1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/62a5d6d82151/ changeset: r5485:62a5d6d82151 user: fubar date: 2011-04-29 18:29:13 summary: gcbias still failing on test - works fine here using same data - clean up of fasta munging affected #: 2 files (166 bytes)
--- a/tools/picard/picard_wrapper.py Fri Apr 29 10:37:59 2011 -0400 +++ b/tools/picard/picard_wrapper.py Fri Apr 29 12:29:13 2011 -0400 @@ -361,19 +361,19 @@ tmp_dir = opts.outdir
# set ref and dict files to use (create if necessary) - if opts.ref_file: + ref_file_name = opts.ref + if opts.ref_file <> None: csd = 'CreateSequenceDictionary' realjarpath = os.path.split(opts.jar)[0] jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname) - ref_file_name = '%s.fa' % tmp_ref_name + ref_file_name = '%s.fasta' % tmp_ref_name # build dict - ## need to change name of fasta to have fasta ext - dict_file_name = ref_file_name.replace( '.fa', '.dict' ) + dict_file_name = '%s.dict' % tmp_ref_name os.symlink( opts.ref_file, ref_file_name ) cl = ['REFERENCE=%s' % ref_file_name] cl.append('OUTPUT=%s' % dict_file_name) - cl.append('URI=%s' % os.path.basename( ref_file_name )) + cl.append('URI=%s' % os.path.basename( ref_file )) cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names) if opts.species_name: cl.append('SPECIES=%s' % opts.species_name) @@ -381,11 +381,9 @@ cl.append('GENOME_ASSEMBLY=%s' % opts.build_name) pic.delme.append(dict_file_name) pic.delme.append(ref_file_name) + pic.delme.append(tmp_ref_name) s = pic.runPic(jarpath, cl) - elif opts.ref: - ref_file_name = opts.ref - - # run relevant command(s) + # run relevant command(s)
cl = ['VALIDATION_STRINGENCY=LENIENT',]
@@ -446,13 +444,15 @@
elif pic.picname == 'CollectAlignmentSummaryMetrics': + # 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)) try: os.symlink(ref_file_name,fakefasta) except: s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' info = s - shutil.copy(ref_file_name,fakefasta) + shutil.copy(ref_file_name,fakefasta) pic.delme.append(fakefasta) cl.append('ASSUME_SORTED=%s' % opts.assumesorted) adaptorseqs = ''.join([' ADAPTER_SEQUENCE=%s' % x for x in opts.adaptors]) @@ -478,13 +478,13 @@ # 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: os.symlink(ref_file_name,fakefasta) except: s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' info = s - shutil.copy(ref_file_name,fakefasta) + shutil.copy(ref_file_name,fakefasta) + pic.delme.append(fakefasta) x = 'rgPicardGCBiasMetrics' pdfname = '%s.pdf' % x jpgname = '%s.jpg' % x
--- a/tools/picard/rgPicardGCBiasMetrics.xml Fri Apr 29 10:37:59 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Fri Apr 29 12:29:13 2011 -0400 @@ -40,7 +40,7 @@ <param name="mingenomefrac" value="0.00001" type="float" label="Minimum Genome Fraction" help="For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." /><param name="maxheap" type="select" help="If in doubt, choose 8G and read Picard documentation please" - label="Java heap size. Java is a pig, the art is long but memory is short"> + label="Java heap size"><option value="1G">1GB: very small data</option><option value="2G" selected="true">2GB</option><option value="4G">4GB for larger datasets </option>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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