May 2010 - galaxy-commits - lists.galaxyproject.org

[hg] galaxy 3770: work around for composite objects without a ba...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7232b61da6d3 changeset: 3770:7232b61da6d3 user: fubar/ross period lazarus at gmail d0t com date: Tue May 11 18:02:39 2010 -0400 description: work around for composite objects without a base_name in grouping.py removed artefacts from Manhattan plot example in the rgManQQ tool help diffstat: lib/galaxy/tools/parameters/grouping.py | 11 ++++++----- lib/galaxy/web/controllers/dataset.py | 1 - static/images/Armitagep_manhattan.png | 0 static/images/Armitagep_qqplot.png | 0 4 files changed, 6 insertions(+), 6 deletions(-) diffs (48 lines): diff -r 69e70e588a8e -r 7232b61da6d3 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Tue May 11 13:25:39 2010 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Tue May 11 18:02:39 2010 -0400 @@ -100,8 +100,7 @@ self.file_type_to_ext = { 'auto':self.default_file_type } self.metadata_ref = 'files_metadata' def get_file_base_name( self, context ): - log.debug('### uploadDataset get base name context = %s' % str(context)) - fd = context.get('files_metadata|base_name','?') + fd = context.get('files_metadata|base_name','Galaxy_Composite_file') return fd def get_file_type( self, context ): return context.get( self.file_type_name, self.default_file_type ) @@ -295,14 +294,16 @@ temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file( dataset ) ), prefix='upload_auto_primary_file' ) dataset.primary_file = temp_name dataset.space_to_tab = False - dataset.precreated_name = dataset.name = dataset.metadata['base_name'] # was 'Uploaded Composite Dataset (%s)' % ( file_type ) + dsn = dataset.metadata.get('base_name','Uploaded Composite Dataset (%s)' % file_type) + dataset.precreated_name = dataset.name = dsn else: file_bunch, warnings = get_one_filename( groups_incoming[ 0 ] ) writable_files_offset = 1 dataset.primary_file = file_bunch.path dataset.space_to_tab = file_bunch.space_to_tab - dataset.precreated_name = dataset.metadata['base_name'] # file_bunch.precreated_name - dataset.name = file_bunch.precreated_name + dsn = dataset.metadata.get('base_name',file_bunch.precreated_name) + dataset.precreated_name = dsn + dataset.name = dsn dataset.warnings.extend( file_bunch.warnings ) if dataset.primary_file is None:#remove this before finish, this should create an empty dataset raise Exception( 'No primary dataset file was available for composite upload' ) diff -r 69e70e588a8e -r 7232b61da6d3 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue May 11 13:25:39 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue May 11 18:02:39 2010 -0400 @@ -246,7 +246,6 @@ ext = data.extension path = data.file_name fname = os.path.split(path)[-1] - basename = data.metadata.base_name efp = data.extra_files_path htmlname = os.path.splitext(outfname)[0] if not htmlname.endswith(ext): diff -r 69e70e588a8e -r 7232b61da6d3 static/images/Armitagep_manhattan.png Binary file static/images/Armitagep_manhattan.png has changed diff -r 69e70e588a8e -r 7232b61da6d3 static/images/Armitagep_qqplot.png Binary file static/images/Armitagep_qqplot.png has changed

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[hg] galaxy 3769: Hack to fix the ghost broken dataset problem a...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/69e70e588a8e changeset: 3769:69e70e588a8e user: fubar/ross period lazarus at gmail d0t com date: Tue May 11 13:25:39 2010 -0400 description: Hack to fix the ghost broken dataset problem after uploading a composite file Delete any precreated datasets leftover.. diffstat: lib/galaxy/tools/actions/upload_common.py | 4 +++- 1 files changed, 3 insertions(+), 1 deletions(-) diffs (14 lines): diff -r 8470f5588775 -r 69e70e588a8e lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue May 11 11:51:49 2010 -0400 +++ b/lib/galaxy/tools/actions/upload_common.py Tue May 11 13:25:39 2010 -0400 @@ -102,7 +102,9 @@ for data in precreated_datasets: log.info( 'Cleaned up unclaimed precreated dataset (%s).' % ( data.id ) ) data.state = data.states.ERROR - data.info = 'No file contents were available.' + data.info = 'Unused precreated dataset to be deleted.' + data.deleted = True + def new_history_upload( trans, uploaded_dataset, state=None ): hda = trans.app.model.HistoryDatasetAssociation( name = uploaded_dataset.name, extension = uploaded_dataset.file_type,

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[hg] galaxy 3767: Add worker threads to SGE runner
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/39268be26944 changeset: 3767:39268be26944 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon May 10 20:59:41 2010 -0400 description: Add worker threads to SGE runner diffstat: lib/galaxy/jobs/runners/sge.py | 66 +++++++++++++++++++++++++++++++++-------- 1 files changed, 52 insertions(+), 14 deletions(-) diffs (148 lines): diff -r f7cf88978f1f -r 39268be26944 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Mon May 10 14:30:18 2010 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Mon May 10 20:59:41 2010 -0400 @@ -75,13 +75,20 @@ # be modified by the monitor thread, which will move items from 'queue' # to 'watched' and then manage the watched jobs. self.watched = [] - self.queue = Queue() + self.monitor_queue = Queue() self.default_cell = self.determine_sge_cell( self.app.config.default_cluster_job_runner ) self.ds = DRMAA.Session() self.ds.init( self.default_cell ) self.monitor_thread = threading.Thread( target=self.monitor ) self.monitor_thread.start() - log.debug( "ready" ) + self.work_queue = Queue() + self.work_threads = [] + nworkers = app.config.cluster_job_queue_workers + for i in range( nworkers ): + worker = threading.Thread( target=self.run_next ) + worker.start() + self.work_threads.append( worker ) + log.debug( "%d workers ready" % nworkers ) def determine_sge_cell( self, url ): """Determine what SGE cell we are using""" @@ -113,6 +120,24 @@ except: return None + def run_next( self ): + """ + Run the next item in the queue (a job waiting to run or finish ) + """ + while 1: + ( op, obj ) = self.work_queue.get() + if op is self.STOP_SIGNAL: + return + try: + if op == 'queue': + self.queue_job( obj ) + elif op == 'finish': + self.finish_job( obj ) + elif op == 'fail': + self.fail_job( obj ) + except: + log.exception( "Uncaught exception %sing job" % op ) + def queue_job( self, job_wrapper ): """Create SGE script for a job and submit it to the SGE queue""" @@ -213,7 +238,7 @@ self.ds.deleteJobTemplate( jt ) # Add to our 'queue' of jobs to monitor - self.queue.put( sge_job_state ) + self.monitor_queue.put( sge_job_state ) def monitor( self ): """ @@ -224,7 +249,7 @@ # Take any new watched jobs and put them on the monitor list try: while 1: - sge_job_state = self.queue.get_nowait() + sge_job_state = self.monitor_queue.get_nowait() if sge_job_state is self.STOP_SIGNAL: # TODO: This is where any cleanup would occur self.ds.exit() @@ -252,13 +277,14 @@ except DRMAA.InvalidJobError: # we should only get here if an orphaned job was put into the queue at app startup log.debug("(%s/%s) job left SGE queue" % ( galaxy_job_id, job_id ) ) - self.finish_job( sge_job_state ) + self.work_queue.put( ( 'finish', sge_job_state ) ) continue except Exception, e: # so we don't kill the monitor thread log.exception("(%s/%s) Unable to check job status" % ( galaxy_job_id, job_id ) ) log.warning("(%s/%s) job will now be errored" % ( galaxy_job_id, job_id ) ) - sge_job_state.job_wrapper.fail( "Cluster could not complete job" ) + sge_job_state.fail_message = "Cluster could not complete job" + self.work_queue.put( ( 'fail', sge_job_state ) ) continue if state != old_state: log.debug("(%s/%s) state change: %s" % ( galaxy_job_id, job_id, DRMAA_state[state] ) ) @@ -266,11 +292,11 @@ sge_job_state.running = True sge_job_state.job_wrapper.change_state( model.Job.states.RUNNING ) if state == DRMAA.Session.DONE: - self.finish_job( sge_job_state ) + self.work_queue.put( ( 'finish', sge_job_state ) ) continue if state == DRMAA.Session.FAILED: - sge_job_state.job_wrapper.fail( "Cluster could not complete job" ) - sge_job_state.job_wrapper.cleanup() + sge_job_state.fail_message = "Cluster could not complete job" + self.work_queue.put( ( 'fail', sge_job_state ) ) continue sge_job_state.old_state = state new_watched.append( sge_job_state ) @@ -304,6 +330,14 @@ # clean up the sge files self.cleanup( ( ofile, efile, job_file ) ) + def fail_job( self, sge_job_state ): + """ + Seperated out so we can use the worker threads for it. + """ + self.stop_job( self.sa_session.query( self.app.model.Job ).get( sge_job_state.job_wrapper.job_id ) ) + sge_job_state.job_wrapper.fail( sge_job_state.fail_message ) + self.cleanup( ( sge_job_state.ofile, sge_job_state.efile, sge_job_state.job_file ) ) + def cleanup( self, files ): if not asbool( self.app.config.get( 'debug', False ) ): for file in files: @@ -312,12 +346,16 @@ def put( self, job_wrapper ): """Add a job to the queue (by job identifier)""" - self.queue_job( job_wrapper ) - + # Change to queued state before handing to worker thread so the runner won't pick it up again + job_wrapper.change_state( model.Job.states.QUEUED ) + self.work_queue.put( ( 'queue', job_wrapper ) ) + def shutdown( self ): """Attempts to gracefully shut down the monitor thread""" log.info( "sending stop signal to worker threads" ) - self.queue.put( self.STOP_SIGNAL ) + self.monitor_queue.put( self.STOP_SIGNAL ) + for i in range( len( self.work_threads ) ): + self.work_queue.put( ( self.STOP_SIGNAL, None ) ) log.info( "sge job runner stopped" ) def stop_job( self, job ): @@ -342,9 +380,9 @@ log.debug( "(%s/%s) is still in running state, adding to the SGE queue" % ( job.id, job.job_runner_external_id ) ) sge_job_state.old_state = DRMAA.Session.RUNNING sge_job_state.running = True - self.queue.put( sge_job_state ) + self.monitor_queue.put( sge_job_state ) elif job.state == model.Job.states.QUEUED: log.debug( "(%s/%s) is still in SGE queued state, adding to the SGE queue" % ( job.id, job.job_runner_external_id ) ) sge_job_state.old_state = DRMAA.Session.QUEUED_ACTIVE sge_job_state.running = False - self.queue.put( sge_job_state ) + self.monitor_queue.put( sge_job_state )

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[hg] galaxy 3768: Add mimetypes to snp/wga datatypes in genetics.py
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8470f5588775 changeset: 3768:8470f5588775 user: fubar/ross period lazarus at gmail d0t com date: Tue May 11 11:51:49 2010 -0400 description: Add mimetypes to snp/wga datatypes in genetics.py Fix edit_attributes to snp/wga composite files in tests diffstat: lib/galaxy/datatypes/genetics.py | 19 ++++++++++++++++++- lib/galaxy/tools/__init__.py | 2 +- test/functional/test_toolbox.py | 6 ++++-- tools/rgenetics/rgCaCo.xml | 1 + tools/rgenetics/rgClean.xml | 1 + tools/rgenetics/rgEigPCA.xml | 1 + tools/rgenetics/rgGLM.xml | 2 ++ tools/rgenetics/rgGRR.xml | 1 + tools/rgenetics/rgHaploView.xml | 1 + tools/rgenetics/rgLDIndep.xml | 1 + tools/rgenetics/rgPedSub.xml | 1 + tools/rgenetics/rgQC.xml | 1 + tools/rgenetics/rgTDT.xml | 1 + 13 files changed, 34 insertions(+), 4 deletions(-) diffs (200 lines): diff -r 39268be26944 -r 8470f5588775 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon May 10 20:59:41 2010 -0400 +++ b/lib/galaxy/datatypes/genetics.py Tue May 11 11:51:49 2010 -0400 @@ -173,6 +173,10 @@ return false return true + def get_mime(self): + """Returns the mime type of the datatype""" + return 'application/vnd.ms-excel' + class rgTabList(Tabular): """ @@ -211,6 +215,10 @@ out = "Can't create peek %s" % exc return out + def get_mime(self): + """Returns the mime type of the datatype""" + return 'text/html' + class rgSampleList(rgTabList): """ @@ -262,7 +270,7 @@ stored in extra files path """ - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='RgeneticsData', readonly=True, set_in_upload=True) composite_type = 'auto_primary_file' @@ -302,6 +310,11 @@ f.write('\n') f.close() + def get_mime(self): + """Returns the mime type of the datatype""" + return 'text/html' + + def set_meta( self, dataset, **kwd ): """ @@ -506,6 +519,10 @@ cannot rename the datasets here - they come with the default unfortunately """ return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' + + def get_mime(self): + """Returns the mime type of the datatype""" + return 'text/html' def get_phecols(self, phenolist=[], maxConc=20): """ diff -r 39268be26944 -r 8470f5588775 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon May 10 20:59:41 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Tue May 11 11:51:49 2010 -0400 @@ -541,7 +541,7 @@ attrib['composite_data'].append( child ) if composite_data_name is None: #generate a unique name; each test uses a fresh history - composite_data_name = '_COMPOSITE_RENAMED %i_' % ( composite_data_names_counter ) + composite_data_name = '_COMPOSITE_RENAMED_%i_' % ( composite_data_names_counter ) composite_data_names_counter += 1 elif child.tag == 'metadata': attrib['metadata'].append( child ) diff -r 39268be26944 -r 8470f5588775 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Mon May 10 20:59:41 2010 -0400 +++ b/test/functional/test_toolbox.py Tue May 11 11:51:49 2010 -0400 @@ -45,8 +45,10 @@ new_name = edit_att.get( 'value', None ) assert new_name, 'You must supply the new dataset name as the value tag of the edit_attributes tag' hda_id = self.get_history_as_data_list()[-1].get( 'id' ) - self.edit_hda_attribute_info( hda_id, new_name = new_name ) - print "Renamed uploaded file to:", new_name + try: + self.edit_hda_attribute_info( hda_id = str(hda_id), new_name = new_name ) + except: + print "### call to edit_hda failed for hda_id",hda_id,"new_name=",new_name else: raise Exception( 'edit_attributes type (%s) is unimplemented' % edit_att.get( 'type', None ) ) # We need to handle the case where we've uploaded a valid compressed file since the upload diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgCaCo.xml Tue May 11 11:51:49 2010 -0400 @@ -28,6 +28,7 @@ <composite_data value='tinywga.bim' /> <composite_data value='tinywga.bed' /> <composite_data value='tinywga.fam' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='name' value='rgCaCotest1' /> <output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' /> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgClean.xml --- a/tools/rgenetics/rgClean.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgClean.xml Tue May 11 11:51:49 2010 -0400 @@ -57,6 +57,7 @@ <composite_data value='tinywga.bim' /> <composite_data value='tinywga.bed' /> <composite_data value='tinywga.fam' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='title' value='rgCleantest1' /> <param name="geno" value="1" /> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgEigPCA.xml --- a/tools/rgenetics/rgEigPCA.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgEigPCA.xml Tue May 11 11:51:49 2010 -0400 @@ -40,6 +40,7 @@ <composite_data value='tinywga.bim' /> <composite_data value='tinywga.bed' /> <composite_data value='tinywga.fam' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='title' value='rgEigPCAtest1' /> <param name="k" value="4" /> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgGLM.xml Tue May 11 11:51:49 2010 -0400 @@ -52,10 +52,12 @@ <composite_data value='tinywga.bim' /> <composite_data value='tinywga.bed' /> <composite_data value='tinywga.fam' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='phef' value='tinywga' ftype='pphe' > <metadata name='base_name' value='tinywga' /> <composite_data value='tinywga.pphe' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='title1' value='rgGLMtest1' /> <param name='predvar' value='c1' /> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgGRR.xml --- a/tools/rgenetics/rgGRR.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgGRR.xml Tue May 11 11:51:49 2010 -0400 @@ -27,6 +27,7 @@ <composite_data value='tinywga.bim' /> <composite_data value='tinywga.bed' /> <composite_data value='tinywga.fam' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='title1' value='rgGRRtest1' /> <param name='n' value='100' /> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgHaploView.xml --- a/tools/rgenetics/rgHaploView.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgHaploView.xml Tue May 11 11:51:49 2010 -0400 @@ -88,6 +88,7 @@ <metadata name='base_name' value='tinywga' /> <composite_data value='tinywga.ped' /> <composite_data value='tinywga.map' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='ucsc_region' value='' /> <param name='title' value='rgHaploViewtest1' /> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgLDIndep.xml --- a/tools/rgenetics/rgLDIndep.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgLDIndep.xml Tue May 11 11:51:49 2010 -0400 @@ -41,6 +41,7 @@ <composite_data value='tinywga.bim' /> <composite_data value='tinywga.bed' /> <composite_data value='tinywga.fam' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='title1' value='rgLDIndeptest1' /> <param name="mind" value="1" /> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgPedSub.xml --- a/tools/rgenetics/rgPedSub.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgPedSub.xml Tue May 11 11:51:49 2010 -0400 @@ -73,6 +73,7 @@ <metadata name='base_name' value='tinywga' /> <composite_data value='tinywga.ped' /> <composite_data value='tinywga.map' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='title' value='rgPedSubtest1' /> <param name="region" value="" /> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgQC.xml Tue May 11 11:51:49 2010 -0400 @@ -25,6 +25,7 @@ <composite_data value='tinywga.bim' /> <composite_data value='tinywga.bed' /> <composite_data value='tinywga.fam' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='out_prefix' value='rgQCtest1' /> <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='280'> diff -r 39268be26944 -r 8470f5588775 tools/rgenetics/rgTDT.xml --- a/tools/rgenetics/rgTDT.xml Mon May 10 20:59:41 2010 -0400 +++ b/tools/rgenetics/rgTDT.xml Tue May 11 11:51:49 2010 -0400 @@ -27,6 +27,7 @@ <composite_data value='tinywga.bim' /> <composite_data value='tinywga.bed' /> <composite_data value='tinywga.fam' /> + <edit_attributes type='name' value='tinywga' /> </param> <param name='title1' value='rgTDTtest1' /> <output name='out_file1' file='rgTDTtest1_TDT.xls' ftype='tabular' compare="diff"/>

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[hg] galaxy 3766: Fix for exporting workflows with input dataset...
by James Taylor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f7cf88978f1f changeset: 3766:f7cf88978f1f user: James Taylor <james(a)jamestaylor.org> date: Mon May 10 14:30:18 2010 -0400 description: Fix for exporting workflows with input dataset modules diffstat: lib/galaxy/workflow/modules.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r dd6d09de392e -r f7cf88978f1f lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py Mon May 10 12:50:09 2010 -0400 +++ b/lib/galaxy/workflow/modules.py Mon May 10 14:30:18 2010 -0400 @@ -122,7 +122,7 @@ .add_text( "name", "Name", value=self.state['name'] ) return self.trans.fill_template( "workflow/editor_generic_form.mako", module=self, form=form ) - def get_state( self ): + def get_state( self, secure=True ): return to_json_string( self.state ) def update_state( self, incoming ):

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[hg] galaxy 3765: Remove builds.txt from source control - use bu...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/dd6d09de392e changeset: 3765:dd6d09de392e user: Nate Coraor <nate(a)bx.psu.edu> date: Mon May 10 12:50:09 2010 -0400 description: Remove builds.txt from source control - use builds.txt.sample instead and copy it over if you don't have one diffstat: run.sh | 7 + setup.sh | 1 + tool-data/shared/ucsc/builds.txt | 819 -------------------------------- tool-data/shared/ucsc/builds.txt.sample | 153 +++++ 4 files changed, 161 insertions(+), 819 deletions(-) diffs (1006 lines): diff -r 4e5ca6c44804 -r dd6d09de392e run.sh --- a/run.sh Mon May 10 12:42:05 2010 -0400 +++ b/run.sh Mon May 10 12:50:09 2010 -0400 @@ -20,4 +20,11 @@ fi fi fi + +# Temporary: since builds.txt is now removed from source control, create it +# from the sample if necessary +if [ ! -f "tool-data/shared/ucsc/builds.txt" ]; then + cp tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/builds.txt +fi + python ./scripts/paster.py serve universe_wsgi.ini $@ diff -r 4e5ca6c44804 -r dd6d09de392e setup.sh --- a/setup.sh Mon May 10 12:42:05 2010 -0400 +++ b/setup.sh Mon May 10 12:50:09 2010 -0400 @@ -26,6 +26,7 @@ tool-data/sequence_index_base.loc.sample tool-data/sequence_index_color.loc.sample tool-data/twobit.loc.sample +tool-data/shared/ucsc/builds.txt.sample " DIRS=" diff -r 4e5ca6c44804 -r dd6d09de392e tool-data/shared/ucsc/builds.txt --- a/tool-data/shared/ucsc/builds.txt Mon May 10 12:42:05 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,819 +0,0 @@ -#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn -? unspecified (?) -hg19Haps hg19Haplotypes Feb. 2009 (GRCh37/hg19Haps) (hg19Haps) -hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) -hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) -hg17 Human May 2004 (NCBI35/hg17) (hg17) -hg16 Human July 2003 (NCBI34/hg16) (hg16) -hg15 Human Apr. 2003 (NCBI33/hg15) (hg15) -venter1 J. Craig Venter Sep. 2007 (HuRef/venter1) (venter1) -panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) -panTro1 Chimp Nov. 2003 (CGSC 1.1/panTro1) (panTro1) -gorGor2 Gorilla Aug. 2009 (Sanger 4/gorGor2) (gorGor2) -gorGor1 Gorilla Oct. 2008 (Sanger 0.1/gorGor1) (gorGor1) -ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2) -rheMac2 Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) -papHam1 Baboon Nov. 2008 (Baylor 1.0/papHam1) (papHam1) -calJac3 Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3) -calJac1 Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1) -otoGar1 Bushbaby Dec. 2006 (Broad/otoGar1) (otoGar1) -micMur1 Mouse lemur Jun. 2003 (Broad/micMur1) (micMur1) -tupBel1 Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1) -mmtv MMTV Nov. 2009 (MMTV/mmtv) (mmtv) -homPan20 chimp/human Jun. 2008 (UCSC Recon/homPan20) (homPan20) -homIni20 orang/human Jun. 2008 (UCSC Recon/homIni20) (homIni20) -sorAra1 Shrew June 2006 (Broad/sorAra1) (sorAra1) -mm9 Mouse July 2007 (NCBI37/mm9) (mm9) -mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) -mm7 Mouse Aug. 2005 (NCBI35/mm7) (mm7) -rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) -rn3 Rat June 2003 (Baylor 3.1/rn3) (rn3) -speTri1 Squirrel Feb. 2008 (Broad/speTri1) (speTri1) -cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3) -oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) -oryCun1 Rabbit May 2005 (Broad/oryCun1) (oryCun1) -ochPri2 Pika Jul. 2008 (Broad/ochPri2) (ochPri2) -eriEur1 Hedgehog June 2006 (Broad/eriEur1) (eriEur1) -felCatV17e Cat Dec. 2008 (NHGRI/GTB V17e/felCatV17e) (felCatV17e) -felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) -ailMel1 Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1) -nemVec1 Starlet sea anemone Jun. 2007 (JGI-PDF/nemVec1) (nemVec1) -canFam2 Dog May 2005 (Broad/canFam2) (canFam2) -canFam1 Dog July 2004 (Broad/canFam1) (canFam1) -canFamPoodle1 Dog May 2003 (TIGR Poodle/canFamPoodle1) (canFamPoodle1) -equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) -equCab1 Horse Jan. 2007 (Broad/equCab1) (equCab1) -susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) -pteVam1 Megabat Jul. 2008 (Broad/pteVam1) (pteVam1) -myoLuc1 Microbat Mar. 2006 (Broad/myoLuc1) (myoLuc1) -susScr1 Pig Apr. 2009 (SGSC 9.53/susScr1) (susScr1) -turTru1 Dolphin Feb. 2008 (Broad/turTru1) (turTru1) -tarSyr1 Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1) -proCap1 Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1) -oviAri1 Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1) -dipOrd1 Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1) -choHof1 Sloth Jul. 2008 (Broad/choHof1) (choHof1) -bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) -bosTau3 Cow Aug. 2006 (Baylor 3.1/bosTau3) (bosTau3) -bosTau2 Cow Mar. 2005 (Baylor 2.0/bosTau2) (bosTau2) -macEug1 Wallaby Nov. 2007 (Baylor 1.0/macEug1) (macEug1) -dasNov2 Armadillo Jul. 2008 (Broad/dasNov2) (dasNov2) -dasNov1 Armadillo May 2005 (Broad/dasNov1) (dasNov1) -echTel1 Tenrec July 2005 (Broad/echTel1) (echTel1) -loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3) -loxAfr2 Elephant Jul. 2008 (Broad/loxAfr2) (loxAfr2) -loxAfr1 Elephant May 2005 (Broad/loxAfr1) (loxAfr1) -monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) -monDom4 Opossum Jan. 2006 (Broad/monDom4) (monDom4) -monDom1 Opossum Oct. 2004 (Broad prelim/monDom1) (monDom1) -ornAna1 Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1) -galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) -galGal2 Chicken Feb. 2004 (WUGSC 1.0/galGal2) (galGal2) -taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) -anoCar1 Lizard Feb. 2007 (Broad/anoCar1) (anoCar1) -xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) -xenTro1 X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) (xenTro1) -danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) -danRer5 Zebrafish July 2007 (Zv7/danRer5) (danRer5) -danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) (danRer4) -danRer3 Zebrafish May 2005 (Zv5/danRer3) (danRer3) -tetNig2 Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2) -tetNig1 Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1) -fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) -fr1 Fugu Aug. 2002 (JGI 3.0/fr1) (fr1) -gasAcu1 Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1) -oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2) -oryLat1 Medaka Apr. 2006 (NIG/UT MEDAKA1/oryLat1) (oryLat1) -petMar1 Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1) -borEut13 Boreoeutherian Apr. 24. 2006 (UCSC Recon/borEut13) (borEut13) -canHg12 Boreoeutherian Nov. 19. 2005 (UCSC Recon/canHg12) (canHg12) -rodEnt13 Rodent Apr. 24. 2006 (UCSC Recon/rodEnt13) (rodEnt13) -priMat13 Primate Apr. 24. 2006 (UCSC Recon/priMat13) (priMat13) -nonAfr13 Non-Afrotheria Apr. 24. 2006 (UCSC Recon/nonAfr13) (nonAfr13) -lauRas13 Laurasiatheria Apr. 24. 2006 (UCSC Recon/lauRas13) (lauRas13) -homIni14 Hominidae Oct. 1. 2006 (UCSC Recon/homIni14) (homIni14) -homIni13 Hominidae Apr. 24. 2006 (UCSC Recon/homIni13) (homIni13) -gliRes13 Glires Apr. 24. 2006 (UCSC Recon/gliRes13) (gliRes13) -eutHer13 Eutheria Apr. 24. 2006 (UCSC Recon/eutHer13) (eutHer13) -euaGli13 Euarchontoglires Apr. 24. 2006 (UCSC Recon/euaGli13) (euaGli13) -catArr1 Catarrhini June 13. 2006 (UCSC Recon/catArr1) (catArr1) -afrOth13 Afrotheria Apr. 24. 2006 (UCSC Recon/afrOth13) (afrOth13) -braFlo1 Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1) -ci2 C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2) -ci1 C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1) -cioSav2 C. savignyi July 2005 (Sidow Lab 2.0/cioSav2) (cioSav2) -cioSav1 C. savignyi Apr. 2003 (Broad/cioSav1) (cioSav1) -strPur2 S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2) -strPur1 S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1) -ce8 C. elegans Jun 2009 (WS204/ce8) (ce8) -ce7 C. elegans Feb 2009 (WS200/ce7) (ce7) -aplCal1 Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1) -ce6 C. elegans May 2008 (WS190/ce6) (ce6) -ce5 C. elegans Aug. 2007 (WS180/ce5) (ce5) -ce4 C. elegans Jan. 2007 (WS170/ce4) (ce4) -ce3 C. elegans March 2005 (WS140/ce3) (ce3) -ce2 C. elegans Mar. 2004 (WS120/ce2) (ce2) -caePb2 C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) -caePb1 C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1) -cb3 C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3) -cb2 C. briggsae Aug 2005 (WUGSC prelim/cb2) (cb2) -cb1 C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1) -caeRem3 C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) -caeRem2 C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) -caeRem1 C. remanei March 2005 (WUGSC prelim/caeRem1) (caeRem1) -caeJap2 C. japonica Jan. 2009 (WUGSC 4.0.1/caeJap2) (caeJap2) -caeJap1 C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) -priPac1 P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) -dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) -dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2) -dm1 D. melanogaster Jan. 2003 (BDGP R3/dm1) (dm1) -droSim1 D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) -droSec1 D. sechellia Oct. 2005 (Broad/droSec1) (droSec1) -droYak2 D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) -droYak1 D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1) -droEre1 D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1) -droAna2 D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2) -droAna1 D. ananassae July 2004 (TIGR/droAna1) (droAna1) -dp3 D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3) -dp2 D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2) -droPer1 D. persimilis Oct. 2005 (Broad/droPer1) (droPer1) -droVir2 D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2) -droVir1 D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1) -droMoj2 D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2) -droMoj1 D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1) -droGri1 D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1) -anoGam1 A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) -apiMel2 A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2) -apiMel1 A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1) -triCas2 T. castaneum Sep. 2005 (Baylor 2.0/triCas2) (triCas2) -falciparum P. falciparum Plasmodium falciparum (?/falciparum) (falciparum) -sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) -sacCer1 S. cerevisiae Oct. 2003 (SGD/sacCer1) (sacCer1) -sc1 SARS coronavirus Apr. 2003 (GenBank Apr. 14 '03/sc1) (sc1) -phiX phiX174 (phiX) -16079 Mycobacterium sp. JLS (16079) -symbTher_IAM14863 Symbiobacterium thermophilum IAM 14863 (symbTher_IAM14863) -16070 Yersinia pseudotuberculosis IP 31758 (16070) -18883 Mycobacterium tuberculosis H37Ra (18883) -nocaJS61 Nocardioides sp. JS614 (nocaJS61) -12521 Clostridium perfringens SM101 (12521) -acidCryp_JF_5 Acidiphilium cryptum JF-5 (acidCryp_JF_5) -lactLact Lactococcus lactis subsp. lactis Il1403 (lactLact) -13082 Bacillus licheniformis ATCC 14580 (13082) -344 Rhizobium leguminosarum bv. viciae 3841 (344) -siliPome_DSS_3 Silicibacter pomeroyi DSS-3 (siliPome_DSS_3) -paraSp_UWE25 Candidatus Protochlamydia amoebophila UWE25 (paraSp_UWE25) -geobKaus_HTA426 Geobacillus kaustophilus HTA426 (geobKaus_HTA426) -rhizEtli_CFN_42 Rhizobium etli CFN 42 (rhizEtli_CFN_42) -13162 Streptococcus thermophilus LMG 18311 (13162) -13163 Streptococcus thermophilus CNRZ1066 (13163) -18817 Methylobacterium radiotolerans JCM 2831 (18817) -28109 Bartonella tribocorum CIP 105476 (28109) -dichNodo_VCS1703A Dichelobacter nodosus VCS1703A (dichNodo_VCS1703A) -12931 Xanthomonas oryzae pv. oryzae KACC10331 (12931) -eschColi_O157H7 Escherichia coli O157:H7 str. Sakai (eschColi_O157H7) -burk383 Burkholderia sp. 383 (burk383) -15759 Psychrobacter sp. PRwf-1 (15759) -15758 Staphylococcus aureus subsp. aureus JH1 (15758) -27835 Microcystis aeruginosa NIES-843 (27835) -campJeju_81_176 Campylobacter jejuni subsp. jejuni 81-176 (campJeju_81_176) -15751 Rhodopseudomonas palustris BisA53 (15751) -15750 Rhodopseudomonas palustris BisB18 (15750) -15757 Staphylococcus aureus subsp. aureus JH9 (15757) -15756 Xanthobacter autotrophicus Py2 (15756) -15755 Rhodobacter sphaeroides ATCC 17025 (15755) -15754 Rhodobacter sphaeroides ATCC 17029 (15754) -13603 Ralstonia eutropha H16 (13603) -shewPutrCN32 Shewanella putrefaciens CN-32 (shewPutrCN32) -aerPer1 Aeropyrum pernix K1 (aerPer1) -18255 Bacillus thuringiensis str. Al Hakam (18255) -acinSp_ADP1 Acinetobacter sp. ADP1 (acinSp_ADP1) -anapMarg_ST_MARIES Anaplasma marginale str. St. Maries (anapMarg_ST_MARIES) -297 Xanthomonas axonopodis pv. citri str. 306 (297) -desuPsyc_LSV54 Desulfotalea psychrophila LSv54 (desuPsyc_LSV54) -17227 Desulfovibrio vulgaris subsp. vulgaris DP4 (17227) -190 Yersinia enterocolitica subsp. enterocolitica 8081 (190) -193 Clostridium botulinum A str. ATCC 3502 (193) -270 Streptococcus pyogenes str. Manfredo (270) -16252 Synechococcus sp. JA-2-3B'a(2-13) (16252) -16251 Synechococcus sp. JA-3-3Ab (16251) -16319 Arcobacter butzleri RM4018 (16319) -276 Listeria monocytogenes EGD-e (276) -277 Streptococcus pneumoniae TIGR4 (277) -13427 Heliobacterium modesticaldum Ice1 (13427) -279 Staphylococcus epidermidis ATCC 12228 (279) -19979 Flavobacterium psychrophilum JIP02/86 (19979) -13548 Prochlorococcus marinus str. AS9601 (13548) -16700 Yersinia pestis Pestoides F (16700) -therTher_HB8 Thermus thermophilus HB8 (therTher_HB8) -28035 Streptococcus pneumoniae Hungary19A-6 (28035) -19575 Bradyrhizobium sp. ORS278 (19575) -18083 Escherichia coli C str. ATCC 8739 (18083) -methStad1 Methanosphaera stadtmanae DSM 3091 (methStad1) -magnMagn_AMB_1 Magnetospirillum magneticum AMB-1 (magnMagn_AMB_1) -13901 Thermoanaerobacter pseudethanolicus ATCC 33223 (13901) -methBurt2 Methanococcoides burtonii DSM 6242 (methBurt2) -13908 Rhodoferax ferrireducens T118 (13908) -13909 Pseudomonas putida F1 (13909) -16400 Haemophilus influenzae PittEE (16400) -16401 Haemophilus influenzae PittGG (16401) -100 Mycoplasma pulmonis UAB CTIP (100) -methMari_C7 Methanococcus maripaludis C7 (methMari_C7) -106 Halobacterium salinarum R1 (106) -geobSulf Geobacter sulfurreducens PCA (geobSulf) -38 Haemophilus ducreyi 35000HP (38) -28247 Synechococcus sp. PCC 7002 (28247) -16791 Coxiella burnetii RSA 331 (16791) -procMari_CCMP1375 Prochlorococcus marinus subsp. marinus str. CCMP1375 (procMari_CCMP1375) -31 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (31) -oenoOeni_PSU_1 Oenococcus oeni PSU-1 (oenoOeni_PSU_1) -16817 Pseudomonas stutzeri A1501 (16817) -wiggBrev Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis (wiggBrev) -10639 Mycoplasma hyopneumoniae 7448 (10639) -10638 Yersinia pestis biovar Microtus str. 91001 (10638) -caldMaqu1 Caldivirga maquilingensis IC-167 (caldMaqu1) -salmEnte_PARATYPI_ATC Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 (salmEnte_PARATYPI_ATC) -onioYell_PHYTOPLASMA Onion yellows phytoplasma OY-M (onioYell_PHYTOPLASMA) -18459 Francisella tularensis subsp. tularensis WY96-3418 (18459) -334 Streptococcus agalactiae NEM316 (334) -mariAqua_VT8 Marinobacter aquaeolei VT8 (mariAqua_VT8) -16719 Fervidobacterium nodosum Rt17-B1 (16719) -330 Streptococcus agalactiae 2603V/R (330) -333 Streptococcus mutans UA159 (333) -9638 Lactobacillus johnsonii NCC 533 (9638) -17729 Anaeromyxobacter sp. Fw109-5 (17729) -shewLoihPV4 Shewanella loihica PV-4 (shewLoihPV4) -candPela_UBIQUE_HTCC1 Candidatus Pelagibacter ubique HTCC1062 (candPela_UBIQUE_HTCC1) -myxoXant_DK_1622 Myxococcus xanthus DK 1622 (myxoXant_DK_1622) -9636 Rickettsia rickettsii str. 'Sheila Smith' (9636) -salmTyph_TY2 Salmonella enterica subsp. enterica serovar Typhi str. Ty2 (salmTyph_TY2) -chloChlo_CAD3 Chlorobium chlorochromatii CaD3 (chloChlo_CAD3) -mesoFlor_L1 Mesoplasma florum L1 (mesoFlor_L1) -28921 Acinetobacter baumannii (28921) -hermArse Herminiimonas arsenicoxydans (hermArse) -methMaze1 Methanosarcina mazei Go1 (methMaze1) -17343 Sphingomonas wittichii RW1 (17343) -99 Mycoplasma pneumoniae M129 (99) -13643 Synechococcus sp. CC9605 (13643) -13642 Synechococcus sp. WH 7803 (13642) -lawsIntr_PHE_MN1_00 Lawsonia intracellularis PHE/MN1-00 (lawsIntr_PHE_MN1_00) -jannCCS1 Jannaschia sp. CCS1 (jannCCS1) -91 Mycobacterium avium subsp. paratuberculosis K-10 (91) -90 Mycobacterium leprae TN (90) -92 Mycobacterium smegmatis str. MC2 155 (92) -95 Tropheryma whipplei str. Twist (95) -13649 Xanthomonas campestris pv. vesicatoria str. 85-10 (13649) -13885 Chlamydia trachomatis A/HAR-13 (13885) -13884 Rickettsia felis URRWXCal2 (13884) -13887 Streptococcus pyogenes MGAS6180 (13887) -13760 Corynebacterium glutamicum ATCC 13032 (13760) -13888 Streptococcus pyogenes MGAS5005 (13888) -ureaUrea Ureaplasma parvum serovar 3 str. ATCC 700970 (ureaUrea) -streCoel Streptomyces coelicolor A3(2) (streCoel) -orieTsut_BORYONG Orientia tsutsugamushi str. Boryong (orieTsut_BORYONG) -polaJS66 Polaromonas sp. JS666 (polaJS66) -rhodRubr_ATCC11170 Rhodospirillum rubrum ATCC 11170 (rhodRubr_ATCC11170) -rhodRHA1 Rhodococcus sp. RHA1 (rhodRHA1) -pireSp Rhodopirellula baltica SH 1 (pireSp) -franTula_TULARENSIS Francisella tularensis subsp. tularensis SCHU S4 (franTula_TULARENSIS) -syneSp_WH8102 Synechococcus sp. WH 8102 (syneSp_WH8102) -19521 Clostridium botulinum A str. Hall (19521) -238 Staphylococcus aureus subsp. aureus COL (238) -15660 Prochlorococcus marinus str. NATL1A (15660) -17823 Xylella fastidiosa M12 (17823) -methPetr_PM1 Methylibium petroleiphilum PM1 (methPetr_PM1) -237 Staphylococcus aureus subsp. aureus NCTC 8325 (237) -thioCrun_XCL_2 Thiomicrospira crunogena XCL-2 (thioCrun_XCL_2) -haloHalo1 Halobacterium sp. NRC-1 (haloHalo1) -16190 Roseiflexus sp. RS-1 (16190) -idioLoih_L2TR Idiomarina loihiensis L2TR (idioLoih_L2TR) -18637 Methylobacterium extorquens PA1 (18637) -sodaGlos_MORSITANS Sodalis glossinidius str. 'morsitans' (sodaGlos_MORSITANS) -18633 Prochlorococcus marinus str. MIT 9215 (18633) -mycoTube_H37RV Mycobacterium tuberculosis H37Rv (mycoTube_H37RV) -polyQLWP Polynucleobacter sp. QLW-P1DMWA-1 (polyQLWP) -peloLute_DSM273 Pelodictyon luteolum DSM 273 (peloLute_DSM273) -burkCeno_AU_1054 Burkholderia cenocepacia AU 1054 (burkCeno_AU_1054) -13942 Streptococcus sanguinis SK36 (13942) -13943 Burkholderia mallei NCTC 10229 (13943) -ente638 Enterobacter sp. 638 (ente638) -13946 Burkholderia mallei NCTC 10247 (13946) -13947 Burkholderia mallei SAVP1 (13947) -16363 Streptococcus pyogenes MGAS9429 (16363) -neorSenn_MIYAYAMA Neorickettsia sennetsu str. Miyayama (neorSenn_MIYAYAMA) -heliAcin_SHEEBA Helicobacter acinonychis str. Sheeba (heliAcin_SHEEBA) -16366 Streptococcus pyogenes MGAS10750 (16366) -16365 Streptococcus pyogenes MGAS2096 (16365) -13473 Nitrobacter hamburgensis X14 (13473) -burkCepa_AMMD Burkholderia ambifaria AMMD (burkCepa_AMMD) -methMari_C5_1 Methanococcus maripaludis C5 (methMari_C5_1) -13478 Aster yellows witches'-broom phytoplasma AYWB (13478) -13370 Actinobacillus succinogenes 130Z (13370) -methBark1 Methanosarcina barkeri str. Fusaro (methBark1) -geobMeta_GS15 Geobacter metallireducens GS-15 (geobMeta_GS15) -eschColi_CFT073 Escherichia coli CFT073 (eschColi_CFT073) -metMar1 Methanococcus maripaludis S2 (metMar1) -enteFaec_V583 Enterococcus faecalis V583 (enteFaec_V583) -17265 Francisella tularensis subsp. holarctica OSU18 (17265) -shigFlex_2A Shigella flexneri 2a str. 301 (shigFlex_2A) -erwiCaro_ATROSEPTICA Pectobacterium atrosepticum SCRI1043 (erwiCaro_ATROSEPTICA) -pseuHalo_TAC125 Pseudoalteromonas haloplanktis TAC125 (pseuHalo_TAC125) -17163 Campylobacter jejuni subsp. doylei 269.97 (17163) -17161 Campylobacter curvus 525.92 (17161) -10690 Mesorhizobium sp. BNC1 (10690) -10694 Ehrlichia canis str. Jake (10694) -10697 Mycoplasma mobile 163K (10697) -25 Bordetella parapertussis 12822 (25) -26 Bordetella pertussis Tohama I (26) -16841 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) (16841) -sulfToko1 Sulfolobus tokodaii str. 7 (sulfToko1) -404 Lactobacillus brevis ATCC 367 (404) -403 Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 (403) -13920 Psychrobacter cryohalolentis K5 (13920) -401 Lactococcus lactis subsp. cremoris SK11 (401) -16137 Bradyrhizobium sp. BTAi1 (16137) -uncuMeth_RCI uncultured methanogenic archaeon RC-I (uncuMeth_RCI) -coryEffi_YS_314 Corynebacterium efficiens YS-314 (coryEffi_YS_314) -13485 Parabacteroides distasonis ATCC 8503 (13485) -409 Mycoplasma gallisepticum R (409) -28743 Yersinia pseudotuberculosis YPIII (28743) -19469 Escherichia coli SECEC SMS-3-5 (19469) -psycArct_273_4 Psychrobacter arcticus 273-4 (psycArct_273_4) -propAcne_KPA171202 Propionibacterium acnes KPA171202 (propAcne_KPA171202) -acidJS42 Acidovorax sp. JS42 (acidJS42) -chroSale_DSM3043 Chromohalobacter salexigens DSM 3043 (chroSale_DSM3043) -19065 Clostridium kluyveri DSM 555 (19065) -18801 Staphylococcus aureus subsp. aureus str. Newman (18801) -13151 Shigella sonnei Ss046 (13151) -18965 Sulfurovum sp. NBC37-1 (18965) -18963 Nitratiruptor sp. SB155-2 (18963) -18809 Methylobacterium sp. 4-46 (18809) -tropWhip_TW08_27 Tropheryma whipplei TW08/27 (tropWhip_TW08_27) -28135 Bordetella petrii DSM 12804 (28135) -natrPhar1 Natronomonas pharaonis DSM 2160 (natrPhar1) -370 Chlamydophila felis Fe/C-56 (370) -377 Gluconacetobacter diazotrophicus PAl 5 (377) -rubrXyla_DSM9941 Rubrobacter xylanophilus DSM 9941 (rubrXyla_DSM9941) -15746 Prochlorococcus marinus str. MIT 9301 (15746) -15747 Rhodopseudomonas palustris HaA2 (15747) -18981 Finegoldia magna ATCC 29328 (18981) -franCcI3 Frankia sp. CcI3 (franCcI3) -15749 Rhodopseudomonas palustris BisB5 (15749) -16549 Janthinobacterium sp. Marseille (16549) -89 Mycobacterium bovis AF2122/97 (89) -12716 Citrobacter koseri ATCC BAA-895 (12716) -82 Lactobacillus acidophilus NCFM (82) -81 Clostridium tetani E88 (81) -16095 Mycoplasma agalactiae PG2 (16095) -87 Corynebacterium diphtheriae NCTC 13129 (87) -84 Lactobacillus gasseri ATCC 33323 (84) -85 Listeria monocytogenes str. 4b F2365 (85) -20197 Francisella tularensis subsp. holarctica FTA (20197) -caldSacc_DSM8903 Caldicellulosiruptor saccharolyticus DSM 8903 (caldSacc_DSM8903) -anabVari_ATCC29413 Anabaena variabilis ATCC 29413 (anabVari_ATCC29413) -lactPlan Lactobacillus plantarum WCFS1 (lactPlan) -carbHydr_Z_2901 Carboxydothermus hydrogenoformans Z-2901 (carbHydr_Z_2901) -13617 Prochlorococcus marinus str. MIT 9515 (13617) -10878 Bacillus anthracis str. Sterne (10878) -16067 Yersinia pestis Angola (16067) -16062 Leuconostoc citreum KM20 (16062) -16148 Leptospira borgpetersenii serovar Hardjo-bovis JB197 (16148) -16146 Leptospira borgpetersenii serovar Hardjo-bovis L550 (16146) -vibrVuln_CMCP6_1 Vibrio vulnificus CMCP6 (vibrVuln_CMCP6_1) -10877 Bacillus thuringiensis serovar konkukian str. 97-27 (10877) -19517 Clostridium botulinum A str. ATCC 19397 (19517) -nitrWino_NB_255 Nitrobacter winogradskyi Nb-255 (nitrWino_NB_255) -16321 Bifidobacterium adolescentis ATCC 15703 (16321) -17629 Pseudomonas putida GB-1 (17629) -17237 Rickettsia bellii OSU 85-389 (17237) -19519 Clostridium botulinum F str. Langeland (19519) -mesoLoti Mesorhizobium loti MAFF303099 (mesoLoti) -coxiBurn Coxiella burnetii RSA 493 (coxiBurn) -247 Chlamydophila pneumoniae AR39 (247) -acidBact_ELLIN345 Acidobacteria bacterium Ellin345 (acidBact_ELLIN345) -241 Salmonella typhimurium LT2 (241) -16249 Bartonella bacilliformis KC583 (16249) -12997 Acaryochloris marina MBIC11017 (12997) -xyleFast Xylella fastidiosa 9a5c (xyleFast) -13435 Lactobacillus sakei subsp. sakei 23K (13435) -11752 Haemophilus influenzae 86-028NP (11752) -16393 Neisseria meningitidis 053442 (16393) -16394 Thermoanaerobacter sp. X514 (16394) -methKand1 Methanopyrus kandleri AV19 (methKand1) -bifiLong Bifidobacterium longum NCC2705 (bifiLong) -leptInte Leptospira interrogans serovar Lai str. 56601 (leptInte) -burkCeno_HI2424 Burkholderia cenocepacia HI2424 (burkCeno_HI2424) -16364 Streptococcus pyogenes MGAS10270 (16364) -13875 Candidatus Blochmannia pennsylvanicus str. BPEN (13875) -buchSp Buchnera aphidicola str. APS (Acyrthosiphon pisum) (buchSp) -178 Burkholderia pseudomallei K96243 (178) -176 Mycoplasma penetrans HF-2 (176) -pyroCali1 Pyrobaculum calidifontis JCM 11548 (pyroCali1) -chloTepi_TLS Chlorobium tepidum TLS (chloTepi_TLS) -13282 Synechococcus elongatus PCC 6301 (13282) -16800 Pseudomonas entomophila L48 (16800) -picrTorr1 Picrophilus torridus DSM 9790 (picrTorr1) -shewANA3 Shewanella sp. ANA-3 (shewANA3) -13443 Listeria welshimeri serovar 6b str. SLCC5334 (13443) -bdelBact Bdellovibrio bacteriovorus HD100 (bdelBact) -gramFors_KT0803 Gramella forsetii KT0803 (gramFors_KT0803) -184 Clavibacter michiganensis subsp. sepedonicus (184) -189 Streptomyces avermitilis MA-4680 (189) -clavMich_NCPPB_382 Clavibacter michiganensis subsp. michiganensis NCPPB 382 (clavMich_NCPPB_382) -peloCarb Pelobacter carbinolicus DSM 2380 (peloCarb) -20083 Campylobacter hominis ATCC BAA-381 (20083) -saliTrop_CNB_440 Salinispora tropica CNB-440 (saliTrop_CNB_440) -17057 Borrelia afzelii PKo (17057) -campJeju Campylobacter jejuni subsp. jejuni NCTC 11168 (campJeju) -17053 Pseudomonas putida W619 (17053) -12 Pseudomonas fluorescens PfO-1 (12) -15 Xanthomonas campestris pv. campestris str. 8004 (15) -12475 Wolbachia endosymbiont strain TRS of Brugia malayi (12475) -13217 Azoarcus sp. BH72 (13217) -dehaEthe_195 Dehalococcoides ethenogenes 195 (dehaEthe_195) -methTherPT1 Methanosaeta thermophila PT (methTherPT1) -shewMR7 Shewanella sp. MR-7 (shewMR7) -shewMR4 Shewanella sp. MR-4 (shewMR4) -15708 Acidovorax avenae subsp. citrulli AAC00-1 (15708) -19087 Ureaplasma parvum serovar 3 str. ATCC 27815 (19087) -geobUran_RF4 Geobacter uraniireducens Rf4 (geobUran_RF4) -shewDeni Shewanella denitrificans OS217 (shewDeni) -pyrFur2 Pyrococcus furiosus DSM 3638 (pyrFur2) -desuRedu_MI_1 Desulfotomaculum reducens MI-1 (desuRedu_MI_1) -syntFuma_MPOB Syntrophobacter fumaroxidans MPOB (syntFuma_MPOB) -278 Streptococcus pneumoniae R6 (278) -13654 Synechococcus sp. RCC307 (13654) -13655 Synechococcus sp. CC9902 (13655) -16313 Staphylococcus aureus subsp. aureus USA300 (16313) -legiPneu_PHILADELPHIA Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (legiPneu_PHILADELPHIA) -20391 Bacillus pumilus SAFR-032 (20391) -chlaPneu_CWL029 Chlamydophila pneumoniae CWL029 (chlaPneu_CWL029) -16259 Escherichia coli UTI89 (16259) -13067 Bacteroides fragilis YCH46 (13067) -gloeViol Gloeobacter violaceus PCC 7421 (gloeViol) -moorTher_ATCC39073 Moorella thermoacetica ATCC 39073 (moorTher_ATCC39073) -323 Pseudomonas syringae pv. syringae B728a (323) -320 Brucella suis 1330 (320) -roseDeni_OCH_114 Roseobacter denitrificans OCh 114 (roseDeni_OCH_114) -326 Streptococcus agalactiae A909 (326) -327 Pseudomonas fluorescens Pf-5 (327) -325 Ehrlichia chaffeensis str. Arkansas (325) -329 Desulfovibrio desulfuricans G20 (329) -16203 Brucella melitensis biovar Abortus 2308 (16203) -12950 Yersinia pseudotuberculosis IP 32953 (12950) -heliPylo_26695 Helicobacter pylori 26695 (heliPylo_26695) -12952 Rickettsia canadensis str. McKiel (12952) -12953 Rickettsia akari str. Hartford (12953) -16208 Mycoplasma capricolum subsp. capricolum ATCC 27343 (16208) -17375 Francisella tularensis subsp. tularensis FSC198 (17375) -19259 Acholeplasma laidlawii PG-8A (19259) -77 Clostridium acetobutylicum ATCC 824 (77) -74 Bacillus cereus ATCC 10987 (74) -15770 Dehalococcoides sp. BAV1 (15770) -79 Clostridium perfringens str. 13 (79) -78 Clostridium difficile 630 (78) -13624 Bacillus cereus subsp. cytotoxis NVH 391-98 (13624) -13623 Bacillus weihenstephanensis KBAB4 (13623) -tricEryt_IMS101 Trichodesmium erythraeum IMS101 (tricEryt_IMS101) -photLumi Photorhabdus luminescens subsp. laumondii TTO1 (photLumi) -peloTher_SI Pelotomaculum thermopropionicum SI (peloTher_SI) -18789 Shewanella sediminis HAW-EB3 (18789) -therKoda1 Thermococcus kodakarensis KOD1 (therKoda1) -oceaIhey Oceanobacillus iheyensis HTE831 (oceaIhey) -16297 Xanthomonas oryzae pv. oryzae MAFF 311018 (16297) -19639 Methanococcus maripaludis C6 (19639) -blocFlor Candidatus Blochmannia floridanus (blocFlor) -shewW318 Shewanella sp. W3-18-1 (shewW318) -16184 Clostridium phytofermentans ISDg (16184) -17477 Acinetobacter baumannii ATCC 17978 (17477) -therElon Thermosynechococcus elongatus BP-1 (therElon) -13403 Bacillus amyloliquefaciens FZB42 (13403) -17679 Petrotoga mobilis SJ95 (17679) -16374 Streptococcus pneumoniae D39 (16374) -16375 Shigella flexneri 5 str. 8401 (16375) -methBoon1 Candidatus Methanoregula boonei 6A8 (methBoon1) -mariMari_MCS10 Maricaulis maris MCS10 (mariMari_MCS10) -ralsEutr_JMP134 Ralstonia eutropha JMP134 (ralsEutr_JMP134) -baciSubt Bacillus subtilis subsp. subtilis str. 168 (baciSubt) -16372 Buchnera aphidicola str. Cc (Cinara cedri) (16372) -213 Prochlorococcus marinus subsp. pastoris str. CCMP1986 (213) -erytLito_HTCC2594 Erythrobacter litoralis HTCC2594 (erytLito_HTCC2594) -acidCell_11B Acidothermus cellulolyticus 11B (acidCell_11B) -pyrAer1 Pyrobaculum aerophilum str. IM2 (pyrAer1) -xantCamp Xanthomonas campestris pv. campestris str. ATCC 33913 (xantCamp) -thioDeni_ATCC25259 Thiobacillus denitrificans ATCC 25259 (thioDeni_ATCC25259) -28583 Chlamydia trachomatis 434/Bu (28583) -deinRadi Deinococcus radiodurans R1 (deinRadi) -yersPest_CO92 Yersinia pestis CO92 (yersPest_CO92) -28585 Chlamydia trachomatis L2b/UCH-1/proctitis (28585) -wolbEndo_OF_DROSOPHIL Wolbachia endosymbiont of Drosophila melanogaster (wolbEndo_OF_DROSOPHIL) -17153 Streptococcus suis 05ZYH33 (17153) -10689 Kineococcus radiotolerans SRS30216 (10689) -17155 Streptococcus suis 98HAH33 (17155) -17159 Campylobacter concisus 13826 (17159) -ralsSola Ralstonia solanacearum GMI1000 (ralsSola) -10687 Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (10687) -17403 Frankia alni ACN14a (17403) -16871 Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 (16871) -12388 Bacillus licheniformis ATCC 14580 (12388) -neisMeni_Z2491_1 Neisseria meningitidis Z2491 (neisMeni_Z2491_1) -saliRube_DSM13855 Salinibacter ruber DSM 13855 (saliRube_DSM13855) -17953 Campylobacter jejuni subsp. jejuni 81116 (17953) -10616 Mycoplasma mycoides subsp. mycoides SC str. PG1 (10616) -13496 Prochlorococcus marinus str. MIT 9303 (13496) -28507 Clostridium botulinum A3 str. Loch Maree (28507) -colwPsyc_34H Colwellia psychrerythraea 34H (colwPsyc_34H) -hyphNept_ATCC15444 Hyphomonas neptunium ATCC 15444 (hyphNept_ATCC15444) -vibrChol1 Vibrio cholerae O1 biovar eltor str. N16961 (vibrChol1) -deinGeot_DSM11300 Deinococcus geothermalis DSM 11300 (deinGeot_DSM11300) -312 Buchnera aphidicola str. Sg (Schizaphis graminum) (312) -311 Streptococcus pyogenes MGAS315 (311) -metaSedu Metallosphaera sedula DSM 5348 (metaSedu) -314 Clostridium thermocellum ATCC 27405 (314) -lactSali_UCC118 Lactobacillus salivarius UCC118 (lactSali_UCC118) -pediPent_ATCC25745 Pediococcus pentosaceus ATCC 25745 (pediPent_ATCC25745) -flavJohn_UW101 Flavobacterium johnsoniae UW101 (flavJohn_UW101) -mannSucc_MBEL55E Mannheimia succiniciproducens MBEL55E (mannSucc_MBEL55E) -haemSomn_129PT Haemophilus somnus 129PT (haemSomn_129PT) -13145 Shigella dysenteriae Sd197 (13145) -13146 Shigella boydii Sb227 (13146) -17491 Legionella pneumophila str. Corby (17491) -nanEqu1 Nanoarchaeum equitans Kin4-M (nanEqu1) -12508 Staphylococcus haemolyticus JCSC1435 (12508) -13384 Pelobacter propionicus DSM 2379 (13384) -chlaTrac Chlamydia trachomatis D/UW-3/CX (chlaTrac) -haloWals1 Haloquadratum walsbyi DSM 16790 (haloWals1) -13389 Shewanella baltica OS195 (13389) -baciHalo Bacillus halodurans C-125 (baciHalo) -hypeButy1 Hyperthermus butylicus DSM 5456 (hypeButy1) -chroViol Chromobacterium violaceum ATCC 12472 (chroViol) -16088 Francisella tularensis subsp. novicida U112 (16088) -methJann1 Methanocaldococcus jannaschii DSM 2661 (methJann1) -384 Bacillus cereus ATCC 14579 (384) -pastMult Pasteurella multocida subsp. multocida str. Pm70 (pastMult) -386 Pseudomonas aeruginosa UCBPP-PA14 (386) -388 Haemophilus somnus 2336 (388) -16083 Alkaliphilus oremlandii OhILAs (16083) -27853 Francisella philomiragia subsp. philomiragia ATCC 25017 (27853) -16081 Mycobacterium sp. KMS (16081) -cytoHutc_ATCC33406 Cytophaga hutchinsonii ATCC 33406 (cytoHutc_ATCC33406) -nitrEuro Nitrosomonas europaea ATCC 19718 (nitrEuro) -12720 Enterobacter sakazakii ATCC BAA-894 (12720) -therMari Thermotoga maritima MSB8 (therMari) -mycoGeni Mycoplasma genitalium G37 (mycoGeni) -vibrFisc_ES114_1 Vibrio fischeri ES114 (vibrFisc_ES114_1) -pyroIsla1 Pyrobaculum islandicum DSM 4184 (pyroIsla1) -17407 Burkholderia multivorans ATCC 17616 (17407) -13030 Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- (13030) -18271 Rickettsia massiliae MTU5 (18271) -21047 Candidatus Desulforudis audaxviator MP104C (21047) -19857 Vibrio harveyi ATCC BAA-1116 (19857) -17639 Parvibaculum lavamentivorans DS-1 (17639) -18059 Mycobacterium bovis BCG str. Pasteur 1173P2 (18059) -vibrPara1 Vibrio parahaemolyticus RIMD 2210633 (vibrPara1) -259 Escherichia coli O157:H7 EDL933 (259) -64 Staphylococcus epidermidis RP62A (64) -neisGono_FA1090_1 Neisseria gonorrhoeae FA 1090 (neisGono_FA1090_1) -66 Streptococcus gordonii str. Challis substr. CH1 (66) -16723 Aeromonas salmonicida subsp. salmonicida A449 (16723) -16230 Mycobacterium ulcerans Agy99 (16230) -16721 Coxiella burnetii Dugway 5J108-111 (16721) -16720 Pseudomonas aeruginosa PA7 (16720) -256 Buchnera aphidicola str. Bp (Baizongia pistaciae) (256) -257 Chlamydophila pneumoniae J138 (257) -novoArom_DSM12444 Novosphingobium aromaticivorans DSM 12444 (novoArom_DSM12444) -15642 Mycobacterium tuberculosis F11 (15642) -azoaSp_EBN1 Azoarcus sp. EbN1 (azoaSp_EBN1) -therTher_HB27 Thermus thermophilus HB27 (therTher_HB27) -metAce1 Methanosarcina acetivorans C2A (metAce1) -glucOxyd_621H Gluconobacter oxydans 621H (glucOxyd_621H) -listInno Listeria innocua Clip11262 (listInno) -sulfAcid1 Sulfolobus acidocaldarius DSM 639 (sulfAcid1) -geobTher_NG80_2 Geobacillus thermodenitrificans NG80-2 (geobTher_NG80_2) -402 Lactobacillus casei ATCC 334 (402) -13960 Escherichia coli E24377A (13960) -13954 Burkholderia pseudomallei 1710b (13954) -17445 Marinomonas sp. MWYL1 (17445) -13967 Corynebacterium jeikeium K411 (13967) -leifXyli_XYLI_CTCB0 Leifsonia xyli subsp. xyli str. CTCB07 (leifXyli_XYLI_CTCB0) -10645 Synechococcus elongatus PCC 7942 (10645) -campFetu_82_40 Campylobacter fetus subsp. fetus 82-40 (campFetu_82_40) -13355 Ehrlichia ruminantium str. Welgevonden (13355) -desuHafn_Y51 Desulfitobacterium hafniense Y51 (desuHafn_Y51) -13356 Ehrlichia ruminantium str. Gardel (13356) -13291 Bacillus clausii KSM-K16 (13291) -16421 Francisella tularensis subsp. holarctica (16421) -therVolc1 Thermoplasma volcanium GSS1 (therVolc1) -soliUsit_ELLIN6076 Solibacter usitatus Ellin6076 (soliUsit_ELLIN6076) -bradJapo Bradyrhizobium japonicum USDA 110 (bradJapo) -methTher1 Methanothermobacter thermautotrophicus str. Delta H (methTher1) -13454 Pseudoalteromonas atlantica T6c (13454) -methAeol1 Methanococcus aeolicus Nankai-3 (methAeol1) -nostSp Nostoc sp. PCC 7120 (nostSp) -sphiAlas_RB2256 Sphingopyxis alaskensis RB2256 (sphiAlas_RB2256) -saccDegr_2_40 Saccharophagus degradans 2-40 (saccDegr_2_40) -408 Shigella flexneri 2a str. 2457T (408) -anaeDeha_2CP_C Anaeromyxobacter dehalogenans 2CP-C (anaeDeha_2CP_C) -bordBron Bordetella bronchiseptica RB50 (bordBron) -rickBell_RML369_C Rickettsia bellii RML369-C (rickBell_RML369_C) -pyroArse1 Pyrobaculum arsenaticum DSM 13514 (pyroArse1) -thioDeni_ATCC33889 Sulfurimonas denitrificans DSM 1251 (thioDeni_ATCC33889) -methSmit1 Methanobrevibacter smithii ATCC 35061 (methSmit1) -halMar1 Haloarcula marismortui ATCC 43049 (halMar1) -9618 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 (9618) -9619 Brucella abortus biovar 1 str. 9-941 (9619) -vermEise_EF01_2 Verminephrobacter eiseniae EF01-2 (vermEise_EF01_2) -granBeth_CGDNIH1 Granulibacter bethesdensis CGDNIH1 (granBeth_CGDNIH1) -alcaBork_SK2 Alcanivorax borkumensis SK2 (alcaBork_SK2) -vibrChol_O395_1 Vibrio cholerae O395 (vibrChol_O395_1) -nitrOcea_ATCC19707 Nitrosococcus oceani ATCC 19707 (nitrOcea_ATCC19707) -campJeju_RM1221 Campylobacter jejuni RM1221 (campJeju_RM1221) -12468 Bacillus cereus E33L (12468) -12469 Streptococcus pyogenes MGAS10394 (12469) -19135 Actinobacillus pleuropneumoniae serovar 3 str. JL03 (19135) -woliSucc Wolinella succinogenes DSM 1740 (woliSucc) -19485 Ochrobactrum anthropi ATCC 49188 (19485) -therPend1 Thermofilum pendens Hrk 5 (therPend1) -19489 Staphylococcus aureus subsp. aureus USA300_TCH1516 (19489) -therFusc_YX Thermobifida fusca YX (therFusc_YX) -12609 Chlorobium phaeobacteroides DSM 266 (12609) -aquiAeol Aquifex aeolicus VF5 (aquiAeol) -heliPylo_J99 Helicobacter pylori J99 (heliPylo_J99) -burkPseu_1106A Burkholderia pseudomallei 1106a (burkPseu_1106A) -azorCaul2 Azorhizobium caulinodans ORS 571 (azorCaul2) -12607 Prosthecochloris vibrioformis DSM 265 (12607) -synePCC6 Synechocystis sp. PCC 6803 (synePCC6) -baumCica_HOMALODISCA Baumannia cicadellinicola str. Hc (Homalodisca coagulata) (baumCica_HOMALODISCA) -355 Chlamydophila abortus S26/3 (355) -28111 Sorangium cellulosum 'So ce 56' (28111) -shewBalt Shewanella baltica OS155 (shewBalt) -therTeng Thermoanaerobacter tengcongensis MB4 (therTeng) -359 Pseudomonas syringae pv. tomato str. DC3000 (359) -19943 Rickettsia rickettsii str. Iowa (19943) -alkaEhrl_MLHE_1 Alkalilimnicola ehrlichei MLHE-1 (alkaEhrl_MLHE_1) -sulSol1 Sulfolobus solfataricus P2 (sulSol1) -15604 Dehalococcoides sp. CBDB1 (15604) -19265 Nitrosopumilus maritimus SCM1 (19265) -19543 Thermotoga sp. RQ2 (19543) -methHung1 Methanospirillum hungatei JF-1 (methHung1) -27803 Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7 (27803) -28505 Clostridium botulinum B1 str. Okra (28505) -15766 Lactobacillus reuteri F275 (15766) -17929 Burkholderia cenocepacia MC0-3 (17929) -15762 Mycobacterium sp. MCS (15762) -15760 Mycobacterium gilvum PYR-GCK (15760) -15761 Mycobacterium vanbaalenii PYR-1 (15761) -18797 Lactococcus lactis subsp. cremoris MG1363 (18797) -20371 Brucella suis ATCC 23445 (20371) -desuVulg_HILDENBOROUG Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (desuVulg_HILDENBOROUG) -20079 Escherichia coli DH10B (20079) -288 Yersinia pestis KIM (288) -13006 Alkaliphilus metalliredigens QYMF (13006) -13001 Acinetobacter baumannii (13001) -4 Treponema denticola ATCC 35405 (4) -283 Agrobacterium tumefaciens str. C58 (283) -methVann1 Methanococcus vannielii SB (methVann1) -285 Xylella fastidiosa Temecula1 (285) -286 Streptococcus pyogenes MGAS8232 (286) -candCars_RUDDII Candidatus Carsonella ruddii PV (candCars_RUDDII) -336 Anaplasma phagocytophilum HZ (336) -burkMall_ATCC23344 Burkholderia mallei ATCC 23344 (burkMall_ATCC23344) -leucMese_ATCC8293 Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 (leucMese_ATCC8293) -burkViet_G4 Burkholderia vietnamiensis G4 (burkViet_G4) -267 Pseudomonas putida KT2440 (267) -266 Staphylococcus aureus subsp. aureus MSSA476 (266) -265 Staphylococcus aureus subsp. aureus MRSA252 (265) -264 Staphylococcus aureus subsp. aureus N315 (264) -17643 Shewanella baltica OS185 (17643) -archFulg1 Archaeoglobus fulgidus DSM 4304 (archFulg1) -13418 Polaromonas naphthalenivorans CJ2 (13418) -18007 Desulfococcus oleovorans Hxd3 (18007) -16304 Sinorhizobium medicae WSM419 (16304) -16306 Caulobacter sp. K31 (16306) -59 Chloroflexus aurantiacus J-10-fl (59) -12530 Synechococcus sp. CC9311 (12530) -13551 Prochlorococcus marinus str. MIT 9211 (13551) -15691 Mycobacterium abscessus (15691) -fusoNucl Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (fusoNucl) -63 Staphylococcus aureus RF122 (63) -heliHepa Helicobacter hepaticus ATCC 51449 (heliHepa) -17249 Thermosipho melanesiensis BI429 (17249) -15596 Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 (15596) -psycIngr_37 Psychromonas ingrahamii 37 (psycIngr_37) -syntAcid_SB Syntrophus aciditrophicus SB (syntAcid_SB) -salmTyph Salmonella enterica subsp. enterica serovar Typhi str. CT18 (salmTyph) -burkXeno_LB400 Burkholderia xenovorans LB400 (burkXeno_LB400) -trepPall Treponema pallidum subsp. pallidum str. Nichols (trepPall) -neisMeni_MC58_1 Neisseria meningitidis MC58 (neisMeni_MC58_1) -syntWolf_GOETTINGEN Syntrophomonas wolfei subsp. wolfei str. Goettingen (syntWolf_GOETTINGEN) -15644 Thermotoga lettingae TMO (15644) -13913 Nitrosomonas eutropha C91 (13913) -17417 Dinoroseobacter shibae DFL 12 (17417) -13911 Prochlorococcus marinus str. NATL2A (13911) -13910 Prochlorococcus marinus str. MIT 9312 (13910) -250 Ralstonia metallidurans CH34 (250) -13915 Frankia sp. EAN1pec (13915) -13914 Ignicoccus hospitalis KIN4/I (13914) -rhodSpha_2_4_1 Rhodobacter sphaeroides 2.4.1 (rhodSpha_2_4_1) -16235 Escherichia coli 536 (16235) -zymoMobi_ZM4 Zymomonas mobilis subsp. mobilis ZM4 (zymoMobi_ZM4) -rhodPalu_CGA009 Rhodopseudomonas palustris CGA009 (rhodPalu_CGA009) -420 Chlamydophila pneumoniae TW-183 (420) -stapMari1 Staphylothermus marinus F1 (stapMari1) -sinoMeli Sinorhizobium meliloti 1021 (sinoMeli) -bartHens_HOUSTON_1 Bartonella henselae str. Houston-1 (bartHens_HOUSTON_1) -301 Streptococcus pyogenes SSI-1 (301) -19193 Corynebacterium glutamicum R (19193) -304 Clostridium perfringens ATCC 13124 (304) -306 Staphylococcus aureus subsp. aureus MW2 (306) -307 Corynebacterium glutamicum ATCC 13032 (307) -caulCres Caulobacter crescentus CB15 (caulCres) -haheChej_KCTC_2396 Hahella chejuensis KCTC 2396 (haheChej_KCTC_2396) -10784 Bacillus anthracis str. 'Ames Ancestor' (10784) -magnMC1 Magnetococcus sp. MC-1 (magnMC1) -heliPylo_HPAG1 Helicobacter pylori HPAG1 (heliPylo_HPAG1) -pyrHor1 Pyrococcus horikoshii OT3 (pyrHor1) -12514 Brucella ovis ATCC 25840 (12514) -12512 Arthrobacter aurescens TC1 (12512) -actiPleu_L20 Actinobacillus pleuropneumoniae L20 (actiPleu_L20) -paraDeni_PD1222 Paracoccus denitrificans PD1222 (paraDeni_PD1222) -borrBurg Borrelia burgdorferi B31 (borrBurg) -strePyog_M1_GAS Streptococcus pyogenes M1 GAS (strePyog_M1_GAS) -pseuAeru Pseudomonas aeruginosa PAO1 (pseuAeru) -16523 Herpetosiphon aurantiacus ATCC 23779 (16523) -16525 Candidatus Korarchaeum cryptofilum OPF8 (16525) -19619 Lysinibacillus sphaericus C3-41 (19619) -19617 Candidatus Sulcia muelleri GWSS (19617) -saccEryt_NRRL_2338 Saccharopolyspora erythraea NRRL 2338 (saccEryt_NRRL_2338) -methCaps_BATH Methylococcus capsulatus str. Bath (methCaps_BATH) -16645 Yersinia pestis Antiqua (16645) -16646 Yersinia pestis Nepal516 (16646) -12637 Clostridium beijerinckii NCIMB 8052 (12637) -ehrlRumi_WELGEVONDEN Ehrlichia ruminantium str. Welgevonden (ehrlRumi_WELGEVONDEN) -methLabrZ_1 Methanocorpusculum labreanum Z (methLabrZ_1) -vibrVuln_YJ016_1 Vibrio vulnificus YJ016 (vibrVuln_YJ016_1) -13773 Streptococcus thermophilus LMD-9 (13773) -20039 Leptothrix cholodnii SP-6 (20039) -shewAmaz Shewanella amazonensis SB2B (shewAmaz) -13126 Legionella pneumophila str. Lens (13126) -13127 Legionella pneumophila str. Paris (13127) -13120 Mycoplasma hyopneumoniae 232 (13120) -18509 Staphylococcus aureus subsp. aureus Mu3 (18509) -13040 Silicibacter sp. TM1040 (13040) -18267 Candidatus Vesicomyosocius okutanii HA (18267) -methFlag_KT Methylobacillus flagellatus KT (methFlag_KT) -therAcid1 Thermoplasma acidophilum DSM 1728 (therAcid1) -therPetr_RKU_1 Thermotoga petrophila RKU-1 (therPetr_RKU_1) -shewFrig Shewanella frigidimarina NCIMB 400 (shewFrig) -photProf_SS9 Photobacterium profundum SS9 (photProf_SS9) -burkThai_E264 Burkholderia thailandensis E264 (burkThai_E264) -17811 Lactobacillus helveticus DPC 4571 (17811) -229 Chlamydia muridarum Nigg (229) -228 Chlamydophila caviae GPIC (228) -nitrMult_ATCC25196 Nitrosospira multiformis ATCC 25196 (nitrMult_ATCC25196) -223 Mycobacterium tuberculosis CDC1551 (223) -220 Prochlorococcus marinus str. MIT 9313 (220) -20241 Shewanella halifaxensis HAW-EB4 (20241) -20243 Brucella canis ATCC 23365 (20243) -88 Mycobacterium avium 104 (88) -19227 Renibacterium salmoninarum ATCC 33209 (19227) -neisMeni_FAM18_1 Neisseria meningitidis FAM18 (neisMeni_FAM18_1) -arthFB24 Arthrobacter sp. FB24 (arthFB24) -10679 Rickettsia typhi str. Wilmington (10679) -17457 Pseudomonas mendocina ymp (17457) -13959 Escherichia coli HS (13959) -17455 Shewanella woodyi ATCC 51908 (17455) -17109 Salinispora arenicola CNS-205 (17109) -17459 Serratia proteamaculans 568 (17459) -13953 Burkholderia pseudomallei 668 (13953) -10676 Mycoplasma synoviae 53 (10676) -10675 Mycoplasma hyopneumoniae J (10675) -16820 Clostridium novyi NT (16820) -nocaFarc_IFM10152 Nocardia farcinica IFM 10152 (nocaFarc_IFM10152) -13378 Bacteroides vulgatus ATCC 8482 (13378) -16351 Escherichia coli W3110 (16351) -porpGing_W83 Porphyromonas gingivalis W83 (porpGing_W83) -17415 Shewanella pealeana ATCC 700345 (17415) -eschColi_APEC_O1 Escherichia coli APEC O1 (eschColi_APEC_O1) -46 Bacteroides fragilis NCTC 9343 (46) -13462 Roseiflexus castenholzii DSM 13941 (13462) -44 Bartonella quintana str. Toulouse (44) -42 Rickettsia conorii str. Malish 7 (42) -43 Rickettsia prowazekii str. Madrid E (43) -bactThet_VPI_5482 Bacteroides thetaiotaomicron VPI-5482 (bactThet_VPI_5482) -17413 Delftia acidovorans SPH-1 (17413) -haemInfl_KW20 Haemophilus influenzae Rd KW20 (haemInfl_KW20) -brucMeli Brucella melitensis 16M (brucMeli) -haloHalo_SL1 Halorhodospira halophila SL1 (haloHalo_SL1) -pyrAby1 Pyrococcus abyssi GE5 (pyrAby1) -mculMari1 Methanoculleus marisnigri JR1 (mculMari1) -12554 Borrelia garinii PBi (12554) -dechArom_RCB Dechloromonas aromatica RCB (dechArom_RCB) -stapAure_MU50 Staphylococcus aureus subsp. aureus Mu50 (stapAure_MU50) -eschColi_K12 Escherichia coli K12 (eschColi_K12) -12416 Pseudomonas syringae pv. phaseolicola 1448A (12416) -aeroHydr_ATCC7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966 (aeroHydr_ATCC7966) -baciAnth_AMES Bacillus anthracis str. Ames (baciAnth_AMES) -shewOnei Shewanella oneidensis MR-1 (shewOnei) -15217 Human herpesvirus 1 (15217) -lMaj5 Leishmania major 2005 (lMaj5) diff -r 4e5ca6c44804 -r dd6d09de392e tool-data/shared/ucsc/builds.txt.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/shared/ucsc/builds.txt.sample Mon May 10 12:50:09 2010 -0400 @@ -0,0 +1,153 @@ +#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn +? unspecified (?) +hg19Haps hg19Haplotypes Feb. 2009 (GRCh37/hg19Haps) (hg19Haps) +hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) +hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) +hg17 Human May 2004 (NCBI35/hg17) (hg17) +hg16 Human July 2003 (NCBI34/hg16) (hg16) +hg15 Human Apr. 2003 (NCBI33/hg15) (hg15) +venter1 J. Craig Venter Sep. 2007 (HuRef/venter1) (venter1) +panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) +panTro1 Chimp Nov. 2003 (CGSC 1.1/panTro1) (panTro1) +gorGor2 Gorilla Aug. 2009 (Sanger 4/gorGor2) (gorGor2) +gorGor1 Gorilla Oct. 2008 (Sanger 0.1/gorGor1) (gorGor1) +ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2) +rheMac2 Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) +papHam1 Baboon Nov. 2008 (Baylor 1.0/papHam1) (papHam1) +calJac3 Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3) +calJac1 Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1) +otoGar1 Bushbaby Dec. 2006 (Broad/otoGar1) (otoGar1) +micMur1 Mouse lemur Jun. 2003 (Broad/micMur1) (micMur1) +tupBel1 Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1) +mmtv MMTV Nov. 2009 (MMTV/mmtv) (mmtv) +homPan20 chimp/human Jun. 2008 (UCSC Recon/homPan20) (homPan20) +homIni20 orang/human Jun. 2008 (UCSC Recon/homIni20) (homIni20) +sorAra1 Shrew June 2006 (Broad/sorAra1) (sorAra1) +mm9 Mouse July 2007 (NCBI37/mm9) (mm9) +mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) +mm7 Mouse Aug. 2005 (NCBI35/mm7) (mm7) +rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) +rn3 Rat June 2003 (Baylor 3.1/rn3) (rn3) +speTri1 Squirrel Feb. 2008 (Broad/speTri1) (speTri1) +cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3) +oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) +oryCun1 Rabbit May 2005 (Broad/oryCun1) (oryCun1) +ochPri2 Pika Jul. 2008 (Broad/ochPri2) (ochPri2) +eriEur1 Hedgehog June 2006 (Broad/eriEur1) (eriEur1) +felCatV17e Cat Dec. 2008 (NHGRI/GTB V17e/felCatV17e) (felCatV17e) +felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) +ailMel1 Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1) +nemVec1 Starlet sea anemone Jun. 2007 (JGI-PDF/nemVec1) (nemVec1) +canFam2 Dog May 2005 (Broad/canFam2) (canFam2) +canFam1 Dog July 2004 (Broad/canFam1) (canFam1) +canFamPoodle1 Dog May 2003 (TIGR Poodle/canFamPoodle1) (canFamPoodle1) +equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) +equCab1 Horse Jan. 2007 (Broad/equCab1) (equCab1) +susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) +pteVam1 Megabat Jul. 2008 (Broad/pteVam1) (pteVam1) +myoLuc1 Microbat Mar. 2006 (Broad/myoLuc1) (myoLuc1) +susScr1 Pig Apr. 2009 (SGSC 9.53/susScr1) (susScr1) +turTru1 Dolphin Feb. 2008 (Broad/turTru1) (turTru1) +tarSyr1 Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1) +proCap1 Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1) +oviAri1 Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1) +dipOrd1 Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1) +choHof1 Sloth Jul. 2008 (Broad/choHof1) (choHof1) +bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) +bosTau3 Cow Aug. 2006 (Baylor 3.1/bosTau3) (bosTau3) +bosTau2 Cow Mar. 2005 (Baylor 2.0/bosTau2) (bosTau2) +macEug1 Wallaby Nov. 2007 (Baylor 1.0/macEug1) (macEug1) +dasNov2 Armadillo Jul. 2008 (Broad/dasNov2) (dasNov2) +dasNov1 Armadillo May 2005 (Broad/dasNov1) (dasNov1) +echTel1 Tenrec July 2005 (Broad/echTel1) (echTel1) +loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3) +loxAfr2 Elephant Jul. 2008 (Broad/loxAfr2) (loxAfr2) +loxAfr1 Elephant May 2005 (Broad/loxAfr1) (loxAfr1) +monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) +monDom4 Opossum Jan. 2006 (Broad/monDom4) (monDom4) +monDom1 Opossum Oct. 2004 (Broad prelim/monDom1) (monDom1) +ornAna1 Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1) +galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) +galGal2 Chicken Feb. 2004 (WUGSC 1.0/galGal2) (galGal2) +taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) +anoCar1 Lizard Feb. 2007 (Broad/anoCar1) (anoCar1) +xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) +xenTro1 X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) (xenTro1) +danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) +danRer5 Zebrafish July 2007 (Zv7/danRer5) (danRer5) +danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) (danRer4) +danRer3 Zebrafish May 2005 (Zv5/danRer3) (danRer3) +tetNig2 Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2) +tetNig1 Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1) +fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) +fr1 Fugu Aug. 2002 (JGI 3.0/fr1) (fr1) +gasAcu1 Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1) +oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2) +oryLat1 Medaka Apr. 2006 (NIG/UT MEDAKA1/oryLat1) (oryLat1) +petMar1 Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1) +borEut13 Boreoeutherian Apr. 24. 2006 (UCSC Recon/borEut13) (borEut13) +canHg12 Boreoeutherian Nov. 19. 2005 (UCSC Recon/canHg12) (canHg12) +rodEnt13 Rodent Apr. 24. 2006 (UCSC Recon/rodEnt13) (rodEnt13) +priMat13 Primate Apr. 24. 2006 (UCSC Recon/priMat13) (priMat13) +nonAfr13 Non-Afrotheria Apr. 24. 2006 (UCSC Recon/nonAfr13) (nonAfr13) +lauRas13 Laurasiatheria Apr. 24. 2006 (UCSC Recon/lauRas13) (lauRas13) +homIni14 Hominidae Oct. 1. 2006 (UCSC Recon/homIni14) (homIni14) +homIni13 Hominidae Apr. 24. 2006 (UCSC Recon/homIni13) (homIni13) +gliRes13 Glires Apr. 24. 2006 (UCSC Recon/gliRes13) (gliRes13) +eutHer13 Eutheria Apr. 24. 2006 (UCSC Recon/eutHer13) (eutHer13) +euaGli13 Euarchontoglires Apr. 24. 2006 (UCSC Recon/euaGli13) (euaGli13) +catArr1 Catarrhini June 13. 2006 (UCSC Recon/catArr1) (catArr1) +afrOth13 Afrotheria Apr. 24. 2006 (UCSC Recon/afrOth13) (afrOth13) +braFlo1 Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1) +ci2 C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2) +ci1 C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1) +cioSav2 C. savignyi July 2005 (Sidow Lab 2.0/cioSav2) (cioSav2) +cioSav1 C. savignyi Apr. 2003 (Broad/cioSav1) (cioSav1) +strPur2 S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2) +strPur1 S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1) +ce8 C. elegans Jun 2009 (WS204/ce8) (ce8) +ce7 C. elegans Feb 2009 (WS200/ce7) (ce7) +aplCal1 Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1) +ce6 C. elegans May 2008 (WS190/ce6) (ce6) +ce5 C. elegans Aug. 2007 (WS180/ce5) (ce5) +ce4 C. elegans Jan. 2007 (WS170/ce4) (ce4) +ce3 C. elegans March 2005 (WS140/ce3) (ce3) +ce2 C. elegans Mar. 2004 (WS120/ce2) (ce2) +caePb2 C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) +caePb1 C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1) +cb3 C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3) +cb2 C. briggsae Aug 2005 (WUGSC prelim/cb2) (cb2) +cb1 C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1) +caeRem3 C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) +caeRem2 C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) +caeRem1 C. remanei March 2005 (WUGSC prelim/caeRem1) (caeRem1) +caeJap2 C. japonica Jan. 2009 (WUGSC 4.0.1/caeJap2) (caeJap2) +caeJap1 C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) +priPac1 P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) +dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) +dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2) +dm1 D. melanogaster Jan. 2003 (BDGP R3/dm1) (dm1) +droSim1 D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) +droSec1 D. sechellia Oct. 2005 (Broad/droSec1) (droSec1) +droYak2 D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) +droYak1 D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1) +droEre1 D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1) +droAna2 D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2) +droAna1 D. ananassae July 2004 (TIGR/droAna1) (droAna1) +dp3 D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3) +dp2 D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2) +droPer1 D. persimilis Oct. 2005 (Broad/droPer1) (droPer1) +droVir2 D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2) +droVir1 D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1) +droMoj2 D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2) +droMoj1 D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1) +droGri1 D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1) +anoGam1 A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) +apiMel2 A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2) +apiMel1 A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1) +triCas2 T. castaneum Sep. 2005 (Baylor 2.0/triCas2) (triCas2) +falciparum P. falciparum Plasmodium falciparum (?/falciparum) (falciparum) +sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) +sacCer1 S. cerevisiae Oct. 2003 (SGD/sacCer1) (sacCer1) +sc1 SARS coronavirus Apr. 2003 (GenBank Apr. 14 '03/sc1) (sc1) +phiX phiX174 (phiX)

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[hg] galaxy 3764: Add 'filter transcripts via tracking' tool to ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4e5ca6c44804 changeset: 3764:4e5ca6c44804 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon May 10 12:42:05 2010 -0400 description: Add 'filter transcripts via tracking' tool to RNA-seq tools. This tool is useful for operating on output files from cufftools suite. diffstat: tool_conf.xml.sample | 1 + tools/ngs_rna/filter_transcripts_via_tracking.py | 70 +++++++++++++++++++++++ tools/ngs_rna/filter_transcripts_via_tracking.xml | 32 ++++++++++ 3 files changed, 103 insertions(+), 0 deletions(-) diffs (121 lines): diff -r 1110a91888e2 -r 4e5ca6c44804 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon May 10 11:55:08 2010 -0400 +++ b/tool_conf.xml.sample Mon May 10 12:42:05 2010 -0400 @@ -239,6 +239,7 @@ <tool file="ngs_rna/cufflinks_wrapper.xml" /> <tool file="ngs_rna/cuffcompare_wrapper.xml" /> <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> </section> <section name="NGS: SAM Tools" id="samtools"> <tool file="samtools/sam_bitwise_flag_filter.xml" /> diff -r 1110a91888e2 -r 4e5ca6c44804 tools/ngs_rna/filter_transcripts_via_tracking.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ngs_rna/filter_transcripts_via_tracking.py Mon May 10 12:42:05 2010 -0400 @@ -0,0 +1,70 @@ +#!/usr/bin/env python +import os, sys, tempfile + +assert sys.version_info[:2] >= ( 2, 4 ) + +def __main__(): + """ + Utility script for analyzing Cufflinks data: uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts + produced by cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the GTF so that the output GTF contains only + transcript found in the tracking file. Because a tracking file has multiple samples, a sample number is used to filter transcripts for + a particular sample. + """ + # Read parms. + tracking_file_name = sys.argv[1] + transcripts_file_name = sys.argv[2] + output_file_name = sys.argv[3] + sample_number = int ( sys.argv[4] ) + + # Open files. + transcripts_file = open( transcripts_file_name, 'r' ) + output_file = open( output_file_name, 'w' ) + + # Read transcript IDs from tracking file. + transcript_ids = {} + for i, line in enumerate( file( tracking_file_name ) ) : + # Split line into elements. Line format is + # [Transfrag ID] [Locus ID] [Ref Gene ID] [Ref Transcript ID] [Class code] [qJ:<gene_id>|<transcript_id>|<FMI>|<FPKM>|<conf_lo>|<conf_hi>] + line = line.rstrip( '\r\n' ) + elems = line.split( '\t' ) + + # Get transcript info. + if sample_number == 1: + transcript_info = elems[4] + elif sample_number == 2: + transcript_info = elems[5] + if not transcript_info.startswith('q'): + # No transcript for this sample. + continue + + # Get and store transcript id. + transcript_id = transcript_info.split('|')[1] + transcript_id = transcript_id.strip('"') + transcript_ids[transcript_id] = "" + + # Filter transcripts file using transcript_ids + for i, line in enumerate( file( transcripts_file_name ) ): + # GTF format: chrom source, name, chromStart, chromEnd, score, strand, frame, attributes. + elems = line.split( '\t' ) + + # Get attributes. + attributes_list = elems[8].split(";") + attributes = {} + for name_value_pair in attributes_list: + pair = name_value_pair.strip().split(" ") + name = pair[0].strip() + if name == '': + continue + # Need to strip double quote from values + value = pair[1].strip(" \"") + attributes[name] = value + + # Get element's transcript id. + transcript_id = attributes['transcript_id'] + if transcript_id in transcript_ids: + output_file.write(line) + + # Clean up. + output_file.close() + +if __name__ == "__main__": __main__() diff -r 1110a91888e2 -r 4e5ca6c44804 tools/ngs_rna/filter_transcripts_via_tracking.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ngs_rna/filter_transcripts_via_tracking.xml Mon May 10 12:42:05 2010 -0400 @@ -0,0 +1,32 @@ +<tool id="filter_combined_via_tracking" name="Filter Combined Transcripts" version="0.1"> + <description>using tracking file</description> + <command interpreter="python"> + filter_transcripts_via_tracking.py + $tracking_file + $transcripts_file + $filtered_transcripts + $sample_num + </command> + <inputs> + <param format="gtf" name="transcripts_file" type="data" label="Cufflinks assembled transcripts" help=""/> + <param format="tabular" name="tracking_file" type="data" label="Cuffcompare tracking file" help=""/> + <param name="sample_num" type="select" label="Sample Number"> + <option value="1">1</option> + <option value="2">2</option> + </param> + </inputs> + + <outputs> + <data format="gtf" name="filtered_transcripts"/> + </outputs> + + <tests> + </tests> + + <help> + Uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts produced by + cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the + GTF so that the output GTF contains only transcript found in the tracking file. Because a tracking file has multiple + samples, a sample number is used to filter transcripts for a particular sample. + </help> +</tool>

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[hg] galaxy 3763: right welcome.html at last
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1110a91888e2 changeset: 3763:1110a91888e2 user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 11:55:08 2010 -0400 description: right welcome.html at last diffstat: static/welcome.html | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (15 lines): diff -r df72c7a8d5cf -r 1110a91888e2 static/welcome.html --- a/static/welcome.html Mon May 10 11:49:25 2010 -0400 +++ b/static/welcome.html Mon May 10 11:55:08 2010 -0400 @@ -8,9 +8,9 @@ <body> <div class="document"> <div class="warningmessagelarge"> - <strong>Welcome to Galaxy at the Channing Laboratory</strong> + <strong>Hello world! It's running...</strong> <hr> - Your jobs will run under SGE on the cluster. + To customize this page edit <code>static/welcome.html</code> </div> <br/> <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" />

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[hg] galaxy 3761: Bug in SGE external metadata
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ecbd01636a92 changeset: 3761:ecbd01636a92 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon May 10 11:22:50 2010 -0400 description: Bug in SGE external metadata diffstat: lib/galaxy/jobs/runners/sge.py | 3 +-- 1 files changed, 1 insertions(+), 2 deletions(-) diffs (17 lines): diff -r f53d06cf2f93 -r ecbd01636a92 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Mon May 10 11:13:51 2010 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Mon May 10 11:22:50 2010 -0400 @@ -166,12 +166,11 @@ script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) if self.app.config.set_metadata_externally: - output_fnames = [ str( o ) for o in job_wrapper.get_output_fnames() ] script += "cd %s\n" % os.path.abspath( os.getcwd() ) script += "%s\n" % job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), tmp_dir = self.app.config.new_file_path, dataset_files_path = self.app.model.Dataset.file_path, - output_fnames = output_fnames, + output_fnames = job_wrapper.get_output_fnames(), set_extension = False, kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior fh = file( jt.remoteCommand, "w" )

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[hg] galaxy 3762: Revert inadvertantly updated tool_conf.xml.sam...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/df72c7a8d5cf changeset: 3762:df72c7a8d5cf user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 11:49:25 2010 -0400 description: Revert inadvertantly updated tool_conf.xml.sample and welcome.html diffstat: static/welcome.html | 3 +- tool_conf.xml.sample | 231 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 233 insertions(+), 1 deletions(-) diffs (256 lines): diff -r ecbd01636a92 -r df72c7a8d5cf static/welcome.html --- a/static/welcome.html Mon May 10 11:22:50 2010 -0400 +++ b/static/welcome.html Mon May 10 11:49:25 2010 -0400 @@ -10,9 +10,10 @@ <div class="warningmessagelarge"> <strong>Welcome to Galaxy at the Channing Laboratory</strong> <hr> + Your jobs will run under SGE on the cluster. </div> <br/> - <img src="images/Armitagep_manhattan.png" alt="manhattan plot" style="display: block; margin-left: auto; margin-right: auto;" /> + <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> <hr/> This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. </div> diff -r ecbd01636a92 -r df72c7a8d5cf tool_conf.xml.sample --- a/tool_conf.xml.sample Mon May 10 11:22:50 2010 -0400 +++ b/tool_conf.xml.sample Mon May 10 11:49:25 2010 -0400 @@ -23,6 +23,237 @@ <tool file="data_source/hbvar.xml" /> <tool file="validation/fix_errors.xml" /> </section> + <section name="Send Data" id="send"> + <tool file="data_destination/epigraph.xml" /> + <tool file="data_destination/epigraph_test.xml" /> + </section> + <section name="ENCODE Tools" id="EncodeTools"> + <tool file="encode/gencode_partition.xml" /> + <tool file="encode/random_intervals.xml" /> + </section> + <section name="Lift-Over" id="liftOver"> + <tool file="extract/liftOver_wrapper.xml" /> + </section> + <section name="Text Manipulation" id="textutil"> + <tool file="filters/fixedValueColumn.xml" /> + <tool file="stats/column_maker.xml" /> + <tool file="filters/catWrapper.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/mergeCols.xml" /> + <tool file="filters/convert_characters.xml" /> + <tool file="filters/CreateInterval.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/changeCase.xml" /> + <tool file="filters/pasteWrapper.xml" /> + <tool file="filters/remove_beginning.xml" /> + <tool file="filters/randomlines.xml" /> + <tool file="filters/headWrapper.xml" /> + <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /> + <tool file="stats/dna_filtering.xml" /> + <tool file="new_operations/tables_arithmetic_operations.xml" /> + </section> + <section name="Filter and Sort" id="filter"> + <tool file="stats/filtering.xml" /> + <tool file="filters/sorter.xml" /> + <tool file="filters/grep.xml" /> + </section> + <section name="Join, Subtract and Group" id="group"> + <tool file="filters/joiner.xml" /> + <tool file="filters/compare.xml"/> + <tool file="new_operations/subtract_query.xml"/> + <tool file="stats/grouping.xml" /> + <tool file="new_operations/column_join.xml" /> + </section> + <section name="Convert Formats" id="convert"> + <tool file="filters/axt_to_concat_fasta.xml" /> + <tool file="filters/axt_to_fasta.xml" /> + <tool file="filters/axt_to_lav.xml" /> + <tool file="filters/bed2gff.xml" /> + <tool file="fasta_tools/fasta_to_tabular.xml" /> + <tool file="filters/gff2bed.xml" /> + <tool file="filters/lav_to_bed.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="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="filters/wiggle_to_simple.xml" /> + <tool file="filters/sff_extractor.xml" /> + <tool file="filters/gtf2bedgraph.xml" /> + </section> + <section name="Extract Features" id="features"> + <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> + <tool file="extract/extract_GFF_Features.xml" /> + </section> + <section name="Fetch Sequences" id="fetchSeq"> + <tool file="extract/extract_genomic_dna.xml" /> + </section> + <section name="Fetch Alignments" id="fetchAlign"> + <tool file="maf/interval2maf_pairwise.xml" /> + <tool file="maf/interval2maf.xml" /> + <tool file="maf/maf_split_by_species.xml"/> + <tool file="maf/interval_maf_to_merged_fasta.xml" /> + <tool file="maf/genebed_maf_to_fasta.xml"/> + <tool file="maf/maf_stats.xml"/> + <tool file="maf/maf_thread_for_species.xml"/> + <tool file="maf/maf_limit_to_species.xml"/> + <tool file="maf/maf_limit_size.xml"/> + <tool file="maf/maf_by_block_number.xml"/> + <tool file="maf/maf_reverse_complement.xml"/> + <tool file="maf/maf_filter.xml"/> + </section> + <section name="Get Genomic Scores" id="scores"> + <tool file="stats/wiggle_to_simple.xml" /> + <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> + <tool file="extract/phastOdds/phastOdds_tool.xml" /> + </section> + <section name="Operate on Genomic Intervals" id="bxops"> + <tool file="new_operations/intersect.xml" /> + <tool file="new_operations/subtract.xml" /> + <tool file="new_operations/merge.xml" /> + <tool file="new_operations/concat.xml" /> + <tool file="new_operations/basecoverage.xml" /> + <tool file="new_operations/coverage.xml" /> + <tool file="new_operations/complement.xml" /> + <tool file="new_operations/cluster.xml" id="cluster" /> + <tool file="new_operations/join.xml" /> + <tool file="new_operations/get_flanks.xml" /> + <tool file="new_operations/flanking_features.xml" /> + <tool file="annotation_profiler/annotation_profiler.xml" /> + </section> + <section name="Statistics" id="stats"> + <tool file="stats/gsummary.xml" /> + <tool file="filters/uniq.xml" /> + <tool file="stats/cor.xml" /> + <tool file="regVariation/t_test_two_samples.xml" /> + <tool file="regVariation/compute_q_values.xml" /> + </section> + <section name="Graph/Display Data" id="plots"> + <tool file="plotting/histogram2.xml" /> + <tool file="plotting/scatterplot.xml" /> + <tool file="plotting/bar_chart.xml" /> + <tool file="plotting/xy_plot.xml" /> + <tool file="plotting/boxplot.xml" /> + <tool file="visualization/GMAJ.xml" /> + <tool file="visualization/LAJ.xml" /> + <tool file="visualization/build_ucsc_custom_track.xml" /> + </section> + <section name="Regional Variation" id="regVar"> + <tool file="regVariation/windowSplitter.xml" /> + <tool file="regVariation/featureCounter.xml" /> + <tool file="regVariation/quality_filter.xml" /> + <tool file="regVariation/maf_cpg_filter.xml" /> + <tool file="regVariation/getIndels_2way.xml" /> + <tool file="regVariation/getIndels_3way.xml" /> + <tool file="regVariation/getIndelRates_3way.xml" /> + <tool file="regVariation/substitutions.xml" /> + <tool file="regVariation/substitution_rates.xml" /> + <tool file="regVariation/microsats_alignment_level.xml" /> + <tool file="regVariation/microsats_mutability.xml" /> + <tool file="regVariation/delete_overlapping_indels.xml" /> + <tool file="regVariation/compute_motifs_frequency.xml" /> + <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /> + <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s + <tool file="regVariation/draw_stacked_barplots.xml" /> + </section> + <section name="Multiple regression" id="multReg"> + <tool file="regVariation/linear_regression.xml" /> + <tool file="regVariation/best_regression_subsets.xml" /> + <tool file="regVariation/rcve.xml" /> + </section> + <section name="Multivariate Analysis" id="multVar"> + <tool file="multivariate_stats/pca.xml" /> + <tool file="multivariate_stats/cca.xml" /> + <tool file="multivariate_stats/kpca.xml" /> + <tool file="multivariate_stats/kcca.xml" /> + </section> + <section name="Evolution" id="hyphy"> + <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> + <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> + <tool file="hyphy/hyphy_dnds_wrapper.xml" /> + <tool file="evolution/mutate_snp_codon.xml" /> + <tool file="evolution/codingSnps.xml" /> + <tool file="evolution/add_scores.xml" /> + </section> + <section name="Metagenomic analyses" id="tax_manipulation"> + <tool file="taxonomy/gi2taxonomy.xml" /> + <tool file="taxonomy/t2t_report.xml" /> + <tool file="taxonomy/t2ps_wrapper.xml" /> + <tool file="taxonomy/find_diag_hits.xml" /> + <tool file="taxonomy/lca.xml" /> + <tool file="taxonomy/poisson2test.xml" /> + </section> + <section name="FASTA manipulation" id="fasta_manipulation"> + <tool file="fasta_tools/fasta_compute_length.xml" /> + <tool file="fasta_tools/fasta_filter_by_length.xml" /> + <tool file="fasta_tools/fasta_concatenate_by_species.xml" /> + <tool file="fasta_tools/fasta_to_tabular.xml" /> + <tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastx_toolkit/fasta_formatter.xml" /> + <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> + <tool file="fastx_toolkit/fastx_collapser.xml" /> + </section> + <section name="NGS: QC and manipulation" id="cshl_library_information"> + <label text="Illumina data" id="illumina" /> + <tool file="fastq/fastq_groomer.xml" /> + <tool file="fastq/fastq_paired_end_splitter.xml" /> + <tool file="fastq/fastq_paired_end_joiner.xml" /> + <tool file="fastq/fastq_stats.xml" /> +  + <label text="Roche-454 data" id="454" /> + <tool file="metag_tools/short_reads_figure_score.xml" /> + <tool file="metag_tools/short_reads_trim_seq.xml" /> + <tool file="fastq/fastq_combiner.xml" /> + <label text="AB-SOLiD data" id="solid" /> + <tool file="next_gen_conversion/solid2fastq.xml" /> + <tool file="solid_tools/solid_qual_stats.xml" /> + <tool file="solid_tools/solid_qual_boxplot.xml" /> + <label text="Generic FASTQ manipulation" id="generic_fastq" /> + <tool file="fastq/fastq_filter.xml" /> + <tool file="fastq/fastq_trimmer.xml" /> + <tool file="fastq/fastq_trimmer_by_quality.xml" /> + <tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /> + <tool file="fastq/fastq_to_tabular.xml" /> + <tool file="fastq/tabular_to_fastq.xml" /> + </section> + <section name="NGS: Mapping" id="solexa_tools"> + <tool file="sr_mapping/lastz_wrapper.xml" /> + <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" /> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bowtie_color_wrapper.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + <tool file="sr_mapping/PerM.xml" /> + </section> + <section name="NGS: Expression Analysis" id="ngs-rna-tools"> + <tool file="ngs_rna/tophat_wrapper.xml" /> + <tool file="ngs_rna/cufflinks_wrapper.xml" /> + <tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + </section> + <section name="NGS: SAM Tools" id="samtools"> + <tool file="samtools/sam_bitwise_flag_filter.xml" /> + <tool file="samtools/sam2interval.xml" /> + <tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/sam_merge.xml" /> + <tool file="samtools/sam_pileup.xml" /> + <tool file="samtools/pileup_parser.xml" /> + <tool file="samtools/pileup_interval.xml" /> + </section> + <section name="NGS: Peak Calling" id="peak_calling"> + <tool file="peak_calling/macs_wrapper.xml" /> + <tool file="genetrack/genetrack_indexer.xml" /> + <tool file="genetrack/genetrack_peak_prediction.xml" /> + </section> <section name="SNP/WGA: Data; Filters" id="rgdat"> <label text="Data: Import and upload" id="rgimport" /> <tool file="data_source/upload.xml"/>

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