2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a1b017b9743f/ changeset: r5477:a1b017b9743f user: fubar date: 2011-04-28 23:28:07 summary: collectgcbias metrics is bitten by the header length bug again - try fakefasta solution again affected #: 1 file (149 bytes) --- a/tools/picard/picard_wrapper.py Thu Apr 28 16:25:09 2011 -0400 +++ b/tools/picard/picard_wrapper.py Thu Apr 28 17:28:07 2011 -0400 @@ -475,7 +475,8 @@ elif pic.picname == 'CollectGcBiasMetrics': assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name - """ + # sigh. Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data. + # why? Dunno fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) pic.delme.append(fakefasta) try: @@ -484,13 +485,12 @@ 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' % ref_file_name) + cl.append('R=%s' % fakefasta) cl.append('WINDOW_SIZE=%s' % opts.windowsize) cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac) cl.append('INPUT=%s' % opts.input) http://bitbucket.org/galaxy/galaxy-central/changeset/c6eed447f43b/ changeset: r5478:c6eed447f43b user: fubar date: 2011-04-29 01:30:48 summary: tweaks to fasta locations for tests for ASM and insertsize affected #: 3 files (62 bytes) --- a/lib/galaxy/web/controllers/dataset.py Thu Apr 28 17:28:07 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Thu Apr 28 19:30:48 2011 -0400 @@ -507,7 +507,7 @@ # If data is binary or an image, stream without template; otherwise, use display template. # TODO: figure out a way to display images in display template. - if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image): + if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image) or isinstance(dataset.datatype, datatypes.images.Html): mime = trans.app.datatypes_registry.get_mimetype_by_extension( dataset.extension.lower() ) trans.response.set_content_type( mime ) return open( dataset.file_name ) --- a/tools/picard/rgPicardASMetrics.xml Thu Apr 28 17:28:07 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Thu Apr 28 19:30:48 2011 -0400 @@ -8,7 +8,7 @@ --ref "$genomeSource.ownFile" #end if #if $genomeSource.refGenomeSource == "indexed": - --ref "${ 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_indexes' ].get_fields() )[0][-1] }" #end if </command><requirements><requirement type="package">picard</requirement></requirements> @@ -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_indexes"><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> --- a/tools/picard/rgPicardInsertSize.xml Thu Apr 28 17:28:07 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Thu Apr 28 19:30:48 2011 -0400 @@ -31,7 +31,7 @@ <param name="tailLimit" value="10000" /><param name="histWidth" value="0" /><param name="minPct" value="0.01" /> - <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" lines_diff="25" /> + <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" lines_diff="30" /></test></tests><help> 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.