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[hg] galaxy 3788: Enable images and binary datasets to work with...
by Nate Coraor 25 May '10

25 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/00a558d5ad25 changeset: 3788:00a558d5ad25 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sat May 15 11:25:05 2010 -0400 description: Enable images and binary datasets to work within the display framework. More work is needed to enable images to work well. diffstat: lib/galaxy/web/controllers/dataset.py | 10 +++++++++- 1 files changed, 9 insertions(+), 1 deletions(-) diffs (20 lines): diff -r 9ab8480354c7 -r 00a558d5ad25 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri May 14 11:25:03 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Sat May 15 11:25:05 2010 -0400 @@ -472,7 +472,15 @@ if dataset: truncated, dataset_data = self.get_data( dataset, preview ) dataset.annotation = self.get_item_annotation_str( trans, dataset.history.user, dataset ) - return trans.fill_template_mako( "/dataset/display.mako", item=dataset, item_data=dataset_data, truncated=truncated ) + + # If data is binary or an image, stream without template; otherwise, use display template. + # TODO: figure out a way to display images in display template. + if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image): + mime = trans.app.datatypes_registry.get_mimetype_by_extension( dataset.extension.lower() ) + trans.response.set_content_type( mime ) + return open( dataset.file_name ) + else: + return trans.fill_template_mako( "/dataset/display.mako", item=dataset, item_data=dataset_data, truncated=truncated ) else: raise web.httpexceptions.HTTPNotFound()

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[hg] galaxy 3789: Better UI flow for changing an HDA's data type.
by Nate Coraor 25 May '10

25 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/11951fe9c714 changeset: 3789:11951fe9c714 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sat May 15 13:12:38 2010 -0400 description: Better UI flow for changing an HDA's data type. diffstat: lib/galaxy/web/controllers/root.py | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r 00a558d5ad25 -r 11951fe9c714 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Sat May 15 11:25:05 2010 -0400 +++ b/lib/galaxy/web/controllers/root.py Sat May 15 13:12:38 2010 -0400 @@ -276,6 +276,7 @@ return trans.show_error_message( "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." ) trans.app.datatypes_registry.change_datatype( data, params.datatype ) trans.sa_session.flush() + return trans.show_ok_message( "Changed the type of dataset '%s' to %s" % ( data.name, params.datatype ), refresh_frames=['history'] ) else: return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) ) elif params.save:

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[hg] galaxy 3787: Fixes for editing tool information and submitt...
by Nate Coraor 25 May '10

25 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9ab8480354c7 changeset: 3787:9ab8480354c7 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri May 14 11:25:03 2010 -0400 description: Fixes for editing tool information and submitting a tool for approval in the community space. diffstat: lib/galaxy/webapps/community/controllers/common.py | 13 +++++++++ lib/galaxy/webapps/community/datatypes/__init__.py | 2 +- templates/webapps/community/tool/edit_tool.mako | 30 +++++++++++----------- 3 files changed, 29 insertions(+), 16 deletions(-) diffs (100 lines): diff -r 48432330228e -r 9ab8480354c7 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Fri May 14 10:37:36 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri May 14 11:25:03 2010 -0400 @@ -43,6 +43,19 @@ message=message, status='done' ) ) elif params.get( 'approval_button', False ): + if params.get( 'in_categories', False ): + in_categories = [ trans.sa_session.query( trans.app.model.Category ).get( x ) for x in util.listify( params.in_categories ) ] + trans.app.security_agent.set_entity_category_associations( tools=[ tool ], categories=in_categories ) + else: + # There must not be any categories associated with the tool + trans.app.security_agent.set_entity_category_associations( tools=[ tool ], categories=[] ) + user_description = util.restore_text( params.get( 'user_description', '' ) ) + if user_description: + tool.user_description = user_description + else: + tool.user_description = '' + trans.sa_session.add( tool ) + trans.sa_session.flush() # Move the state from NEW to WAITING event = trans.app.model.Event( state=trans.app.model.Tool.states.WAITING ) tea = trans.app.model.ToolEventAssociation( tool, event ) diff -r 48432330228e -r 9ab8480354c7 lib/galaxy/webapps/community/datatypes/__init__.py --- a/lib/galaxy/webapps/community/datatypes/__init__.py Fri May 14 10:37:36 2010 -0400 +++ b/lib/galaxy/webapps/community/datatypes/__init__.py Fri May 14 11:25:03 2010 -0400 @@ -122,7 +122,7 @@ raise DatatypeVerificationError( 'Tool XML file does not conform to the specification. Missing required <tool> tag attribute: %s' % e ) rval.description = '' desc_tag = root.find( 'description' ) - if desc_tag: + if desc_tag is not None: description = desc_tag.text if description: rval.description = description.strip() diff -r 48432330228e -r 9ab8480354c7 templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Fri May 14 10:37:36 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Fri May 14 11:25:03 2010 -0400 @@ -16,6 +16,13 @@ $(function(){ $("input:text:first").focus(); }) + function confirmSubmit() { + if ( confirm( "After you have submitted your tool to be published, you will no longer be able to modify it. Click OK to submit it." ) ) { + return true; + } else { + return false; + } + } </script> </%def> @@ -89,9 +96,6 @@ %endif <div style="clear: both"></div> </div> - <div class="form-row"> - <input type="submit" id="edit_tool_button" name="edit_tool_button" value="Save"> - </div> </div> </div> <p/> @@ -115,29 +119,25 @@ </div> </div> </div> - </form> - <p/> - <div class="toolForm"> + <p/> %if tool.is_new(): - <div class="toolFormTitle">Get approval for publishing</div> - <div class="toolFormBody"> - <form name="get_approval" id="get_approval" action="${h.url_for( controller='common', action='edit_tool' )}" method="post" > - <input type="hidden" name="id" value="${trans.app.security.encode_id( tool.id )}"/> - <input type="hidden" name="cntrller" value="${cntrller}"/> + <div class="toolForm"> + <div class="toolFormTitle">Get approval for publishing</div> + <div class="toolFormBody"> <div class="form-row"> - <input type="submit" name="approval_button" value="Submit for approval"/> + <input type="submit" name="approval_button" id="approval_button" value="Submit for approval" onClick="return confirmSubmit()" /> </div> <div class="form-row"> <div class="toolParamHelp" style="clear: both;"> Tools must be approved before they are made available to others in the community. After you have submitted your tool to be published, you will no longer be able to modify it, so make sure the information above is - correct and and save any changes before submitting for approval. + correct before submitting for approval. </div> </div> - </form> + </div> </div> %endif - </div> + </form> %else: ${render_msg( "You are not allowed to edit this tool", "error" )} %endif

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[hg] galaxy 3786: Use PBS exit_status (if keep_completed is set)...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/48432330228e changeset: 3786:48432330228e user: Nate Coraor <nate(a)bx.psu.edu> date: Fri May 14 10:37:36 2010 -0400 description: Use PBS exit_status (if keep_completed is set) so we can detect PBS failures. diffstat: eggs.ini | 2 +- lib/galaxy/jobs/runners/pbs.py | 133 ++++++++++++++++++++++++++-------------- 2 files changed, 86 insertions(+), 49 deletions(-) diffs (200 lines): diff -r 5ead6e4c2ef4 -r 48432330228e eggs.ini --- a/eggs.ini Fri May 14 10:19:12 2010 -0400 +++ b/eggs.ini Fri May 14 10:37:36 2010 -0400 @@ -17,7 +17,7 @@ DRMAA_python = 0.2 MySQL_python = 1.2.3c1 numpy = 1.3.0 -pbs_python = 2.9.4 +pbs_python = 2.9.8 psycopg2 = 2.0.13 pycrypto = 2.0.1 pysam = 0.1.1 diff -r 5ead6e4c2ef4 -r 48432330228e lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Fri May 14 10:19:12 2010 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Fri May 14 10:37:36 2010 -0400 @@ -50,6 +50,19 @@ %s """ +# From pbs' job.h +JOB_EXIT_STATUS = { + 0: "job exec successful", + -1: "job exec failed, before files, no retry", + -2: "job exec failed, after files, no retry", + -3: "job execution failed, do retry", + -4: "job aborted on MOM initialization", + -5: "job aborted on MOM init, chkpt, no migrate", + -6: "job aborted on MOM init, chkpt, ok migrate", + -7: "job restart failed", + -8: "exec() of user command failed", +} + class PBSJobState( object ): def __init__( self ): """ @@ -65,6 +78,7 @@ self.efile = None self.runner_url = None self.check_count = 0 + self.stop_job = False class PBSJobRunner( object ): """ @@ -193,8 +207,9 @@ pbs_options = self.determine_pbs_options( runner_url ) c = pbs.pbs_connect( pbs_server_name ) if c <= 0: + errno, text = pbs.error() job_wrapper.fail( "Unable to queue job for execution. Resubmitting the job may succeed." ) - log.error( "Connection to PBS server for submit failed" ) + log.error( "Connection to PBS server for submit failed: %s: %s" % ( errno, text ) ) return # define job attributes @@ -336,58 +351,78 @@ log.debug( "(%s/%s) Skipping state check because PBS server connection failed" % ( galaxy_job_id, job_id ) ) new_watched.append( pbs_job_state ) continue - if statuses.has_key( job_id ): + try: status = statuses[job_id] - if status.job_state != old_state: - log.debug("(%s/%s) job state changed from %s to %s" % ( galaxy_job_id, job_id, old_state, status.job_state ) ) - if status.job_state == "R" and not pbs_job_state.running: - pbs_job_state.running = True - pbs_job_state.job_wrapper.change_state( model.Job.states.RUNNING ) - if status.job_state == "R" and ( pbs_job_state.check_count % 20 ) == 0: - # Every 20th time the job status is checked, do limit checks (if configured) - if self.app.config.output_size_limit > 0: - # Check the size of the job outputs - fail = False - for outfile, size in pbs_job_state.job_wrapper.check_output_sizes(): - if size > self.app.config.output_size_limit: - pbs_job_state.fail_message = 'Job output grew too large (greater than %s), please try different job parameters or' \ - % nice_size( self.app.config.output_size_limit ) - log.warning( '(%s/%s) Dequeueing job due to output %s growing larger than %s limit' \ - % ( galaxy_job_id, job_id, os.path.basename( outfile ), nice_size( self.app.config.output_size_limit ) ) ) - self.work_queue.put( ( 'fail', pbs_job_state ) ) - fail = True - break - if fail: - continue - if self.job_walltime is not None: - # Check the job's execution time - if status.get( 'resources_used', False ): - # resources_used may not be in the status for new jobs - h, m, s = [ int( i ) for i in status.resources_used.walltime.split( ':' ) ] - time_executing = timedelta( 0, s, 0, 0, m, h ) - if time_executing > self.job_walltime: - pbs_job_state.fail_message = 'Job ran longer than maximum allowed execution time (%s), please try different job parameters or' \ - % self.app.config.job_walltime - log.warning( '(%s/%s) Dequeueing job since walltime has been reached' \ - % ( galaxy_job_id, job_id ) ) - self.work_queue.put( ( 'fail', pbs_job_state ) ) - continue - pbs_job_state.old_state = status.job_state - new_watched.append( pbs_job_state ) - else: + except KeyError: try: - # recheck to make sure it wasn't a communication problem + # Recheck to make sure it wasn't a communication problem self.check_single_job( pbs_server_name, job_id ) - log.warning( "(%s/%s) job was not in state check list, but was found with individual state check" % ( galaxy_job_id, job_id ) ) + log.warning( "(%s/%s) PBS job was not in state check list, but was found with individual state check" % ( galaxy_job_id, job_id ) ) new_watched.append( pbs_job_state ) except: errno, text = pbs.error() - if errno != 15001: - log.info("(%s/%s) state check resulted in error (%d): %s" % (galaxy_job_id, job_id, errno, text) ) + if errno == 15001: + # 15001 == job not in queue + log.debug("(%s/%s) PBS job has left queue" % (galaxy_job_id, job_id) ) + self.work_queue.put( ( 'finish', pbs_job_state ) ) + else: + # Unhandled error, continue to monitor + log.info("(%s/%s) PBS state check resulted in error (%d): %s" % (galaxy_job_id, job_id, errno, text) ) new_watched.append( pbs_job_state ) - else: - log.debug("(%s/%s) job has left queue" % (galaxy_job_id, job_id) ) - self.work_queue.put( ( 'finish', pbs_job_state ) ) + continue + if status.job_state != old_state: + log.debug("(%s/%s) PBS job state changed from %s to %s" % ( galaxy_job_id, job_id, old_state, status.job_state ) ) + if status.job_state == "R" and not pbs_job_state.running: + pbs_job_state.running = True + pbs_job_state.job_wrapper.change_state( model.Job.states.RUNNING ) + if status.job_state == "R" and ( pbs_job_state.check_count % 20 ) == 0: + # Every 20th time the job status is checked, do limit checks (if configured) + if self.app.config.output_size_limit > 0: + # Check the size of the job outputs + fail = False + for outfile, size in pbs_job_state.job_wrapper.check_output_sizes(): + if size > self.app.config.output_size_limit: + pbs_job_state.fail_message = 'Job output grew too large (greater than %s), please try different job parameters or' \ + % nice_size( self.app.config.output_size_limit ) + log.warning( '(%s/%s) Dequeueing job due to output %s growing larger than %s limit' \ + % ( galaxy_job_id, job_id, os.path.basename( outfile ), nice_size( self.app.config.output_size_limit ) ) ) + pbs_job_state.stop_job = True + self.work_queue.put( ( 'fail', pbs_job_state ) ) + fail = True + break + if fail: + continue + if self.job_walltime is not None: + # Check the job's execution time + if status.get( 'resources_used', False ): + # resources_used may not be in the status for new jobs + h, m, s = [ int( i ) for i in status.resources_used.walltime.split( ':' ) ] + time_executing = timedelta( 0, s, 0, 0, m, h ) + if time_executing > self.job_walltime: + pbs_job_state.fail_message = 'Job ran longer than maximum allowed execution time (%s), please try different job parameters or' \ + % self.app.config.job_walltime + log.warning( '(%s/%s) Dequeueing job since walltime has been reached' \ + % ( galaxy_job_id, job_id ) ) + pbs_job_state.stop_job = True + self.work_queue.put( ( 'fail', pbs_job_state ) ) + continue + elif status.job_state == "C": + # "keep_completed" is enabled in PBS, so try to check exit status + try: + assert int( status.exit_status ) == 0 + log.debug("(%s/%s) PBS job has completed successfully" % ( galaxy_job_id, job_id ) ) + except AssertionError: + pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error. Please retry or' + log.error( '(%s/%s) PBS job failed: %s' % ( galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ), 'Unknown error: %s' % status.exit_status ) ) ) + self.work_queue.put( ( 'fail', pbs_job_state ) ) + continue + except AttributeError: + # No exit_status, can't verify proper completion so we just have to assume success. + log.debug("(%s/%s) PBS job has completed" % ( galaxy_job_id, job_id ) ) + self.work_queue.put( ( 'finish', pbs_job_state ) ) + continue + pbs_job_state.old_state = status.job_state + new_watched.append( pbs_job_state ) # Replace the watch list with the updated version self.watched = new_watched @@ -411,9 +446,10 @@ log.debug("connection to PBS server %s for state check failed" % pbs_server_name ) failures.append( pbs_server_name ) continue - stat_attrl = pbs.new_attrl(2) + stat_attrl = pbs.new_attrl(3) stat_attrl[0].name = pbs.ATTR_state stat_attrl[1].name = pbs.ATTR_used + stat_attrl[2].name = pbs.ATTR_exitstat jobs = pbs.pbs_statjob( c, None, stat_attrl, None ) pbs.pbs_disconnect( c ) statuses.update( self.convert_statjob_to_bunches( jobs ) ) @@ -480,7 +516,8 @@ """ Seperated out so we can use the worker threads for it. """ - self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) ) + if pbs_job_state.stop_job: + self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) ) pbs_job_state.job_wrapper.fail( pbs_job_state.fail_message ) self.cleanup( ( pbs_job_state.ofile, pbs_job_state.efile, pbs_job_state.job_file ) )

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[hg] galaxy 3784: Add GFF filtering tool. Tool filters GFF file ...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b5391bd3e9c7 changeset: 3784:b5391bd3e9c7 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri May 14 10:15:48 2010 -0400 description: Add GFF filtering tool. Tool filters GFF file based on an attribute value. diffstat: test-data/gff_filtering_in1.gff | 200 +++++++++++++++++++++++++++++++++++++++ test-data/gff_filtering_out1.gff | 46 ++++++++ tool_conf.xml.sample | 13 +- tools/ngs_rna/gff_filtering.py | 137 ++++++++++++++++++++++++++ tools/ngs_rna/gff_filtering.xml | 58 +++++++++++ 5 files changed, 449 insertions(+), 5 deletions(-) diffs (481 lines): diff -r e972d3f8413e -r b5391bd3e9c7 test-data/gff_filtering_in1.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff_filtering_in1.gff Fri May 14 10:15:48 2010 -0400 @@ -0,0 +1,200 @@ +chr1 Cufflinks exon 21199802 21199861 1000 + . gene_id "CUFF.1383"; transcript_id "CUFF.1383.1"; exon_number "1"; FPKM "5.0037092300"; frac "1.000000"; conf_lo "0.000000"; conf_hi "15.011128"; cov "0.284211"; +chr1 Cufflinks transcript 55716264 55716295 1000 . . gene_id "CUFF.5021"; transcript_id "CUFF.5021.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; +chr1 Cufflinks transcript 74904128 74904154 1000 . . gene_id "CUFF.7563"; transcript_id "CUFF.7563.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 134487086 134487123 1000 . . gene_id "CUFF.11837"; transcript_id "CUFF.11837.1"; exon_number "1"; FPKM "25.0185461500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "60.400113"; cov "1.421053"; +chr1 Cufflinks exon 136200923 136200959 1000 . . gene_id "CUFF.12099"; transcript_id "CUFF.12099.1"; exon_number "1"; FPKM "38.5420846095"; frac "1.000000"; conf_lo "0.000000"; conf_hi "83.046650"; cov "2.189189"; +chr1 Cufflinks transcript 138116837 138116866 1000 . . gene_id "CUFF.12557"; transcript_id "CUFF.12557.1"; FPKM "31.6901584567"; frac "1.000000"; conf_lo "0.000000"; conf_hi "76.506810"; cov "1.800000"; +chr1 Cufflinks exon 152240694 152240779 1000 . . gene_id "CUFF.13107"; transcript_id "CUFF.13107.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; +chr1 Cufflinks exon 157633998 157634024 1000 . . gene_id "CUFF.13967"; transcript_id "CUFF.13967.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 167704819 167704854 1000 . . gene_id "CUFF.15347"; transcript_id "CUFF.15347.1"; exon_number "1"; FPKM "26.4084653806"; frac "1.000000"; conf_lo "0.000000"; conf_hi "63.755675"; cov "1.500000"; +chr1 Cufflinks transcript 184245403 184245429 1000 . . gene_id "CUFF.17679"; transcript_id "CUFF.17679.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr10 Cufflinks exon 12731734 12731826 1000 . . gene_id "CUFF.19287"; transcript_id "CUFF.19287.1"; exon_number "1"; FPKM "10.2226317602"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.679616"; cov "0.580645"; +chr10 Cufflinks transcript 42305464 42305515 1000 . . gene_id "CUFF.21709"; transcript_id "CUFF.21709.1"; FPKM "18.2827837250"; frac "1.000000"; conf_lo "0.000000"; conf_hi "44.138544"; cov "1.038462"; +chr10 Cufflinks exon 52431636 52431662 1000 . . gene_id "CUFF.22495"; transcript_id "CUFF.22495.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr10 Cufflinks transcript 62044837 62045189 1000 . . gene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611"; +chr10 Cufflinks transcript 75372919 75373002 1000 . . gene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429"; +chr10 Cufflinks transcript 80362428 80363292 1000 - . gene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449"; +chr10 Cufflinks exon 87908564 87908597 1000 + . gene_id "CUFF.27209"; transcript_id "CUFF.27209.1"; exon_number "2"; FPKM "11.4913582411"; frac "1.000000"; conf_lo "0.000000"; conf_hi "30.264098"; cov "0.652709"; +chr10 Cufflinks exon 89142681 89142707 1000 . . gene_id "CUFF.27307"; transcript_id "CUFF.27307.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr10 Cufflinks exon 93425781 93425807 1000 . . gene_id "CUFF.28101"; transcript_id "CUFF.28101.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr10 Cufflinks exon 108207916 108207986 1000 . . gene_id "CUFF.29319"; transcript_id "CUFF.29319.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; +chr10 Cufflinks transcript 117583959 117584039 1000 . . gene_id "CUFF.30522"; transcript_id "CUFF.30522.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.934890"; cov "1.000000"; +chr11 Cufflinks transcript 3357264 3357347 1000 . . gene_id "CUFF.32520"; transcript_id "CUFF.32520.1"; FPKM "16.9768706018"; frac "1.000000"; conf_lo "0.000000"; conf_hi "36.580072"; cov "0.964286"; +chr11 Cufflinks transcript 5005248 5005351 1000 . . gene_id "CUFF.33024"; transcript_id "CUFF.33024.1"; FPKM "9.1413918625"; frac "1.000000"; conf_lo "0.000000"; conf_hi "22.069272"; cov "0.519231"; +chr11 Cufflinks transcript 7904565 7904642 1000 . . gene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633"; +chr11 Cufflinks exon 49932116 49932142 1000 . . gene_id "CUFF.37546"; transcript_id "CUFF.37546.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr11 Cufflinks transcript 60046420 60046446 1000 . . gene_id "CUFF.39152"; transcript_id "CUFF.39152.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr11 Cufflinks exon 78140156 78140259 1000 . . gene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385"; +chr11 Cufflinks transcript 79846512 79846547 1000 . . gene_id "CUFF.43570"; transcript_id "CUFF.43570.1"; FPKM "26.4084653806"; frac "1.000000"; conf_lo "0.000000"; conf_hi "63.755675"; cov "1.500000"; +chr11 Cufflinks transcript 85583926 85583952 1000 . . gene_id "CUFF.44478"; transcript_id "CUFF.44478.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr11 Cufflinks transcript 98554214 98554301 1000 . . gene_id "CUFF.46823"; transcript_id "CUFF.46823.1"; FPKM "10.8034631102"; frac "1.000000"; conf_lo "0.000000"; conf_hi "26.081867"; cov "0.613636"; +chr11 Cufflinks transcript 100797512 100797539 1000 . . gene_id "CUFF.47191"; transcript_id "CUFF.47191.1"; FPKM "33.9537412036"; frac "1.000000"; conf_lo "0.000000"; conf_hi "81.971583"; cov "1.928571"; +chr11 Cufflinks exon 105616462 105616737 1000 . . gene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087"; +chr11 Cufflinks transcript 106985457 106985483 1000 . . gene_id "CUFF.48949"; transcript_id "CUFF.48949.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr11 Cufflinks exon 120257794 120257821 1000 . . gene_id "CUFF.51205"; transcript_id "CUFF.51205.1"; exon_number "1"; FPKM "50.9306118054"; frac "1.000000"; conf_lo "0.000000"; conf_hi "109.740217"; cov "2.892857"; +chr12 Cufflinks transcript 16542765 16542791 1000 . . gene_id "CUFF.52907"; transcript_id "CUFF.52907.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr12 Cufflinks exon 21319385 21319483 1000 . . gene_id "CUFF.53189"; transcript_id "CUFF.53189.1"; exon_number "1"; FPKM "9.6030783202"; frac "1.000000"; conf_lo "0.000000"; conf_hi "23.183882"; cov "0.545455"; +chr12 Cufflinks transcript 30469129 30469156 1000 . . gene_id "CUFF.53733"; transcript_id "CUFF.53733.1"; FPKM "33.9537412036"; frac "1.000000"; conf_lo "0.000000"; conf_hi "81.971583"; cov "1.928571"; +chr12 Cufflinks transcript 30557416 30557442 1000 . . gene_id "CUFF.53863"; transcript_id "CUFF.53863.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr12 Cufflinks exon 30701762 30702509 1000 . . gene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412"; +chr12 Cufflinks transcript 56895077 56895103 1000 . . gene_id "CUFF.55817"; transcript_id "CUFF.55817.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr12 Cufflinks transcript 81915713 81915797 1000 . . gene_id "CUFF.58203"; transcript_id "CUFF.58203.1"; FPKM "22.3695236165"; frac "1.000000"; conf_lo "0.000000"; conf_hi "44.739047"; cov "1.270588"; +chr12 Cufflinks transcript 118458135 118458232 1000 . . gene_id "CUFF.63640"; transcript_id "CUFF.63640.1"; FPKM "9.7010689153"; frac "1.000000"; conf_lo "0.000000"; conf_hi "23.420452"; cov "0.551020"; +chr13 Cufflinks exon 8262302 8262372 1000 . . gene_id "CUFF.64064"; transcript_id "CUFF.64064.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; +chr13 Cufflinks transcript 14110852 14110956 1000 . . gene_id "CUFF.64684"; transcript_id "CUFF.64684.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "29.264058"; cov "0.771429"; +chr13 Cufflinks transcript 14146567 14146593 1000 . . gene_id "CUFF.64702"; transcript_id "CUFF.64702.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr13 Cufflinks transcript 14564150 14564243 1000 . . gene_id "CUFF.64894"; transcript_id "CUFF.64894.1"; FPKM "15.1708205378"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.688575"; cov "0.861702"; +chr13 Cufflinks transcript 17823162 17823188 1000 . . gene_id "CUFF.65082"; transcript_id "CUFF.65082.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr13 Cufflinks transcript 29757640 29757666 1000 . . gene_id "CUFF.65972"; transcript_id "CUFF.65972.1"; FPKM "70.4225743482"; frac "1.000000"; conf_lo "0.000000"; conf_hi "140.845149"; cov "4.000000"; +chr13 Cufflinks transcript 42402998 42403051 1000 . . gene_id "CUFF.66816"; transcript_id "CUFF.66816.1"; FPKM "26.4084653806"; frac "1.000000"; conf_lo "0.000000"; conf_hi "56.902335"; cov "1.500000"; +chr13 Cufflinks transcript 42853325 42853406 1000 . . gene_id "CUFF.66850"; transcript_id "CUFF.66850.1"; FPKM "17.3909406165"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.472269"; cov "0.987805"; +chr13 Cufflinks exon 42990504 42990546 1000 . . gene_id "CUFF.66994"; transcript_id "CUFF.66994.1"; exon_number "1"; FPKM "33.1641193151"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.458746"; cov "1.883721"; +chr13 Cufflinks exon 49159496 49159569 1000 . . gene_id "CUFF.67788"; transcript_id "CUFF.67788.1"; exon_number "1"; FPKM "44.9657653777"; frac "1.000000"; conf_lo "10.974842"; conf_hi "78.956689"; cov "2.554054"; +chr13 Cufflinks exon 49243161 49243187 1000 + . gene_id "CUFF.67842"; transcript_id "CUFF.67842.1"; exon_number "2"; FPKM "17.3246767151"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.848677"; cov "0.984041"; +chr13 Cufflinks transcript 74671517 74671579 1000 . . gene_id "CUFF.70454"; transcript_id "CUFF.70454.1"; FPKM "18.8363155420"; frac "1.000000"; conf_lo "0.000000"; conf_hi "42.679570"; cov "1.069902"; +chr13 Cufflinks exon 100759121 100759147 1000 . . gene_id "CUFF.72728"; transcript_id "CUFF.72728.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr13 Cufflinks transcript 100200304 100200330 1000 . . gene_id "CUFF.73108"; transcript_id "CUFF.73108.1"; FPKM "123.2395051093"; frac "1.000000"; conf_lo "30.079196"; conf_hi "216.399814"; cov "7.000000"; +chr13 Cufflinks exon 107766857 107766915 1000 . . gene_id "CUFF.73428"; transcript_id "CUFF.73428.1"; exon_number "1"; FPKM "16.1136398932"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.901768"; cov "0.915254"; +chr13 Cufflinks transcript 115623552 115623640 1000 . . gene_id "CUFF.74362"; transcript_id "CUFF.74362.1"; FPKM "21.3641517686"; frac "1.000000"; conf_lo "0.000000"; conf_hi "42.728304"; cov "1.213483"; +chr14 Cufflinks transcript 31651249 31651275 1000 . . gene_id "CUFF.77182"; transcript_id "CUFF.77182.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr14 Cufflinks transcript 31949103 31949152 1000 . . gene_id "CUFF.77316"; transcript_id "CUFF.77316.1"; FPKM "85.5634278330"; frac "1.000000"; conf_lo "28.521143"; conf_hi "142.605713"; cov "4.860000"; +chr14 Cufflinks transcript 32190589 32190685 1000 . . gene_id "CUFF.77438"; transcript_id "CUFF.77438.1"; FPKM "14.7016199026"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.677588"; cov "0.835052"; +chr14 Cufflinks exon 55013239 55013265 1000 . . gene_id "CUFF.79372"; transcript_id "CUFF.79372.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr14 Cufflinks exon 55250464 55250514 1000 . . gene_id "CUFF.79616"; transcript_id "CUFF.79616.1"; exon_number "1"; FPKM "18.6412696804"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.004006"; cov "1.058824"; +chr14 Cufflinks exon 67604227 67604668 1000 . . gene_id "CUFF.81446"; transcript_id "CUFF.81446.1"; exon_number "1"; FPKM "123.6776546104"; frac "1.000000"; conf_lo "100.611653"; conf_hi "146.743656"; cov "7.024887"; +chr14 Cufflinks exon 75165582 75165744 1000 . . gene_id "CUFF.82088"; transcript_id "CUFF.82088.1"; exon_number "1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509"; +chr15 Cufflinks transcript 8254591 8254734 1000 . . gene_id "CUFF.85556"; transcript_id "CUFF.85556.1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "26.408465"; cov "0.750000"; +chr15 Cufflinks transcript 34371407 34371433 1000 . . gene_id "CUFF.87246"; transcript_id "CUFF.87246.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr15 Cufflinks exon 65980225 65980255 1000 + . gene_id "CUFF.89502"; transcript_id "CUFF.89502.1"; exon_number "2"; FPKM "14.1193775302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "30.423030"; cov "0.801980"; +chr15 Cufflinks transcript 85895971 85896018 1000 . . gene_id "CUFF.92834"; transcript_id "CUFF.92834.1"; FPKM "19.8063490354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "47.816756"; cov "1.125000"; +chr15 Cufflinks exon 90828279 90828371 1000 . . gene_id "CUFF.93426"; transcript_id "CUFF.93426.1"; exon_number "1"; FPKM "15.3339476403"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.040065"; cov "0.870968"; +chr15 Cufflinks exon 99013431 99013472 1000 . . gene_id "CUFF.94604"; transcript_id "CUFF.94604.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; +chr15 Cufflinks transcript 102336976 102337075 1000 . . gene_id "CUFF.95298"; transcript_id "CUFF.95298.1"; FPKM "9.5070475370"; frac "1.000000"; conf_lo "0.000000"; conf_hi "22.952043"; cov "0.540000"; +chr16 Cufflinks transcript 10417989 10425202 1000 - . gene_id "CUFF.97232"; transcript_id "CUFF.97232.1"; FPKM "21.1642179587"; frac "1.000000"; conf_lo "0.000000"; conf_hi "44.805591"; cov "1.202127"; +chr16 Cufflinks transcript 40788986 40789084 1000 . . gene_id "CUFF.101774"; transcript_id "CUFF.101774.1"; FPKM "9.6030783202"; frac "1.000000"; conf_lo "0.000000"; conf_hi "23.183882"; cov "0.545455"; +chr16 Cufflinks transcript 57154027 57154067 1000 . . gene_id "CUFF.103364"; transcript_id "CUFF.103364.1"; FPKM "162.3154457537"; frac "1.000000"; conf_lo "75.554191"; conf_hi "249.076701"; cov "9.219512"; +chr16 Cufflinks exon 74862302 74862560 1000 . . gene_id "CUFF.105450"; transcript_id "CUFF.105450.1"; exon_number "1"; FPKM "11.0120241741"; frac "1.000000"; conf_lo "2.020744"; conf_hi "20.003304"; cov "0.625483"; +chr16 Cufflinks exon 91023578 91023669 1000 . . gene_id "CUFF.106912"; transcript_id "CUFF.106912.1"; exon_number "1"; FPKM "10.3337473228"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.947873"; cov "0.586957"; +chr16 Cufflinks transcript 98168779 98168914 1000 . . gene_id "CUFF.107834"; transcript_id "CUFF.107834.1"; FPKM "24.4666664555"; frac "1.000000"; conf_lo "5.971605"; conf_hi "42.961728"; cov "1.389706"; +chr17 Cufflinks exon 8483212 8483268 1000 . . gene_id "CUFF.108498"; transcript_id "CUFF.108498.1"; exon_number "1"; FPKM "50.0370923000"; frac "1.000000"; conf_lo "9.181978"; conf_hi "90.892207"; cov "2.842105"; +chr17 Cufflinks transcript 17478023 17478102 1000 . . gene_id "CUFF.109264"; transcript_id "CUFF.109264.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "47.535238"; cov "1.350000"; +chr17 Cufflinks exon 24611086 24611151 1000 . . gene_id "CUFF.110088"; transcript_id "CUFF.110088.1"; exon_number "1"; FPKM "21.6069262205"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.556456"; cov "1.227273"; +chr17 Cufflinks exon 30355791 30355913 1000 . . gene_id "CUFF.111759"; transcript_id "CUFF.111759.1"; exon_number "1"; FPKM "19.3232673516"; frac "1.000000"; conf_lo "2.040012"; conf_hi "36.606523"; cov "1.097561"; +chr17 Cufflinks exon 31608702 31608787 1000 . . gene_id "CUFF.111943"; transcript_id "CUFF.111943.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; +chr17 Cufflinks transcript 32414547 32414573 1000 . . gene_id "CUFF.112117"; transcript_id "CUFF.112117.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr17 Cufflinks transcript 33245409 33245463 1000 . . gene_id "CUFF.112363"; transcript_id "CUFF.112363.1"; FPKM "17.2855409764"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.730987"; cov "0.981818"; +chr17 Cufflinks transcript 56750339 56750374 1000 . . gene_id "CUFF.115617"; transcript_id "CUFF.115617.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "105.633862"; cov "3.000000"; +chr17 Cufflinks transcript 57144800 57144939 1000 . . gene_id "CUFF.115679"; transcript_id "CUFF.115679.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.162993"; cov "0.771429"; +chr17 Cufflinks exon 71694628 71694708 1000 . . gene_id "CUFF.117117"; transcript_id "CUFF.117117.1"; exon_number "1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; +chr17 Cufflinks transcript 71698227 71698263 1000 . . gene_id "CUFF.117119"; transcript_id "CUFF.117119.1"; FPKM "25.6947230730"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.032549"; cov "1.459459"; +chr17 Cufflinks exon 87862079 87862105 1000 . . gene_id "CUFF.118851"; transcript_id "CUFF.118851.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr18 Cufflinks transcript 39571718 39571880 1000 . . gene_id "CUFF.123569"; transcript_id "CUFF.123569.1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509"; +chr18 Cufflinks exon 46452826 46452864 1000 . . gene_id "CUFF.124197"; transcript_id "CUFF.124197.1"; exon_number "1"; FPKM "48.7540899334"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.508180"; cov "2.769231"; +chr18 Cufflinks exon 50151390 50151416 1000 . . gene_id "CUFF.124439"; transcript_id "CUFF.124439.1"; exon_number "1"; FPKM "17.5638395629"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.733298"; cov "0.997626"; +chr18 Cufflinks exon 65106749 65106787 1000 . . gene_id "CUFF.125675"; transcript_id "CUFF.125675.1"; exon_number "1"; FPKM "48.7540899334"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.508180"; cov "2.769231"; +chr18 Cufflinks transcript 65202282 65202424 1000 . . gene_id "CUFF.125729"; transcript_id "CUFF.125729.1"; FPKM "13.2965699818"; frac "1.000000"; conf_lo "0.000000"; conf_hi "26.593140"; cov "0.755245"; +chr18 Cufflinks exon 69735254 69735280 1000 . . gene_id "CUFF.126371"; transcript_id "CUFF.126371.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr19 Cufflinks transcript 5370466 5370492 1000 . . gene_id "CUFF.129319"; transcript_id "CUFF.129319.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr19 Cufflinks exon 17633088 17633203 1000 . . gene_id "CUFF.131333"; transcript_id "CUFF.131333.1"; exon_number "1"; FPKM "20.4893265884"; frac "1.000000"; conf_lo "2.163116"; conf_hi "38.815537"; cov "1.163793"; +chr19 Cufflinks transcript 41997624 41997859 1000 . . gene_id "CUFF.133569"; transcript_id "CUFF.133569.1"; FPKM "28.1988698132"; frac "1.000000"; conf_lo "13.125940"; conf_hi "43.271800"; cov "1.601695"; +chr19 Cufflinks transcript 53311236 53311262 1000 . . gene_id "CUFF.134885"; transcript_id "CUFF.134885.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr19 Cufflinks exon 56516515 56516684 1000 . . gene_id "CUFF.135203"; transcript_id "CUFF.135203.1"; exon_number "1"; FPKM "33.5542854247"; frac "1.000000"; conf_lo "14.181710"; conf_hi "52.926861"; cov "1.905882"; +chr2 Cufflinks transcript 3246910 3246936 1000 . . gene_id "CUFF.136019"; transcript_id "CUFF.136019.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr2 Cufflinks transcript 4543774 4543977 1000 . . gene_id "CUFF.136435"; transcript_id "CUFF.136435.1"; FPKM "37.2825393608"; frac "1.000000"; conf_lo "18.641270"; conf_hi "55.923809"; cov "2.117647"; +chr2 Cufflinks exon 7271328 7271354 1000 . . gene_id "CUFF.137407"; transcript_id "CUFF.137407.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr2 Cufflinks exon 11509202 11509287 1000 . . gene_id "CUFF.137559"; transcript_id "CUFF.137559.1"; exon_number "1"; FPKM "22.1094128768"; frac "1.000000"; conf_lo "0.000000"; conf_hi "44.218826"; cov "1.255814"; +chr2 Cufflinks transcript 30200331 30200938 1000 . . gene_id "CUFF.140289"; transcript_id "CUFF.140289.1"; FPKM "100.0741846001"; frac "1.000000"; conf_lo "82.383401"; conf_hi "117.764968"; cov "5.684211"; +chr2 Cufflinks transcript 49559781 49559842 1000 . . gene_id "CUFF.143035"; transcript_id "CUFF.143035.1"; FPKM "15.3339476403"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.019424"; cov "0.870968"; +chr2 Cufflinks transcript 78736720 78736746 1000 . . gene_id "CUFF.146383"; transcript_id "CUFF.146383.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr2 Cufflinks transcript 97470595 97470703 1000 . . gene_id "CUFF.148117"; transcript_id "CUFF.148117.1"; FPKM "17.4441239211"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.888248"; cov "0.990826"; +chr2 Cufflinks transcript 106644220 106644341 1000 . . gene_id "CUFF.148977"; transcript_id "CUFF.148977.1"; FPKM "27.2743167045"; frac "1.000000"; conf_lo "6.656871"; conf_hi "47.891762"; cov "1.549180"; +chr2 Cufflinks transcript 118960859 118961004 1000 . . gene_id "CUFF.150015"; transcript_id "CUFF.150015.1"; FPKM "9.7675145928"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.046069"; cov "0.554795"; +chr2 Cufflinks exon 125388931 125389219 1000 . . gene_id "CUFF.151331"; transcript_id "CUFF.151331.1"; exon_number "1"; FPKM "23.0274507817"; frac "1.000000"; conf_lo "10.718761"; conf_hi "35.336141"; cov "1.307958"; +chr2 Cufflinks transcript 145141669 145141755 1000 . . gene_id "CUFF.153993"; transcript_id "CUFF.153993.1"; FPKM "10.9276408471"; frac "1.000000"; conf_lo "0.000000"; conf_hi "26.381659"; cov "0.620690"; +chr2 Cufflinks exon 178035510 178035611 1000 . . gene_id "CUFF.158329"; transcript_id "CUFF.158329.1"; exon_number "1"; FPKM "9.3206348402"; frac "1.000000"; conf_lo "0.000000"; conf_hi "22.502003"; cov "0.529412"; +chr2 Cufflinks transcript 181047445 181047471 1000 . . gene_id "CUFF.158989"; transcript_id "CUFF.158989.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr3 Cufflinks transcript 55664118 55664197 1000 . . gene_id "CUFF.163141"; transcript_id "CUFF.163141.1"; FPKM "11.8838094213"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.690054"; cov "0.675000"; +chr3 Cufflinks exon 66896354 66896433 1000 . . gene_id "CUFF.163935"; transcript_id "CUFF.163935.1"; exon_number "1"; FPKM "5.9419047106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "17.825714"; cov "0.337500"; +chr3 Cufflinks transcript 80648745 80648771 1000 . . gene_id "CUFF.164995"; transcript_id "CUFF.164995.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr3 Cufflinks exon 107424385 107424452 1000 . . gene_id "CUFF.169311"; transcript_id "CUFF.169311.1"; exon_number "1"; FPKM "13.9809522603"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.753005"; cov "0.794118"; +chr3 Cufflinks transcript 130936639 130936898 1000 . . gene_id "CUFF.171349"; transcript_id "CUFF.171349.1"; FPKM "20.1110620975"; frac "1.000000"; conf_lo "7.983635"; conf_hi "32.238489"; cov "1.142308"; +chr3 Cufflinks exon 136592671 136592771 1000 . . gene_id "CUFF.171861"; transcript_id "CUFF.171861.1"; exon_number "1"; FPKM "32.9452142371"; frac "1.000000"; conf_lo "8.040973"; conf_hi "57.849455"; cov "1.871287"; +chr3 Cufflinks transcript 152641383 152641451 1000 . . gene_id "CUFF.172987"; transcript_id "CUFF.172987.1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "44.532262"; cov "1.173913"; +chr3 Cufflinks transcript 152861374 152861508 1000 . . gene_id "CUFF.173007"; transcript_id "CUFF.173007.1"; FPKM "24.6479010219"; frac "1.000000"; conf_lo "6.015839"; conf_hi "43.279963"; cov "1.400000"; +chr3 Cufflinks transcript 157698536 157698562 1000 . . gene_id "CUFF.173579"; transcript_id "CUFF.173579.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr4 Cufflinks exon 13715310 13715630 1000 . . gene_id "CUFF.174817"; transcript_id "CUFF.174817.1"; exon_number "1"; FPKM "19.2510308382"; frac "1.000000"; conf_lo "8.572480"; conf_hi "29.929581"; cov "1.093458"; +chr4 Cufflinks transcript 62063768 62063821 1000 . . gene_id "CUFF.179577"; transcript_id "CUFF.179577.1"; FPKM "26.3875633685"; frac "1.000000"; conf_lo "0.000000"; conf_hi "56.869362"; cov "1.498813"; +chr4 Cufflinks transcript 77180436 77180462 1000 . . gene_id "CUFF.181019"; transcript_id "CUFF.181019.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr4 Cufflinks transcript 102112070 102112096 1000 . . gene_id "CUFF.183381"; transcript_id "CUFF.183381.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr4 Cufflinks exon 117233771 117233830 1000 + . gene_id "CUFF.185373"; transcript_id "CUFF.185373.1"; exon_number "1"; FPKM "4.8015391601"; frac "1.000000"; conf_lo "0.000000"; conf_hi "14.404617"; cov "0.272727"; +chr4 Cufflinks exon 135563059 135563110 1000 . . gene_id "CUFF.189099"; transcript_id "CUFF.189099.1"; exon_number "1"; FPKM "18.2827837250"; frac "1.000000"; conf_lo "0.000000"; conf_hi "44.138544"; cov "1.038462"; +chr4 Cufflinks exon 147515029 147515097 1000 . . gene_id "CUFF.190627"; transcript_id "CUFF.190627.1"; exon_number "1"; FPKM "34.4458244094"; frac "1.000000"; conf_lo "3.636542"; conf_hi "65.255106"; cov "1.956522"; +chr5 Cufflinks exon 3949522 3949685 1000 . . gene_id "CUFF.192485"; transcript_id "CUFF.192485.1"; exon_number "1"; FPKM "23.1879208220"; frac "1.000000"; conf_lo "6.791585"; conf_hi "39.584257"; cov "1.317073"; +chr5 Cufflinks exon 22635516 22635542 1000 . . gene_id "CUFF.194445"; transcript_id "CUFF.194445.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr5 Cufflinks exon 34172212 34172238 1000 . . gene_id "CUFF.196463"; transcript_id "CUFF.196463.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr5 Cufflinks transcript 35362816 35362905 1000 . . gene_id "CUFF.196905"; transcript_id "CUFF.196905.1"; FPKM "10.5633861522"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.502270"; cov "0.600000"; +chr5 Cufflinks transcript 37083127 37083166 1000 . . gene_id "CUFF.197139"; transcript_id "CUFF.197139.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; +chr5 Cufflinks transcript 68089694 68089831 1000 . . gene_id "CUFF.199409"; transcript_id "CUFF.199409.1"; FPKM "17.2229122047"; frac "1.000000"; conf_lo "1.818271"; conf_hi "32.627553"; cov "0.978261"; +chr5 Cufflinks exon 98615179 98615254 1000 . . gene_id "CUFF.201693"; transcript_id "CUFF.201693.1"; exon_number "1"; FPKM "12.5092730750"; frac "1.000000"; conf_lo "0.000000"; conf_hi "30.200057"; cov "0.710526"; +chr5 Cufflinks exon 105915104 105915181 1000 . . gene_id "CUFF.202385"; transcript_id "CUFF.202385.1"; exon_number "1"; FPKM "12.1885224833"; frac "1.000000"; conf_lo "0.000000"; conf_hi "29.425696"; cov "0.692308"; +chr5 Cufflinks transcript 116136788 116136814 1000 . . gene_id "CUFF.204349"; transcript_id "CUFF.204349.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr5 Cufflinks exon 122819526 122819619 1000 . . gene_id "CUFF.205487"; transcript_id "CUFF.205487.1"; exon_number "1"; FPKM "25.2486782797"; frac "1.000000"; conf_lo "2.649470"; conf_hi "47.847887"; cov "1.434124"; +chr5 Cufflinks exon 132055557 132055583 1000 . . gene_id "CUFF.207163"; transcript_id "CUFF.207163.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr5 Cufflinks transcript 145619548 145619710 1000 . . gene_id "CUFF.209965"; transcript_id "CUFF.209965.1"; FPKM "40.8278115086"; frac "1.000000"; conf_lo "19.004428"; conf_hi "62.651195"; cov "2.319018"; +chr6 Cufflinks exon 48466822 48466848 1000 . . gene_id "CUFF.215907"; transcript_id "CUFF.215907.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr6 Cufflinks exon 63803818 63803844 1000 . . gene_id "CUFF.217337"; transcript_id "CUFF.217337.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr6 Cufflinks transcript 77393088 77393138 1000 . . gene_id "CUFF.218387"; transcript_id "CUFF.218387.1"; FPKM "18.6412696804"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.004006"; cov "1.058824"; +chr6 Cufflinks transcript 82379452 82379478 1000 . . gene_id "CUFF.218947"; transcript_id "CUFF.218947.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr6 Cufflinks exon 83928984 83929105 1000 . . gene_id "CUFF.219317"; transcript_id "CUFF.219317.1"; exon_number "1"; FPKM "46.7559714935"; frac "1.000000"; conf_lo "19.761399"; conf_hi "73.750544"; cov "2.655738"; +chr6 Cufflinks exon 103658447 103658521 1000 . . gene_id "CUFF.221849"; transcript_id "CUFF.221849.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "40.969681"; cov "1.080000"; +chr6 Cufflinks exon 113781332 113781358 1000 . . gene_id "CUFF.222775"; transcript_id "CUFF.222775.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr6 Cufflinks exon 118857949 118858148 1000 . . gene_id "CUFF.223543"; transcript_id "CUFF.223543.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "5.569100"; conf_hi "32.459091"; cov "1.080000"; +chr6 Cufflinks transcript 124996314 124996340 1000 . . gene_id "CUFF.224545"; transcript_id "CUFF.224545.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr6 Cufflinks transcript 127077329 127077364 1000 . . gene_id "CUFF.225409"; transcript_id "CUFF.225409.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "105.633862"; cov "3.000000"; +chr6 Cufflinks exon 136038245 136038304 1000 . . gene_id "CUFF.225521"; transcript_id "CUFF.225521.1"; exon_number "1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.212101"; cov "1.350000"; +chr7 Cufflinks exon 13845893 13845919 1000 . . gene_id "CUFF.227869"; transcript_id "CUFF.227869.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr7 Cufflinks exon 56060938 56061023 1000 . . gene_id "CUFF.232920"; transcript_id "CUFF.232920.1"; exon_number "1"; FPKM "11.0547064384"; frac "1.000000"; conf_lo "0.000000"; conf_hi "26.688422"; cov "0.627907"; +chr7 Cufflinks exon 71484947 71484992 1000 . . gene_id "CUFF.234766"; transcript_id "CUFF.234766.1"; exon_number "1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; +chr7 Cufflinks transcript 71784522 71784548 1000 . . gene_id "CUFF.234810"; transcript_id "CUFF.234810.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr7 Cufflinks exon 72605044 72605070 1000 . . gene_id "CUFF.234948"; transcript_id "CUFF.234948.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr7 Cufflinks transcript 85554210 85554343 1000 . . gene_id "CUFF.235778"; transcript_id "CUFF.235778.1"; FPKM "17.7370289869"; frac "1.000000"; conf_lo "1.872548"; conf_hi "33.601510"; cov "1.007463"; +chr7 Cufflinks transcript 98723325 98723416 1000 . . gene_id "CUFF.237594"; transcript_id "CUFF.237594.1"; FPKM "10.3337473228"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.947873"; cov "0.586957"; +chr7 Cufflinks exon 104055491 104055589 1000 . . gene_id "CUFF.238474"; transcript_id "CUFF.238474.1"; exon_number "1"; FPKM "28.8092349606"; frac "1.000000"; conf_lo "5.286593"; conf_hi "52.331877"; cov "1.636364"; +chr7 Cufflinks exon 107603711 107603748 1000 . . gene_id "CUFF.239180"; transcript_id "CUFF.239180.1"; exon_number "1"; FPKM "25.0185461500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "60.400113"; cov "1.421053"; +chr7 Cufflinks exon 133792511 133792572 1000 . . gene_id "CUFF.242136"; transcript_id "CUFF.242136.1"; exon_number "1"; FPKM "15.3339476403"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.019424"; cov "0.870968"; +chr8 Cufflinks exon 9970398 9970545 1000 . . gene_id "CUFF.245320"; transcript_id "CUFF.245320.1"; exon_number "1"; FPKM "22.4828826889"; frac "1.000000"; conf_lo "5.487421"; conf_hi "39.478345"; cov "1.277027"; +chr8 Cufflinks transcript 10425062 10425088 1000 . . gene_id "CUFF.245408"; transcript_id "CUFF.245408.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr8 Cufflinks transcript 13018897 13018981 1000 . . gene_id "CUFF.245840"; transcript_id "CUFF.245840.1"; FPKM "16.7771427124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "36.149718"; cov "0.952941"; +chr8 Cufflinks transcript 14745123 14745149 1000 . . gene_id "CUFF.246146"; transcript_id "CUFF.246146.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr8 Cufflinks exon 29820895 29820930 1000 . . gene_id "CUFF.247504"; transcript_id "CUFF.247504.1"; exon_number "1"; FPKM "26.4084653806"; frac "1.000000"; conf_lo "0.000000"; conf_hi "63.755675"; cov "1.500000"; +chr8 Cufflinks transcript 36676568 36676665 1000 . . gene_id "CUFF.248480"; transcript_id "CUFF.248480.1"; FPKM "9.7010689153"; frac "1.000000"; conf_lo "0.000000"; conf_hi "23.420452"; cov "0.551020"; +chr8 Cufflinks transcript 50146533 50146584 1000 . . gene_id "CUFF.249617"; transcript_id "CUFF.249617.1"; FPKM "27.4241755875"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.090886"; cov "1.557692"; +chr8 Cufflinks exon 51010775 51010850 1000 . . gene_id "CUFF.249695"; transcript_id "CUFF.249695.1"; exon_number "1"; FPKM "18.7639096125"; frac "1.000000"; conf_lo "0.000000"; conf_hi "40.430606"; cov "1.065789"; +chr8 Cufflinks exon 63391023 63391095 1000 . . gene_id "CUFF.250329"; transcript_id "CUFF.250329.1"; exon_number "1"; FPKM "13.0233527904"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.441155"; cov "0.739726"; +chr8 Cufflinks transcript 73858591 73858706 1000 . . gene_id "CUFF.251697"; transcript_id "CUFF.251697.1"; FPKM "12.2935959530"; frac "1.000000"; conf_lo "0.000000"; conf_hi "26.489018"; cov "0.698276"; +chr8 Cufflinks transcript 75514699 75514725 1000 . . gene_id "CUFF.252263"; transcript_id "CUFF.252263.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr8 Cufflinks exon 86101515 86101548 1000 . . gene_id "CUFF.252891"; transcript_id "CUFF.252891.1"; exon_number "1"; FPKM "27.9619045206"; frac "1.000000"; conf_lo "0.000000"; conf_hi "67.506009"; cov "1.588235"; +chr8 Cufflinks transcript 93627215 93627241 1000 . . gene_id "CUFF.254225"; transcript_id "CUFF.254225.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr8 Cufflinks exon 108148187 108148357 1000 . . gene_id "CUFF.255477"; transcript_id "CUFF.255477.1"; exon_number "1"; FPKM "11.1193538445"; frac "1.000000"; conf_lo "0.000000"; conf_hi "22.238708"; cov "0.631579"; +chr8 Cufflinks exon 108190587 108190664 1000 . . gene_id "CUFF.255507"; transcript_id "CUFF.255507.1"; exon_number "1"; FPKM "12.1885224833"; frac "1.000000"; conf_lo "0.000000"; conf_hi "29.425696"; cov "0.692308"; +chr8 Cufflinks exon 120931685 120931769 1000 . . gene_id "CUFF.257375"; transcript_id "CUFF.257375.1"; exon_number "1"; FPKM "16.7771427124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "36.149718"; cov "0.952941"; +chr9 Cufflinks transcript 20449846 20449932 1000 . . gene_id "CUFF.260747"; transcript_id "CUFF.260747.1"; FPKM "234.9313045507"; frac "1.000000"; conf_lo "163.275950"; conf_hi "306.586659"; cov "13.344091"; +chr9 Cufflinks exon 25083606 25083643 1000 . . gene_id "CUFF.261551"; transcript_id "CUFF.261551.1"; exon_number "1"; FPKM "25.0185461500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "60.400113"; cov "1.421053"; +chr9 Cufflinks transcript 27906894 27906964 1000 . . gene_id "CUFF.261925"; transcript_id "CUFF.261925.1"; FPKM "26.7804155972"; frac "1.000000"; conf_lo "0.000000"; conf_hi "53.560831"; cov "1.521127"; +chr9 Cufflinks transcript 34418034 34418065 1000 . . gene_id "CUFF.262975"; transcript_id "CUFF.262975.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; +chr9 Cufflinks exon 34710789 34710815 1000 . . gene_id "CUFF.263065"; transcript_id "CUFF.263065.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr9 Cufflinks transcript 40823051 40823090 1000 . . gene_id "CUFF.263747"; transcript_id "CUFF.263747.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; +chr9 Cufflinks exon 59236547 59236671 1000 . . gene_id "CUFF.267045"; transcript_id "CUFF.267045.1"; exon_number "1"; FPKM "12.1905895442"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.808020"; cov "0.692425"; +chr9 Cufflinks transcript 66418162 66418188 1000 . . gene_id "CUFF.268423"; transcript_id "CUFF.268423.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr9 Cufflinks transcript 95913236 95913262 1000 . . gene_id "CUFF.270957"; transcript_id "CUFF.270957.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr9 Cufflinks exon 103101949 103102030 1000 . . gene_id "CUFF.271979"; transcript_id "CUFF.271979.1"; exon_number "1"; FPKM "11.5939604110"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.990296"; cov "0.658537"; +chr9 Cufflinks transcript 105579135 105579173 1000 . . gene_id "CUFF.272347"; transcript_id "CUFF.272347.1"; FPKM "24.3770449667"; frac "1.000000"; conf_lo "0.000000"; conf_hi "58.851393"; cov "1.384615"; +chr9 Cufflinks exon 107445870 107445930 1000 . . gene_id "CUFF.272761"; transcript_id "CUFF.272761.1"; exon_number "1"; FPKM "38.9633095779"; frac "1.000000"; conf_lo "4.113466"; conf_hi "73.813153"; cov "2.213115"; +chr9 Cufflinks exon 113779194 113779220 1000 . . gene_id "CUFF.274445"; transcript_id "CUFF.274445.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr9 Cufflinks transcript 120860476 120860606 1000 . . gene_id "CUFF.275115"; transcript_id "CUFF.275115.1"; FPKM "25.4005086867"; frac "1.000000"; conf_lo "6.199529"; conf_hi "44.601488"; cov "1.442748"; +chrX Cufflinks exon 10274057 10274087 1000 . . gene_id "CUFF.276147"; transcript_id "CUFF.276147.1"; exon_number "1"; FPKM "99.5432248142"; frac "1.000000"; conf_lo "21.405127"; conf_hi "177.681323"; cov "5.654052"; +chrX Cufflinks transcript 39881431 39881678 1000 . . gene_id "CUFF.277419"; transcript_id "CUFF.277419.1"; FPKM "42.1683560109"; frac "1.000000"; conf_lo "24.187709"; conf_hi "60.149003"; cov "2.395161"; +chrX Cufflinks transcript 90114645 90131913 1000 - . gene_id "CUFF.279771"; transcript_id "CUFF.279771.1"; FPKM "6.8891648819"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.667495"; cov "0.391304"; +chrX Cufflinks transcript 148249672 148249713 1000 . . gene_id "CUFF.282847"; transcript_id "CUFF.282847.1"; FPKM "56.5895686726"; frac "1.000000"; conf_lo "5.974320"; conf_hi "107.204818"; cov "3.214286"; +chrX Cufflinks transcript 148481505 148482455 1000 + . gene_id "CUFF.282965"; transcript_id "CUFF.282965.1"; FPKM "40.1706233958"; frac "1.000000"; conf_lo "16.978103"; conf_hi "63.363144"; cov "2.281690"; +chrX Cufflinks transcript 158986411 158986471 1000 . . gene_id "CUFF.283831"; transcript_id "CUFF.283831.1"; FPKM "15.5853238312"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.626300"; cov "0.885246"; \ No newline at end of file diff -r e972d3f8413e -r b5391bd3e9c7 test-data/gff_filtering_out1.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff_filtering_out1.gff Fri May 14 10:15:48 2010 -0400 @@ -0,0 +1,46 @@ +chr10 Cufflinks transcript 62044837 62045189 1000 . . gene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611"; +chr10 Cufflinks transcript 75372919 75373002 1000 . . gene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429"; +chr10 Cufflinks transcript 80362428 80363292 1000 - . gene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449"; +chr11 Cufflinks transcript 7904565 7904642 1000 . . gene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633"; +chr11 Cufflinks exon 78140156 78140259 1000 . . gene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385"; +chr11 Cufflinks exon 105616462 105616737 1000 . . gene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087"; +chr12 Cufflinks exon 30701762 30702509 1000 . . gene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412"; +chr13 Cufflinks exon 49159496 49159569 1000 . . gene_id "CUFF.67788"; transcript_id "CUFF.67788.1"; exon_number "1"; FPKM "44.9657653777"; frac "1.000000"; conf_lo "10.974842"; conf_hi "78.956689"; cov "2.554054"; +chr13 Cufflinks transcript 100200304 100200330 1000 . . gene_id "CUFF.73108"; transcript_id "CUFF.73108.1"; FPKM "123.2395051093"; frac "1.000000"; conf_lo "30.079196"; conf_hi "216.399814"; cov "7.000000"; +chr14 Cufflinks transcript 31949103 31949152 1000 . . gene_id "CUFF.77316"; transcript_id "CUFF.77316.1"; FPKM "85.5634278330"; frac "1.000000"; conf_lo "28.521143"; conf_hi "142.605713"; cov "4.860000"; +chr14 Cufflinks exon 67604227 67604668 1000 . . gene_id "CUFF.81446"; transcript_id "CUFF.81446.1"; exon_number "1"; FPKM "123.6776546104"; frac "1.000000"; conf_lo "100.611653"; conf_hi "146.743656"; cov "7.024887"; +chr14 Cufflinks exon 75165582 75165744 1000 . . gene_id "CUFF.82088"; transcript_id "CUFF.82088.1"; exon_number "1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509"; +chr16 Cufflinks transcript 57154027 57154067 1000 . . gene_id "CUFF.103364"; transcript_id "CUFF.103364.1"; FPKM "162.3154457537"; frac "1.000000"; conf_lo "75.554191"; conf_hi "249.076701"; cov "9.219512"; +chr16 Cufflinks exon 74862302 74862560 1000 . . gene_id "CUFF.105450"; transcript_id "CUFF.105450.1"; exon_number "1"; FPKM "11.0120241741"; frac "1.000000"; conf_lo "2.020744"; conf_hi "20.003304"; cov "0.625483"; +chr16 Cufflinks transcript 98168779 98168914 1000 . . gene_id "CUFF.107834"; transcript_id "CUFF.107834.1"; FPKM "24.4666664555"; frac "1.000000"; conf_lo "5.971605"; conf_hi "42.961728"; cov "1.389706"; +chr17 Cufflinks exon 8483212 8483268 1000 . . gene_id "CUFF.108498"; transcript_id "CUFF.108498.1"; exon_number "1"; FPKM "50.0370923000"; frac "1.000000"; conf_lo "9.181978"; conf_hi "90.892207"; cov "2.842105"; +chr17 Cufflinks exon 30355791 30355913 1000 . . gene_id "CUFF.111759"; transcript_id "CUFF.111759.1"; exon_number "1"; FPKM "19.3232673516"; frac "1.000000"; conf_lo "2.040012"; conf_hi "36.606523"; cov "1.097561"; +chr18 Cufflinks transcript 39571718 39571880 1000 . . gene_id "CUFF.123569"; transcript_id "CUFF.123569.1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509"; +chr19 Cufflinks exon 17633088 17633203 1000 . . gene_id "CUFF.131333"; transcript_id "CUFF.131333.1"; exon_number "1"; FPKM "20.4893265884"; frac "1.000000"; conf_lo "2.163116"; conf_hi "38.815537"; cov "1.163793"; +chr19 Cufflinks transcript 41997624 41997859 1000 . . gene_id "CUFF.133569"; transcript_id "CUFF.133569.1"; FPKM "28.1988698132"; frac "1.000000"; conf_lo "13.125940"; conf_hi "43.271800"; cov "1.601695"; +chr19 Cufflinks exon 56516515 56516684 1000 . . gene_id "CUFF.135203"; transcript_id "CUFF.135203.1"; exon_number "1"; FPKM "33.5542854247"; frac "1.000000"; conf_lo "14.181710"; conf_hi "52.926861"; cov "1.905882"; +chr2 Cufflinks transcript 4543774 4543977 1000 . . gene_id "CUFF.136435"; transcript_id "CUFF.136435.1"; FPKM "37.2825393608"; frac "1.000000"; conf_lo "18.641270"; conf_hi "55.923809"; cov "2.117647"; +chr2 Cufflinks transcript 30200331 30200938 1000 . . gene_id "CUFF.140289"; transcript_id "CUFF.140289.1"; FPKM "100.0741846001"; frac "1.000000"; conf_lo "82.383401"; conf_hi "117.764968"; cov "5.684211"; +chr2 Cufflinks transcript 106644220 106644341 1000 . . gene_id "CUFF.148977"; transcript_id "CUFF.148977.1"; FPKM "27.2743167045"; frac "1.000000"; conf_lo "6.656871"; conf_hi "47.891762"; cov "1.549180"; +chr2 Cufflinks exon 125388931 125389219 1000 . . gene_id "CUFF.151331"; transcript_id "CUFF.151331.1"; exon_number "1"; FPKM "23.0274507817"; frac "1.000000"; conf_lo "10.718761"; conf_hi "35.336141"; cov "1.307958"; +chr3 Cufflinks transcript 130936639 130936898 1000 . . gene_id "CUFF.171349"; transcript_id "CUFF.171349.1"; FPKM "20.1110620975"; frac "1.000000"; conf_lo "7.983635"; conf_hi "32.238489"; cov "1.142308"; +chr3 Cufflinks exon 136592671 136592771 1000 . . gene_id "CUFF.171861"; transcript_id "CUFF.171861.1"; exon_number "1"; FPKM "32.9452142371"; frac "1.000000"; conf_lo "8.040973"; conf_hi "57.849455"; cov "1.871287"; +chr3 Cufflinks transcript 152861374 152861508 1000 . . gene_id "CUFF.173007"; transcript_id "CUFF.173007.1"; FPKM "24.6479010219"; frac "1.000000"; conf_lo "6.015839"; conf_hi "43.279963"; cov "1.400000"; +chr4 Cufflinks exon 13715310 13715630 1000 . . gene_id "CUFF.174817"; transcript_id "CUFF.174817.1"; exon_number "1"; FPKM "19.2510308382"; frac "1.000000"; conf_lo "8.572480"; conf_hi "29.929581"; cov "1.093458"; +chr4 Cufflinks exon 147515029 147515097 1000 . . gene_id "CUFF.190627"; transcript_id "CUFF.190627.1"; exon_number "1"; FPKM "34.4458244094"; frac "1.000000"; conf_lo "3.636542"; conf_hi "65.255106"; cov "1.956522"; +chr5 Cufflinks exon 3949522 3949685 1000 . . gene_id "CUFF.192485"; transcript_id "CUFF.192485.1"; exon_number "1"; FPKM "23.1879208220"; frac "1.000000"; conf_lo "6.791585"; conf_hi "39.584257"; cov "1.317073"; +chr5 Cufflinks transcript 68089694 68089831 1000 . . gene_id "CUFF.199409"; transcript_id "CUFF.199409.1"; FPKM "17.2229122047"; frac "1.000000"; conf_lo "1.818271"; conf_hi "32.627553"; cov "0.978261"; +chr5 Cufflinks exon 122819526 122819619 1000 . . gene_id "CUFF.205487"; transcript_id "CUFF.205487.1"; exon_number "1"; FPKM "25.2486782797"; frac "1.000000"; conf_lo "2.649470"; conf_hi "47.847887"; cov "1.434124"; +chr5 Cufflinks transcript 145619548 145619710 1000 . . gene_id "CUFF.209965"; transcript_id "CUFF.209965.1"; FPKM "40.8278115086"; frac "1.000000"; conf_lo "19.004428"; conf_hi "62.651195"; cov "2.319018"; +chr6 Cufflinks exon 83928984 83929105 1000 . . gene_id "CUFF.219317"; transcript_id "CUFF.219317.1"; exon_number "1"; FPKM "46.7559714935"; frac "1.000000"; conf_lo "19.761399"; conf_hi "73.750544"; cov "2.655738"; +chr6 Cufflinks exon 118857949 118858148 1000 . . gene_id "CUFF.223543"; transcript_id "CUFF.223543.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "5.569100"; conf_hi "32.459091"; cov "1.080000"; +chr7 Cufflinks transcript 85554210 85554343 1000 . . gene_id "CUFF.235778"; transcript_id "CUFF.235778.1"; FPKM "17.7370289869"; frac "1.000000"; conf_lo "1.872548"; conf_hi "33.601510"; cov "1.007463"; +chr7 Cufflinks exon 104055491 104055589 1000 . . gene_id "CUFF.238474"; transcript_id "CUFF.238474.1"; exon_number "1"; FPKM "28.8092349606"; frac "1.000000"; conf_lo "5.286593"; conf_hi "52.331877"; cov "1.636364"; +chr8 Cufflinks exon 9970398 9970545 1000 . . gene_id "CUFF.245320"; transcript_id "CUFF.245320.1"; exon_number "1"; FPKM "22.4828826889"; frac "1.000000"; conf_lo "5.487421"; conf_hi "39.478345"; cov "1.277027"; +chr9 Cufflinks transcript 20449846 20449932 1000 . . gene_id "CUFF.260747"; transcript_id "CUFF.260747.1"; FPKM "234.9313045507"; frac "1.000000"; conf_lo "163.275950"; conf_hi "306.586659"; cov "13.344091"; +chr9 Cufflinks exon 107445870 107445930 1000 . . gene_id "CUFF.272761"; transcript_id "CUFF.272761.1"; exon_number "1"; FPKM "38.9633095779"; frac "1.000000"; conf_lo "4.113466"; conf_hi "73.813153"; cov "2.213115"; +chr9 Cufflinks transcript 120860476 120860606 1000 . . gene_id "CUFF.275115"; transcript_id "CUFF.275115.1"; FPKM "25.4005086867"; frac "1.000000"; conf_lo "6.199529"; conf_hi "44.601488"; cov "1.442748"; +chrX Cufflinks exon 10274057 10274087 1000 . . gene_id "CUFF.276147"; transcript_id "CUFF.276147.1"; exon_number "1"; FPKM "99.5432248142"; frac "1.000000"; conf_lo "21.405127"; conf_hi "177.681323"; cov "5.654052"; +chrX Cufflinks transcript 39881431 39881678 1000 . . gene_id "CUFF.277419"; transcript_id "CUFF.277419.1"; FPKM "42.1683560109"; frac "1.000000"; conf_lo "24.187709"; conf_hi "60.149003"; cov "2.395161"; +chrX Cufflinks transcript 148249672 148249713 1000 . . gene_id "CUFF.282847"; transcript_id "CUFF.282847.1"; FPKM "56.5895686726"; frac "1.000000"; conf_lo "5.974320"; conf_hi "107.204818"; cov "3.214286"; +chrX Cufflinks transcript 148481505 148482455 1000 + . gene_id "CUFF.282965"; transcript_id "CUFF.282965.1"; FPKM "40.1706233958"; frac "1.000000"; conf_lo "16.978103"; conf_hi "63.363144"; cov "2.281690"; diff -r e972d3f8413e -r b5391bd3e9c7 tool_conf.xml.sample --- a/tool_conf.xml.sample Thu May 13 15:35:41 2010 -0400 +++ b/tool_conf.xml.sample Fri May 14 10:15:48 2010 -0400 @@ -237,11 +237,14 @@ <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" /> - <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> + <label text="RNA-seq" id="rna_seq" /> + <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" /> + <label text="Filtering" id="filtering" /> + <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> + <tool file="ngs_rna/gff_filtering.xml" /> </section> <section name="NGS: SAM Tools" id="samtools"> <tool file="samtools/sam_bitwise_flag_filter.xml" /> diff -r e972d3f8413e -r b5391bd3e9c7 tools/ngs_rna/gff_filtering.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ngs_rna/gff_filtering.py Fri May 14 10:15:48 2010 -0400 @@ -0,0 +1,137 @@ +#!/usr/bin/env python +# This tool takes a gff file as input and creates filters on attributes based on certain properties. +# The tool will skip over invalid lines within the file, informing the user about the number of lines skipped. +# TODO: much of this code is copied from the Filter1 tool (filtering.py in this directory). The commonalities should be +# abstracted and leveraged in each filtering tool. + +from __future__ import division +import sys, re, os.path + +# Older py compatibility +try: + set() +except: + from sets import Set as set + +assert sys.version_info[:2] >= ( 2, 4 ) + +def get_operands( filter_condition ): + # Note that the order of all_operators is important + items_to_strip = ['+', '-', '**', '*', '//', '/', '%', '<<', '>>', '&', '|', '^', '~', '<=', '<', '>=', '>', '==', '!=', '<>', ' and ', ' or ', ' not ', ' is ', ' is not ', ' in ', ' not in '] + for item in items_to_strip: + if filter_condition.find( item ) >= 0: + filter_condition = filter_condition.replace( item, ' ' ) + operands = set( filter_condition.split( ' ' ) ) + return operands + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +in_fname = sys.argv[1] +out_fname = sys.argv[2] +attribute_type = sys.argv[3] +attribute_name = sys.argv[4] +cond_text = sys.argv[5] + +# Unescape if input has been escaped +mapped_str = { + '__lt__': '<', + '__le__': '<=', + '__eq__': '==', + '__ne__': '!=', + '__gt__': '>', + '__ge__': '>=', + '__sq__': '\'', + '__dq__': '"', +} +for key, value in mapped_str.items(): + cond_text = cond_text.replace( key, value ) + +# Add attribute name to condition text. +cond_text = attribute_name + cond_text + +# Attempt to determine if the condition includes executable stuff and, if so, exit +secured = dir() +operands = get_operands(cond_text) +for operand in operands: + try: + check = int( operand ) + except: + if operand in secured: + stop_err( "Illegal value '%s' in condition '%s'" % ( operand, cond_text ) ) + +# Set up assignment. +assignment = "%s = attributes[ '%s' ]" % ( attribute_name, attribute_name ) + +# Set up type casting based on attribute type. +type_cast = "%s = %s(%s)" % ( attribute_name, attribute_type, attribute_name) + +# Stats +skipped_lines = 0 +first_invalid_line = 0 +invalid_line = None +lines_kept = 0 +total_lines = 0 +out = open( out_fname, 'wt' ) + +# Read and filter input file, skipping invalid lines +code = ''' +for i, line in enumerate( file( in_fname ) ): + total_lines += 1 + line = line.rstrip( '\\r\\n' ) + if not line or line.startswith( '#' ): + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + try: + # GTF format: chrom source, name, chromStart, chromEnd, score, strand, frame, attributes. + # Attributes format: name1 "value1" ; name2 "value2" ; ... + elems = line.split( '\t' ) + attributes_list = elems[8].split(";") + attributes = {} + for name_value_pair in attributes_list: + pair = name_value_pair.strip().split(" ") + if pair == '': + continue + name = pair[0].strip() + if name == '': + continue + # Need to strip double quote from values + value = pair[1].strip(" \\"") + attributes[name] = value + %s + %s + if %s: + lines_kept += 1 + print >> out, line + except: + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line +''' % ( assignment, type_cast, cond_text ) + +valid_filter = True +try: + exec code +except Exception, e: + out.close() + if str( e ).startswith( 'invalid syntax' ): + valid_filter = False + stop_err( 'Filter condition "%s" likely invalid. See tool tips, syntax and examples.' % cond_text ) + else: + stop_err( str( e ) ) + +if valid_filter: + out.close() + valid_lines = total_lines - skipped_lines + print 'Filtering with %s, ' % ( cond_text ) + if valid_lines > 0: + print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines ) + else: + print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text + if skipped_lines > 0: + print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) diff -r e972d3f8413e -r b5391bd3e9c7 tools/ngs_rna/gff_filtering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ngs_rna/gff_filtering.xml Fri May 14 10:15:48 2010 -0400 @@ -0,0 +1,58 @@ +<tool id="gff_filtering" name="Filter GFF" version="0.1"> + <description>file on any attribute using simple expressions</description> + <command interpreter="python"> + gff_filtering.py $input $out_file1 "$attribute_type" "$attribute_name" "$cond" + </command> + <inputs> + <param format="gff" name="input" type="data" label="Filter" help="Query missing? See TIP below."/> + <param name="attribute_name" size="40" type="text" label="Attribute name" help=""> + <validator type="empty_field" message="Enter a valid attribute name."/> + </param> + <param name="attribute_type" type="select" label="Attribute type"> + <option value="float">Float</option> + <option value="integer">Integer</option> + <option value="str">String</option> + </param> + <param name="cond" size="40" type="text" value=">0" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool."> + <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="input" value="gff_filtering_in1.gff"/> + <param name="attribute_name" value="conf_lo"/> + <param name="attribute_type" value="float"/> + <param name="cond" value=">0"/> + <output name="out_file1" file="gff_filtering_out1.gff"/> + </test> + </tests> + + <help> + +.. class:: warningmark + +Double equal signs, ==, must be used as *"equal to"* (e.g., **c1 == 'chr22'**) + +.. class:: infomark + +**TIP:** Attempting to apply a filtering condition may throw exceptions if the data type (e.g., string, integer) in every line of the attribute being filtered is not appropriate for the condition (e.g., attempting certain numerical calculations on strings). If an exception is thrown when applying the condition to a line, that line is skipped as invalid for the filter condition. The number of invalid skipped lines is documented in the resulting history item as a "Condition/data issue". + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + +----- + +**Syntax** + +The filter tool allows you to restrict the dataset using simple conditional statements. + +- Make sure that multi-character operators contain no white space ( e.g., **<=** is valid while **< =** is not valid ) +- When using 'equal-to' operator **double equal sign '==' must be used** ( e.g., **attribute_name=='chr1'** ) +- Non-numerical values must be included in single or double quotes ( e.g., **attribute_name=='XX22'** ) + +</help> +</tool>

1 0

[hg] galaxy 3785: Fix comment.
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5ead6e4c2ef4 changeset: 3785:5ead6e4c2ef4 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri May 14 10:19:12 2010 -0400 description: Fix comment. diffstat: tools/ngs_rna/gff_filtering.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r b5391bd3e9c7 -r 5ead6e4c2ef4 tools/ngs_rna/gff_filtering.py --- a/tools/ngs_rna/gff_filtering.py Fri May 14 10:15:48 2010 -0400 +++ b/tools/ngs_rna/gff_filtering.py Fri May 14 10:19:12 2010 -0400 @@ -1,7 +1,7 @@ #!/usr/bin/env python # This tool takes a gff file as input and creates filters on attributes based on certain properties. # The tool will skip over invalid lines within the file, informing the user about the number of lines skipped. -# TODO: much of this code is copied from the Filter1 tool (filtering.py in this directory). The commonalities should be +# TODO: much of this code is copied from the Filter1 tool (filtering.py in tools/stats/). The commonalities should be # abstracted and leveraged in each filtering tool. from __future__ import division

1 0

[hg] galaxy 3783: Add track definition to bedgraph files generat...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e972d3f8413e changeset: 3783:e972d3f8413e user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu May 13 15:35:41 2010 -0400 description: Add track definition to bedgraph files generated by gtf2bedgraph. diffstat: test-data/gtf2bedgraph_out.bedgraph | 2 +- tools/filters/gtf_to_bedgraph_converter.py | 25 ++++++++++++++++--------- 2 files changed, 17 insertions(+), 10 deletions(-) diffs (61 lines): diff -r 0c1cb2c76b84 -r e972d3f8413e test-data/gtf2bedgraph_out.bedgraph --- a/test-data/gtf2bedgraph_out.bedgraph Thu May 13 14:10:37 2010 -0400 +++ b/test-data/gtf2bedgraph_out.bedgraph Thu May 13 15:35:41 2010 -0400 @@ -1,3 +1,4 @@ +track type=bedGraph chr1 36425949 36426026 4.8386844109 chr1 46891971 46892996 8.4688567539 chr1 71654477 71654594 0.4686878995 @@ -98,4 +99,3 @@ chr9 57867099 57867303 0.5359102332 chr9 106815437 106815604 5.4023275754 chr9 119703053 119703292 0.0814657030 -track type=bedGraph diff -r 0c1cb2c76b84 -r e972d3f8413e tools/filters/gtf_to_bedgraph_converter.py --- a/tools/filters/gtf_to_bedgraph_converter.py Thu May 13 14:10:37 2010 -0400 +++ b/tools/filters/gtf_to_bedgraph_converter.py Thu May 13 15:35:41 2010 -0400 @@ -9,16 +9,14 @@ output_name = sys.argv[2] attribute_name = sys.argv[3] - # Create temp file. - tmp_name = tempfile.NamedTemporaryFile().name + # Create temp files. + tmp_name1 = tempfile.NamedTemporaryFile().name + tmp_name2 = tempfile.NamedTemporaryFile().name # Do conversion. skipped_lines = 0 first_skipped_line = 0 - out = open( tmp_name, 'w' ) - - # Write track definition line. - out.write( "track type=bedGraph\n") + out = open( tmp_name1, 'w' ) # Write track data to temporary file. i = 0 @@ -56,11 +54,20 @@ first_skipped_line = i + 1 out.close() - # Sort tmp file to create bedgraph file; sort by chromosome name and chromosome start. - cmd = "sort -k1,1 -k2,2n < %s > %s" % ( tmp_name, output_name ) + # Sort tmp file by chromosome name and chromosome start to create ordered track data. + cmd = "sort -k1,1 -k2,2n < %s > %s" % ( tmp_name1, tmp_name2 ) try: os.system(cmd) - os.remove(tmp_name) + os.remove(tmp_name1) + except Exception, ex: + sys.stderr.write( "%s\n" % ex ) + sys.exit(1) + + # Create bedgraph file by combining track definition with ordered track data. + cmd = "echo 'track type=bedGraph' | cat - %s > %s " % ( tmp_name2, output_name ) + try: + os.system(cmd) + os.remove(tmp_name2) except Exception, ex: sys.stderr.write( "%s\n" % ex ) sys.exit(1)

1 0

[hg] galaxy 3782: Fix for editing category information in the co...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0c1cb2c76b84 changeset: 3782:0c1cb2c76b84 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu May 13 14:10:37 2010 -0400 description: Fix for editing category information in the community space. diffstat: lib/galaxy/webapps/community/controllers/admin.py | 32 +++++++++++----------- 1 files changed, 16 insertions(+), 16 deletions(-) diffs (47 lines): diff -r 17e1d798a59f -r 0c1cb2c76b84 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Thu May 13 12:14:52 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Thu May 13 14:10:37 2010 -0400 @@ -756,27 +756,27 @@ status='error' ) ) category = get_category( trans, id ) if params.get( 'edit_category_button', False ): - old_name = category.name - new_name = util.restore_text( params.name ) - new_description = util.restore_text( params.description ) - if old_name != new_name: + new_name = util.restore_text( params.get( 'name', '' ) ).strip() + new_description = util.restore_text( params.get( 'description', '' ) ).strip() + if category.name != new_name or category.description != new_description: if not new_name: message = 'Enter a valid name' status = 'error' - elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): + elif category.name != new_name and \ + trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): message = 'A category with that name already exists' status = 'error' - else: - category.name = new_name - category.description = new_description - trans.sa_session.add( category ) - trans.sa_session.flush() - message = "The information has been saved for category '%s'" % ( new_name ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='manage_categories', - webapp=webapp, - message=util.sanitize_text( message ), - status='done' ) ) + else: + category.name = new_name + category.description = new_description + trans.sa_session.add( category ) + trans.sa_session.flush() + message = "The information has been saved for category '%s'" % ( category.name ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='manage_categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='done' ) ) return trans.fill_template( '/webapps/community/category/edit_category.mako', category=category, webapp=webapp,

1 0

[hg] galaxy 3781: Only use search+select when jquery autocomplet...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/17e1d798a59f changeset: 3781:17e1d798a59f user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu May 13 12:14:52 2010 -0400 description: Only use search+select when jquery autocomplete plugin is defined. diffstat: static/scripts/galaxy.base.js | 16 ++++------------ static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/galaxy.workflow_editor.canvas.js | 2 +- 3 files changed, 6 insertions(+), 14 deletions(-) diffs (56 lines): diff -r 0c2b174f18e9 -r 17e1d798a59f static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Thu May 13 12:03:17 2010 -0400 +++ b/static/scripts/galaxy.base.js Thu May 13 12:14:52 2010 -0400 @@ -147,6 +147,10 @@ // Replace select box with a text input box + autocomplete. // TODO: make work with selects where refresh_on_change=True and refresh_on_change_values="..." function replace_big_select_inputs(min_length) { + // To do replace, jQuery's autocomplete plugin must be loaded. + if (typeof jQuery().autocomplete == "undefined") + return; + // Set default for min_length. if (min_length === undefined) min_length = 20; @@ -182,11 +186,6 @@ var text = $(this).text(); var value = $(this).attr('value'); - // HACK: dbkey-specific: ignore values that are '?' - if (value == '?') { - return; - } - // Set options and mapping. Mapping is (i) [from text to value] AND (ii) [from value to value]. This // enables a user to type the value directly rather than select the text that represents the value. select_options.push( text ); @@ -199,13 +198,6 @@ } }); - // HACK: dbkey-specific: add an unspecified option. We need to add this at the end b/c adding it first mucks - // up the autocomplete sorting for some reason. (I.e. All options that start with the first character of the - // first option are listed before the other, alphabetized options.) - select_options.push( "unspecified (?)" ); - select_mapping[ "unspecified (?)" ] = "?"; - select_mapping[ "?" ] = "?"; - // Set initial text if it's empty. if ( text_input_elt.attr('value') == '' ) { text_input_elt.attr('value', 'Click to Search or Select'); diff -r 0c2b174f18e9 -r 17e1d798a59f static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Thu May 13 12:03:17 2010 -0400 +++ b/static/scripts/packed/galaxy.base.js Thu May 13 12:14:52 2010 -0400 @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen! u(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString()! .toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).sp lit(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a){if(a===undefined){a=20}$('select[refresh_on_change!="true"]').each(function(){var b=$(this);if(b.find("option").length<a){return}var c=b.attr("value");var d=$("<input type='text' class='text-and-autocomplete-select'></input>");d.attr("size",40);d.attr("name",b.attr("name"));d.attr("id",b.attr("id"));d.click(function(){var i=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",i);$(this).select()});var h=[];var g={};b.children("option").each(function(){var j=$(this).text();var i=$(this).attr("value");if(i=="?"){return}h.push(j);g[j]=i;g[i]=i;if(i==c){d.attr("value",j! )}});h.push("unspecified (?)");g["unspecified (?)"]="?";g["?"]="?";if(d.attr("value")==""){d.attr("value","Click to Search or Select")}h=h.sort(naturalSort);var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};d.autocomplete(h,f);b.replaceWith(d);var e=function(){var j=d.attr("value");var i=g[j];if(i!==null&&i!==undefined){d.attr("value",i)}else{if(c!=""){d.attr("value",c)}else{d.attr("value","?")}}};d.parents("form").submit(function(){e()});$(document).bind("convert_dbkeys",function(){e()})})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup! 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){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*! f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canv as.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callou! t'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag",function(i){var h=function(){var k=$(i.dragProx! y).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dr agProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=! g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j)! )});workflow.node_changed(this)},update_field_data:function(f){var c=$ (this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div")! .remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,too! l_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input _connections:f,position:$(d.element).position(),annotation:d.annotation};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.a! ctive_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by! _level,function(k,l){l.sort(function(p,o){return $(d[p].element).posit ion().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_cont! ainer.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function! (){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#can vas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.ext! end(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:f! unction(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2); f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview! -border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_! viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a! ){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*! f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canv as.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callou! t'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag",function(i){var h=function(){var k=$(i.dragProx! y).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dr agProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=! g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j)! )});workflow.node_changed(this)},update_field_data:function(f){var c=$ (this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div")! .remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,too! l_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input _connections:f,position:$(d.element).position(),annotation:d.annotation};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.a! ctive_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80! ;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(functi on(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g! ,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../ima! ges/delete_icon_dark.png")},function(){$(this).attr("src","../images/d elete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}functi! on ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(! CanvasManager.prototype,{init_drag:function(){var b=this;var a=functio n(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:! f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);! i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file

1 0

[hg] galaxy 3780: Fix for issue where connecting to a Workflow S...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0c2b174f18e9 changeset: 3780:0c2b174f18e9 user: Dannon Baker <dannon.baker(a)emory.edu> date: Thu May 13 12:03:17 2010 -0400 description: Fix for issue where connecting to a Workflow Step that had been changed wasn't being saved diffstat: static/scripts/galaxy.workflow_editor.canvas.js | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r 6dab2b0a9801 -r 0c2b174f18e9 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu May 13 09:35:57 2010 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu May 13 12:03:17 2010 -0400 @@ -473,6 +473,7 @@ this.has_changes = true; if ( this.active_node == node ) { // Reactive with new form_html + this.check_changes_in_active_form(); //Force changes to be saved even on new connection (previously dumped) parent.show_form_for_tool( node.form_html + node.tooltip, node ); } },

1 0

[hg] galaxy 3779: Fix for changing a library dataset's data type...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6dab2b0a9801 changeset: 3779:6dab2b0a9801 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu May 13 09:35:57 2010 -0400 description: Fix for changing a library dataset's data type ( resolves ticket # 333 ), add the library dataset's data type to the library dataset info page, and add <pre> tags to the tool description on the tool information page in the community space. diffstat: templates/library/common/ldda_edit_info.mako | 1 + templates/library/common/ldda_info.mako | 5 +++++ templates/webapps/community/tool/edit_tool.mako | 2 +- templates/webapps/community/tool/view_tool.mako | 2 +- 4 files changed, 8 insertions(+), 2 deletions(-) diffs (50 lines): diff -r eb91e90d3405 -r 6dab2b0a9801 templates/library/common/ldda_edit_info.mako --- a/templates/library/common/ldda_edit_info.mako Wed May 12 17:43:29 2010 -0400 +++ b/templates/library/common/ldda_edit_info.mako Thu May 13 09:35:57 2010 -0400 @@ -101,6 +101,7 @@ %if ldda.datatype.allow_datatype_change: <form name="change_datatype" action="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), use_panels=use_panels, show_deleted=show_deleted, )}" method="post"> <div class="form-row"> + <input type="hidden" name="id" value="${trans.security.encode_id( ldda.id )}"/> <label>New Type:</label> ${datatype( ldda, file_formats )} <div class="toolParamHelp" style="clear: both;"> diff -r eb91e90d3405 -r 6dab2b0a9801 templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Wed May 12 17:43:29 2010 -0400 +++ b/templates/library/common/ldda_info.mako Thu May 13 09:35:57 2010 -0400 @@ -80,6 +80,11 @@ <div style="clear: both"></div> </div> <div class="form-row"> + <label>Data type:</label> + ${ldda.ext} + <div style="clear: both"></div> + </div> + <div class="form-row"> <label>Build:</label> ${ldda.dbkey} <div style="clear: both"></div> diff -r eb91e90d3405 -r 6dab2b0a9801 templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Wed May 12 17:43:29 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Thu May 13 09:35:57 2010 -0400 @@ -83,7 +83,7 @@ <div class="form-row"> <label>Description:</label> %if tool.user_description: - <div class="form-row-input"><textarea name="user_description" rows="5" cols="35">${tool.user_description}</textarea></div> + <div class="form-row-input"><pre><textarea name="user_description" rows="5" cols="35">${tool.user_description}</textarea></pre></div> %else: <div class="form-row-input"><textarea name="user_description" rows="5" cols="35"></textarea></div> %endif diff -r eb91e90d3405 -r 6dab2b0a9801 templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Wed May 12 17:43:29 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Thu May 13 09:35:57 2010 -0400 @@ -119,7 +119,7 @@ <div class="form-row"> <label>Description:</label> %if tool.user_description: - ${tool.user_description} + <pre>${tool.user_description}</pre> %endif <div style="clear: both"></div> </div>

1 0

[hg] galaxy 3778: trackster:
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/eb91e90d3405 changeset: 3778:eb91e90d3405 user: Kanwei Li <kanwei(a)gmail.com> date: Wed May 12 17:43:29 2010 -0400 description: trackster: - Prompt when leaving a viz with unsaved changes - Can only add datatypes of the same dbkey diffstat: lib/galaxy/web/controllers/tracks.py | 8 ++++++++ static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 28 ++++++++++++++++------------ templates/tracks/browser.mako | 20 ++++++++++++++------ 4 files changed, 39 insertions(+), 19 deletions(-) diffs (191 lines): diff -r b762ea8e5508 -r eb91e90d3405 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Wed May 12 15:57:05 2010 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Wed May 12 17:43:29 2010 -0400 @@ -48,6 +48,13 @@ } class DatasetSelectionGrid( grids.Grid ): + class DbKeyColumn( grids.GridColumn ): + def filter( self, trans, user, query, dbkey ): + """ Filter by dbkey. """ + # use raw SQL b/c metadata is a BLOB + dbkey = dbkey.replace("'", "\\'") + return query.filter( "metadata like '%%\"dbkey\": [\"%s\"]%%' OR metadata like '%%\"dbkey\": \"%s\"%%'" % (dbkey, dbkey) ) + # Grid definition. available_tracks = None title = "Add Tracks" @@ -61,6 +68,7 @@ columns = [ grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), grids.GridColumn( "Filetype", key="extension" ), + DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) ] def build_initial_query( self, session ): diff -r b762ea8e5508 -r eb91e90d3405 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Wed May 12 15:57:05 2010 -0400 +++ b/static/scripts/packed/trackster.js Wed May 12 17:43:29 2010 -0400 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern! (right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.! max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;t his.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor! ,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.high-this.lo! w)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(t his.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0! );'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position:! relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.c hildren(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.vi! ew,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertica! l_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:nu ll,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.da! ta_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;! h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}els e{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":t! his.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.h! eight_px=100;this.container_div.addClass("feature-track");this.dataset _id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data! _queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u! =this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if (this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_s! lots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L! [3];if(ag<=ac&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ce il(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Ma! th.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<l! abel></label>").attr("for",e).text("Block color:"),l=$("<input></input >").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.! vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file +var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern! (right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.! max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;t his.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0;this.has_changes=false};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=t! his.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-t! his.low<30){return}if(a){this.center=a/b.width()*(this.high-this.low)+ this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var! f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug"! ).text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relati ve;'></div>"),l=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(Labe! lTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{! init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range =undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*! d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var! u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if (m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Disp! lay mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(! this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.c ontainer_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,! d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var! q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by_tile[a ][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("hei! ght",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.lengt! h;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=ac&&T>=D ){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=nul! l;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div />").addClass("for! m-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e) .text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="Rea! dTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file diff -r b762ea8e5508 -r eb91e90d3405 static/scripts/trackster.js --- a/static/scripts/trackster.js Wed May 12 15:57:05 2010 -0400 +++ b/static/scripts/trackster.js Wed May 12 17:43:29 2010 -0400 @@ -102,6 +102,7 @@ this.zoom_factor = 3; this.zoom_level = 0; this.track_id_counter = 0; + this.has_changes = false; }; $.extend( View.prototype, { add_track: function ( track ) { @@ -117,10 +118,12 @@ this.label_tracks.push( label_track ); }, remove_track: function( track ) { + this.has_changes = true; track.container_div.fadeOut('slow', function() { $(this).remove(); }); delete this.tracks[this.tracks.indexOf(track)]; }, update_options: function() { + this.has_changes = true; var sorted = $("ul#sortable-ul").sortable('toArray'); for (var id_i in sorted) { var id = sorted[id_i].split("_li")[0].split("track_")[1]; @@ -215,7 +218,7 @@ init_global: function () { this.header_div = $("<div class='track-header'>").text( this.name ); this.content_div = $("<div class='track-content'>"); - this.container_div = $("<div></div>").addClass('track').append( this.header_div ).append( this.content_div ); + this.container_div = $("<div />").addClass('track').append( this.header_div ).append( this.content_div ); this.parent_element.append( this.container_div ); }, init_each: function(params, success_fn) { @@ -392,8 +395,8 @@ $('#linetrack_' + track_id + '_minval').remove(); $('#linetrack_' + track_id + '_maxval').remove(); - var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); - var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); + var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); + var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); max_label.css({ position: "relative", top: "25px", left: "10px" }); max_label.prependTo(track.container_div); @@ -537,7 +540,7 @@ parent_element.append( canvas ); return canvas; }, gen_options: function(track_id) { - var container = $("<div></div>").addClass("form-row"); + var container = $("<div />").addClass("form-row"); var minval = 'track_' + track_id + '_minval', maxval = 'track_' + track_id + '_maxval', @@ -604,7 +607,8 @@ init: function() { var track = this, key = track.view.max_low + '_' + track.view.max_high; - this.init_each({ low: track.view.max_low, + + this.init_each({ low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom, resolution: this.view.resolution }, function (result) { track.data_cache.set(key, result); @@ -948,18 +952,18 @@ parent_element.append( new_canvas ); return new_canvas; }, gen_options: function(track_id) { - var container = $("<div></div>").addClass("form-row"); + var container = $("<div />").addClass("form-row"); var block_color = 'track_' + track_id + '_block_color', - block_color_label = $('<label></label>').attr("for", block_color).text("Block color:"), - block_color_input = $('<input></input>').attr("id", block_color).attr("name", block_color).val(this.prefs.block_color), + block_color_label = $('<label />').attr("for", block_color).text("Block color:"), + block_color_input = $('<input />').attr("id", block_color).attr("name", block_color).val(this.prefs.block_color), label_color = 'track_' + track_id + '_label_color', - label_color_label = $('<label></label>').attr("for", label_color).text("Text color:"), - label_color_input = $('<input></input>').attr("id", label_color).attr("name", label_color).val(this.prefs.label_color), + label_color_label = $('<label />').attr("for", label_color).text("Text color:"), + label_color_input = $('<input />').attr("id", label_color).attr("name", label_color).val(this.prefs.label_color), show_count = 'track_' + track_id + '_show_count', - show_count_label = $('<label></label>').attr("for", show_count).text("Show summary counts"), + show_count_label = $('<label />').attr("for", show_count).text("Show summary counts"), show_count_input = $('<input type="checkbox" style="float:left;"></input>').attr("id", show_count).attr("name", show_count).attr("checked", this.prefs.show_counts), - show_count_div = $('<div></div>').append(show_count_input).append(show_count_label); + show_count_div = $('<div />').append(show_count_input).append(show_count_label); return container.append(block_color_label).append(block_color_input).append(label_color_label).append(label_color_input).append(show_count_div); }, update_options: function(track_id) { diff -r b762ea8e5508 -r eb91e90d3405 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Wed May 12 15:57:05 2010 -0400 +++ b/templates/tracks/browser.mako Wed May 12 17:43:29 2010 -0400 @@ -110,7 +110,7 @@ error: function() { alert( "Couldn't create new browser" ) }, success: function(form_html) { show_modal("New Track Browser", form_html, { - "Cancel": function() { window.location = "/"; }, + "Cancel": function() { window.location = "${h.url_for( controller='visualization', action='list' )}"; }, "Continue": function() { $(document).trigger("convert_dbkeys"); continue_fn(); } }); $("#new-title").focus(); @@ -119,6 +119,12 @@ }); %endif + window.onbeforeunload = function() { + if ( view.has_changes ) { + return "There are unsaved changes to your visualization which will be lost."; + } + }; + // Execute this when everything is ready function init() { $("ul#sortable-ul").sortable({ @@ -192,7 +198,7 @@ $("#add-track").bind( "click", function(e) { $.ajax({ url: "${h.url_for( action='list_datasets' )}", - data: {}, + data: { "f-dbkey": view.dbkey }, error: function() { alert( "Grid refresh failed" ); }, success: function(table_html) { show_modal("Add Track — Select Dataset(s)", table_html, { @@ -219,6 +225,7 @@ break; } view.add_track(new_track); + view.has_changes = true; sidebar_box(new_track); } }); @@ -262,13 +269,15 @@ }, success: function(vis_id) { view.vis_id = vis_id; + view.has_changes = false; hide_modal(); - } + }, + error: function() { alert("Could not save visualization"); } }); }); - view.add_label_track( new LabelTrack( $("#top-labeltrack" ) ) ); - view.add_label_track( new LabelTrack( $("#nav-labeltrack" ) ) ); + view.add_label_track( new LabelTrack( $("#top-labeltrack") ) ); + view.add_label_track( new LabelTrack( $("#nav-labeltrack") ) ); $.ajax({ url: "${h.url_for( action='chroms' )}", @@ -328,7 +337,6 @@ del_icon.bind("click", function() { $("#track_" + track_id + "_li").fadeOut('slow', function() { $("#track_" + track_id + "_li").remove(); }); view.remove_track(track); - view.update_options(); }); icon_div.append(edit_icon).append(del_icon); title.append(label).prepend(icon_div);

1 0

[hg] galaxy 3777: Several Fixes for Uploading Composite datatype...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b762ea8e5508 changeset: 3777:b762ea8e5508 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed May 12 15:57:05 2010 -0400 description: Several Fixes for Uploading Composite datatypes. Revert changeset 3769:69e70e588a8e. diffstat: lib/galaxy/tools/actions/upload_common.py | 3 +-- lib/galaxy/tools/parameters/grouping.py | 23 +++++++++++++++-------- lib/galaxy/web/controllers/tool_runner.py | 2 +- tools/data_source/upload.py | 2 +- 4 files changed, 18 insertions(+), 12 deletions(-) diffs (101 lines): diff -r 997d55c65f49 -r b762ea8e5508 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Wed May 12 15:18:40 2010 -0400 +++ b/lib/galaxy/tools/actions/upload_common.py Wed May 12 15:57:05 2010 -0400 @@ -102,8 +102,7 @@ for data in precreated_datasets: log.info( 'Cleaned up unclaimed precreated dataset (%s).' % ( data.id ) ) data.state = data.states.ERROR - data.info = 'Unused precreated dataset to be deleted.' - data.deleted = True + data.info = 'No file contents were available.' def new_history_upload( trans, uploaded_dataset, state=None ): hda = trans.app.model.HistoryDatasetAssociation( name = uploaded_dataset.name, diff -r 997d55c65f49 -r b762ea8e5508 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Wed May 12 15:18:40 2010 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed May 12 15:57:05 2010 -0400 @@ -99,6 +99,17 @@ self.default_file_type = 'txt' self.file_type_to_ext = { 'auto':self.default_file_type } self.metadata_ref = 'files_metadata' + def get_composite_dataset_name( self, context ): + #FIXME: HACK + #Special case of using 'base_name' metadata for use as Dataset name needs to be done in a General Fashion, as defined within a particular Datatype. + + #We get two different types of contexts here, one straight from submitted parameters, the other after being parsed into tool inputs + dataset_name = context.get('files_metadata|base_name', None ) + if dataset_name is None: + dataset_name = context.get('files_metadata', {} ).get( 'base_name', None ) + if dataset_name is None: + dataset_name = 'Uploaded Composite Dataset (%s)' % self.get_file_type( context ) + return dataset_name def get_file_base_name( self, context ): fd = context.get('files_metadata|base_name','Galaxy_Composite_file') return fd @@ -241,6 +252,7 @@ for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ): if file_bunch.path: break + file_bunch.space_to_tab = space_to_tab return file_bunch, warnings def get_filenames( context ): rval = [] @@ -287,24 +299,18 @@ if meta_spec.set_in_upload: if meta_name in files_metadata: dataset.metadata[ meta_name ] = files_metadata[ meta_name ] - dataset_name = None - dataset_info = None + dataset.precreated_name = dataset.name = self.get_composite_dataset_name( context ) if dataset.datatype.composite_type == 'auto_primary_file': #replace sniff here with just creating an empty file 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 - 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 - dsn = dataset.metadata.get('base_name',file_bunch.precreated_name) - dataset.precreated_name = dsn - dataset.name = dsn - dataset.warnings.extend( file_bunch.warnings ) + dataset.warnings.extend( 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' ) keys = [ value.name for value in writable_files.values() ] @@ -315,6 +321,7 @@ dataset.composite_files[ key ] = None else: file_bunch, warnings = get_one_filename( group_incoming ) + dataset.warnings.extend( warnings ) if file_bunch.path: dataset.composite_files[ key ] = file_bunch.__dict__ else: diff -r 997d55c65f49 -r b762ea8e5508 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Wed May 12 15:18:40 2010 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Wed May 12 15:57:05 2010 -0400 @@ -203,7 +203,7 @@ d_type = dataset_upload_input.get_datatype( trans, kwd ) if d_type.composite_type is not None: - datasets.append( create_dataset( 'Uploaded Composite Dataset (%s)' % dataset_upload_input.get_datatype_ext( trans, kwd ) ) ) + datasets.append( create_dataset( dataset_upload_input.get_composite_dataset_name( kwd ) ) ) else: params = Bunch( ** tool_state.inputs[dataset_upload_input.name][0] ) if params.file_data not in [ None, "" ]: diff -r 997d55c65f49 -r b762ea8e5508 tools/data_source/upload.py --- a/tools/data_source/upload.py Wed May 12 15:18:40 2010 -0400 +++ b/tools/data_source/upload.py Wed May 12 15:57:05 2010 -0400 @@ -299,7 +299,7 @@ break elif dataset.composite_file_paths[value.name] is not None: if not value.is_binary: - if uploaded_dataset.composite_files[ value.name ].space_to_tab: + if value.space_to_tab: sniff.convert_newlines_sep2tabs( dataset.composite_file_paths[ value.name ][ 'path' ] ) else: sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] )

1 0

[hg] galaxy 3776: Remove the hack I just committed for changing ...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/997d55c65f49 changeset: 3776:997d55c65f49 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed May 12 15:18:40 2010 -0400 description: Remove the hack I just committed for changing modENCODE fly and worm dbkeys, and translate the values in the tool configs. diffstat: lib/galaxy/tools/__init__.py | 6 ------ tools/data_source/fly_modencode.xml | 5 +++++ tools/data_source/worm_modencode.xml | 5 +++++ 3 files changed, 10 insertions(+), 6 deletions(-) diffs (46 lines): diff -r 70747a610c28 -r 997d55c65f49 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed May 12 14:50:25 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Wed May 12 15:18:40 2010 -0400 @@ -1646,12 +1646,6 @@ data.name = param_dict.get( 'name', data.name ) data.info = param_dict.get( 'info', data.name ) data.dbkey = param_dict.get( 'dbkey', data.dbkey ) - # HACK to map modENCODEfly dbkey, which is always "fly" to be dm2 - # and modENCODEworm dbkey, which is always "worm" to be ce6 - if data.dbkey == 'fly': - data.dbkey = 'dm2' - elif data.dbkey == 'worm': - data.dbkey = 'ce6' data.extension = param_dict.get( 'data_type', data.extension ) #TODO: these should be possible as part of data_source.py and external set_meta, see the upload tool: if data.extension in [ 'txt', 'tabular' ]: diff -r 70747a610c28 -r 997d55c65f49 tools/data_source/fly_modencode.xml --- a/tools/data_source/fly_modencode.xml Wed May 12 14:50:25 2010 -0400 +++ b/tools/data_source/fly_modencode.xml Wed May 12 15:18:40 2010 -0400 @@ -7,6 +7,11 @@ <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" /> </inputs> <request_param_translation> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="dm2" > + <value_translation> + <value galaxy_value="dm2" remote_value="fly" /> + </value_translation> + </request_param> <request_param galaxy_name="URL" remote_name="URL" missing=""> <append_param separator="&" first_separator="?" join="="> <value name="d" missing="" /> diff -r 70747a610c28 -r 997d55c65f49 tools/data_source/worm_modencode.xml --- a/tools/data_source/worm_modencode.xml Wed May 12 14:50:25 2010 -0400 +++ b/tools/data_source/worm_modencode.xml Wed May 12 15:18:40 2010 -0400 @@ -7,6 +7,11 @@ <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" /> </inputs> <request_param_translation> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="ce6" > + <value_translation> + <value galaxy_value="ce6" remote_value="worm" /> + </value_translation> + </request_param> <request_param galaxy_name="URL" remote_name="URL" missing=""> <append_param separator="&" first_separator="?" join="="> <value name="d" missing="" />

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[hg] galaxy 3775: Force modENCODE worm dbkey to be ce6 and modEN...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/70747a610c28 changeset: 3775:70747a610c28 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed May 12 14:50:25 2010 -0400 description: Force modENCODE worm dbkey to be ce6 and modENCODE fly dbkey to be dm2. diffstat: lib/galaxy/tools/__init__.py | 6 ++++++ tools/data_source/fly_modencode.xml | 2 +- tools/data_source/worm_modencode.xml | 2 +- 3 files changed, 8 insertions(+), 2 deletions(-) diffs (40 lines): diff -r 58500dfab084 -r 70747a610c28 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed May 12 14:37:00 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Wed May 12 14:50:25 2010 -0400 @@ -1646,6 +1646,12 @@ data.name = param_dict.get( 'name', data.name ) data.info = param_dict.get( 'info', data.name ) data.dbkey = param_dict.get( 'dbkey', data.dbkey ) + # HACK to map modENCODEfly dbkey, which is always "fly" to be dm2 + # and modENCODEworm dbkey, which is always "worm" to be ce6 + if data.dbkey == 'fly': + data.dbkey = 'dm2' + elif data.dbkey == 'worm': + data.dbkey = 'ce6' data.extension = param_dict.get( 'data_type', data.extension ) #TODO: these should be possible as part of data_source.py and external set_meta, see the upload tool: if data.extension in [ 'txt', 'tabular' ]: diff -r 58500dfab084 -r 70747a610c28 tools/data_source/fly_modencode.xml --- a/tools/data_source/fly_modencode.xml Wed May 12 14:37:00 2010 -0400 +++ b/tools/data_source/fly_modencode.xml Wed May 12 14:50:25 2010 -0400 @@ -10,7 +10,7 @@ <request_param galaxy_name="URL" remote_name="URL" missing=""> <append_param separator="&" first_separator="?" join="="> <value name="d" missing="" /> - <value name="dbkey" missing="" /> + <value name="dbkey" missing="dm2" /> <value name="q" missing="" /> <value name="s" missing="" /> <value name="t" missing="" /> diff -r 58500dfab084 -r 70747a610c28 tools/data_source/worm_modencode.xml --- a/tools/data_source/worm_modencode.xml Wed May 12 14:37:00 2010 -0400 +++ b/tools/data_source/worm_modencode.xml Wed May 12 14:50:25 2010 -0400 @@ -10,7 +10,7 @@ <request_param galaxy_name="URL" remote_name="URL" missing=""> <append_param separator="&" first_separator="?" join="="> <value name="d" missing="" /> - <value name="dbkey" missing="" /> + <value name="dbkey" missing="ce6" /> <value name="q" missing="" /> <value name="s" missing="" /> <value name="t" missing="" />

1 0

[hg] galaxy 3774: Fixes for displaying appropriate datasets in G...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/58500dfab084 changeset: 3774:58500dfab084 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed May 12 14:37:00 2010 -0400 description: Fixes for displaying appropriate datasets in GBrowse wormbase, modENCODE worm, and modENCODE fly. diffstat: lib/galaxy/config.py | 2 +- lib/galaxy/datatypes/interval.py | 32 ++++++++++++++++++------ tool-data/shared/gbrowse/gbrowse_build_sites.txt | 11 ++++++- tool_conf.xml.sample | 2 + universe_wsgi.ini.sample | 2 +- 5 files changed, 37 insertions(+), 12 deletions(-) diffs (120 lines): diff -r f5f6b6e0a784 -r 58500dfab084 lib/galaxy/config.py --- a/lib/galaxy/config.py Wed May 12 11:43:57 2010 -0400 +++ b/lib/galaxy/config.py Wed May 12 14:37:00 2010 -0400 @@ -84,7 +84,7 @@ self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.bx_display_sites = kwargs.get( 'bx_display_sites', "main" ).lower().split(",") self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "main,test,tair" ).lower().split(",") + self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly" ).lower().split(",") self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' ) diff -r f5f6b6e0a784 -r 58500dfab084 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Wed May 12 11:43:57 2010 -0400 +++ b/lib/galaxy/datatypes/interval.py Wed May 12 14:37:00 2010 -0400 @@ -582,7 +582,7 @@ """Initialize datatype, by adding GBrowse display app""" Tabular.__init__(self, **kwd) self.add_display_app( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) - self.add_display_app( 'c_elegans', 'display in Wormbase', 'as_gbrowse_display_file', 'gbrowse_links' ) + self.add_display_app( 'gbrowse', 'display in Gbrowse', 'as_gbrowse_display_file', 'gbrowse_links' ) def set_meta( self, dataset, overwrite = True, **kwd ): i = 0 for i, line in enumerate( file ( dataset.file_name ) ): @@ -628,10 +628,24 @@ continue if line.startswith( '##sequence-region' ): # ##sequence-region IV 6000000 6030000 elems = line.split() - seqid = elems[1] # IV - start = elems[2] # 6000000 - stop = elems[3] # 6030000 - break + if len( elems ) > 3: + # line looks like: + # ##sequence-region ctg123 1 1497228 + seqid = elems[1] # IV + start = elems[2] # 6000000 + stop = elems[3] # 6030000 + break + elif len( elems ) == 2 and elems[1].find( '..' ) > 0: + # line looks like this: + # ##sequence-region X:120000..140000 + elems = elems[1].split( ':' ) + seqid = elems[0] + start = elems[1].split( '..' )[0] + stop = elems[1].split( '..' )[1] + break + else: + log.exception( "line (%s) uses an unsupported ##sequence-region definition." % str( line ) ) + break # Allow UCSC style browser and track info in the GFF file if line.startswith("browser position"): pos_info = line.split()[-1] @@ -652,7 +666,8 @@ break if i > 10: break - except: + except Exception, e: + log.exception( str( e ) ) seqid, start, stop = ( '', '', '' ) return ( seqid, str( start ), str( stop ) ) else: @@ -681,8 +696,9 @@ if seqid and start and stop: for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ): if site_name in app.config.gbrowse_display_sites: - redirect_url = urllib.quote_plus( "%s%s/?ref=%s&start=%s&stop=%s&eurl=%%s" % - ( site_url, dataset.dbkey, seqid, start, stop ) ) + # Old method, the one uncommented below now seems to be the way GBrowse wants the request + # redirect_url = urllib.quote_plus( "%s%s/?ref=%s&start=%s&stop=%s&eurl=%%s" % ( site_url, dataset.dbkey, seqid, start, stop ) ) + redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s" % ( site_url, seqid, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) ret_val.append( ( site_name, link ) ) return ret_val diff -r f5f6b6e0a784 -r 58500dfab084 tool-data/shared/gbrowse/gbrowse_build_sites.txt --- a/tool-data/shared/gbrowse/gbrowse_build_sites.txt Wed May 12 11:43:57 2010 -0400 +++ b/tool-data/shared/gbrowse/gbrowse_build_sites.txt Wed May 12 14:37:00 2010 -0400 @@ -1,4 +1,11 @@ # wormbase sites / supported genomes -main http://www.wormbase.org/db/seq/gbgff/c_elegans/ c_elegans,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi -test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ c_elegans,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi +wormbase http://www.wormbase.org/db/gb2/gbrowse/c_elegans ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb3,cb2,cb1,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap2,caeJap1 +#test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb3,cb2,cb1,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap2,caeJap1 + +# UCSC mirror that includes arabidopsis tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis + +# modENCODE worm and fly +modencode_worm http://modencode.oicr.on.ca/fgb2/gbrowse/worm ce6 +modencode_fly http://modencode.oicr.on.ca/fgb2/gbrowse/fly dm2 + diff -r f5f6b6e0a784 -r 58500dfab084 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed May 12 11:43:57 2010 -0400 +++ b/tool_conf.xml.sample Wed May 12 14:37:00 2010 -0400 @@ -10,10 +10,12 @@ <tool file="data_source/biomart.xml" /> <tool file="data_source/biomart_test.xml" /> <tool file="data_source/gramene_mart.xml" /> + <tool file="data_source/fly_modencode.xml" /> <tool file="data_source/flymine.xml" /> <tool file="data_source/flymine_test.xml" /> <tool file="data_source/modmine.xml" /> <tool file="data_source/ratmine.xml" /> + <tool file="data_source/worm_modencode.xml" /> <tool file="data_source/wormbase.xml" /> <tool file="data_source/wormbase_test.xml" /> <tool file="data_source/eupathdb.xml" /> diff -r f5f6b6e0a784 -r 58500dfab084 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Wed May 12 11:43:57 2010 -0400 +++ b/universe_wsgi.ini.sample Wed May 12 14:37:00 2010 -0400 @@ -108,7 +108,7 @@ # Comma separated list of bx / UCSC / gbrowse / GeneTrack browsers to use for viewing bx_display_sites = main ucsc_display_sites = main,test,archaea,ucla -gbrowse_display_sites = main,test,tair +gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly # Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt #genetrack_display_sites =

1 0

[hg] galaxy 3773: Fix buildbot's builds.txt
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f5f6b6e0a784 changeset: 3773:f5f6b6e0a784 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed May 12 11:43:57 2010 -0400 description: Fix buildbot's builds.txt diffstat: buildbot_setup.sh | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r ef70e978e3fe -r f5f6b6e0a784 buildbot_setup.sh --- a/buildbot_setup.sh Wed May 12 09:51:31 2010 -0400 +++ b/buildbot_setup.sh Wed May 12 11:43:57 2010 -0400 @@ -55,6 +55,7 @@ SAMPLES=" datatypes_conf.xml.sample universe_wsgi.ini.sample +tool-data/shared/ucsc/builds.txt.sample " DIRS="

1 0

[hg] galaxy 3772: Enable viewing of datasets via history/view wh...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ef70e978e3fe changeset: 3772:ef70e978e3fe user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed May 12 09:51:31 2010 -0400 description: Enable viewing of datasets via history/view when user is not logged in and/or when user does not have public username. diffstat: templates/root/history_common.mako | 12 ++++++++++-- 1 files changed, 10 insertions(+), 2 deletions(-) diffs (22 lines): diff -r dea0ad16553e -r ef70e978e3fe templates/root/history_common.mako --- a/templates/root/history_common.mako Wed May 12 09:18:05 2010 -0400 +++ b/templates/root/history_common.mako Wed May 12 09:51:31 2010 -0400 @@ -38,8 +38,16 @@ if for_editing: display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) else: - display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', - username=data.history.user.username, slug=dataset_id ) + # Get URL for display only. + if data.history.user and data.history.user.username: + display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', + username=data.history.user.username, slug=dataset_id ) + else: + # HACK: revert to for_editing display URL when there is no user/username. This should only happen when + # there's no user/username because dataset is being displayed by history/view after error reported. + # There are no security concerns here because both dataset/display and dataset/display_by_username_and_slug + # check user permissions (to the same degree) before displaying. + display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) %> <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}" %if for_editing:

1 0

[hg] galaxy 3771: Fixes for uploading a tool to the community sp...
by Nate Coraor 20 May '10

20 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/dea0ad16553e changeset: 3771:dea0ad16553e user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed May 12 09:18:05 2010 -0400 description: Fixes for uploading a tool to the community space, and keep None from being displayed if there is no user_description. diffstat: lib/galaxy/webapps/community/controllers/common.py | 12 +- lib/galaxy/webapps/community/controllers/upload.py | 199 ++++++++++---------- lib/galaxy/webapps/community/datatypes/__init__.py | 10 +- templates/webapps/community/tool/edit_tool.mako | 6 +- templates/webapps/community/tool/view_tool.mako | 10 +- 5 files changed, 131 insertions(+), 106 deletions(-) diffs (321 lines): diff -r 7232b61da6d3 -r dea0ad16553e lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Tue May 11 18:02:39 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Wed May 12 09:18:05 2010 -0400 @@ -28,8 +28,11 @@ else: # There must not be any categories associated with the tool trans.app.security_agent.set_entity_category_associations( tools=[ tool ], categories=[] ) - if params.get( 'description', False ): - tool.user_description = util.restore_text( params.get( 'description', '' ) ) + user_description = util.restore_text( params.get( 'user_description', '' ) ) + if user_description: + tool.user_description = user_description + else: + tool.user_description = '' trans.sa_session.add( tool ) trans.sa_session.flush() message="Tool '%s' description and category associations have been saved" % tool.name @@ -236,7 +239,10 @@ def get_tool( trans, id ): return trans.sa_session.query( trans.model.Tool ).get( trans.app.security.decode_id( id ) ) def get_tools( trans ): - return trans.sa_session.query( trans.model.Tool ).order_by( trans.model.Tool.name ) + # Return only the latest version of each tool + return trans.sa_session.query( trans.model.Tool ) \ + .filter( trans.model.Tool.newer_version_id == None ) \ + .order_by( trans.model.Tool.name ) def get_approved_tools( trans, category=None ): # TODO: write this as a query using eagerload - will be much faster. ids = [] diff -r 7232b61da6d3 -r dea0ad16553e lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Tue May 11 18:02:39 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Wed May 12 09:18:05 2010 -0400 @@ -26,112 +26,119 @@ replace_version = None uploaded_file = None categories = get_categories( trans ) - if not get_categories( trans ): + if not categories: return trans.response.send_redirect( web.url_for( controller='tool', action='browse_tools', cntrller='tool', message='No categories have been configured in this instance of the Galaxy Community. An administrator needs to create some via the Administrator control panel before anything can be uploaded', status='error' ) ) - elif params.file_data == '' and params.url.strip() == '': - message = 'No files were entered on the upload form.' - status = 'error' - elif params.file_data == '': - try: - uploaded_file = urllib2.urlopen( params.url.strip() ) - except ( ValueError, urllib2.HTTPError ), e: - message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e + if params.get( 'upload_button', False ): + + url_paste = params.get( 'url', '' ).strip() + file_data = params.get( 'file_data', '' ) + if file_data == '' and url_paste == '': + message = 'No files were entered on the upload form.' status = 'error' - except urllib2.URLError, e: - message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e.reason - status = 'error' - elif params.file_data not in ( '', None ): - uploaded_file = params.file_data.file - if params.upload_button and uploaded_file: - datatype = trans.app.datatypes_registry.get_datatype_by_extension( params.upload_type ) - if datatype is None: - message = 'An unknown file type was selected. This should not be possible, please report the error.' - status = 'error' - else: + elif file_data == '': try: - # Initialize the tool object - meta = datatype.verify( uploaded_file ) - meta.user = trans.user - meta.guid = trans.app.security.get_new_guid() - obj = datatype.create_model_object( meta ) - trans.sa_session.add( obj ) - if isinstance( obj, trans.app.model.Tool ): - existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).first() - if existing and replace_id is None: - raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) - elif existing: - replace_version = trans.sa_session.query( trans.app.model.Tool ).get( trans.security.decode_id( replace_id ) ) - if replace_version.newer_version: - # If the user has picked an old version, switch to the newest version - replace_version = get_versions( trans, replace_version )[0] - if replace_version.tool_id != meta.id: - raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Check the tool XML file' % ( meta.id, replace_version.tool_id ) ) - for old_version in get_versions( trans, replace_version ): - if old_version.version == meta.version: - raise UploadError( 'The new version (%s) matches an old version. Check your version in the tool XML file' % meta.version ) - if old_version.is_new(): - raise UploadError( 'There is an existing version of this tool which has not yet been submitted for approval, so either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', - action='view_tool', - cntrller='tool', - id=trans.security.encode_id( old_version.id ) ) ) - if old_version.is_waiting(): - raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' ) - # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed - if category_ids: - for category_id in category_ids: - category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) - # Initialize the tool category - tca = trans.app.model.ToolCategoryAssociation( obj, category ) - trans.sa_session.add( tca ) - # Initialize the tool event - event = trans.app.model.Event( state=trans.app.model.Tool.states.NEW ) - # Flush to get an event id - trans.sa_session.add( event ) + uploaded_file = urllib2.urlopen( url_paste ) + except ( ValueError, urllib2.HTTPError ), e: + message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e + status = 'error' + except urllib2.URLError, e: + message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e.reason + status = 'error' + elif file_data not in ( '', None ): + uploaded_file = file_data.file + if uploaded_file: + # TODO: tool should no longer be the default when we upload histories and workflows + upload_type = params.get( 'upload_type', 'tool' ) + datatype = trans.app.datatypes_registry.get_datatype_by_extension( upload_type ) + if datatype is None: + message = 'An unknown file type was selected. This should not be possible, please report the error.' + status = 'error' + else: + try: + # Initialize the tool object + meta = datatype.verify( uploaded_file ) + meta.user = trans.user + meta.guid = trans.app.security.get_new_guid() + obj = datatype.create_model_object( meta ) + trans.sa_session.add( obj ) + if isinstance( obj, trans.app.model.Tool ): + existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).first() + if existing and replace_id is None: + raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) + elif existing: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( trans.security.decode_id( replace_id ) ) + if replace_version.newer_version: + # If the user has picked an old version, switch to the newest version + replace_version = get_versions( trans, replace_version )[0] + if replace_version.tool_id != meta.id: + raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Check the tool XML file' % ( meta.id, replace_version.tool_id ) ) + for old_version in get_versions( trans, replace_version ): + if old_version.version == meta.version: + raise UploadError( 'The new version (%s) matches an old version. Check your version in the tool XML file' % meta.version ) + if old_version.is_new(): + raise UploadError( 'There is an existing version of this tool which has not yet been submitted for approval, so either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.security.encode_id( old_version.id ) ) ) + if old_version.is_waiting(): + raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' ) + # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed + if category_ids: + for category_id in category_ids: + category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) + # Initialize the tool category + tca = trans.app.model.ToolCategoryAssociation( obj, category ) + trans.sa_session.add( tca ) + # Initialize the tool event + event = trans.app.model.Event( state=trans.app.model.Tool.states.NEW ) + # Flush to get an event id + trans.sa_session.add( event ) + trans.sa_session.flush() + tea = trans.app.model.ToolEventAssociation( obj, event ) + trans.sa_session.add( tea ) + if replace_version and replace_id: + replace_version.newer_version_id = obj.id + trans.sa_session.add( replace_version ) trans.sa_session.flush() - tea = trans.app.model.ToolEventAssociation( obj, event ) - trans.sa_session.add( tea ) - if replace_version and replace_id: - replace_version.newer_version_id = obj.id - trans.sa_session.add( replace_version ) - trans.sa_session.flush() - try: - os.link( uploaded_file.name, obj.file_name ) - except OSError: - shutil.copy( uploaded_file.name, obj.file_name ) - # We're setting cntrller to 'tool' since that is the only controller from which we can upload + try: + os.link( uploaded_file.name, obj.file_name ) + except OSError: + shutil.copy( uploaded_file.name, obj.file_name ) + # We're setting cntrller to 'tool' since that is the only controller from which we can upload + # TODO: this will need tweaking when we can upload histories or workflows + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='tool', + id=trans.app.security.encode_id( obj.id ), + message='Uploaded %s' % meta.message, + status='done' ) ) + except ( datatypes.DatatypeVerificationError, UploadError ), e: + message = str( e ) + status = 'error' + uploaded_file.close() + elif replace_id is not None: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + old_version = None + for old_version in get_versions( trans, replace_version ): + if old_version.is_new(): + message = 'There is an existing version of this tool which has not been submitted for approval, so either submit or delete it before uploading a new version.' + break + if old_version.is_waiting(): + message = 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' + break + else: + old_version = None + if old_version is not None: return trans.response.send_redirect( web.url_for( controller='common', - action='edit_tool', + action='view_tool', cntrller='tool', - id=trans.app.security.encode_id( obj.id ), - message='Uploaded %s' % meta.message, - status='done' ) ) - except ( datatypes.DatatypeVerificationError, UploadError ), e: - message = str( e ) - status = 'error' - uploaded_file.close() - elif replace_id is not None: - replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) - old_version = None - for old_version in get_versions( trans, replace_version ): - if old_version.is_new(): - message = 'There is an existing version of this tool which has not been submitted for approval, so either submit or delete it before uploading a new version.' - break - if old_version.is_waiting(): - message = 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' - break - else: - old_version = None - if old_version is not None: - return trans.response.send_redirect( web.url_for( controller='common', - action='view_tool', - cntrller='tool', - id=trans.app.security.encode_id( old_version.id ), - message=message, - status='error' ) ) + id=trans.app.security.encode_id( old_version.id ), + message=message, + status='error' ) ) selected_upload_type = params.get( 'type', 'tool' ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/upload/upload.mako', diff -r 7232b61da6d3 -r dea0ad16553e lib/galaxy/webapps/community/datatypes/__init__.py --- a/lib/galaxy/webapps/community/datatypes/__init__.py Tue May 11 18:02:39 2010 -0400 +++ b/lib/galaxy/webapps/community/datatypes/__init__.py Wed May 12 09:18:05 2010 -0400 @@ -120,11 +120,13 @@ rval.version = root.attrib['version'] except KeyError, e: raise DatatypeVerificationError( 'Tool XML file does not conform to the specification. Missing required <tool> tag attribute: %s' % e ) - rval.description = None + rval.description = '' desc_tag = root.find( 'description' ) - if desc_tag is not None: - rval.description = desc_tag.text.strip() - rval.message = 'Tool: %s %s, Version: %s, ID: %s' % ( rval.name, rval.description or '', rval.version, rval.id ) + if desc_tag: + description = desc_tag.text + if description: + rval.description = description.strip() + rval.message = 'Tool: %s %s, Version: %s, ID: %s' % ( str( rval.name ), str( rval.description ), str( rval.version ), str( rval.id ) ) return rval else: raise DatatypeVerificationError( 'Unable to find a properly formatted tool XML file' ) diff -r 7232b61da6d3 -r dea0ad16553e templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Tue May 11 18:02:39 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Wed May 12 09:18:05 2010 -0400 @@ -82,7 +82,11 @@ </div> <div class="form-row"> <label>Description:</label> - <div class="form-row-input"><textarea name="description" rows="5" cols="35">${tool.user_description}</textarea></div> + %if tool.user_description: + <div class="form-row-input"><textarea name="user_description" rows="5" cols="35">${tool.user_description}</textarea></div> + %else: + <div class="form-row-input"><textarea name="user_description" rows="5" cols="35"></textarea></div> + %endif <div style="clear: both"></div> </div> <div class="form-row"> diff -r 7232b61da6d3 -r dea0ad16553e templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Tue May 11 18:02:39 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Wed May 12 09:18:05 2010 -0400 @@ -4,8 +4,12 @@ from galaxy.web.framework.helpers import time_ago from urllib import quote_plus + menu_label = 'Edit information' + if cntrller in [ 'tool' ]: can_edit = trans.app.security_agent.can_edit_item( trans.user, tool ) + if can_edit: + menu_label = 'Edit information or submit for approval' can_upload_new_version = trans.app.security_agent.can_upload_new_version( trans.user, tool, versions ) visible_versions = [] @@ -89,7 +93,7 @@ <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="tool-${tool.id}-popup"> %if cntrller=='admin' or can_edit: - <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">${menu_label}</a> %endif <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> %if cntrller=='admin' or trans.user==tool.user: @@ -114,7 +118,9 @@ </div> <div class="form-row"> <label>Description:</label> - ${tool.user_description} + %if tool.user_description: + ${tool.user_description} + %endif <div style="clear: both"></div> </div> <div class="form-row">

1 0

[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

1 0

[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,

1 0

[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"/>

1 0

[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 )

1 0

[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 ):

1 0

[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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