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commit/galaxy-central: natefoo: Instead of raising in exception, default to english if a locale is set by the client but not installed on the server.
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2b7295ac12dc/ changeset: r5051:2b7295ac12dc user: natefoo date: 2011-02-11 22:15:18 summary: Instead of raising in exception, default to english if a locale is set by the client but not installed on the server. affected #: 1 file (177 bytes) --- a/lib/galaxy/web/framework/__init__.py Fri Feb 11 15:32:13 2011 -0500 +++ b/lib/galaxy/web/framework/__init__.py Fri Feb 11 16:15:18 2011 -0500 @@ -27,7 +27,7 @@ pkg_resources.require( "Babel" ) from babel.support import Translations -from babel import Locale +from babel import Locale, UnknownLocaleError pkg_resources.require( "SQLAlchemy >= 0.4" ) from sqlalchemy import and_ @@ -198,11 +198,16 @@ # and such). self.workflow_building_mode = False def setup_i18n( self ): + locales = [] if 'HTTP_ACCEPT_LANGUAGE' in self.environ: # locales looks something like: ['en', 'en-us;q=0.7', 'ja;q=0.3'] locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split( ',' ) - locales = [ Locale.parse(l.split( ';' )[0], sep='-').language for l in locales ] - else: + for locale in locales: + try: + locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language ) + except UnknownLocaleError: + pass + if not locales: # Default to English locales = 'en' t = Translations.load( dirname='locale', locales=locales, domain='ginga' ) 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: natefoo: The Galaxy-side job runner for execution via LWR, a light weight cluster setup written by John Chilton. For more information on implementing the cluster, see: https://bitbucket.org/jmchilton/lwr/
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/74048a9ab689/ changeset: r5050:74048a9ab689 user: natefoo date: 2011-02-11 21:32:13 summary: The Galaxy-side job runner for execution via LWR, a light weight cluster setup written by John Chilton. For more information on implementing the cluster, see: https://bitbucket.org/jmchilton/lwr/ affected #: 1 file (0 bytes) 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: natefoo: Handle bugs encountered when fetching an egg during a version conflict and a sys.path item has been removed.
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a5846ac40596/ changeset: r5049:a5846ac40596 user: natefoo date: 2011-02-11 21:01:04 summary: Handle bugs encountered when fetching an egg during a version conflict and a sys.path item has been removed. affected #: 1 file (939 bytes) --- a/lib/galaxy/eggs/__init__.py Fri Feb 11 14:17:22 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Fri Feb 11 15:01:04 2011 -0500 @@ -45,6 +45,7 @@ self.crate = crate self.distribution = None self.dir = None + self.removed_location = None if self.name is not None and self.version is not None: self.set_distribution() def set_dir( self ): @@ -103,34 +104,50 @@ pkg_resources.compatible_platforms( tmp_dist.platform, pkg_resources.get_platform() ): return file return None - if self.url is None: - return None - alternative = None - try: - url = self.url + '/' + self.distribution.egg_name() + '.egg' - URLRetriever().retrieve( url, self.distribution.location ) - log.debug( "Fetched %s" % url ) - except IOError, e: - if e[1] == 404 and self.distribution.platform != py: - alternative = find_alternative() - if alternative is None: - return None - else: - return None - if alternative is not None: + def _fetch(): + if self.url is None: + return False + alternative = None try: - url = '/'.join( ( self.url, alternative ) ) - URLRetriever().retrieve( url, os.path.join( self.dir, alternative ) ) + url = self.url + '/' + self.distribution.egg_name() + '.egg' + URLRetriever().retrieve( url, self.distribution.location ) log.debug( "Fetched %s" % url ) except IOError, e: - return None - self.platform = alternative.split( '-', 2 )[-1].rsplit( '.egg', 1 )[0] - self.set_distribution() - self.unpack_if_needed() - self.remove_doppelgangers() - global env - env = get_env() # reset the global Environment object now that we've obtained a new egg - return self.distribution + if e[1] == 404 and self.distribution.platform != py: + alternative = find_alternative() + if alternative is None: + return False + else: + return False + if alternative is not None: + try: + url = '/'.join( ( self.url, alternative ) ) + URLRetriever().retrieve( url, os.path.join( self.dir, alternative ) ) + log.debug( "Fetched %s" % url ) + except IOError, e: + return False + self.platform = alternative.split( '-', 2 )[-1].rsplit( '.egg', 1 )[0] + self.set_distribution() + self.unpack_if_needed() + self.remove_doppelgangers() + return True + # If being called from a version conflict, that code has removed a + # directory from sys.path. That directory could be Python's main lib + # directory (e.g. in the case of wsgiref under 2.6). Temporarily put + # it back during the execution of this code. + if self.removed_location: + sys.path.append( self.removed_location ) + try: + assert _fetch() + rval = self.distribution + except: + rval = None + if self.removed_location: + sys.path.remove( self.removed_location ) + if rval is not None: + global env + env = get_env() # reset the global Environment object now that we've obtained a new egg + return rval def unpack_if_needed( self ): meta = pkg_resources.EggMetadata( zipimport.zipimporter( self.distribution.location ) ) if meta.has_metadata( 'not-zip-safe' ): @@ -200,7 +217,10 @@ sys.path.remove(entry) # if the conflict is a dpeendent egg, fetch that specific egg if egg: + # Store the removed path so the fetch method can use it + egg.removed_location = location r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) + egg.removed_location = None else: r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env ) # re-add the path if it's a non-egg dir, in case more deps live there 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: natefoo: Fix a minor bug which mad it completely impossible to run a job.
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4397e753ec2c/ changeset: r5048:4397e753ec2c user: natefoo date: 2011-02-11 20:17:22 summary: Fix a minor bug which mad it completely impossible to run a job. affected #: 1 file (1 byte) --- a/lib/galaxy/jobs/__init__.py Fri Feb 11 13:12:27 2011 -0500 +++ b/lib/galaxy/jobs/__init__.py Fri Feb 11 14:17:22 2011 -0500 @@ -1033,7 +1033,7 @@ for obj in module.__all__: display_name = ':'.join( ( module_name, obj ) ) runner = getattr( module, obj ) - self.job_runners[obj] = runner( self.app ) + self.job_runners[name] = runner( self.app ) log.debug( 'Loaded job runner: %s' % display_name ) def put( self, job_wrapper ): 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: natefoo: Make loading of job runners dynamic. Changes to lib/galaxy/config.py and lib/galaxy/jobs/__init__.py are no longer required. Existing runners which are not part of the Galaxy source will need to define the class name to instantiate in the __all__ list in the runner. See the included runners for an example.
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6937b1a3b3a2/ changeset: r5047:6937b1a3b3a2 user: natefoo date: 2011-02-11 19:12:27 summary: Make loading of job runners dynamic. Changes to lib/galaxy/config.py and lib/galaxy/jobs/__init__.py are no longer required. Existing runners which are not part of the Galaxy source will need to define the class name to instantiate in the __all__ list in the runner. See the included runners for an example. affected #: 7 files (2.2 KB) --- a/lib/galaxy/config.py Fri Feb 11 09:27:10 2011 -0500 +++ b/lib/galaxy/config.py Fri Feb 11 13:12:27 2011 -0500 @@ -189,16 +189,6 @@ for path in self.tool_config, self.datatypes_config: if not os.path.isfile(path): raise ConfigurationError("File not found: %s" % path ) - # Check job runners so the admin can scramble dependent egg. - if self.start_job_runners is not None: - runner_to_egg = dict( pbs = 'pbs_python', sge = 'DRMAA_python', drmaa = 'drmaa' ) - for runner in self.start_job_runners.split( ',' ): - try: - pkg_resources.require( runner_to_egg[runner] ) - except eggs.EggNotFetchable, e: - raise eggs.EggNotFetchable( 'You must scramble the %s egg to use the %s job runner. Instructions are available at:\n http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster' % ( runner_to_egg[runner], runner ) ) - except KeyError: - raise Exception( 'No such job runner: %s. Please double-check the value of start_job_runners in universe_wsgi.ini' % runner ) # Check for deprecated options. for key in self.config_dict.keys(): if key in self.deprecated_options: --- a/lib/galaxy/jobs/__init__.py Fri Feb 11 09:27:10 2011 -0500 +++ b/lib/galaxy/jobs/__init__.py Fri Feb 11 13:12:27 2011 -0500 @@ -1015,44 +1015,58 @@ start_job_runners.extend( app.config.start_job_runners.split(",") ) if app.config.use_tasked_jobs: start_job_runners.append("tasks") - for runner_name in start_job_runners: - if runner_name == "local": - import runners.local - self.job_runners[runner_name] = runners.local.LocalJobRunner( app ) - elif runner_name == "tasks": - import runners.tasks - self.job_runners[runner_name] = runners.tasks.TaskedJobRunner( app ) - elif runner_name == "pbs": - import runners.pbs - self.job_runners[runner_name] = runners.pbs.PBSJobRunner( app ) - elif runner_name == "sge": - import runners.sge - self.job_runners[runner_name] = runners.sge.SGEJobRunner( app ) - elif runner_name == "drmaa": - import runners.drmaa - self.job_runners[runner_name] = runners.drmaa.DRMAAJobRunner( app ) - else: - log.error( "Unable to start unknown job runner: '%s'" %runner_name ) + for name in start_job_runners: + self._load_plugin( name ) + + def _load_plugin( self, name ): + module_name = 'galaxy.jobs.runners.' + name + try: + module = __import__( module_name ) + except: + log.exception( 'Job runner is not loadable: %s' % module_name ) + return + for comp in module_name.split( "." )[1:]: + module = getattr( module, comp ) + if '__all__' not in dir( module ): + log.error( 'Runner "%s" does not contain a list of exported classes in __all__' % module_name ) + return + for obj in module.__all__: + display_name = ':'.join( ( module_name, obj ) ) + runner = getattr( module, obj ) + self.job_runners[obj] = runner( self.app ) + log.debug( 'Loaded job runner: %s' % display_name ) def put( self, job_wrapper ): - if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper): - runner_name = "tasks" - log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) - self.job_runners[runner_name].put( job_wrapper ) - else: - runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0] - log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) - self.job_runners[runner_name].put( job_wrapper ) + try: + if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper): + runner_name = "tasks" + log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) + self.job_runners[runner_name].put( job_wrapper ) + else: + runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0] + log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) + self.job_runners[runner_name].put( job_wrapper ) + except KeyError: + log.error( 'put(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) + job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) def stop( self, job ): runner_name = ( job.job_runner_name.split(":", 1) )[0] log.debug( "stopping job %d in %s runner" %( job.id, runner_name ) ) - self.job_runners[runner_name].stop_job( job ) + try: + self.job_runners[runner_name].stop_job( job ) + except KeyError: + log.error( 'stop(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) + # Job and output dataset states have already been updated, so nothing is done here. def recover( self, job, job_wrapper ): runner_name = ( job.job_runner_name.split(":", 1) )[0] log.debug( "recovering job %d in %s runner" %( job.id, runner_name ) ) - self.job_runners[runner_name].recover( job, job_wrapper ) + try: + self.job_runners[runner_name].recover( job, job_wrapper ) + except KeyError: + log.error( 'recover(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) + job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) def shutdown( self ): for runner in self.job_runners.itervalues(): --- a/lib/galaxy/jobs/runners/drmaa.py Fri Feb 11 09:27:10 2011 -0500 +++ b/lib/galaxy/jobs/runners/drmaa.py Fri Feb 11 13:12:27 2011 -0500 @@ -8,29 +8,29 @@ import pkg_resources -try: - if sys.version_info[:2] == ( 2, 4 ): - pkg_resources.require( "ctypes" ) - pkg_resources.require( "drmaa" ) - drmaa = __import__( "drmaa" ) -except Exception, e: - drmaa = str( e ) +if sys.version_info[:2] == ( 2, 4 ): + pkg_resources.require( "ctypes" ) +pkg_resources.require( "drmaa" ) +# We foolishly named this file the same as the name exported by the drmaa +# library... 'import drmaa' import itself. +drmaa = __import__( "drmaa" ) log = logging.getLogger( __name__ ) -if type( drmaa ) != str: - drmaa_state = { - drmaa.JobState.UNDETERMINED: 'process status cannot be determined', - drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active', - drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold', - drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold', - drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold', - drmaa.JobState.RUNNING: 'job is running', - drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended', - drmaa.JobState.USER_SUSPENDED: 'job is user suspended', - drmaa.JobState.DONE: 'job finished normally', - drmaa.JobState.FAILED: 'job finished, but failed', - } +__all__ = [ 'DRMAAJobRunner' ] + +drmaa_state = { + drmaa.JobState.UNDETERMINED: 'process status cannot be determined', + drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active', + drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold', + drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold', + drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold', + drmaa.JobState.RUNNING: 'job is running', + drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended', + drmaa.JobState.USER_SUSPENDED: 'job is user suspended', + drmaa.JobState.DONE: 'job finished normally', + drmaa.JobState.FAILED: 'job finished, but failed', +} drm_template = """#!/bin/sh #$ -S /bin/sh @@ -70,8 +70,6 @@ def __init__( self, app ): """Initialize this job runner and start the monitor thread""" # Check if drmaa was importable, fail if not - if type( drmaa ) == str: - raise Exception( "DRMAAJobRunner requires drmaa module which could not be loaded: %s" % drmaa ) self.app = app self.sa_session = app.model.context # 'watched' and 'queue' are both used to keep track of jobs to watch. --- a/lib/galaxy/jobs/runners/local.py Fri Feb 11 09:27:10 2011 -0500 +++ b/lib/galaxy/jobs/runners/local.py Fri Feb 11 13:12:27 2011 -0500 @@ -12,6 +12,8 @@ log = logging.getLogger( __name__ ) +__all__ = [ 'LocalJobRunner' ] + class LocalJobRunner( BaseJobRunner ): """ Job runner backed by a finite pool of worker threads. FIFO scheduling --- a/lib/galaxy/jobs/runners/pbs.py Fri Feb 11 09:27:10 2011 -0500 +++ b/lib/galaxy/jobs/runners/pbs.py Fri Feb 11 13:12:27 2011 -0500 @@ -11,14 +11,28 @@ import pkg_resources +egg_message = """ + +The 'pbs' runner depends on 'pbs_python' which is not installed or not +configured properly. Galaxy's "scramble" system should make this installation +simple, please follow the instructions found at: + + http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster + +Additional errors may follow: +%s +""" + try: pkg_resources.require( "pbs_python" ) - pbs = __import__( "pbs" ) -except: - pbs = None + import pbs +except Exception, e: + raise Exception( egg_message % str( e ) ) log = logging.getLogger( __name__ ) +__all__ = [ 'PBSJobRunner' ] + pbs_template = """#!/bin/sh GALAXY_LIB="%s" if [ "$GALAXY_LIB" != "None" ]; then --- a/lib/galaxy/jobs/runners/sge.py Fri Feb 11 09:27:10 2011 -0500 +++ b/lib/galaxy/jobs/runners/sge.py Fri Feb 11 13:12:27 2011 -0500 @@ -8,27 +8,42 @@ import pkg_resources +egg_message = """ + +The 'sge' runner depends on 'DRMAA_python' which is not installed. Galaxy's +"scramble" system should make this installation simple, please follow the +instructions found at: + + http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster + +Additional errors may follow: +%s +""" + + try: pkg_resources.require( "DRMAA_python" ) - DRMAA = __import__( "DRMAA" ) -except: - DRMAA = None + import DRMAA +except Exception, e: + raise Exception( egg_message % str( e ) ) + log = logging.getLogger( __name__ ) -if DRMAA is not None: - DRMAA_state = { - DRMAA.Session.UNDETERMINED: 'process status cannot be determined', - DRMAA.Session.QUEUED_ACTIVE: 'job is queued and waiting to be scheduled', - DRMAA.Session.SYSTEM_ON_HOLD: 'job is queued and in system hold', - DRMAA.Session.USER_ON_HOLD: 'job is queued and in user hold', - DRMAA.Session.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold', - DRMAA.Session.RUNNING: 'job is running', - DRMAA.Session.SYSTEM_SUSPENDED: 'job is system suspended', - DRMAA.Session.USER_SUSPENDED: 'job is user suspended', - DRMAA.Session.DONE: 'job finished normally', - DRMAA.Session.FAILED: 'job finished, but failed', - } +__all__ = [ 'SGEJobRunner' ] + +DRMAA_state = { + DRMAA.Session.UNDETERMINED: 'process status cannot be determined', + DRMAA.Session.QUEUED_ACTIVE: 'job is queued and waiting to be scheduled', + DRMAA.Session.SYSTEM_ON_HOLD: 'job is queued and in system hold', + DRMAA.Session.USER_ON_HOLD: 'job is queued and in user hold', + DRMAA.Session.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold', + DRMAA.Session.RUNNING: 'job is running', + DRMAA.Session.SYSTEM_SUSPENDED: 'job is system suspended', + DRMAA.Session.USER_SUSPENDED: 'job is user suspended', + DRMAA.Session.DONE: 'job finished normally', + DRMAA.Session.FAILED: 'job finished, but failed', +} sge_template = """#!/bin/sh #$ -S /bin/sh @@ -67,9 +82,6 @@ STOP_SIGNAL = object() def __init__( self, app ): """Initialize this job runner and start the monitor thread""" - # Check if SGE was importable, fail if not - if DRMAA is None: - raise Exception( "SGEJobRunner requires DRMAA_python which was not found" ) self.app = app self.sa_session = app.model.context # 'watched' and 'queue' are both used to keep track of jobs to watch. --- a/lib/galaxy/jobs/runners/tasks.py Fri Feb 11 09:27:10 2011 -0500 +++ b/lib/galaxy/jobs/runners/tasks.py Fri Feb 11 13:12:27 2011 -0500 @@ -12,6 +12,8 @@ log = logging.getLogger( __name__ ) +__all__ = [ 'TaskedJobRunner' ] + class TaskedJobRunner( object ): """ Job runner backed by a finite pool of worker threads. FIFO scheduling 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: guru: Updated path to sputnik binary in 'Extract orthologous microsatellites for multiple (>2) species alignments' tool
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/68c394e5dda8/ changeset: r5046:68c394e5dda8 user: guru date: 2011-02-11 15:27:10 summary: Updated path to sputnik binary in 'Extract orthologous microsatellites for multiple (>2) species alignments' tool affected #: 1 file (52 bytes) --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Fri Feb 11 08:42:05 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Fri Feb 11 09:27:10 2011 -0500 @@ -18,7 +18,7 @@ #------------------------------------------------------------------------------- # WHICH SPUTNIK USED? my $sputnikpath = (); -$sputnikpath = "/Users/ydk/work/rhesus_microsat/codes/./sputnik_Mac-PowerPC"; +$sputnikpath = "sputnik"; #print "sputnik_Mac-PowerPC non-existant\n" if !-e $sputnikpath; #exit if !-e $sputnikpath; #$sputnikpath = "bx-sputnik" ; 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: jgoecks: Fix searching functionality and labels in published item grids.
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a8bfcfeca73b/ changeset: r5045:a8bfcfeca73b user: jgoecks date: 2011-02-11 14:42:05 summary: Fix searching functionality and labels in published item grids. affected #: 4 files (174 bytes) --- a/lib/galaxy/web/controllers/history.py Fri Feb 11 00:53:49 2011 -0500 +++ b/lib/galaxy/web/controllers/history.py Fri Feb 11 08:42:05 2011 -0500 @@ -135,15 +135,15 @@ columns = [ NameURLColumn( "Name", key="name", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [] --- a/lib/galaxy/web/controllers/page.py Fri Feb 11 00:53:49 2011 -0500 +++ b/lib/galaxy/web/controllers/page.py Fri Feb 11 08:42:05 2011 -0500 @@ -63,15 +63,15 @@ columns = [ grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ], + "Search title, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) def build_initial_query( self, trans, **kwargs ): --- a/lib/galaxy/web/controllers/visualization.py Fri Feb 11 00:53:49 2011 -0500 +++ b/lib/galaxy/web/controllers/visualization.py Fri Feb 11 08:42:05 2011 -0500 @@ -50,15 +50,15 @@ columns = [ grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ], + "Search title, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) def build_initial_query( self, trans, **kwargs ): --- a/lib/galaxy/web/controllers/workflow.py Fri Feb 11 00:53:49 2011 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Fri Feb 11 08:42:05 2011 -0500 @@ -66,15 +66,15 @@ columns = [ grids.PublicURLColumn( "Name", key="name", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: trackster: Properly return NO_DATA for LineTrack datasets, fix error when no data is available
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/384f3b803e64/ changeset: r5044:384f3b803e64 user: kanwei date: 2011-02-11 06:53:49 summary: trackster: Properly return NO_DATA for LineTrack datasets, fix error when no data is available affected #: 3 files (329 bytes) --- a/lib/galaxy/datatypes/interval.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/datatypes/interval.py Fri Feb 11 00:53:49 2011 -0500 @@ -1161,7 +1161,7 @@ resolution = max( resolution, 1 ) return resolution def get_track_type( self ): - return "LineTrack", {"data": "bigwig"} + return "LineTrack", {"data": "bigwig", "index": "bigwig"} class CustomTrack ( Tabular ): """UCSC CustomTrack""" --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Fri Feb 11 00:53:49 2011 -0500 @@ -48,13 +48,13 @@ # Override. pass - def has_data( self, chrom, start, end ): + def has_data( self, chrom, start, end, **kwargs ): """ Returns true if dataset has data in the specified genome window, false otherwise. """ # Override. - return False + pass def get_data( self, chrom, start, end, **kwargs ): """ Returns data in region defined by chrom, start, and end. """ @@ -140,10 +140,9 @@ else: return results, stats[level]["max"], stats[level]["avg"], stats[level]["delta"] - def has_data( self, chrom, start, end ): + def has_data( self, chrom ): """ - Returns true if dataset has data in the specified genome window, false - otherwise. + Returns true if dataset has data for this chrom """ # Get summary tree. @@ -154,8 +153,7 @@ self.CACHE[filename] = st # Check for data. - level = ceil( log( 100000, st.block_size ) ) - 1 - return ( st.query( chrom, int(start), int(end), level ) is not None ) + return st.chrom_blocks.get(chrom, None) is not None class VcfDataProvider( TracksDataProvider ): """ @@ -405,14 +403,24 @@ """ BigWig data provider for the Galaxy track browser. """ - - def get_data( self, chrom, start, end, **kwargs ): - # Bigwig has the possibility of it being a standalone bigwig file, in which case we use - # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset + def _get_dataset( self ): if self.converted_dataset is not None: f = open( self.converted_dataset.file_name ) else: f = open( self.original_dataset.file_name ) + return f + + def has_data( self, chrom ): + f = self._get_dataset() + bw = BigWigFile(file=f) + all_dat = bw.query(chrom, 0, 2147483647, 1) + f.close() + return all_dat is not None + + def get_data( self, chrom, start, end, **kwargs ): + # Bigwig has the possibility of it being a standalone bigwig file, in which case we use + # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset + f = self._get_dataset() bw = BigWigFile(file=f) if 'stats' in kwargs: @@ -426,7 +434,6 @@ 'min': float( all_dat['min'] ), \ 'total_frequency': float( all_dat['coverage'] ) } - start = int(start) end = int(end) num_points = 2000 @@ -439,9 +446,10 @@ pos = start step_size = (end - start) / num_points result = [] - for dat_dict in data: - result.append( (pos, float_nan(dat_dict['mean']) ) ) - pos += step_size + if data: + for dat_dict in data: + result.append( (pos, float_nan(dat_dict['mean']) ) ) + pos += step_size return result --- a/lib/galaxy/web/controllers/tracks.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 11 00:53:49 2011 -0500 @@ -458,13 +458,17 @@ return msg # Check for data in the genome window. - # TODO: Not all tracks have an index data source, so need to try alternative data sources to check for data. - if chrom and low and high and data_sources.get( 'index' ): + if data_sources.get( 'index' ): tracks_dataset_type = data_sources['index']['name'] indexer = get_data_provider( tracks_dataset_type )( dataset.get_converted_dataset( trans, tracks_dataset_type ), dataset ) - if not indexer.has_data( chrom, low, high ): + if not indexer.has_data( chrom ): return messages.NO_DATA - + else: + # Standalone data provider + standalone_provider = get_data_provider(data_sources['data_standalone']['name'])( dataset ) + kwargs = {"stats": True} + if not standalone_provider.has_data( chrom ): + return messages.NO_DATA return messages.DATA @web.json 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: kanwei: trackster: Remove content-div margin and border-top
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7234805d1f92/ changeset: r5043:7234805d1f92 user: kanwei date: 2011-02-10 23:43:39 summary: trackster: Remove content-div margin and border-top affected #: 2 files (63 bytes) --- a/static/june_2007_style/blue/trackster.css Thu Feb 10 17:19:40 2011 -0500 +++ b/static/june_2007_style/blue/trackster.css Thu Feb 10 17:43:39 2011 -0500 @@ -22,7 +22,7 @@ .track{background:white;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:0px;} -.track-content{overflow:hidden;text-align:center;margin-bottom:2px;border-top:1px solid #eee;border-bottom:#eee solid 1px;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} +.track-content{overflow:hidden;text-align:center;border-bottom:1px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} .label-track .track-content{background:white;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;} --- a/static/june_2007_style/trackster.css.tmpl Thu Feb 10 17:19:40 2011 -0500 +++ b/static/june_2007_style/trackster.css.tmpl Thu Feb 10 17:43:39 2011 -0500 @@ -146,9 +146,8 @@ .track-content { overflow: hidden; text-align: center; - margin-bottom: 2px; - border-top: 1px solid #eee; - border-bottom: #eee solid 1px; +/* border-top: 1px solid #eee; */ + border-bottom: 1px solid #eee; background: #eee url('/static/images/tracks/diag_bg.gif'); min-height: 16px; } 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: jgoecks: Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c2d187cf4428/ changeset: r5042:c2d187cf4428 user: jgoecks date: 2011-02-10 23:19:40 summary: Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality. affected #: 5 files (5.5 KB) --- a/lib/galaxy/datatypes/util/gff_util.py Thu Feb 10 15:53:06 2011 -0500 +++ b/lib/galaxy/datatypes/util/gff_util.py Thu Feb 10 17:19:40 2011 -0500 @@ -257,4 +257,18 @@ # Could not split attributes string, so entire string must be # 'group' attribute. This is the case for strictly GFF files. attributes['group'] = attr_str - return attributes \ No newline at end of file + return attributes + +def gff_attributes_to_str( attrs, gff_format ): + """ + Convert GFF attributes to string. Supported formats are GFF3, GTF. + """ + if gff_format == 'GTF': + format_string = '%s "%s"' + elif gff_format == 'GFF3': + format_string = '%s=%s' + attrs_strs = [] + for name, value in attrs.items(): + attrs_strs.append( format_string % ( name, value ) ) + return " ; ".join( attrs_strs ) + \ No newline at end of file --- a/tools/extract/extract_genomic_dna.py Thu Feb 10 15:53:06 2011 -0500 +++ b/tools/extract/extract_genomic_dna.py Thu Feb 10 17:19:40 2011 -0500 @@ -5,17 +5,19 @@ -d, --dbkey=N: Genome build of input file -o, --output_format=N: the data type of the output file -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc + -I, --interpret_features: if true, complete features are interpreted when input is GFF + -F, --fasta=<genomic_sequences>: genomic sequences to use for extraction -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format. """ from galaxy import eggs import pkg_resources pkg_resources.require( "bx-python" ) -import sys, string, os, re +import sys, string, os, re, tempfile, subprocess from bx.cookbook import doc_optparse import bx.seq.nib import bx.seq.twobit from galaxy.tools.util.galaxyops import * -from galaxy.datatypes.util.gff_util import * +from galaxy.datatypes.util import gff_util assert sys.version_info[:2] >= ( 2, 4 ) @@ -44,16 +46,20 @@ seq_path = fields[2].strip() break return seq_path - def __main__(): + # + # Parse options, args. + # options, args = doc_optparse.parse( __doc__ ) try: chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols ) dbkey = options.dbkey output_format = options.output_format gff_format = options.gff + interpret_features = options.interpret_features GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR + fasta_file = options.fasta input_filename, output_filename = args except: doc_optparse.exception() @@ -62,11 +68,49 @@ strand = None nibs = {} twobits = {} - seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ) - if not os.path.exists( seq_path ): - # If this occurs, we need to fix the metadata validator. - stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey ) + + # + # Set path to sequence data. + # + if fasta_file: + # Need to create 2bit file from fasta file. + try: + seq_path = tempfile.NamedTemporaryFile( dir="." ).name + cmd = "faToTwoBit %s %s" % ( fasta_file, seq_path ) + + tmp_name = tempfile.NamedTemporaryFile( dir="." ).name + tmp_stderr = open( tmp_name, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # Get stderr, allowing for case where it's very large. + tmp_stderr = open( tmp_name, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + + # Error checking. + if returncode != 0: + raise Exception, stderr + except Exception, e: + stop_err( 'Error running faToTwoBit. ' + str( e ) ) + else: + seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ) + if not os.path.exists( seq_path ): + # If this occurs, we need to fix the metadata validator. + stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey ) + + # + # Fetch sequences. + # skipped_lines = 0 first_invalid_line = 0 invalid_line = '' @@ -74,106 +118,134 @@ warnings = [] warning = '' twobitfile = None - - for i, line in enumerate( open( input_filename ) ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( "#" ): - fields = line.split( '\t' ) + file_iterator = open( input_filename ) + if gff_format and interpret_features: + file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=True ) + for i, feature in enumerate( file_iterator ): + if gff_format and interpret_features: + # Processing features. + gff_util.convert_gff_coords_to_bed( feature ) + chrom = feature.chrom + start = feature.start + end = feature.end + strand = feature.strand + else: + # Processing lines, either interval or GFF format. + line = feature.rstrip( '\r\n' ) + if line and not line.startswith( "#" ): + fields = line.split( '\t' ) + try: + chrom = fields[chrom_col] + start = int( fields[start_col] ) + end = int( fields[end_col] ) + if gff_format: + start, end = gff_util.convert_gff_coords_to_bed( [start, end] ) + if includes_strand_col: + strand = fields[strand_col] + except: + warning = "Invalid chrom, start or end column values. " + warnings.append( warning ) + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + if start > end: + warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end ) + warnings.append( warning ) + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + + if strand not in ['+', '-']: + strand = '+' + sequence = '' + + # Open sequence file and get sequence for feature/interval. + if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ): + # TODO: improve support for GFF-nib interaction. + if chrom in nibs: + nib = nibs[chrom] + else: + nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) ) try: - chrom = fields[chrom_col] - start = int( fields[start_col] ) - end = int( fields[end_col] ) - if gff_format: - start, end = convert_gff_coords_to_bed( [start, end] ) - if includes_strand_col: - strand = fields[strand_col] + sequence = nib.get( start, end-start ) except: - warning = "Invalid chrom, start or end column values. " + warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) warnings.append( warning ) skipped_lines += 1 if not invalid_line: first_invalid_line = i + 1 invalid_line = line continue - if start > end: - warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end ) + elif seq_path and os.path.isfile( seq_path ): + if not(twobitfile): + twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) ) + try: + if options.gff and interpret_features: + # Create sequence from intervals within a feature. + sequence = '' + for interval in feature.intervals: + sequence += twobitfile[interval.chrom][interval.start:interval.end] + else: + sequence = twobitfile[chrom][start:end] + except: + warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) warnings.append( warning ) skipped_lines += 1 if not invalid_line: first_invalid_line = i + 1 invalid_line = line continue + else: + warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey ) + warnings.append( warning ) + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + if sequence == '': + warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " \ + % ( chrom, start, end, dbkey ) + warnings.append( warning ) + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + if includes_strand_col and strand == "-": + sequence = reverse_complement( sequence ) - if strand not in ['+', '-']: - strand = '+' - sequence = '' - - if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ): - if chrom in nibs: - nib = nibs[chrom] - else: - nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) ) - try: - sequence = nib.get( start, end-start ) - except: - warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) - warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line - continue - elif seq_path and os.path.isfile( seq_path ): - if not(twobitfile): - twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) ) - try: - sequence = twobitfile[chrom][start:end] - except: - warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) - warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line - continue + if output_format == "fasta" : + l = len( sequence ) + c = 0 + if gff_format: + start, end = gff_util.convert_bed_coords_to_gff( [ start, end ] ) + fields = [dbkey, str( chrom ), str( start ), str( end ), strand] + meta_data = "_".join( fields ) + fout.write( ">%s\n" % meta_data ) + while c < l: + b = min( c + 50, l ) + fout.write( "%s\n" % str( sequence[c:b] ) ) + c = b + else: # output_format == "interval" + if interpret_features: + # TODO: need better GFF Reader to capture all information needed + # to produce this line. + meta_data = "\t".join( + [feature.chrom, "galaxy_extract_genomic_dna", "interval", \ + str( feature.start ), str( feature.end ), feature.score, feature.strand, + ".", gff_util.gff_attributes_to_str( feature.attributes, "GTF" ) ] ) else: - warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey ) - warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line - continue - if sequence == '': - warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " %( chrom, start, end, dbkey ) - warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line - continue - if includes_strand_col and strand == "-": - sequence = reverse_complement( sequence ) - - if output_format == "fasta" : - l = len( sequence ) - c = 0 - if gff_format: - start, end = convert_bed_coords_to_gff( [ start, end ] ) - fields = [dbkey, str( chrom ), str( start ), str( end ), strand] - meta_data = "_".join( fields ) - fout.write( ">%s\n" % meta_data ) - while c < l: - b = min( c + 50, l ) - fout.write( "%s\n" % str( sequence[c:b] ) ) - c = b - else: # output_format == "interval" meta_data = "\t".join( fields ) - if gff_format: - format_str = "%s seq \"%s\";\n" - else: - format_str = "%s\t%s\n" - fout.write( format_str % ( meta_data, str( sequence ) ) ) + if gff_format: + format_str = "%s seq \"%s\";\n" + else: + format_str = "%s\t%s\n" + fout.write( format_str % ( meta_data, str( sequence ) ) ) fout.close() --- a/tools/extract/extract_genomic_dna.xml Thu Feb 10 15:53:06 2011 -0500 +++ b/tools/extract/extract_genomic_dna.xml Thu Feb 10 17:19:40 2011 -0500 @@ -1,57 +1,112 @@ <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.1"><description>using coordinates from assembled/unassembled genomes</description><command interpreter="python"> - extract_genomic_dna.py $input $out_file1 -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR} + extract_genomic_dna.py $input $out_file1 -o $out_format -d $dbkey + + #if str( $interpret_features ) == "yes": + -I + #end if + + ## Columns to use in input file. #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): -1 1,4,5,7 --gff #else: -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} #end if + + #if $seq_source.index_source == "cached": + ## Genomic data from cache. + -g ${GALAXY_DATA_INDEX_DIR} + #else: + ## Genomic data from history. + -F $seq_source.ref_file + #end if </command><inputs> - <param format="interval,gff" name="input" type="data" label="Fetch sequences corresponding to Query"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="seq" /> - </param> - <param name="out_format" type="select" label="Output data type"> - <option value="fasta">FASTA</option> - <option value="interval">Interval</option> - </param> + <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"> + <validator type="unspecified_build" /> + </param> + <param name="interpret_features" type="select" label="Interpret features when possible" help="Only meaningful for GFF, GTF datasets."> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Source for Genomic Data"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <param name="out_format" type="select" label="Output data type"> + <option value="fasta">FASTA</option> + <option value="interval">Interval</option> + </param></inputs><outputs> - <data format="input" name="out_file1" metadata_source="input"> - <change_format> - <when input="out_format" value="fasta" format="fasta" /> - </change_format> - </data> + <data format="input" name="out_file1" metadata_source="input"> + <change_format> + <when input="out_format" value="fasta" format="fasta" /> + </change_format> + </data></outputs><tests><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> + <param name="interpret_features" value="yes"/> + <param name="index_source" value="cached"/><param name="out_format" value="fasta"/><output name="out_file1" file="extract_genomic_dna_out1.fasta" /></test><test><param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" /> + <param name="interpret_features" value="yes"/> + <param name="index_source" value="cached"/><param name="out_format" value="fasta"/><output name="out_file1" file="extract_genomic_dna_out2.fasta" /></test><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> + <param name="interpret_features" value="no"/> + <param name="index_source" value="cached"/><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out3.interval" /></test><test><param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> + <param name="interpret_features" value="no"/> + <param name="index_source" value="cached"/><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out4.gff" /></test><test><param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> + <param name="interpret_features" value="no"/><param name="out_format" value="fasta"/> + <param name="index_source" value="cached"/><output name="out_file1" file="extract_genomic_dna_out5.fasta" /></test> +  + <test> + <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> + <param name="interpret_features" value="no"/> + <param name="index_source" value="history"/> + <param name="ref_file" value="tophat_in1.fasta"/> + <param name="out_format" value="fasta"/> + <output name="out_file1" file="extract_genomic_dna_out6.fasta" /> + </test> + <test> + <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> + <param name="interpret_features" value="yes"/> + <param name="index_source" value="history"/> + <param name="ref_file" value="tophat_in1.fasta"/> + <param name="out_format" value="fasta"/> + <output name="out_file1" file="extract_genomic_dna_out7.fasta" /> + </test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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