- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Partial implementation of Circos visualization using D3.
by Bitbucket 25 May '12

25 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4288ffb1bd16/ changeset: 4288ffb1bd16 user: jgoecks date: 2012-05-25 21:13:25 summary: Partial implementation of Circos visualization using D3. affected #: 7 files Diff too large to display. 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.

1 0

commit/galaxy-central: guru: Suppressed R package-loading messages which were previously being written into stderr
by Bitbucket 25 May '12

25 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8cbbb813f286/ changeset: 8cbbb813f286 user: guru date: 2012-05-25 16:54:03 summary: Suppressed R package-loading messages which were previously being written into stderr affected #: 1 file diff -r 8335baa6881520cabfd3eb41986d7df203dc3183 -r 8cbbb813f2865de22ff671c980816cde5e225be5 tools/regVariation/logistic_regression_vif.py --- a/tools/regVariation/logistic_regression_vif.py +++ b/tools/regVariation/logistic_regression_vif.py @@ -5,16 +5,10 @@ from rpy import * import numpy -#export PYTHONPATH=~/galaxy/lib/ - def stop_err(msg): sys.stderr.write(msg) sys.exit() -#infile = 'logreg_inp.tab' -#y_col=3 -#x_cols=[1,2,3] -#outfile='logreg_out.txt' -#python logistic_regression_vif.py logreg_inp.tab 4 1,2,3 logreg_out2.tabular # running test + infile = sys.argv[1] y_col = int(sys.argv[2])-1 x_cols = sys.argv[3].split(',') @@ -84,17 +78,11 @@ set_default_mode(NO_CONVERSION) try: linear_model = r.glm(r("y ~ x"), data = r.na_exclude(dat),family="binomial") - #r('library(car)') - #r.assign('dat',dat) - #r.assign('ncols',len(x_cols)) - #r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')).as_py() - except RException, rex: stop_err("Error performing logistic regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.") if len(x_cols)>1: try: - - r('library(car)') + r('suppressPackageStartupMessages(library(car))') r.assign('dat',dat) r.assign('ncols',len(x_cols)) vif=r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')) @@ -163,9 +151,6 @@ rsq= r.round(float((null_deviance-residual_deviance)/null_deviance), digits=5) null_deviance= r.round(float(null_deviance), digits=5) residual_deviance= r.round(float(residual_deviance), digits=5) - - #rsq = r.round(float(rsq), digits=5) - except: pass 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.

1 0

commit/galaxy-central: fubar: Reverse order of job manager and instance in warning
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8335baa68815/ changeset: 8335baa68815 user: fubar date: 2012-05-25 07:48:49 summary: Reverse order of job manager and instance in warning affected #: 1 file diff -r 3f1150fee33c6d7270549e0760fd84b7c35fdb50 -r 8335baa6881520cabfd3eb41986d7df203dc3183 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2380,7 +2380,7 @@ msg = None status = None if self.app.config.job_manager != self.app.config.server_name: - return trans.show_error_message( 'This Galaxy instance (%s) is not the job manager (%s). If using multiple servers, please directly access the job manager instance to manage jobs.' % ( self.app.config.job_manager,self.app.config.server_name) ) + return trans.show_error_message( 'This Galaxy instance (%s) is not the job manager (%s). If using multiple servers, please directly access the job manager instance to manage jobs.' % (self.app.config.server_name, self.app.config.job_manager) ) job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated' 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.

1 0

commit/galaxy-central: fubar: Fix for bogus double negative compare - allows job management from admin screen when only one job manager running
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3f1150fee33c/ changeset: 3f1150fee33c user: fubar date: 2012-05-25 07:40:44 summary: Fix for bogus double negative compare - allows job management from admin screen when only one job manager running affected #: 1 file diff -r 3fa05d052e820d21f1a6e5ae206d90edcc1a8782 -r 3f1150fee33c6d7270549e0760fd84b7c35fdb50 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2379,8 +2379,8 @@ deleted = [] msg = None status = None - if not self.app.config.job_manager != self.app.config.server_name: - return trans.show_error_message( 'This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs.' ) + if self.app.config.job_manager != self.app.config.server_name: + return trans.show_error_message( 'This Galaxy instance (%s) is not the job manager (%s). If using multiple servers, please directly access the job manager instance to manage jobs.' % ( self.app.config.job_manager,self.app.config.server_name) ) job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated' 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.

1 0

commit/galaxy-central: greg: Fix a typo in the community common cntroller.
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fa05d052e82/ changeset: 3fa05d052e82 user: greg date: 2012-05-24 22:47:25 summary: Fix a typo in the community common cntroller. affected #: 1 file diff -r 676546e7038ae833e524bbc4b4b26c81c71954bd -r 3fa05d052e820d21f1a6e5ae206d90edcc1a8782 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -774,7 +774,7 @@ break if in_ctx: tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, dir=work_dir ) - element_tree = util.parse_xml( tmp_config ) + element_tree = util.parse_xml( tmp_tool_config ) element_tree_root = element_tree.getroot() # Look for code files required by the tool config. tmp_code_files = [] 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.

1 0

commit/galaxy-central: greg: Enhance setting metadata on tool shed repositories tha tinclude tools that require entries in the tool_data_table_conf.xml file.
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/676546e7038a/ changeset: 676546e7038a user: greg date: 2012-05-24 22:36:32 summary: Enhance setting metadata on tool shed repositories tha tinclude tools that require entries in the tool_data_table_conf.xml file. affected #: 5 files diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py @@ -8,6 +8,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require('ssh' ) pkg_resources.require( 'Fabric' ) from fabric.api import env, lcd, local diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,4 +1,5 @@ import sys, os, tempfile, shutil, logging, string, urllib2 +import galaxy.tools.data from datetime import date, datetime, timedelta from time import strftime, gmtime from galaxy import util @@ -528,10 +529,11 @@ exported_workflow_dict = from_json_string( workflow_text ) if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) - # This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) + if 'tools' in metadata_dict: + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) + if tool_dependencies_config: + metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) return metadata_dict def generate_tool_guid( repository_clone_url, tool ): """ @@ -1026,6 +1028,8 @@ # Reload the tool into the local list of repository_tools_tups. repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( app ) return repository_tools_tups def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ): """ @@ -1398,6 +1402,9 @@ if uninstall: # Write the current in-memory version of the integrated_tool_panel.xml file to disk. trans.app.toolbox.write_integrated_tool_panel_config_file() +def reset_tool_data_tables( app ): + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + app.tool_data_tables = galaxy.tools.data.ToolDataTableManager( app.config.tool_data_table_config_path ) def strip_path( fpath ): file_path, file_name = os.path.split( fpath ) return file_name diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -7,7 +7,7 @@ from galaxy.util.hash_util import * from galaxy.util.shed_util import copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_configured_ui, handle_sample_tool_data_table_conf_file -from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, strip_path, to_html_escaped, to_html_str, update_repository +from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, strip_path, to_html_escaped, to_html_str, update_repository from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -245,6 +245,8 @@ correction_msg = "This file refers to a file named %s. " % str( index_file ) correction_msg += "Upload a file named %s.sample to the repository to correct this error." % str( index_file_name ) invalid_files.append( ( xml_file_in_ctx, correction_msg ) ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) return sample_files_copied, can_set_metadata, invalid_files def clean_repository_metadata( trans, id, changeset_revisions ): # Delete all repository_metadata reecords associated with the repository that have a changeset_revision that is not in changeset_revisions. @@ -437,16 +439,20 @@ work_dir = make_tmp_directory() datatypes_config = get_config( 'datatypes_conf.xml', repo, repo_dir, ctx, work_dir ) if datatypes_config: - metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) sample_files = get_sample_files( repo, repo_dir, dir=work_dir ) + # Handle the tool_data_table_conf.xml.sample file if it is included in the repository. + if 'tool_data_table_conf.xml.sample' in sample_files: + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) if sample_files: trans.app.config.tool_data_path = work_dir for filename in ctx: # Find all tool configs. ctx_file_name = strip_path( filename ) if ctx_file_name not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - valid, tool = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) - if valid and tool is not None: + is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) + if is_tool_config and valid and tool is not None: sample_files_copied, can_set_metadata, invalid_files = check_tool_input_params( trans, repo, repo_dir, @@ -484,9 +490,11 @@ os.unlink( os.path.join( original_tool_data_path, copied_file ) ) except: pass - elif tool is not None: - # We have a tool config but it is invalid. - invalid_files.append( ( ctx_file_name, 'Problems loading tool.' ) ) + elif is_tool_config: + if not error_message: + error_message = 'Unknown problems loading tool.' + # We have a tool config but it is invalid or the tool does not properly load. + invalid_files.append( ( ctx_file_name, error_message ) ) invalid_tool_configs.append( ctx_file_name ) # Find all exported workflows. elif filename.endswith( '.ga' ): @@ -498,15 +506,18 @@ metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( ctx_file_name, str( e ) ) ) - # Find tool_dependencies.xml if it exists. This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, repo_dir, ctx, work_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) + if 'tools' in metadata_dict: + # Find tool_dependencies.xml if it exists. This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, repo_dir, ctx, work_dir ) + if tool_dependencies_config: + metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs if sample_files: # Don't forget to reset the value of trans.app.config.tool_data_path! trans.app.config.tool_data_path = original_tool_data_path + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) try: shutil.rmtree( work_dir ) except: @@ -737,9 +748,14 @@ repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) tool = None message = '' work_dir = make_tmp_directory() + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) + if tool_data_table_config: + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) if changeset_revision == repository.tip: try: copied_tool_config = copy_file_from_disk( tool_config, repo_files_dir, work_dir ) @@ -750,7 +766,6 @@ else: # Get the tool config file name from the hgweb url, something like: /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( repo, changeset_revision ) in_ctx = False for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) @@ -784,14 +799,18 @@ pass else: tool = None + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) try: shutil.rmtree( work_dir ) except: pass return tool, message def load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, dir ): + is_tool_config = False tool = None valid = False + error_message = '' tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir=dir ) if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] or check_bz2( tmp_config )[ 0 ] or check_zip( tmp_config ) ): @@ -799,11 +818,15 @@ # Make sure we're looking at a tool config and not a display application config or something else. element_tree = util.parse_xml( tmp_config ) element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' + is_tool_config = element_tree_root.tag == 'tool' except Exception, e: log.debug( "Error parsing %s, exception: %s" % ( tmp_config, str( e ) ) ) - is_tool = False - if is_tool: + is_tool_config = False + if is_tool_config: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', dir ) + if tool_data_table_config: + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) # Look for code files required by the tool config. The directory to which dir refers should be removed by the caller. for code_elem in element_tree_root.findall( 'code' ): code_file_name = code_elem.get( 'file' ) @@ -814,9 +837,17 @@ try: tool = load_tool( trans, tmp_config ) valid = True - except: + except KeyError, e: valid = False - return valid, tool + error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) + error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' + error_message += 'this error. ' + except Exception, e: + valid = False + error_message = str( e ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) + return is_tool_config, valid, tool, error_message def new_tool_metadata_required( trans, id, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata @@ -1049,13 +1080,11 @@ error_message, status = reset_all_metadata_on_repository( trans, id, **kwd ) if error_message: # If there is an error, display it. - message += '%s %s ' % ( message, error_message ) - status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, - message=message, - status=status ) ) + message=error_message, + status='error' ) ) def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): # This method id deprecated, but we'll keep it around for a while in case we need it. The problem is that hg purge # is not supported by the mercurial API. diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -950,7 +950,12 @@ for filename in ctx: # Find all tool configs in this repository changeset_revision. if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - valid, tool = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) + is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, + repo, + repo_dir, + ctx, + filename, + work_dir ) if valid and tool is not None: tool_guids.append( generate_tool_guid( trans, repository, tool ) ) tool_guids.sort() diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -3,7 +3,7 @@ from galaxy.model.orm import * from galaxy.datatypes.checkers import * from common import * -from galaxy.util.shed_util import get_configured_ui, handle_sample_tool_data_table_conf_file +from galaxy.util.shed_util import get_configured_ui, reset_tool_data_tables, handle_sample_tool_data_table_conf_file from galaxy import eggs eggs.require('mercurial') @@ -168,6 +168,8 @@ status=status ) ) else: status = 'error' + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', repository=repository, 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.

1 0

commit/galaxy-central: jgoecks: Full and proper sorting for GTF datasets: sort by, in order, transcript_id, chrom, and start.
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/95c05fcbbceb/ changeset: 95c05fcbbceb user: jgoecks date: 2012-05-24 19:26:48 summary: Full and proper sorting for GTF datasets: sort by, in order, transcript_id, chrom, and start. affected #: 2 files diff -r a0d6e382f2e198e46613705ad8a3962d0bc58fca -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 lib/galaxy/datatypes/util/gff_util.py --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -1,9 +1,12 @@ """ Provides utilities for working with GFF files. """ + +import copy import pkg_resources; pkg_resources.require( "bx-python" ) from bx.intervals.io import * from bx.tabular.io import Header, Comment +from galaxy.util.odict import odict class GFFInterval( GenomicInterval ): """ @@ -48,7 +51,8 @@ def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4, \ strand_col=6, score_col=5, default_strand='.', fix_strand=False, intervals=[], \ raw_size=0 ): - GFFInterval.__init__( self, reader, intervals[0].fields, chrom_col, feature_col, \ + # Use copy so that first interval and feature do not share fields. + GFFInterval.__init__( self, reader, copy.deepcopy( intervals[0].fields ), chrom_col, feature_col, \ start_col, end_col, strand_col, score_col, default_strand, \ fix_strand=fix_strand ) self.intervals = intervals @@ -356,4 +360,46 @@ for name, value in attrs.items(): attrs_strs.append( format_string % ( name, value ) ) return " ; ".join( attrs_strs ) - \ No newline at end of file + +def read_unordered_gtf( iterator ): + """ + Returns GTF features found in an iterator. GTF lines need not be ordered + or clustered for reader to work. Reader returns GFFFeature objects sorted + by transcript_id, chrom, and start position. + """ + + # Aggregate intervals by transcript_id. + feature_intervals = odict() + for count, line in enumerate( iterator ): + line_attrs = parse_gff_attributes( line.split('\t')[8] ) + transcript_id = line_attrs[ 'transcript_id' ] + if transcript_id in feature_intervals: + feature = feature_intervals[ transcript_id ] + else: + feature = [] + feature_intervals[ transcript_id ] = feature + feature.append( GFFInterval( None, line.split( '\t' ) ) ) + + # Create features. + chroms_features = {} + for count, intervals in enumerate( feature_intervals.values() ): + # Sort intervals by start position. + intervals.sort( lambda a,b: cmp( a.start, b.start ) ) + feature = GFFFeature( None, intervals=intervals ) + if feature.chrom not in chroms_features: + chroms_features[ feature.chrom ] = [] + chroms_features[ feature.chrom ].append( feature ) + + # Sort features by chrom, start position. + chroms_features_sorted = [] + for chrom_features in chroms_features.values(): + chroms_features_sorted.append( chrom_features ) + chroms_features_sorted.sort( lambda a,b: cmp( a[0].chrom, b[0].chrom ) ) + for features in chroms_features_sorted: + features.sort( lambda a,b: cmp( a.start, b.start ) ) + + # Yield. + for chrom_features in chroms_features_sorted: + for feature in chrom_features: + yield feature + \ No newline at end of file diff -r a0d6e382f2e198e46613705ad8a3962d0bc58fca -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 tools/filters/gff/sort_gtf.py --- /dev/null +++ b/tools/filters/gff/sort_gtf.py @@ -0,0 +1,28 @@ +#!/usr/bin/env python + +import sys +from galaxy import eggs +from galaxy.datatypes.util.gff_util import read_unordered_gtf + +# Older py compatibility +try: + set() +except: + from sets import Set as set + +assert sys.version_info[:2] >= ( 2, 4 ) + +# +# Process inputs. +# + +in_fname = sys.argv[1] +out_fname = sys.argv[2] + +out = open( out_fname, 'w' ) +for feature in read_unordered_gtf( open( in_fname, 'r' ) ): + # Print feature. + for interval in feature.intervals: + out.write( "\t".join(interval.fields) ) + +# TODO: print status information: how many lines processed and features found. \ No newline at end of file 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.

1 0

commit/galaxy-central: 4 new changesets
by Bitbucket 24 May '12

24 May '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4bb4d6d97649/ changeset: 4bb4d6d97649 branch: add_weblogo_requirement user: natefoo date: 2012-05-24 17:13:01 summary: Closed branch add_weblogo_requirement affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/changeset/8e00c7e646b3/ changeset: 8e00c7e646b3 user: natefoo date: 2012-05-24 17:13:32 summary: Merged add_weblogo_requirement. affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/changeset/aad87a713970/ changeset: aad87a713970 branch: add_clustalw2_requirement user: natefoo date: 2012-05-24 17:14:02 summary: Closed branch add_clustalw2_requirement affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/changeset/a0d6e382f2e1/ changeset: a0d6e382f2e1 user: natefoo date: 2012-05-24 17:14:17 summary: Merged add_clustalw2_requirement. affected #: 0 files 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.

1 0

commit/galaxy-central: natefoo: Add ssh egg and fix a requirement for the Tool Shed.
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a45a4d1023af/ changeset: a45a4d1023af user: natefoo date: 2012-05-24 16:05:55 summary: Add ssh egg and fix a requirement for the Tool Shed. affected #: 2 files diff -r fdb66f9df9de8ad9e0ed34f5301f13f06674fa78 -r a45a4d1023afcceee66372790fa7586f19e12b2e eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -54,6 +54,7 @@ Routes = 1.12.3 SQLAlchemy = 0.5.6 sqlalchemy_migrate = 0.5.4 +ssh = 1.7.14 SVGFig = 1.1.6 Tempita = 0.1 twill = 0.9 diff -r fdb66f9df9de8ad9e0ed34f5301f13f06674fa78 -r a45a4d1023afcceee66372790fa7586f19e12b2e lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py @@ -8,7 +8,7 @@ from galaxy import eggs import pkg_resources -pkg_resources.require( 'fabric' ) +pkg_resources.require( 'Fabric' ) from fabric.api import env, lcd, local 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.

1 0

commit/galaxy-central: dannon: History API undelete bug pointed out by Ed Kirton. Resolves BB Issue #763.
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fdb66f9df9de/ changeset: fdb66f9df9de user: dannon date: 2012-05-24 14:18:49 summary: History API undelete bug pointed out by Ed Kirton. Resolves BB Issue #763. affected #: 1 file diff -r e5a406a8345b8933035ec6530643d9078aa74d72 -r fdb66f9df9de8ad9e0ed34f5301f13f06674fa78 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -153,7 +153,7 @@ POST /api/histories/deleted/{encoded_quota_id}/undelete Undeletes a quota """ - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False, deleted=True ) + history = self.get_history( trans, id, check_ownership=True, check_accessible=False, deleted=True ) history.deleted = False trans.sa_session.add( history ) trans.sa_session.flush() 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.

1 0