- galaxy-dev - lists.galaxyproject.org

dynamic_options
by Ross 15 Sep '08

15 Sep '08

I see from the parameters code that dynamic_options are to be replaced with options as part of workflow buildout. I'm finding lots of use cases where the dynamic_options returned by code from an included module makes some complicated things really easy for users. For example. In the new gene expression tools, each expression experiment is stored as a new Galaxy datatype based on the Bioconductor representation (affybatch, eset etc). Each of those structures has (optional!) accompanying experimental metadata (phenodata) which at the time the affybatch is being created, is in the form of a tab delimited file with a header row. For constructing design and contrast matrices for analyses, the user has to choose one or more of those phenodata columns for that experiment - and the choice typically might be limited to those columns containing *exactly* two values - ie dichotomous contrasts. I have code working that allows the user to choose an input (eg affybatch) experiment file from their history, then to choose from among *only* the dichotomous phenotype columns, and run the analysis - you cannot imagine what a big deal this is compared with trying to teach people to generate design and contrast matrices interactively in R! But of course, these miracles all rely on dynamic_options calling some code included with the tool. What's the best way forward for a situation where we need to obtain this kind of drop down list for a tool, that depends on the choice on a previous page, that will be compatible with workflows in the long-haul? I guess one approach is that when generating the (eg affybatch) metadata, I guess I could create all the option lists I'm going to ever need as additional metadata datastructures that could be used like the options from files are used elsewhere - the catch is that they'd all have to be precomputed rather than being computed on the fly by the tool - is that reasonable or is there some way to allow dynamic computing on the metadata (and it's a little complex, involving parsing the phenodata and constructing a concordance of the values in each column and eg returning only the columns with exactly two values) -- python -c "foo = map(None,'moc.liamg(a)surazal.ssor'); foo.reverse(); print ''.join(foo)"

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[hg] galaxy 1503: Lastz with additional short read changes
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/777e41dbdf1f changeset: 1503:777e41dbdf1f user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 12 15:14:20 2008 -0400 description: Lastz with additional short read changes 10 file(s) affected in this change: test-data/lastz_census.txt test-data/lastz_diffs.txt test-data/lastz_diffs_ref_name.txt test-data/lastz_maf.txt tool_conf.xml.sample tools/metag_tools/blat_wrapper.xml tools/metag_tools/megablast_wrapper.xml tools/sr_mapping/fastq_statistics.xml tools/sr_mapping/lastz_code.py tools/sr_mapping/lastz_wrapper.xml diffs (truncated from 7931 to 3000 lines): diff -r 6bb33bc9903f -r 777e41dbdf1f test-data/lastz_census.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_census.txt Fri Sep 12 15:14:20 2008 -0400 @@ -0,0 +1,5386 @@ +phiX 1 255 +phiX 2 255 +phiX 3 255 +phiX 4 255 +phiX 5 255 +phiX 6 255 +phiX 7 255 +phiX 8 255 +phiX 9 255 +phiX 10 255 +phiX 11 255 +phiX 12 255 +phiX 13 255 +phiX 14 255 +phiX 15 255 +phiX 16 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[hg] galaxy 1502: Prevent workflow editor form loading in IE6 an...
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/6bb33bc9903f changeset: 1502:6bb33bc9903f user: James Taylor <james(a)jamestaylor.org> date: Fri Sep 12 07:13:09 2008 -0400 description: Prevent workflow editor form loading in IE6 and print a message 1 file(s) affected in this change: templates/workflow/editor.mako diffs (25 lines): diff -r 362a1c02da3d -r 6bb33bc9903f templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Sep 11 12:22:32 2008 -0400 +++ b/templates/workflow/editor.mako Fri Sep 12 07:13:09 2008 -0400 @@ -28,9 +28,21 @@ <script type='text/javascript' src="/static/scripts/galaxy.workflow_editor.canvas.js"> </script> +  + <script type='text/javascript'> $( function() { + if ( window.lt_ie_7 ) { + show_modal( + "Browser not supported", + "Sorry, the workflow editor is not supported for IE6 and below." + ); + return; + } // Initialize workflow state reset(); // Load the datatype info

1 0

[hg] galaxy 1501: Upgrade bx-python to r448.
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/362a1c02da3d changeset: 1501:362a1c02da3d user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 11 12:22:32 2008 -0400 description: Upgrade bx-python to r448. 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 30f4ab3cc266 -r 362a1c02da3d eggs.ini --- a/eggs.ini Wed Sep 10 09:58:29 2008 -0400 +++ b/eggs.ini Thu Sep 11 12:22:32 2008 -0400 @@ -55,12 +55,12 @@ MySQL_python = _5.0.51a_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r427 +bx_python = _dev_r448 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r427.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r448.tar.bz2 Cheetah = http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.51a.tar.gz

1 0

[hg] galaxy 1500: Allow complete logging configuration to be spe...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/30f4ab3cc266 changeset: 1500:30f4ab3cc266 user: James Taylor <james(a)jamestaylor.org> date: Wed Sep 10 09:58:29 2008 -0400 description: Allow complete logging configuration to be specified in the ini file, in which case this is used instead of the "log_level" and "log_format" keys under the app configuration. PasteScript actually handles this, so we just do nothing related to logging config if the ini file contains a "[loggers]" section. For example, you could add this to the end of your universe_wsgi.ini to include SQLAlchemy debugging and include the thread name with every log message. # Logger overrides [loggers] keys = root, sqlalchemy.engine, sqlalchemy.orm.unitofwork, paste.httpserver.ThreadPool [logger_root] level = DEBUG handlers = console [logger_sqlalchemy.engine] level = INFO handlers = console qualname = sqlalchemy.engine [logger_sqlalchemy.orm.unitofwork] level = DEBUG handlers = console qualname = sqlalchemy.orm.unitofwork [logger_paste.httpserver.ThreadPool] level = INFO handlers = console qualname = paste.httpserver.ThreadPool [handlers] keys = console [handler_console] class = StreamHandler args = (sys.stderr,) level = NOTSET formatter = generic [formatters] keys = generic [formatter_generic] format = %(threadName)s %(name)s %(levelname)s %(asctime)s %(message)s 1 file(s) affected in this change: lib/galaxy/config.py diffs (28 lines): diff -r f9d00dbefdec -r 30f4ab3cc266 lib/galaxy/config.py --- a/lib/galaxy/config.py Mon Sep 08 16:00:49 2008 -0400 +++ b/lib/galaxy/config.py Wed Sep 10 09:58:29 2008 -0400 @@ -64,9 +64,10 @@ self.bugs_email = kwargs.get( 'bugs_email', None ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) - #Parse global_conf + # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() + self.global_conf_parser = global_conf_parser if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) #Store per-tool runner config @@ -118,6 +119,12 @@ Allow some basic logging configuration to be read from the cherrpy config. """ + # PasteScript will have already configured the logger if the appropriate + # sections were found in the config file, so we do nothing if the + # config has a loggers section, otherwise we do some simple setup + # using the 'log_*' values from the config. + if config.global_conf_parser.has_section( "loggers" ): + return format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] destination = config.get( "log_destination", "stdout" )

1 0

[hg] galaxy 1499: Update GMAJ tool to allow the specifying of an...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f9d00dbefdec changeset: 1499:f9d00dbefdec user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Sep 08 16:00:49 2008 -0400 description: Update GMAJ tool to allow the specifying of annotations in two styles. 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (144 lines): diff -r ad69f789d1cd -r f9d00dbefdec tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Mon Sep 08 14:54:40 2008 -0400 +++ b/tools/visualization/GMAJ.xml Mon Sep 08 16:00:49 2008 -0400 @@ -1,21 +1,40 @@ -<tool id="gmaj_1" name="GMAJ" Version="2.0.0"> +<tool id="gmaj_1" name="GMAJ" Version="2.0.1"> <description>Multiple Alignment Viewer</description> <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> <repeat name="annotations" title="Annotations"> - <param name="species" type="select" label="Species of Annotation" multiple="False"> - <options> - <filter type="data_meta" ref="maf_input" key="species" /> - </options> - </param> - <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> - <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> - <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> - <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> - <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> - <param name="offset" label="Offset" value="0" type="integer"/> + <conditional name="annotation_style"> + <param name="style" type="select" label="Annotation Style" help="If your data is not in a style similar to what is available from Galaxy (and the UCSC table browser), choose 'Basic'."> + <option value="galaxy" selected="true">Galaxy</option> + <option value="basic">Basic</option> + </param> + <when value="galaxy"> + <param name="species" type="select" label="Species of Annotation" multiple="False"> + <options> + <filter type="data_meta" ref="maf_input" key="species" /> + </options> + </param> + <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> + <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> + <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> + <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> + <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> + <param name="offset" label="Offset" value="0" type="integer"/> + </when> + <when value="basic"> + <param name="seq_name" label="Full Sequence Name" value="" type="text"> + <validator type="empty_field" message="You must supply the sequence name"/> + </param> + <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> + <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> + <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> + <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> + <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> + <param name="offset" label="Offset" value="0" type="integer"/> + </when> + </conditional> </repeat> <param name="nowarn" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Warnings to Suppress" separator=" " help="These do not affect behavior, only suppress warning messages."> <options> @@ -81,52 +100,59 @@ #end if #set $seq_count = 0 -#for $spec_count, $annotation in $enumerate( $annotations ): -#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: -#set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]] -#else -#set $seq_names = [$annotation['species'].value] +#for $annotation_count, $annotation in $enumerate( $annotations ): +#if $annotation.annotation_style.style == "galaxy": +#if $maf_input.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: +#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#set $aliases = [ " %s" % $chrom for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#else: +#set $seq_names = [$annotation.annotation_style['species']] +#set $aliases = [""] #end if -#for $seq_name in $seq_names: +#else: +#set $seq_names = [$annotation.annotation_style['seq_name']] +#set $aliases = [""] +#end if +#for $seq_name, $alias in $zip( $seq_names, $aliases ): seq ${seq_count}: seqname = $seq_name -#if $annotation['exons_file'].dataset: -exons = ${spec_count}.exons.${annotation['exons_file'].extension} +#if $annotation.annotation_style['exons_file'].dataset: +exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}$alias #end if -#if $annotation['repeats_file'].dataset: -repeats = ${spec_count}.repeats.${annotation['repeats_file'].extension} +#if $annotation.annotation_style['repeats_file'].dataset: +repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}$alias #end if -#if $annotation['links_file'].dataset: -links = ${spec_count}.links.${annotation['links_file'].extension} +#if $annotation.annotation_style['links_file'].dataset: +links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}$alias #end if -#if $annotation['underlays_file'].dataset: -underlays = ${spec_count}.underlays.${annotation['underlays_file'].extension} +#if $annotation.annotation_style['underlays_file'].dataset: +underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}$alias #end if -#if $annotation['highlights_file'].dataset: -highlights = ${spec_count}.highlights.${annotation['highlights_file'].extension} +#if $annotation.annotation_style['highlights_file'].dataset: +highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}$alias #end if -offset = $annotation['offset'] +offset = $annotation.annotation_style['offset'] #set $seq_count = $seq_count + 1 #end for #end for </configfile> <configfile name="filenames_file"> -#for $spec_count, $annotation in $enumerate( $annotations ): -#if $annotation['exons_file'].dataset: -$annotation['exons_file'] = ${spec_count}.exons.${annotation['exons_file'].extension} +#for $annotation_count, $annotation in $enumerate( $annotations ): +#if $annotation.annotation_style['exons_file'].dataset: +$annotation.annotation_style['exons_file'] = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension} #end if -#if $annotation['repeats_file'].dataset: -$annotation['repeats_file'] = ${spec_count}.repeats.${annotation['repeats_file'].extension} +#if $annotation.annotation_style['repeats_file'].dataset: +$annotation.annotation_style['repeats_file'] = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension} #end if -#if $annotation['links_file'].dataset: -$annotation['links_file'] = ${spec_count}.links.${annotation['links_file'].extension} +#if $annotation.annotation_style['links_file'].dataset: +$annotation.annotation_style['links_file'] = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension} #end if -#if $annotation['underlays_file'].dataset: -$annotation['underlays_file'] = ${spec_count}.underlays.${annotation['underlays_file'].extension} +#if $annotation.annotation_style['underlays_file'].dataset: +$annotation.annotation_style['underlays_file'] = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension} #end if -#if $annotation['highlights_file'].dataset: -$annotation['highlights_file'] = ${spec_count}.highlights.${annotation['highlights_file'].extension} +#if $annotation.annotation_style['highlights_file'].dataset: +$annotation.annotation_style['highlights_file'] = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension} #end if #end for </configfile>

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[hg] galaxy 1496: The interval to BED converter will now use the...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/2a361ee9ce3e changeset: 1496:2a361ee9ce3e user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Sep 08 11:15:58 2008 -0400 description: The interval to BED converter will now use the name field specified via metadata, if available. 2 file(s) affected in this change: lib/galaxy/datatypes/converters/interval_to_bed_converter.py lib/galaxy/datatypes/converters/interval_to_bed_converter.xml diffs (48 lines): diff -r 49fe600b9499 -r 2a361ee9ce3e lib/galaxy/datatypes/converters/interval_to_bed_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Mon Sep 08 09:47:37 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Mon Sep 08 11:15:58 2008 -0400 @@ -31,18 +31,28 @@ strandCol = int( sys.argv[6] ) - 1 except: strandCol = -1 + try: + nameCol = int( sys.argv[7] ) - 1 + except: + nameCol = -1 skipped_lines = 0 first_skipped_line = 0 - count = 0 out = open( output_name,'w' ) - for region in bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ): + for count, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ) ): try: - out.write( region.chrom + "\t" + str( region.start ) + "\t" + str( region.end ) + "\tregion_" + str( count ) + "\t" + "0\t" + region.strand + "\n" ) + if nameCol >= 0: + name = region.fields[nameCol] + else: + raise IndexError + except: + name = "region_%i" % count + try: + + out.write( "%s\t%i\t%i\t%s\t%i\t%s\n" % ( region.chrom, region.start, region.end, name, 0, region.strand ) ) except: skipped_lines += 1 if not first_skipped_line: first_skipped_line = count + 1 - count += 1 out.close() info_msg = "%i regions converted to BED." % ( count - skipped_lines ) if skipped_lines > 0: diff -r 49fe600b9499 -r 2a361ee9ce3e lib/galaxy/datatypes/converters/interval_to_bed_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Sep 08 09:47:37 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Sep 08 11:15:58 2008 -0400 @@ -1,7 +1,7 @@ <tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED">   - <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command> + <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol}</command> <inputs> <page> <param format="interval" name="input1" type="data" label="Choose intervals"/>

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[hg] galaxy 1497: Fix for scatterplot.py: Handling an uncaught e...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/a17b2cd3d9a4 changeset: 1497:a17b2cd3d9a4 user: guru date: Mon Sep 08 14:36:37 2008 -0400 description: Fix for scatterplot.py: Handling an uncaught exception. 1 file(s) affected in this change: tools/plotting/scatterplot.py diffs (15 lines): diff -r 2a361ee9ce3e -r a17b2cd3d9a4 tools/plotting/scatterplot.py --- a/tools/plotting/scatterplot.py Mon Sep 08 11:15:58 2008 -0400 +++ b/tools/plotting/scatterplot.py Mon Sep 08 14:36:37 2008 -0400 @@ -44,7 +44,10 @@ skipped_lines += 1 if not first_invalid_line: first_invalid_line = i + 1 - invalid_value = fields[column] + try: + invalid_value = fields[column] + except: + invalid_value = '' invalid_column = column + 1 break else:

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[hg] galaxy 1498: Fix for grouping.py: New line character append...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ad69f789d1cd changeset: 1498:ad69f789d1cd user: guru date: Mon Sep 08 14:54:40 2008 -0400 description: Fix for grouping.py: New line character appended when grouping by the last column will now be trimmed. 1 file(s) affected in this change: tools/stats/grouping.py diffs (11 lines): diff -r a17b2cd3d9a4 -r ad69f789d1cd tools/stats/grouping.py --- a/tools/stats/grouping.py Mon Sep 08 14:36:37 2008 -0400 +++ b/tools/stats/grouping.py Mon Sep 08 14:54:40 2008 -0400 @@ -90,6 +90,7 @@ for ii, line in enumerate( file( tmpfile.name )): if line and not line.startswith( '#' ): + line = line.strip() try: fields = line.split("\t") item = fields[group_col]

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Main is at rev 1495:49fe600b9499
by Greg Von Kuster 08 Sep '08

08 Sep '08

1 0