June 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: kanwei: Copy datasets:
by Bitbucket 10 Jun '11

10 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/93e4915c0508/ changeset: 93e4915c0508 user: kanwei date: 2011-06-10 18:36:16 summary: Copy datasets: - Now copy datasets in the order they were listed in source history. Fixes #483 - Properly refresh current history if data is copied into it - Add link to switch to new history if one is created affected #: 3 files (1.1 KB) --- a/lib/galaxy/web/controllers/dataset.py Fri Jun 10 08:46:11 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Jun 10 12:36:16 2011 -0400 @@ -789,10 +789,11 @@ else: target_history_ids = [] done_msg = error_msg = "" + new_history = None if do_copy: invalid_datasets = 0 if not source_dataset_ids or not ( target_history_ids or new_history_name ): - error_msg = "You must provide both source datasets and target histories." + error_msg = "You must provide both source datasets and target histories. " else: if new_history_name: new_history = trans.app.model.History() @@ -807,23 +808,28 @@ target_histories = [ history ] if len( target_histories ) != len( target_history_ids ): error_msg = error_msg + "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) ) - for data in map( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get, source_dataset_ids ): - if data is None: - error_msg = error_msg + "You tried to copy a dataset that does not exist. " + source_hdas = map( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get, source_dataset_ids ) + source_hdas.sort(key=lambda hda: hda.hid) + for hda in source_hdas: + if hda is None: + error_msg = error_msg + "You tried to copy a dataset that does not exist. " invalid_datasets += 1 - elif data.history != history: - error_msg = error_msg + "You tried to copy a dataset which is not in your current history. " + elif hda.history != history: + error_msg = error_msg + "You tried to copy a dataset which is not in your current history. " invalid_datasets += 1 else: for hist in target_histories: - hist.add_dataset( data.copy( copy_children = True ) ) + hist.add_dataset( hda.copy( copy_children = True ) ) if history in target_histories: refresh_frames = ['history'] trans.sa_session.flush() hist_names_str = ", ".join( [ hist.name for hist in target_histories ] ) num_source = len( source_dataset_ids ) - invalid_datasets num_target = len(target_histories) - done_msg = "%i %s copied to %i %s: %s" % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str ) + done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str ) + if new_history is not None: + done_msg += " <a href=\"%s\" target=\"_top\">Switch to the new history.</a>" % url_for( + controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) ) trans.sa_session.refresh( history ) source_datasets = history.visible_datasets target_histories = [history] --- a/lib/galaxy/web/controllers/history.py Fri Jun 10 08:46:11 2011 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri Jun 10 12:36:16 2011 -0400 @@ -1182,3 +1182,13 @@ else: msg = '%d cloned histories are now included in your previously stored histories.' % len( histories ) return trans.show_ok_message( msg ) + + @web.expose + @web.require_login( "switch to a history" ) + def switch_to_history( self, trans, hist_id=None ): + decoded_id = trans.security.decode_id(hist_id) + hist = trans.sa_session.query( trans.app.model.History ).get( decoded_id ) + + trans.set_history( hist ) + return trans.response.send_redirect( url_for( "/" ) ) + \ No newline at end of file --- a/templates/dataset/copy_view.mako Fri Jun 10 08:46:11 2011 -0400 +++ b/templates/dataset/copy_view.mako Fri Jun 10 12:36:16 2011 -0400 @@ -1,21 +1,29 @@ <%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="javascripts" /><%def name="title()">Copy History Items</%def><%def name="javascripts()"> -${parent.javascripts()} -${h.js( "jquery", "galaxy.base" )} -<script type="text/javascript"> - $(function() { - $("#select-multiple").click(function() { - $("#single-dest-select").val(""); - $("#single-destination").hide(); - $("#multiple-destination").show(); + ${parent.javascripts()} + ${h.js( "jquery", "galaxy.base" )} + + <script type="text/javascript"> + $(function() { + $("#select-multiple").click(function() { + $("#single-dest-select").val(""); + $("#single-destination").hide(); + $("#multiple-destination").show(); + }); }); - }); -</script> - + %if 'history' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + if ( parent.force_right_panel ) { + parent.force_right_panel( 'show' ); + } + } + %endif + </script> + </%def> %if error_msg: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Write a newline between intervals in BedDataProvider.write_data_to_file.
by Bitbucket 10 Jun '11

10 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1edea6b133ce/ changeset: 1edea6b133ce user: dan date: 2011-06-10 14:46:11 summary: Write a newline between intervals in BedDataProvider.write_data_to_file. affected #: 1 file (9 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Jun 09 18:35:42 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Fri Jun 10 08:46:11 2011 -0400 @@ -604,7 +604,7 @@ iterator = self.get_iterator( chrom, start, end ) out = open( filename, "w" ) for line in iterator: - out.write( line ) + out.write( "%s\n" % line ) out.close() class VcfDataProvider( TabixDataProvider ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Better handling of implict datatype conversion and dynamic options. Still lots of cleanup to do.
by Bitbucket 09 Jun '11

09 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0886ed0a8c9f/ changeset: 0886ed0a8c9f user: dan date: 2011-06-10 00:35:42 summary: Better handling of implict datatype conversion and dynamic options. Still lots of cleanup to do. affected #: 4 files (815 bytes) --- a/lib/galaxy/tools/__init__.py Thu Jun 09 17:49:20 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Jun 09 18:35:42 2011 -0400 @@ -798,6 +798,8 @@ elif elem.tag == "param": param = self.parse_param_elem( elem, enctypes, context ) rval[param.name] = param + if hasattr( param, 'data_ref' ): + param.ref_input = context[ param.data_ref ] return rval def parse_param_elem( self, input_elem, enctypes, context ): @@ -923,8 +925,6 @@ if not self.check_values: return for input in self.inputs.itervalues(): - if input.name not in value: - value[input.name] = input.get_initial_value( None, value ) if isinstance( input, ToolParameter ): callback( "", input, value[input.name] ) else: --- a/lib/galaxy/tools/actions/__init__.py Thu Jun 09 17:49:20 2011 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Thu Jun 09 18:35:42 2011 -0400 @@ -37,7 +37,7 @@ if data and not isinstance( data.datatype, formats ): # Need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion trans.sa_session.refresh( data ) - target_ext, converted_dataset = data.find_conversion_destination( formats, converter_safe = input.converter_safe( param_values, trans ) ) + target_ext, converted_dataset = data.find_conversion_destination( formats ) if target_ext: if converted_dataset: data = converted_dataset --- a/lib/galaxy/tools/parameters/basic.py Thu Jun 09 17:49:20 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Thu Jun 09 18:35:42 2011 -0400 @@ -714,6 +714,9 @@ # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ): return True + #dataset not ready yet + if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): + return True # Dynamic, but all dependenceis are known and have values return False def get_initial_value( self, trans, context ): @@ -844,6 +847,7 @@ self.force_select = string_as_bool( elem.get( "force_select", True )) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) + self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True def from_html( self, value, trans=None, context={} ): @@ -939,7 +943,7 @@ if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending: + if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): return True # No late validation return False @@ -1321,7 +1325,7 @@ selected = ( value and ( hda in value ) ) field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) else: - target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + target_ext, converted_dataset = hda.find_conversion_destination( self.formats ) if target_ext: if converted_dataset: hda = converted_dataset @@ -1370,13 +1374,22 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) ) + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats ) if target_ext is not None: return True return False for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): - if self.options and self._options_filter_attribute( data ) != filter_value: + if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: + is_valid = False + if isinstance( data.datatype, self.formats ): + is_valid = True + else: + target_ext, converted_dataset = data.find_conversion_destination( self.formats ) + if target_ext: + is_valid = True + if converted_dataset: + data = converted_dataset + if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ): continue most_recent_dataset[0] = data # Also collect children via association object --- a/lib/galaxy/tools/parameters/dynamic_options.py Thu Jun 09 17:49:20 2011 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Thu Jun 09 18:35:42 2011 -0400 @@ -440,6 +440,9 @@ # Load Validators for validator in elem.findall( 'validator' ): self.validators.append( validation.Validator.from_element( self.tool_param, validator ) ) + + if self.dataset_ref_name: + tool_param.data_ref = self.dataset_ref_name def parse_column_definitions( self, elem ): for column_elem in elem.findall( 'column' ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: VCF can take floats
by Bitbucket 09 Jun '11

09 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3f2e99f97694/ changeset: 3f2e99f97694 user: kanwei date: 2011-06-09 23:49:20 summary: VCF can take floats affected #: 2 files (98 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Jun 09 15:58:25 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Thu Jun 09 17:49:20 2011 -0400 @@ -637,7 +637,7 @@ # alternative base(s) feature[4], # phred quality score - int( feature[5] )] + float( feature[5] )] rval.append(payload) return { 'data_type' : 'vcf', 'data': rval, 'message': message } --- a/lib/galaxy_utils/sequence/vcf.py Thu Jun 09 15:58:25 2011 -0400 +++ b/lib/galaxy_utils/sequence/vcf.py Thu Jun 09 17:49:20 2011 -0400 @@ -1,6 +1,5 @@ #Dan Blankenberg -#See: http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3 -#See: http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:variant_call_… +# See http://www.1000genomes.org/wiki/Analysis/variant-call-format NOT_A_NUMBER = float( 'NaN' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Some fixes for trackster/visual analytics.
by Bitbucket 09 Jun '11

09 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/90c81fa6114f/ changeset: 90c81fa6114f user: dan date: 2011-06-09 21:58:25 summary: Some fixes for trackster/visual analytics. affected #: 1 file (157 bytes) --- a/lib/galaxy/web/controllers/tracks.py Thu Jun 09 12:06:07 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Thu Jun 09 15:58:25 2011 -0400 @@ -412,6 +412,7 @@ return msg # Return data. + data = None if isinstance( dataset.datatype, Gff ): data = GFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' @@ -768,7 +769,9 @@ # for jida in original_job.input_datasets: input_dataset = jida.dataset - if run_on_region and hasattr( input_dataset.datatype, 'get_track_type' ): + if input_dataset is None: #optional dataset and dataset wasn't selected + tool_params[ jida.name ] = None + elif run_on_region and hasattr( input_dataset.datatype, 'get_track_type' ): # Dataset is indexed and hence a subset can be extracted and used # as input. track_type, data_sources = input_dataset.datatype.get_track_type() @@ -802,7 +805,7 @@ trans.sa_session.flush() # Add dataset to tool's parameters. - tool_params[ jida.name ] = new_dataset + tool_params[ jida.name ] = new_dataset.id # # Execute tool and handle outputs. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Make Cuffcompare wrapper compatible with v1.0.3
by Bitbucket 09 Jun '11

09 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389/ changeset: f4b98c453389 user: jgoecks date: 2011-06-09 18:06:07 summary: Make Cuffcompare wrapper compatible with v1.0.3 affected #: 6 files (890 bytes) --- a/test-data/cuffcompare_out1.tmap Thu Jun 09 11:38:37 2011 -0400 +++ b/test-data/cuffcompare_out1.tmap Thu Jun 09 12:06:07 2011 -0400 @@ -1,51 +1,51 @@ ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 - -- - u CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 - -- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - -- - u CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 - -- - u CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 - -- - u CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 - -- - u CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 - -- - u CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 - -- - u CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 - -- - u CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 - -- - u CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 - -- - u CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 - -- - u CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 - -- - u CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 - -- - u CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 - -- - u CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 - -- - u CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 - -- - u CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 - -- - u CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 - -- - u CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 - -- - u CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 - -- - u CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 - -- - u CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 - +- - u CUFF.1 CUFF.1.1 100 0.000000 0.000000 0.000000 0.000000 41 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 0.000000 0.000000 0.000000 0.000000 31 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 0.000000 0.000000 0.000000 0.000000 169 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 0.000000 0.000000 0.000000 0.000000 404 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 100 0.000000 0.000000 0.000000 0.000000 97 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 100 0.000000 0.000000 0.000000 0.000000 72 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 100 0.000000 0.000000 0.000000 0.000000 61 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 100 0.000000 0.000000 0.000000 0.000000 54 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 100 0.000000 0.000000 0.000000 0.000000 290 CUFF.25.1 - +- - u CUFF.27 CUFF.27.1 100 0.000000 0.000000 0.000000 0.000000 37 CUFF.27.1 - +- - u CUFF.29 CUFF.29.1 100 0.000000 0.000000 0.000000 0.000000 142 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 0.000000 0.000000 0.000000 0.000000 31 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 100 0.000000 0.000000 0.000000 0.000000 131 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 100 0.000000 0.000000 0.000000 0.000000 69 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 100 0.000000 0.000000 0.000000 0.000000 53 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 100 0.000000 0.000000 0.000000 0.000000 80 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 100 0.000000 0.000000 0.000000 0.000000 102 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 100 0.000000 0.000000 0.000000 0.000000 41 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.59.1 - +- - u CUFF.61 CUFF.61.1 100 0.000000 0.000000 0.000000 0.000000 28 CUFF.61.1 - +- - u CUFF.63 CUFF.63.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.63.1 - +- - u CUFF.65 CUFF.65.1 100 0.000000 0.000000 0.000000 0.000000 55 CUFF.65.1 - +- - u CUFF.67 CUFF.67.1 100 0.000000 0.000000 0.000000 0.000000 65 CUFF.67.1 - +- - u CUFF.69 CUFF.69.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.69.1 - +- - u CUFF.71 CUFF.71.1 100 0.000000 0.000000 0.000000 0.000000 98 CUFF.71.1 - +- - u CUFF.73 CUFF.73.1 100 0.000000 0.000000 0.000000 0.000000 55 CUFF.73.1 - +- - u CUFF.75 CUFF.75.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.75.1 - +- - u CUFF.77 CUFF.77.1 100 0.000000 0.000000 0.000000 0.000000 52 CUFF.77.1 - +- - u CUFF.79 CUFF.79.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.79.1 - +- - u CUFF.81 CUFF.81.1 100 0.000000 0.000000 0.000000 0.000000 64 CUFF.81.1 - +- - u CUFF.83 CUFF.83.1 100 0.000000 0.000000 0.000000 0.000000 96 CUFF.83.1 - +- - u CUFF.85 CUFF.85.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.85.1 - +- - u CUFF.87 CUFF.87.1 100 0.000000 0.000000 0.000000 0.000000 49 CUFF.87.1 - +- - u CUFF.89 CUFF.89.1 100 0.000000 0.000000 0.000000 0.000000 51 CUFF.89.1 - +- - u CUFF.91 CUFF.91.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.91.1 - +- - u CUFF.93 CUFF.93.1 100 0.000000 0.000000 0.000000 0.000000 39 CUFF.93.1 - +- - u CUFF.95 CUFF.95.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.95.1 - +- - u CUFF.97 CUFF.97.1 100 0.000000 0.000000 0.000000 0.000000 59 CUFF.97.1 - +- - u CUFF.99 CUFF.99.1 100 0.000000 0.000000 0.000000 0.000000 58 CUFF.99.1 - --- a/test-data/cuffcompare_out3.tmap Thu Jun 09 11:38:37 2011 -0400 +++ b/test-data/cuffcompare_out3.tmap Thu Jun 09 12:06:07 2011 -0400 @@ -1,51 +1,51 @@ ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - -- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - -- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 - -- - u CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 - -- - u CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 - -- - u CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 - -- - u CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 - -- - u CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 - -- - u CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 - -- - u CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 - -- - u CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 - -- - u CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 - -- - u CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 - -- - u CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 - -- - u CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 - -- - u CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 - -- - u CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 - -- - u CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 - -- - u CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 - -- - u CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 - -- - u CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 - -- - u CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 - -- - u CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 - +- - u CUFF.1 CUFF.1.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 0.000000 0.000000 0.000000 0.000000 576 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 0.000000 0.000000 0.000000 0.000000 565 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 0.000000 0.000000 0.000000 0.000000 979 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 100 0.000000 0.000000 0.000000 0.000000 86 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 100 0.000000 0.000000 0.000000 0.000000 88 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.25.1 - +- - u CUFF.26 CUFF.26.1 100 0.000000 0.000000 0.000000 0.000000 32 CUFF.26.1 - +- - u CUFF.29 CUFF.29.1 100 0.000000 0.000000 0.000000 0.000000 70 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 100 0.000000 0.000000 0.000000 0.000000 40 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 100 0.000000 0.000000 0.000000 0.000000 124 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 100 0.000000 0.000000 0.000000 0.000000 33 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 100 0.000000 0.000000 0.000000 0.000000 81 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 100 0.000000 0.000000 0.000000 0.000000 46 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 100 0.000000 0.000000 0.000000 0.000000 477 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.59.1 - +- - u CUFF.61 CUFF.61.1 100 0.000000 0.000000 0.000000 0.000000 72 CUFF.61.1 - +- - u CUFF.63 CUFF.63.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.63.1 - +- - u CUFF.65 CUFF.65.1 100 0.000000 0.000000 0.000000 0.000000 61 CUFF.65.1 - +- - u CUFF.67 CUFF.67.1 100 0.000000 0.000000 0.000000 0.000000 197 CUFF.67.1 - +- - u CUFF.69 CUFF.69.1 100 0.000000 0.000000 0.000000 0.000000 354 CUFF.69.1 - +- - u CUFF.71 CUFF.71.1 100 0.000000 0.000000 0.000000 0.000000 42 CUFF.71.1 - +- - u CUFF.73 CUFF.73.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.73.1 - +- - u CUFF.75 CUFF.75.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.75.1 - +- - u CUFF.77 CUFF.77.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.77.1 - +- - u CUFF.79 CUFF.79.1 100 0.000000 0.000000 0.000000 0.000000 71 CUFF.79.1 - +- - u CUFF.81 CUFF.81.1 100 0.000000 0.000000 0.000000 0.000000 212 CUFF.81.1 - +- - u CUFF.83 CUFF.83.1 100 0.000000 0.000000 0.000000 0.000000 45 CUFF.83.1 - +- - u CUFF.85 CUFF.85.1 100 0.000000 0.000000 0.000000 0.000000 100 CUFF.85.1 - +- - u CUFF.87 CUFF.87.1 100 0.000000 0.000000 0.000000 0.000000 59 CUFF.87.1 - +- - u CUFF.89 CUFF.89.1 100 0.000000 0.000000 0.000000 0.000000 48 CUFF.89.1 - +- - u CUFF.91 CUFF.91.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.91.1 - +- - u CUFF.93 CUFF.93.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.93.1 - +- - u CUFF.95 CUFF.95.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.95.1 - +- - u CUFF.97 CUFF.97.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.97.1 - +- - u CUFF.99 CUFF.99.1 100 0.000000 0.000000 0.000000 0.000000 97 CUFF.99.1 - --- a/test-data/cuffcompare_out6.tracking Thu Jun 09 11:38:37 2011 -0400 +++ b/test-data/cuffcompare_out6.tracking Thu Jun 09 12:06:07 2011 -0400 @@ -1,100 +1,100 @@ -TCONS_00000001 XLOC_000001 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000002 XLOC_000002 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - -TCONS_00000003 XLOC_000006 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - -TCONS_00000004 XLOC_000006 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - -TCONS_00000005 XLOC_000006 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - -TCONS_00000006 XLOC_000008 - u q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|- - -TCONS_00000007 XLOC_000008 - u q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|- - -TCONS_00000008 XLOC_000010 - u q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|- - -TCONS_00000009 XLOC_000011 - u q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000010 XLOC_000013 - u q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|- - -TCONS_00000011 XLOC_000014 - u q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|- - -TCONS_00000012 XLOC_000015 - u q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000013 XLOC_000016 - u q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000014 XLOC_000018 - u q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000015 XLOC_000019 - u q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000016 XLOC_000020 - u q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000017 XLOC_000021 - u q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000018 XLOC_000022 - u q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000019 XLOC_000024 - u q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|- - -TCONS_00000020 XLOC_000025 - u q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000021 XLOC_000028 - u q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|- - -TCONS_00000022 XLOC_000030 - u q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000023 XLOC_000032 - u q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000024 XLOC_000034 - u q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000025 XLOC_000035 - u q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|- - -TCONS_00000026 XLOC_000037 - u q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|- - -TCONS_00000027 XLOC_000040 - u q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|- - -TCONS_00000028 XLOC_000042 - u q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|- - -TCONS_00000029 XLOC_000044 - u q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|- - -TCONS_00000030 XLOC_000046 - u q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|- - -TCONS_00000031 XLOC_000048 - u q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|- - -TCONS_00000032 XLOC_000049 - u q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000033 XLOC_000052 - u q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000034 XLOC_000057 - u q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|- - -TCONS_00000035 XLOC_000059 - u q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|- - -TCONS_00000036 XLOC_000059 - u q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|- - -TCONS_00000037 XLOC_000060 - u q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000038 XLOC_000062 - u q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000039 XLOC_000065 - u q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|- - -TCONS_00000040 XLOC_000068 - u q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000041 XLOC_000071 - u q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - -TCONS_00000042 XLOC_000073 - u q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - -TCONS_00000043 XLOC_000075 - u q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000044 XLOC_000077 - u q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - -TCONS_00000045 XLOC_000080 - u q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - -TCONS_00000046 XLOC_000083 - u q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000047 XLOC_000084 - u q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - -TCONS_00000048 XLOC_000085 - 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u - q2:CUFF.77|CUFF.77.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000090 XLOC_000067 - u - q2:CUFF.79|CUFF.79.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000091 XLOC_000068 - u - q2:CUFF.81|CUFF.81.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000092 XLOC_000069 - u - q2:CUFF.83|CUFF.83.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000093 XLOC_000070 - u - q2:CUFF.85|CUFF.85.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000094 XLOC_000072 - u - q2:CUFF.87|CUFF.87.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000095 XLOC_000074 - u - q2:CUFF.89|CUFF.89.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000096 XLOC_000076 - u - q2:CUFF.91|CUFF.91.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000097 XLOC_000078 - u - q2:CUFF.93|CUFF.93.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000098 XLOC_000079 - u - q2:CUFF.95|CUFF.95.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000099 XLOC_000081 - u - q2:CUFF.97|CUFF.97.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000100 XLOC_000082 - u - q2:CUFF.99|CUFF.99.1|100|0.000000|0.000000|0.000000|0.000000|- --- a/test-data/cuffcompare_out7.txt Thu Jun 09 11:38:37 2011 -0400 +++ b/test-data/cuffcompare_out7.txt Thu Jun 09 12:06:07 2011 -0400 @@ -1,19 +1,11 @@ -# Cuffcompare v1.0.1 | Command line was: -#cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf +# Cuffcompare v1.0.3 | Command line was: +#cuffcompare -o cc_output -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf # -#> Genomic sequence: chr1 -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 0 in 0 loci (0 multi-exon) #= Summary for dataset: cuffcompare_in1.gtf : # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) # Reference mRNAs : 0 in 0 loci (0 multi-exon) -#> Genomic sequence: chr1 -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 0 in 0 loci (0 multi-exon) #= Summary for dataset: cuffcompare_in2.gtf : # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) --- a/tools/ngs_rna/cuffcompare_wrapper.py Thu Jun 09 11:38:37 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Thu Jun 09 12:06:07 2011 -0400 @@ -116,7 +116,7 @@ raise Exception, stderr # check that there are results in the output file - cc_output_fname = "cc_output" + cc_output_fname = "cc_output.stats" if len( open( cc_output_fname, 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: --- a/tools/ngs_rna/cuffcompare_wrapper.xml Thu Jun 09 11:38:37 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Thu Jun 09 12:06:07 2011 -0400 @@ -35,9 +35,7 @@ <inputs><param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/><repeat name="input_files" title="Additional GTF Input Files"> - <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""> - <validator type="unspecified_build" /> - </param> + <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/></repeat><conditional name="annotation"><param name="use_ref_annotation" type="select" label="Use Reference Annotation"> @@ -73,13 +71,16 @@ </inputs><outputs> - <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" from_work_dir="cc_output" /> - <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: ${first_input.hid} data tmap file" from_work_dir="input1.tmap" /> - <data format="tabular" name="input1_refmap" label="${tool.name} on ${on_string}: data ${first_input.hid} refmap file" from_work_dir="input1.refmap"/> - <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} tmap file" from_work_dir="input2.tmap"> + <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" + from_work_dir="cc_output.stats" /> + <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: ${first_input.hid} data tmap file" + from_work_dir="cc_output.input1.tmap" /> + <data format="tabular" name="input1_refmap" label="${tool.name} on ${on_string}: data ${first_input.hid} refmap file" + from_work_dir="cc_output.input1.refmap"/> + <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} tmap file" from_work_dir="cc_output.input2.tmap"><filter>len( input_files ) > 0</filter></data> - <data format="tabular" name="input2_refmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} refmap file" from_work_dir="input2.refmap"> + <data format="tabular" name="input2_refmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} refmap file" from_work_dir="cc_output.input2.refmap"><filter>len( input_files ) > 0</filter></data><data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: remove errant print statement from fastqc wrapper
by Bitbucket 09 Jun '11

09 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5e6254f2b9e3/ changeset: 5e6254f2b9e3 user: fubar date: 2011-06-09 17:38:37 summary: remove errant print statement from fastqc wrapper affected #: 1 file (61 bytes) --- a/tools/rgenetics/rgFastQC.py Thu Jun 09 11:26:41 2011 -0400 +++ b/tools/rgenetics/rgFastQC.py Thu Jun 09 11:38:37 2011 -0400 @@ -123,7 +123,6 @@ sauce = os.path.join(adir,f) dest = os.path.join(self.opts.outputdir,f) shutil.move(sauce,dest) - print 'moved %s to %s' % (sauce,dest) os.rmdir(adir) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Some fixes for interplay between DataToolParameter, implicit datatype conversion and dynamic select lists. Closes #491.
by Bitbucket 09 Jun '11

09 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/894112e0b9d5/ changeset: 894112e0b9d5 user: dan date: 2011-06-09 17:26:41 summary: Some fixes for interplay between DataToolParameter, implicit datatype conversion and dynamic select lists. Closes #491. TODO: Revamp this interplay to allow the use of implicit datatype conversion by allowing manual input of selections by e.g. Text Boxes. affected #: 3 files (327 bytes) --- a/lib/galaxy/tools/__init__.py Thu Jun 09 11:24:19 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Jun 09 11:26:41 2011 -0400 @@ -923,6 +923,8 @@ if not self.check_values: return for input in self.inputs.itervalues(): + if input.name not in value: + value[input.name] = input.get_initial_value( None, value ) if isinstance( input, ToolParameter ): callback( "", input, value[input.name] ) else: --- a/lib/galaxy/tools/parameters/basic.py Thu Jun 09 11:24:19 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Thu Jun 09 11:26:41 2011 -0400 @@ -699,8 +699,8 @@ # Old style dynamic options, no dependency information so there isn't # a lot we can do: if we're dealing with workflows, have to assume # late validation no matter what. - if self.dynamic_options is not None: - return ( trans is None or trans.workflow_building_mode ) + if self.dynamic_options is not None and ( trans is None or trans.workflow_building_mode ): + return True # If we got this far, we can actually look at the dependencies # to see if their values will not be available until runtime. for dep_name in self.get_dependencies(): @@ -1354,7 +1354,7 @@ happens twice (here and when generating HTML). """ # Can't look at history in workflow mode - if trans.workflow_building_mode: + if trans is None or trans.workflow_building_mode: return DummyDataset() assert trans is not None, "DataToolParameter requires a trans" history = trans.get_history() @@ -1370,7 +1370,7 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( None, trans ) ) + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) ) if target_ext is not None: return True return False --- a/lib/galaxy/util/expressions.py Thu Jun 09 11:24:19 2011 -0400 +++ b/lib/galaxy/util/expressions.py Thu Jun 09 11:26:41 2011 -0400 @@ -21,6 +21,8 @@ if self.parent is not None and key in self.parent: return self.parent[key] raise KeyError( key ) + def __setitem__( self, key, value ): + self.dict[key] = value def __contains__( self, key ): if key in self.dict: return True @@ -29,4 +31,7 @@ return False def __str__( self ): return str( self.dict ) - + def __nonzero__( self ): + if not self.dict and not self.parent: + return False + return True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 09 Jun '11

09 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1131b031cec7/ changeset: 1131b031cec7 user: natefoo date: 2011-06-09 17:22:23 summary: Fix for either a bug or undocumented feature in ElementTree that broke megablast and blast+ XML parsing in Python 2.7. affected #: 2 files (2 bytes) --- a/tools/metag_tools/megablast_xml_parser.py Wed Jun 08 23:50:07 2011 -0400 +++ b/tools/metag_tools/megablast_xml_parser.py Thu Jun 09 11:22:23 2011 -0400 @@ -53,7 +53,7 @@ query = elem.findtext( "Iteration_query-def" ) qLen = elem.findtext( "Iteration_query-len" ) # for every <Hit> within <Iteration> - for hit in elem.findall( "Iteration_hits/Hit/" ): + for hit in elem.findall( "Iteration_hits/Hit" ): subject = hit.findtext( "Hit_id" ) if re.search( '^gi', subject ): subject = subject.split('|')[1] --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Wed Jun 08 23:50:07 2011 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Jun 09 11:22:23 2011 -0400 @@ -138,7 +138,7 @@ qlen = int(elem.findtext("Iteration_query-len")) # for every <Hit> within <Iteration> - for hit in elem.findall("Iteration_hits/Hit/"): + for hit in elem.findall("Iteration_hits/Hit"): #Expecting either this, # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> # <Hit_def>RecName: Full=Rhodopsin</Hit_def> http://bitbucket.org/galaxy/galaxy-central/changeset/d394deb322a9/ changeset: d394deb322a9 user: natefoo date: 2011-06-09 17:24:19 summary: Rebuild the bx_python egg for numpy 1.6.0. Python 2.7 support officially in beta (tests are passing nicely). affected #: 1 file (9 bytes) --- a/eggs.ini Thu Jun 09 11:22:23 2011 -0400 +++ b/eggs.ini Thu Jun 09 11:24:19 2011 -0400 @@ -67,7 +67,7 @@ psycopg2 = _8.4.2_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static -bx_python = _494c2d1d68b3 +bx_python = _494c2d1d68b3_rebuild1 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 pysam = _kanwei_b10f6e722e9a Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Testing Python 2.7.
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a6868407f0e8/ changeset: a6868407f0e8 user: natefoo date: 2011-06-09 05:50:07 summary: Testing Python 2.7. affected #: 4 files (1.9 KB) --- a/dist-eggs.ini Wed Jun 08 17:47:36 2011 -0400 +++ b/dist-eggs.ini Wed Jun 08 23:50:07 2011 -0400 @@ -13,33 +13,43 @@ py2.5-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.5 py2.6-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.6 py2.6-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.6 +py2.7-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.7 +py2.7-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.7 py2.4-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.4 py2.4-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.4 py2.5-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.5 py2.5-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5 py2.6-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.6 py2.6-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 -py2.4-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.4 -py2.5-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.5 -py2.6-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.6 +py2.7-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.7 +py2.7-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 +py2.4-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /usr/local/bin/python2.4 +py2.5-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /usr/local/bin/python2.5 +py2.6-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /usr/local/bin/python2.6 +py2.7-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /usr/local/bin/python2.7 py2.6-macosx-10.6-universal-ucs2 = fanty.bx.psu.edu /usr/bin/python2.6 py2.4-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6 +py2.7-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.7 py2.4-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.6 +py2.7-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.7 py2.4-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.4 py2.5-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 py2.6-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 +py2.7-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.7 py2.4-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.4 py2.5-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.5 py2.6-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.6 +py2.7-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.7 ; these hosts are used to build eggs with no C extensions py2.4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.4 py2.5 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5 py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 +py2.7 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 [groups] py2.4-linux-i686 = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 @@ -48,34 +58,42 @@ py2.5-linux-x86_64 = py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-i686 = py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.6-linux-x86_64 = py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 +py2.7-linux-i686 = py2.7-linux-i686-ucs2 py2.7-linux-i686-ucs4 +py2.7-linux-x86_64 = py2.7-linux-x86_64-ucs2 py2.7-linux-x86_64-ucs4 py2.4-linux = py2.4-linux-i686 py2.4-linux-x86_64 py2.5-linux = py2.5-linux-i686 py2.5-linux-x86_64 py2.6-linux = py2.6-linux-i686 py2.6-linux-x86_64 -linux-i686 = py2.4-linux-i686 py2.5-linux-i686 py2.6-linux-i686 -linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 py2.6-linux-x86_64 +py2.7-linux = py2.7-linux-i686 py2.7-linux-x86_64 +linux-i686 = py2.4-linux-i686 py2.5-linux-i686 py2.6-linux-i686 py2.7-linux-i686 +linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 py2.6-linux-x86_64 py2.7-linux-x86_64 linux = linux-i686 linux-x86_64 py2.4-macosx = py2.4-macosx-10.3-fat-ucs2 py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 -macosx = py2.4-macosx py2.5-macosx py2.6-macosx +py2.7-macosx = py2.7-macosx-10.3-fat-ucs2 +macosx = py2.4-macosx py2.5-macosx py2.6-macosx py2.7-macosx py2.4-solaris-i86pc = py2.4-solaris-2.10-i86pc_32-ucs2 py2.4-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-i86pc = py2.5-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-i86pc = py2.6-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 +py2.7-solaris-i86pc = py2.7-solaris-2.10-i86pc_32-ucs2 py2.7-solaris-2.10-i86pc_64-ucs2 py2.4-solaris-sun4u = py2.4-solaris-2.10-sun4u_32-ucs2 py2.4-solaris-2.10-sun4u_64-ucs2 py2.5-solaris-sun4u = py2.5-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-sun4u = py2.6-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 +py2.7-solaris-sun4u = py2.7-solaris-2.10-sun4u_32-ucs2 py2.7-solaris-2.10-sun4u_64-ucs2 py2.4-solaris = py2.4-solaris-i86pc py2.4-solaris-sun4u py2.5-solaris = py2.5-solaris-i86pc py2.5-solaris-sun4u py2.6-solaris = py2.6-solaris-i86pc py2.6-solaris-sun4u -solaris-i86pc = py2.4-solaris-i86pc py2.5-solaris-i86pc py2.6-solaris-i86pc -solaris-sun4u = py2.4-solaris-sun4u py2.5-solaris-sun4u py2.6-solaris-sun4u +py2.7-solaris = py2.7-solaris-i86pc py2.7-solaris-sun4u +solaris-i86pc = py2.4-solaris-i86pc py2.5-solaris-i86pc py2.6-solaris-i86pc py2.7-solaris-i86pc +solaris-sun4u = py2.4-solaris-sun4u py2.5-solaris-sun4u py2.6-solaris-sun4u py2.7-solaris-sun4u solaris = solaris-i86pc solaris-sun4u py2.4-all = py2.4-linux py2.4-macosx py2.4-solaris py2.5-all = py2.5-linux py2.5-macosx py2.5-solaris py2.6-all = py2.6-linux py2.6-macosx py2.6-solaris +py2.7-all = py2.7-linux py2.7-macosx py2.7-solaris ; group for building pysam on solaris 10 sparc -solaris-2.10-sun4u = py2.4-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.4-solaris-2.10-sun4u_64-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 +;solaris-2.10-sun4u = py2.4-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.4-solaris-2.10-sun4u_64-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 ; the 'all' key is used internally by the build system to specify which hosts ; to build on when no hosts are specified on the dist-eggs.py command line. @@ -83,10 +101,10 @@ ; the 'noplatform' key, likewise, is for which build hosts should be used when ; building pure python (noplatform) eggs. -noplatform = py2.4 py2.5 py2.6 +noplatform = py2.4 py2.5 py2.6 py2.7 ; don't build these eggs on these platforms: [ignore] GeneTrack = py2.4 python-daemon = py2.4 -ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 +ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.7-linux-i686-ucs2 py2.7-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.7-linux-x86_64-ucs2 py2.7-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.7-macosx-10.3-fat-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.7-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.7-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.7-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 py2.7-solaris-2.10-sun4u_64-ucs2 --- a/eggs.ini Wed Jun 08 17:47:36 2011 -0400 +++ b/eggs.ini Wed Jun 08 23:50:07 2011 -0400 @@ -18,7 +18,7 @@ DRMAA_python = 0.2 MarkupSafe = 0.12 MySQL_python = 1.2.3c1 -numpy = 1.3.0 +numpy = 1.6.0 pbs_python = 4.1.0 psycopg2 = 2.0.13 pycrypto = 2.0.1 --- a/scripts/check_python.py Wed Jun 08 17:47:36 2011 -0400 +++ b/scripts/check_python.py Wed Jun 08 23:50:07 2011 -0400 @@ -8,7 +8,7 @@ def check_python(): try: - assert sys.version_info[:2] >= ( 2, 4 ) and sys.version_info[:2] <= ( 2, 6 ) + assert sys.version_info[:2] >= ( 2, 4 ) and sys.version_info[:2] <= ( 2, 7 ) except AssertionError: print >>sys.stderr, msg raise --- a/scripts/scramble/lib/scramble_lib.py Wed Jun 08 17:47:36 2011 -0400 +++ b/scripts/scramble/lib/scramble_lib.py Wed Jun 08 23:50:07 2011 -0400 @@ -26,7 +26,7 @@ depf = open( '.galaxy_deps', 'r' ) except: return [] - c = eggs.Crate() + c = eggs.Crate( None ) for dep in depf: c[dep.strip()].require() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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