 +821,21 @@ #user_tool_section_filters = examples:restrict_text #user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode -# ---- Galaxy Message Queue ------------------------------------------------- +# Galaxy Application Internal Message Queue + +# Galaxy uses AMQP internally TODO more documentation on what for. +# For examples, see http://ask.github.io/kombu/userguide/connections.html +# +# Without specifying anything here, galaxy will first attempt to use your +# specified database_connection above. If that's not specified either, Galaxy +# 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" + + + +# ---- Galaxy External Message Queue ------------------------------------------------- # Galaxy uses AMQ protocol to receive messages from external sources like # bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. 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: dannon: Initial internal control message queue for IPC implementation. Needs significant refactoring, as noted in some TODOs, but this is a minimally functional version so it makes the next-stable cutoff. Currently only handles reloading tools and data tables, but adding additional tasks is simple and should be straightforward.
by commits-noreply＠bitbucket.org 19 May '14

19 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c822084e6e54/ Changeset: c822084e6e54 Branch: next-stable User: dannon Date: 2014-05-19 22:56:08 Summary: Initial internal control message queue for IPC implementation. Needs significant refactoring, as noted in some TODOs, but this is a minimally functional version so it makes the next-stable cutoff. Currently only handles reloading tools and data tables, but adding additional tasks is simple and should be straightforward. Affected #: 7 files diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -18,6 +18,7 @@ from galaxy.tools.data_manager.manager import DataManagers from galaxy.jobs import metrics as job_metrics from galaxy.web.base import pluginframework +from galaxy.queue_worker import GalaxyQueueWorker import logging log = logging.getLogger( __name__ ) @@ -146,6 +147,10 @@ # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self ) self.model.engine.dispose() + self.control_worker = GalaxyQueueWorker(self, + galaxy.queues.control_queue_from_config(self.config), + galaxy.queue_worker.control_message_to_task) + self.control_worker.start() def shutdown( self ): self.job_manager.shutdown() diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -340,6 +340,17 @@ amqp_config = {} for k, v in amqp_config: self.amqp[k] = v + # Galaxy internal control queue configuration. + # If specified in universe, use it, otherwise we use whatever 'real' + # database is specified. Lastly, we create and use new sqlite database + # (to minimize locking) as a final option. + if 'amqp_internal_connection' in kwargs: + self.amqp_internal_connection = kwargs.get('amqp_internal_connection') + # TODO Get extra amqp args as necessary for ssl + elif 'database_connection' in kwargs: + self.amqp_internal_connection = "sqlalchemy+"+self.database_connection + else: + self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path( "database/control.sqlite", self.root ) self.biostar_url = kwargs.get( 'biostar_url', None ) self.biostar_key_name = kwargs.get( 'biostar_key_name', None ) self.biostar_key = kwargs.get( 'biostar_key', None ) diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/queue_worker.py --- /dev/null +++ b/lib/galaxy/queue_worker.py @@ -0,0 +1,94 @@ +""" +Galaxy control queue and worker. This is used to handle 'app' control like +reloading the toolbox, etc., across multiple processes. +""" + +import logging +import threading +import galaxy.queues +from galaxy import eggs, util +eggs.require('kombu') + +from kombu import Connection +from kombu.mixins import ConsumerMixin +from kombu.pools import producers + + +log = logging.getLogger(__name__) + + +class GalaxyQueueWorker(ConsumerMixin, threading.Thread): + """ + This is a flexible worker for galaxy's queues. Each process, web or + handler, will have one of these used for dispatching so called 'control' + tasks. + """ + def __init__(self, app, queue, task_mapping): + super(GalaxyQueueWorker, self).__init__() + log.info("Initalizing Galaxy Queue Worker on %s" % app.config.amqp_internal_connection) + self.connection = Connection(app.config.amqp_internal_connection) + self.app = app + # Eventually we may want different workers w/ their own queues and task + # mappings. Right now, there's only the one. + self.control_queue = queue + self.task_mapping = task_mapping + self.declare_queues = galaxy.queues.all_control_queues_for_declare(app.config) + # TODO we may want to purge the queue at the start to avoid executing + # stale 'reload_tool', etc messages. This can happen if, say, a web + # process goes down and messages get sent before it comes back up. + # Those messages will no longer be useful (in any current case) + + def get_consumers(self, Consumer, channel): + return [Consumer(queues=self.control_queue, + callbacks=[self.process_task])] + + def process_task(self, body, message): + if body['task'] in self.task_mapping: + if body.get('noop', None) != self.app.config.server_name: + try: + f = self.task_mapping[body['task']] + log.debug("Instance recieved '%s' task, executing now." % body['task']) + f(self.app, **body['kwargs']) + except Exception: + # this shouldn't ever throw an exception, but... + log.exception("Error running control task type: %s" % body['task']) + else: + log.warning("Recieved a malformed task message:\n%s" % body) + message.ack() + + +def send_control_task(trans, task, noop_self=False, kwargs={}): + log.info("Sending %s control task." % task) + payload = {'task': task, + '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') + + +# Tasks -- to be reorganized into a separate module as appropriate. This is +# just an example method. Ideally this gets pushed into atomic tasks, whether +# where they're currently invoked, or elsewhere. (potentially using a dispatch +# decorator). +def reload_tool(app, **kwargs): + params = util.Params(kwargs) + tool_id = params.get('tool_id', None) + log.debug("Executing reload tool task for %s" % tool_id) + if tool_id: + app.toolbox.reload_tool_by_id( tool_id ) + else: + log.error("Reload tool invoked without tool id.") + + +def reload_tool_data_tables(app, **kwargs): + params = util.Params(kwargs) + log.debug("Executing tool data table reload for %s" % params.get('table_names', 'all tables')) + table_names = app.tool_data_tables.reload_tables( table_names=params.get('table_name', None)) + log.debug("Finished data table reload for %s" % table_names) + +control_message_to_task = { 'reload_tool': reload_tool, + 'reload_tool_data_tables': reload_tool_data_tables} diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/queues.py --- /dev/null +++ b/lib/galaxy/queues.py @@ -0,0 +1,32 @@ +""" + +All message queues used by Galaxy + +""" + +from galaxy import eggs + +eggs.require("kombu") +from kombu import Exchange, Queue + +ALL_CONTROL = "control.*" +galaxy_exchange = Exchange('galaxy_core_exchange', type='topic') + + +def all_control_queues_for_declare(config): + """ + For in-memory routing (used by sqlalchemy-based transports), we need to be able to + build the entire routing table in producers. + + Refactor later to actually persist this somewhere instead of building it repeatedly. + """ + return [Queue('control.%s' % q, galaxy_exchange, routing_key='control') for q in config.server_names] + + +def control_queue_from_config(config): + """ + Returns a Queue instance with the correct name and routing key for this + galaxy process's config + """ + return Queue("control.%s" % config.server_name, galaxy_exchange, + routing_key='control') diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -5,6 +5,7 @@ from galaxy.util import inflector from galaxy.web.form_builder import CheckboxField from string import punctuation as PUNCTUATION +import galaxy.queue_worker log = logging.getLogger( __name__ ) @@ -62,8 +63,9 @@ toolbox = self.app.toolbox tool_id = None if params.get( 'reload_tool_button', False ): - tool_id = params.tool_id - message, status = toolbox.reload_tool_by_id( tool_id ) + tool_id = params.get('tool_id', None) + galaxy.queue_worker.send_control_task(trans, 'reload_tool', noop_self=True, kwargs={'tool_id': tool_id} ) + message, status = trans.app.toolbox.reload_tool_by_id( tool_id) return trans.fill_template( '/admin/reload_tool.mako', tool_id=tool_id, toolbox=toolbox, diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -1,6 +1,7 @@ +import galaxy.queue_worker from galaxy import web +from galaxy.util.json import from_json_string from galaxy.web.base.controller import BaseUIController -from galaxy.util.json import from_json_string import pkg_resources; pkg_resources.require( "Paste" ) @@ -90,6 +91,9 @@ table_name = table_name.split( "," ) # Reload the tool data tables table_names = self.app.tool_data_tables.reload_tables( table_names=table_name ) + galaxy.queue_worker.send_control_task(trans, 'reload_tool_data_tables', + noop_self=True, + kwargs={'table_name': table_name} ) redirect_url = None if table_names: status = 'done' diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -821,7 +821,21 @@ #user_tool_section_filters = examples:restrict_text #user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode -# ---- Galaxy Message Queue ------------------------------------------------- +# Galaxy Application Internal Message Queue + +# Galaxy uses AMQP internally TODO more documentation on what for. +# For examples, see http://ask.github.io/kombu/userguide/connections.html +# +# Without specifying anything here, galaxy will first attempt to use your +# specified database_connection above. If that's not specified either, Galaxy +# 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" + + + +# ---- Galaxy External Message Queue ------------------------------------------------- # Galaxy uses AMQ protocol to receive messages from external sources like # bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. 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 19 May '14

19 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da128dd1ab03/ Changeset: da128dd1ab03 Branch: next-stable User: davebgx Date: 2014-05-19 22:38:58 Summary: Remove migrated tools from main's tool_conf.xml Affected #: 1 file diff -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 -r da128dd1ab03d905da0cf8dafec70443267cff64 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -41,12 +41,10 @@ </section><section id="convert" name="Convert Formats"><tool file="filters/bed2gff.xml" /> - <tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="filters/gff2bed.xml" /><tool file="maf/maf_to_bed.xml" /><tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" /> - <tool file="fasta_tools/tabular_to_fasta.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/wig_to_bigwig.xml" /><tool file="filters/bed_to_bigbed.xml" /> https://bitbucket.org/galaxy/galaxy-central/commits/174b6a2281e5/ Changeset: 174b6a2281e5 User: davebgx Date: 2014-05-19 22:39:25 Summary: Merge with next-stable. Affected #: 1 file diff -r 9b33b543fb1448f8f775ac975e2605ac610c8f63 -r 174b6a2281e53793a8188ba2b2792d0dd220d362 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -41,12 +41,10 @@ </section><section id="convert" name="Convert Formats"><tool file="filters/bed2gff.xml" /> - <tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="filters/gff2bed.xml" /><tool file="maf/maf_to_bed.xml" /><tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" /> - <tool file="fasta_tools/tabular_to_fasta.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/wig_to_bigwig.xml" /><tool file="filters/bed_to_bigbed.xml" /> 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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