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commit/galaxy-central: natefoo: Minor fix for setting the username during user creation under use_remote_user = True. Converts the user portion of the user's email to lowercase and replaces invalid characters with '-' as per the public name format requirements.
by Bitbucket 29 Apr '11

29 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4933de88cdb0/ changeset: r5483:4933de88cdb0 user: natefoo date: 2011-04-29 16:35:42 summary: Minor fix for setting the username during user creation under use_remote_user = True. Converts the user portion of the user's email to lowercase and replaces invalid characters with '-' as per the public name format requirements. affected #: 1 file (231 bytes) --- a/lib/galaxy/web/framework/__init__.py Thu Apr 28 22:07:58 2011 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Apr 29 10:35:42 2011 -0400 @@ -437,14 +437,17 @@ if not user.default_permissions: self.app.security_agent.user_set_default_permissions( user, history=True, dataset=True ) elif user is None: - username = remote_user_email.split( '@', 1 )[0] + username = remote_user_email.split( '@', 1 )[0].lower() random.seed() user = self.app.model.User( email=remote_user_email ) user.set_password_cleartext( ''.join( random.sample( string.letters + string.digits, 12 ) ) ) user.external = True + # Replace invalid characters in the username + for char in filter( lambda x: x not in string.ascii_lowercase + string.digits + '-', username ): + username = username.replace( char, '-' ) # Find a unique username - user can change it later if ( self.sa_session.query( self.app.model.User ).filter_by( username=username ).first() ): - i = 0 + i = 1 while ( self.sa_session.query( self.app.model.User ).filter_by( username=(username + '-' + str(i) ) ).first() ): i += 1 username += '-' + str(i) 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: fubar: ok. back to all_fasta.loc - they must be somewhere
by Bitbucket 29 Apr '11

29 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/bb39eef087d4/ changeset: r5482:bb39eef087d4 user: fubar date: 2011-04-29 04:07:58 summary: ok. back to all_fasta.loc - they must be somewhere affected #: 2 files (8 bytes) --- a/tools/picard/rgPicardASMetrics.xml Thu Apr 28 21:44:35 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Thu Apr 28 22:07:58 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 ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].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="bwa_indexes"> + <options from_data_table="all_fasta"><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/rgPicardGCBiasMetrics.xml Thu Apr 28 21:44:35 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 22:07:58 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 ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].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="bwa_indexes"> + <options from_data_table="all_fasta"><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> 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: fubar: Finally I think. fasta not .fa for asmetrics and gcbias
by Bitbucket 29 Apr '11

29 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/640ff3d819e5/ changeset: r5481:640ff3d819e5 user: fubar date: 2011-04-29 03:44:35 summary: Finally I think. fasta not .fa for asmetrics and gcbias affected #: 2 files (29 bytes) --- a/tools/picard/rgPicardASMetrics.xml Thu Apr 28 21:14:46 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Thu Apr 28 21:44:35 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 ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'bwa_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="srma_indexes"> + <options from_data_table="bwa_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/rgPicardGCBiasMetrics.xml Thu Apr 28 21:14:46 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 21:44:35 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 ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'bwa_indexes' ].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="srma_indexes"> + <options from_data_table="bwa_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> @@ -43,8 +43,8 @@ label="Java heap size. Java is a pig, the art is long but memory is short"><option value="1G">1GB: very small data</option><option value="2G" selected="true">2GB</option> - <option value="4G">4GB will work for small sized datasets </option> - <option value="8G" >8GB - should generally work...</option> + <option value="4G">4GB for larger datasets </option> + <option value="8G" >8GB use if 4GB fails</option><option value="16G">16GB - try this if 8GB fails</option></param> 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: fubar: typo in selected for gcbias. Still broken on test - no idea why - wonder if it's an old version of picard?
by Bitbucket 29 Apr '11

29 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d6aa5ad56d2b/ changeset: r5480:d6aa5ad56d2b user: fubar date: 2011-04-29 03:14:46 summary: typo in selected for gcbias. Still broken on test - no idea why - wonder if it's an old version of picard? affected #: 1 file (16 bytes) --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 19:57:32 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 21:14:46 2011 -0400 @@ -44,7 +44,7 @@ <option value="1G">1GB: very small data</option><option value="2G" selected="true">2GB</option><option value="4G">4GB will work for small sized datasets </option> - <option value="8G" selected="true" >8GB - should generally work...</option> + <option value="8G" >8GB - should generally work...</option><option value="16G">16GB - try this if 8GB fails</option></param> 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: fubar: gcbias still failing - try 2GB of java heap...
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8f1cabffa8f8/ changeset: r5479:8f1cabffa8f8 user: fubar date: 2011-04-29 01:57:32 summary: gcbias still failing - try 2GB of java heap... affected #: 1 file (25 bytes) --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 19:30:48 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 19:57:32 2011 -0400 @@ -41,10 +41,11 @@ 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"> + <option value="1G">1GB: very small data</option> + <option value="2G" selected="true">2GB</option><option value="4G">4GB will work for small sized datasets </option><option value="8G" selected="true" >8GB - should generally work...</option><option value="16G">16GB - try this if 8GB fails</option> - <option value="32G">32GB - please use only if absolutely necessary</option></param></inputs> 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 28 Apr '11

28 Apr '11

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.

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commit/galaxy-central: fubar: fix for missing html ref in picard_reordersam and for data index srma_indexes in gcbias
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d2032d37013f/ changeset: r5476:d2032d37013f user: fubar date: 2011-04-28 22:25:09 summary: fix for missing html ref in picard_reordersam and for data index srma_indexes in gcbias affected #: 3 files (41 bytes) --- a/tools/picard/picard_ReorderSam.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Thu Apr 28 16:25:09 2011 -0400 @@ -121,7 +121,7 @@ **Picard documentation** -This is a Galaxy interface for Picard-tool_'s ReorderSam tool, a part of Picard-tools_, which is supported by SAMTools_. +This is a Galaxy interface for Picard-tools_'s ReorderSam tool, a part of Picard-tools_, which is supported by SAMTools_. .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/ --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 16:25:09 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 ), $__app__.tool_data_tables[ 'srma_index' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" #end if </command> @@ -25,7 +25,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome"> - <options from_data_table="srma_index"> + <options from_data_table="srma_indexes"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options> --- a/tools/rgenetics/rgfakePhe.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/rgenetics/rgfakePhe.xml Thu Apr 28 16:25:09 2011 -0400 @@ -1,6 +1,5 @@ <tool id="fakePhe1" name="Null phenotypes"><description>for testing</description> - <code file="rgfakePhe_code.py"/><command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name' "$title1" '$ppheout' '$ppheout.files_path' '$script_file' </command> 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 28 Apr '11

28 Apr '11

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.

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commit/galaxy-central: kanwei: trackster: Fix filters, restore name of IntervalIndex provider
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0cb1f1f68a86/ changeset: r5473:0cb1f1f68a86 user: kanwei date: 2011-04-28 19:17:51 summary: trackster: Fix filters, restore name of IntervalIndex provider affected #: 1 file (11 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Apr 28 12:11:27 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Thu Apr 28 13:17:51 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.

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commit/galaxy-central: fubar: The Buildbot tells me that it's easiest to install FastQC under tool-data/shared/jars - adjusted the tool appropriately
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d6be25b05259/ changeset: r5472:d6be25b05259 user: fubar date: 2011-04-28 18:11:27 summary: The Buildbot tells me that it's easiest to install FastQC under tool-data/shared/jars - adjusted the tool appropriately affected #: 1 file (5 bytes) --- a/tools/rgenetics/rgFastQC.xml Thu Apr 28 11:48:52 2011 -0400 +++ b/tools/rgenetics/rgFastQC.xml Thu Apr 28 12:11:27 2011 -0400 @@ -1,7 +1,7 @@ <tool name="Fastqc: Fastqc QC" id="fastqc" version="0.1"><description>using FastQC from Babraham</description><command interpreter="python"> - rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/FastQC/fastqc + rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc #if $contaminants.dataset and str($contaminants) > '' -c "$contaminants" #end if 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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