2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/493c62279136/ changeset: r5474:493c62279136 user: fubar date: 2011-04-28 19:40:20 summary: odd problem with gcbias on test - may be due to missing picard_index.loc - sample only is there so shifting to srma_index for testing affected #: 2 files (21 bytes) --- a/tools/picard/picard_wrapper.py Thu Apr 28 12:11:27 2011 -0400 +++ b/tools/picard/picard_wrapper.py Thu Apr 28 13:40:20 2011 -0400 @@ -475,6 +475,7 @@ elif pic.picname == 'CollectGcBiasMetrics': assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name + """ fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) pic.delme.append(fakefasta) try: @@ -483,13 +484,13 @@ s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' info = s shutil.copy(ref_file_name,fakefasta) - + """ x = 'rgPicardGCBiasMetrics' pdfname = '%s.pdf' % x jpgname = '%s.jpg' % x tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out') temppdf = os.path.join(opts.outdir,pdfname) - cl.append('R=%s' % fakefasta) + cl.append('R=%s' % ref_file_name) cl.append('WINDOW_SIZE=%s' % opts.windowsize) cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac) cl.append('INPUT=%s' % opts.input) --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 12:11:27 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 13:40:20 2011 -0400 @@ -7,7 +7,7 @@ #if $genomeSource.refGenomeSource == "history": --own_ref "$genomeSource.ownFile" #else: - --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_index' ].get_fields() )[0][-1] }" #end if </command> @@ -25,7 +25,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome"> - <options from_data_table="all_fasta"> + <options from_data_table="srma_index"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options> http://bitbucket.org/galaxy/galaxy-central/changeset/2b057869b72f/ changeset: r5475:2b057869b72f user: fubar date: 2011-04-28 19:40:41 summary: branch merge affected #: 1 file (11 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Apr 28 13:40:20 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Thu Apr 28 13:40:41 2011 -0400 @@ -417,7 +417,7 @@ return filters -class TabixDataProvider( TracksDataProvider, FilterableMixin ): +class TabixDataProvider( FilterableMixin, TracksDataProvider ): """ Tabix index data provider for the Galaxy track browser. """ @@ -448,7 +448,7 @@ iterator = self.get_iterator( chrom, start, end ) return self.process_data(iterator, **kwargs) -class GffDataProvider( TracksDataProvider, FilterableMixin ): +class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } def write_data_to_file( self, chrom, start, end, filename ): @@ -653,7 +653,7 @@ # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { "tabix": { Vcf: VcfDataProvider, Bed: BedDataProvider, "default" : TabixDataProvider }, - "interval_index": { Gff: GffDataProvider, Gtf: GffDataProvider }, + "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, "summary_tree": SummaryTreeDataProvider, "bigwig": BigWigDataProvider, 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.