galaxy-commits February 2011

galaxy-commits@lists.galaxyproject.org

1 participants
166 discussions

commit/galaxy-central: dan: Remove unused parameters from TopHat and Cufflinks tool tests.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/25a02a5c286f/ changeset: r5146:25a02a5c286f user: dan date: 2011-02-28 21:17:35 summary: Remove unused parameters from TopHat and Cufflinks tool tests. affected #: 2 files (171 bytes) --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 15:03:45 2011 -0500 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 15:17:35 2011 -0500 @@ -105,7 +105,6 @@ <test><param name="sPaired" value="No"/><param name="input" value="cufflinks_in.sam"/> - <param name="mean_inner_distance" value="20"/><param name="max_intron_len" value="300000"/><param name="min_isoform_fraction" value="0.05"/><param name="pre_mrna_fraction" value="0.05"/> --- a/tools/ngs_rna/tophat_wrapper.xml Mon Feb 28 15:03:45 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Mon Feb 28 15:17:35 2011 -0500 @@ -448,7 +448,6 @@ <param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/><param name="max_intron_length" value="500000"/> - <param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/><param name="min_segment_intron" value="50" /> @@ -494,7 +493,6 @@ <param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/><param name="max_intron_length" value="500000"/> - <param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/><param name="min_segment_intron" value="50" /> 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.

1 0

commit/galaxy-central: rc: Adding tests for vcf extract and filter tools
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/162fb94f7621/ changeset: r5145:162fb94f7621 user: rc date: 2011-02-28 21:03:45 summary: Adding tests for vcf extract and filter tools affected #: 11 files (3.1 KB) Diff too large to display. 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.

1 0

commit/galaxy-central: dannon: mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/05b089557d0d/ changeset: r5144:05b089557d0d user: dannon date: 2011-02-28 20:32:36 summary: mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag. affected #: 1 file (18 bytes) --- a/tools/sr_mapping/mosaik.xml Mon Feb 28 14:04:53 2011 -0500 +++ b/tools/sr_mapping/mosaik.xml Mon Feb 28 14:32:36 2011 -0500 @@ -13,8 +13,7 @@ #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': - ##$genomeSource.indexReference - ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } + ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } #else: $genomeSource.historyReference #end if @@ -95,7 +94,7 @@ <param name="act" value="35"/><param name="bw" value="19"/><param name="mhp" value="100"/> - <output name="output" ftype="sam" file="mosaik_test_out.sam" sort="True"/> + <output name="output" ftype="sam" file="mosaik_test_out.sam" compare="sim_size" delta="0"/></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.

1 0

commit/galaxy-central: guru: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3dce98e473f1/ changeset: r5143:3dce98e473f1 user: guru date: 2011-02-28 20:04:53 summary: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool. Also, fixed a bug in microsatellite birth/death tool - cases where microsatellite boundaries aren't defined are skipped. affected #: 4 files (317 bytes) --- a/test-data/q_values.tabular Mon Feb 28 12:16:28 2011 -0500 +++ b/test-data/q_values.tabular Mon Feb 28 14:04:53 2011 -0500 @@ -1,4 +1,4 @@ -pi0: 0.243863648325601 +pi0: 0.243864 FDR level: 0.05 --- a/tools/regVariation/compute_q_values.pl Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/compute_q_values.pl Mon Feb 28 14:04:53 2011 -0500 @@ -11,6 +11,8 @@ use strict; use warnings; use IO::Handle; +use File::Temp qw/ tempfile tempdir /; +my $tdir = tempdir( CLEANUP => 0 ); # check to make sure having correct input and output files my $usage = "usage: compute_q_values.pl [TABULAR.in] [lambda] [pi0_method] [fdr_level] [robust] [TABULAR.out] [PDF.out] \n"; @@ -44,7 +46,8 @@ my $r_script; # R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values -# construct an R script file and save it in the same directory where the perl file is located +# construct an R script file and save it in a temp directory +chdir $tdir; $r_script = "q_values_computation.r"; open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; @@ -76,6 +79,7 @@ dev.off(); #save the q-values in the output file $q_valuesOutputFile + qobj\$pi0 <- signif(qobj\$pi0,digits=6) qwrite(qobj, filename=\"$q_valuesOutputFile\"); #options(show.error.messages = TRUE); --- a/tools/regVariation/compute_q_values.xml Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/compute_q_values.xml Mon Feb 28 14:04:53 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="compute_q_values" name="Compute q-values" version="1.0.0"> +<tool id="compute_q_values" name="Compute q-values" version="1.0.1"><description>based on multiple simultaneous tests p-values</description><command interpreter="perl"> --- a/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 14:04:53 2011 -0500 @@ -643,7 +643,11 @@ my %microsatstarts=(); #1 WITHIN EACH ALIGNMENT, IF THERE EXISTS A MICROSATELLITE #2 THIS HASH CONTAINS THE START SITE OF THE MICROSATELLITE #3 WIHIN THE ALIGNMENT - + next if !defined $extreme_start; + next if !defined $extreme_end; + next if $extreme_start > length($sequences{$tags[0]}); + next if $extreme_start < 0; + next if $extreme_end > length($sequences{$tags[0]}); for my $i (0 ... $#tags){ #1 NOW THAT WE HAVE GATHERED INFORMATION REGARDING #2 SEQUENCE ALIGNMENT AND MICROSATELLITE COORDINATES @@ -3977,3 +3981,4 @@ foreach my $line (@_) {print "$line\n";} print "::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<\n"; } + 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.

1 0

commit/galaxy-central: dan: Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4d2d7c952d87/ changeset: r5142:4d2d7c952d87 user: dan date: 2011-02-28 18:16:28 summary: Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/. affected #: 16 files (2.5 KB) --- a/lib/galaxy/tools/test.py Mon Feb 28 09:59:30 2011 -0500 +++ b/lib/galaxy/tools/test.py Mon Feb 28 12:16:28 2011 -0500 @@ -1,4 +1,5 @@ import new, sys +import os.path import galaxy.util import parameters from parameters import basic @@ -12,7 +13,7 @@ """ Encapsulates information about a tool test, and allows creation of a dynamic TestCase class (the unittest framework is very class oriented, - doing dynamic tests in this was allows better integration) + doing dynamic tests in this way allows better integration) """ def __init__( self, tool, name, maxseconds ): self.tool = tool @@ -26,19 +27,17 @@ def add_param( self, name, value, extra ): try: if name not in self.tool.inputs: + found_parameter = False for input_name, input_value in self.tool.inputs.items(): - if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ): - self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) - elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files: - name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ] - if name_change: - name_change = name_change[-1].get( 'value' ) #only the last name change really matters - if value is None and not name_change: - assert self.tool.inputs[name].optional, '%s is not optional. You must provide a valid filename.' % name - else: - self.required_files.append( ( value, extra ) ) #these files will be uploaded - if name_change: - value = name_change #change value for select to renamed uploaded file for e.g. composite dataset + if isinstance( input_value, grouping.Group ): + found_parameter, new_value = self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) + if found_parameter: + value = new_value + break + if not found_parameter: + raise ValueError( "Unable to determine parameter type of test input '%s'. Ensure that the parameter exists and that any container groups are defined first." % name ) + elif isinstance( self.tool.inputs[name], basic.DataToolParameter ): + value = self.__add_uploaded_dataset( name, value, extra, self.tool.inputs[name] ) except Exception, e: log.debug( "Error in add_param for %s: %s" % ( name, e ) ) self.inputs.append( ( name, value, extra ) ) @@ -47,27 +46,65 @@ def __expand_grouping_for_data_input( self, name, value, extra, grouping_name, grouping_value ): # Currently handles grouping.Conditional and grouping.Repeat if isinstance( grouping_value, grouping.Conditional ): - if name != grouping_value.test_param.name: - for case in grouping_value.cases: - for case_input_name, case_input_value in case.inputs.items(): - if case_input_name == name and isinstance( case_input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files: - if value is None: - assert case_input_value.optional, '%s is not optional. You must provide a valid filename.' % name - else: - self.required_files.append( ( value, extra ) ) - return True - elif isinstance( case_input_value, grouping.Conditional ): - self.__expand_grouping_for_data_input(name, value, extra, case_input_name, case_input_value) + if name == grouping_value.test_param.name: + return True, value + case_test_param_value = None + for input in self.inputs: + if input[0] == grouping_value.test_param.name: + case_test_param_value = input[1] + break + if case_test_param_value is None: + #case for this group has not been set yet + return False, value + for case in grouping_value.cases: + if case.value == case_test_param_value: + break + if case.value != case_test_param_value: + return False, value + #assert case.value == case_test_param_value, "Current case could not be determined for parameter '%s'. Provided value '%s' could not be found in '%s'." % ( grouping_value.name, value, grouping_value.test_param.name ) + if name in case.inputs: + if isinstance( case.inputs[name], basic.DataToolParameter ): + return True, self.__add_uploaded_dataset( name, value, extra, case.inputs[name] ) + else: + return True, value + else: + for input_name, input_parameter in case.inputs.iteritems(): + if isinstance( input_parameter, grouping.Group ): + found_parameter, new_value = self.__expand_grouping_for_data_input( name, value, extra, input_name, input_parameter ) + if found_parameter: + return True, new_value elif isinstance( grouping_value, grouping.Repeat ): # FIXME: grouping.Repeat can only handle 1 repeat param element since the param name # is something like "input2" and the expanded page display is something like "queries_0|input2". # The problem is that the only param name on the page is "input2", and adding more test input params - # with the same name ( "input2" ) is not yet supported in our test code ( the lat one added is the only - # one used ). - for input_name, input_value in grouping_value.inputs.items(): - if input_name == name and isinstance( input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files: - if value is None: - assert input_value.optional, '%s is not optional. You must provide a valid filename.' % name - else: - self.required_files.append( ( value, extra ) ) - return True + # with the same name ( "input2" ) is not yet supported in our test code ( the last one added is the only + # one used ). + if name in grouping_value.inputs: + if isinstance( grouping_value.inputs[name], basic.DataToolParameter ): + return True, self.__add_uploaded_dataset( name, value, extra, grouping_value.inputs[name] ) + else: + return True, value + else: + for input_name, input_parameter in grouping_value.inputs.iteritems(): + if isinstance( input_parameter, grouping.Group ): + found_parameter, new_value = self.__expand_grouping_for_data_input( name, value, extra, input_name, input_parameter ) + if found_parameter: + return True, new_value + return False, value + def __add_uploaded_dataset( self, name, value, extra, input_parameter ): + if value is None: + assert input_parameter.optional, '%s is not optional. You must provide a valid filename.' % name + return value + if ( value, extra ) not in self.required_files: + self.required_files.append( ( value, extra ) ) #these files will be uploaded + name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ] + if name_change: + name_change = name_change[-1].get( 'value' ) #only the last name change really matters + value = name_change #change value for select to renamed uploaded file for e.g. composite dataset + else: + for end in [ '.zip', '.gz' ]: + if value.endswith( end ): + value = value[ :-len( end ) ] + break + value = os.path.basename( value ) #if uploading a file in a path other than root of test-data + return value --- a/test/functional/test_toolbox.py Mon Feb 28 09:59:30 2011 -0500 +++ b/test/functional/test_toolbox.py Mon Feb 28 12:16:28 2011 -0500 @@ -1,5 +1,4 @@ import sys, new -import os.path from galaxy.tools.parameters import grouping from galaxy.tools.parameters import basic from base.twilltestcase import TwillTestCase @@ -56,12 +55,6 @@ # tool will have uncompressed it on the fly. all_inputs = {} for name, value, _ in testdef.inputs: - if value: - for end in [ '.zip', '.gz' ]: - if value.endswith( end ): - value = value[ :-len( end ) ] - break - value = os.path.basename( value ) #if uploading a file in a path other than root of test-data all_inputs[ name ] = value # See if we have a grouping.Repeat element repeat_name = None --- a/tools/human_genome_variation/ldtools.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/human_genome_variation/ldtools.xml Mon Feb 28 12:16:28 2011 -0500 @@ -24,7 +24,7 @@ <param name="input" value="ldInput1.txt" /><param name="rsquare" value="0.64" /><param name="freq" value="0.00" /> - <param name="output" file="ldOutput1.txt" /> + <output name="output" file="ldOutput1.txt" /></test></tests> --- a/tools/maf/maf_to_fasta.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/maf/maf_to_fasta.xml Mon Feb 28 12:16:28 2011 -0500 @@ -38,15 +38,15 @@ <tests><test><param name="input1" value="3.maf" ftype="maf"/> + <param name="fasta_type" value="concatenated"/><param name="species" value="canFam1"/> - <param name="fasta_type" value="concatenated"/><output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/></test><test><param name="input1" value="4.maf" ftype="maf"/> + <param name="fasta_type" value="multiple"/><param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/><param name="complete_blocks" value="partial_allowed"/> - <param name="fasta_type" value="multiple"/><output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/></test></tests> --- a/tools/new_operations/intersect.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/new_operations/intersect.xml Mon Feb 28 12:16:28 2011 -0500 @@ -38,7 +38,6 @@ <code file="operation_filter.py"/><tests><test> - <param name="type" value="Interval"/><param name="input1" value="1.bed" /><param name="input2" value="2.bed" /><param name="min" value="1" /> @@ -46,7 +45,6 @@ <output name="output" file="gops_intersect_out.bed" /></test><test> - <param name="type" value="Interval"/><param name="input1" value="1.bed" /><param name="input2" value="2_mod.bed" ftype="interval"/><param name="min" value="1" /> --- a/tools/next_gen_conversion/solid2fastq.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/next_gen_conversion/solid2fastq.xml Mon Feb 28 12:16:28 2011 -0500 @@ -54,9 +54,9 @@ <test><param name="input1" value="fr.csfasta" ftype="csfasta"/><param name="input2" value="fr.qualsolid" ftype="qualsolid" /> + <param name="paired" value="yes"/><param name="input3" value="rr.csfasta" ftype="csfasta"/><param name="input4" value="rr.qualsolid" ftype="qualsolid" /> - <param name="paired" value="yes"/><param name="qual" value="0" /><param name="trim_first_base" value="No" /><param name="trim_name" value="Yes" /> --- a/tools/peak_calling/macs_wrapper.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/peak_calling/macs_wrapper.xml Mon Feb 28 12:16:28 2011 -0500 @@ -140,10 +140,10 @@ </configfiles><tests><test> + <param name="input_type_selector" value="single_end" /><param name="input_chipseq_file1" value="chipseq_enriched.bed.gz" ftype="bed" /><param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /> - <param name="input_type_selector" value="single_end" /><param name="tsize" value="36" /><param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /> @@ -166,10 +166,10 @@ </output></test><test> + <param name="input_type_selector" value="single_end" /><param name="input_chipseq_file1" value="chipseq_enriched.bed.gz" ftype="bed" /><param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /> - <param name="input_type_selector" value="single_end" /><param name="tsize" value="36" /><param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /> @@ -190,10 +190,10 @@ </output></test><param name="input1" value="3.bam" ftype="bam" /> - <param name="output1" file="bam_to_sam_out2.sam" sorted="True" /> + <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /></test></tests><help> --- a/tools/samtools/sam2interval.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/samtools/sam2interval.xml Mon Feb 28 12:16:28 2011 -0500 @@ -15,13 +15,11 @@ <tests><test><param name="input1" value="sam_bioinf_example.sam" ftype="sam"/> - <param name="flags" value="Read is mapped in a proper pair"/><param name="print_all" value="Yes"/><output name="out_file1" file="sam2interval_printAll.dat" ftype="interval"/></test><test><param name="input1" value="sam_bioinf_example.sam" ftype="sam"/> - <param name="flags" value="Read is mapped in a proper pair"/><param name="print_all" value="No"/><output name="out_file1" file="sam2interval_noprintAll.dat" ftype="interval"/></test> --- a/tools/samtools/sam_to_bam.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/samtools/sam_to_bam.xml Mon Feb 28 12:16:28 2011 -0500 @@ -60,7 +60,7 @@ --><param name="index_source" value="cached" /><param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" /> - <param name="output1" file="sam_to_bam_out2.bam" /> + <output name="output1" file="sam_to_bam_out2.bam" /></test></tests><help> --- a/tools/samtools/samtools_flagstat.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/samtools/samtools_flagstat.xml Mon Feb 28 12:16:28 2011 -0500 @@ -14,7 +14,7 @@ <tests><test><param name="input1" value="3.bam" ftype="bam" /> - <param name="output1" file="samtools_flagstat_out1.txt" /> + <output name="output1" file="samtools_flagstat_out1.txt" /></test></tests><help> --- a/tools/sr_mapping/bfast_wrapper.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/sr_mapping/bfast_wrapper.xml Mon Feb 28 12:16:28 2011 -0500 @@ -368,8 +368,6 @@ <param name="indices" value="phiX_nt_50" /><param name="source_select" value="pre_set" /><param name="suppressHeader" value="False" /> - <param name="indexing_repeatmasker" value="" /> - <param name="indexing_option_selector" value="default" /><output name="output" ftype="sam" file="bfast_out3.sam" lines_diff="2" /></test></tests> 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.

1 0

commit/galaxy-central: jgoecks: Fix bad value in cufflinks functional test.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4146f64da13d/ changeset: r5141:4146f64da13d user: jgoecks date: 2011-02-28 15:59:30 summary: Fix bad value in cufflinks functional test. affected #: 1 file (4 bytes) --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 09:52:17 2011 -0500 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 09:59:30 2011 -0500 @@ -103,7 +103,7 @@ Simple test that uses test data included with cufflinks. --><test> - <param name="sPaired" value="single"/> + <param name="sPaired" value="No"/><param name="input" value="cufflinks_in.sam"/><param name="mean_inner_distance" value="20"/><param name="max_intron_len" value="300000"/> 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.

1 0

commit/galaxy-central: natefoo: Bugfix for the last commit when running functional tests with sqlite.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2e88578ef7e1/ changeset: r5140:2e88578ef7e1 user: natefoo date: 2011-02-28 15:52:17 summary: Bugfix for the last commit when running functional tests with sqlite. affected #: 1 file (49 bytes) --- a/scripts/functional_tests.py Mon Feb 28 09:35:36 2011 -0500 +++ b/scripts/functional_tests.py Mon Feb 28 09:52:17 2011 -0500 @@ -139,13 +139,15 @@ if psu_production: global_conf = None + if not database_connection.startswith( 'sqlite://' ): + kwargs['database_engine_option_max_overflow'] = '20' + # Build the Universe Application app = UniverseApplication( job_queue_workers = 5, id_secret = 'changethisinproductiontoo', template_path = "templates", database_connection = database_connection, database_engine_option_pool_size = '10', - database_engine_option_max_overflow = '20', file_path = file_path, new_file_path = new_file_path, tool_path = tool_path, 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.

1 0

commit/galaxy-central: natefoo: Require ctypes egg before pysam on Python 2.4
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b9b772f2e4eb/ changeset: r5139:b9b772f2e4eb user: natefoo date: 2011-02-28 15:35:36 summary: Require ctypes egg before pysam on Python 2.4 affected #: 2 files (157 bytes) --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Mon Feb 28 08:33:48 2011 -0500 +++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Mon Feb 28 09:35:36 2011 -0500 @@ -4,7 +4,11 @@ import sys from galaxy import eggs -import pkg_resources; pkg_resources.require( "pysam" ) +import pkg_resources + +if sys.version_info[:2] == (2, 4): + pkg_resources.require( "ctypes" ) +pkg_resources.require( "pysam" ) from pysam import csamtools from galaxy.visualization.tracks.summary import * @@ -24,4 +28,4 @@ st.write(out_fname) if __name__ == "__main__": - main() \ No newline at end of file + main() --- a/lib/galaxy/visualization/tracks/data_providers.py Mon Feb 28 08:33:48 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Feb 28 09:35:36 2011 -0500 @@ -2,9 +2,14 @@ Data providers for tracks visualizations. """ +import sys from math import floor, ceil, log, pow import pkg_resources -pkg_resources.require( "bx-python" ); pkg_resources.require( "pysam" ); pkg_resources.require( "numpy" ) +pkg_resources.require( "bx-python" ) +if sys.version_info[:2] == (2, 4): + pkg_resources.require( "ctypes" ) +pkg_resources.require( "pysam" ) +pkg_resources.require( "numpy" ) from galaxy.datatypes.util.gff_util import * from bx.interval_index_file import Indexes from bx.arrays.array_tree import FileArrayTreeDict @@ -671,4 +676,4 @@ blocks = zip( block_sizes, block_starts ) payload.append( [ ( feature.start + block[1], feature.start + block[1] + block[0] ) for block in blocks ] ) - return payload \ No newline at end of file + return payload 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.

1 0

commit/galaxy-central: natefoo: Add ccat_configurations.loc to buildbot_setup.sh
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/16cafc8da6f3/ changeset: r5138:16cafc8da6f3 user: natefoo date: 2011-02-28 14:33:48 summary: Add ccat_configurations.loc to buildbot_setup.sh affected #: 1 file (46 bytes) --- a/buildbot_setup.sh Mon Feb 28 07:58:52 2011 -0500 +++ b/buildbot_setup.sh Mon Feb 28 08:33:48 2011 -0500 @@ -40,6 +40,7 @@ /galaxy/data/location/bowtie_indices_color.loc /galaxy/data/location/bwa_index.loc /galaxy/data/location/bwa_index_color.loc +/galaxy/data/location/ccat_configurations.loc /galaxy/data/location/codingSnps.loc /galaxy/data/location/encode_datasets.loc /galaxy/home/universe/encode_feature_partitions 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.

1 0

commit/galaxy-central: natefoo: Increase the SQLAlchemy SuquePool limits for functional tests.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5bced201f40a/ changeset: r5137:5bced201f40a user: natefoo date: 2011-02-28 13:58:52 summary: Increase the SQLAlchemy SuquePool limits for functional tests. affected #: 1 file (155 bytes) --- a/scripts/functional_tests.py Sun Feb 27 14:48:23 2011 -0500 +++ b/scripts/functional_tests.py Mon Feb 28 07:58:52 2011 -0500 @@ -144,6 +144,8 @@ id_secret = 'changethisinproductiontoo', template_path = "templates", database_connection = database_connection, + database_engine_option_pool_size = '10', + database_engine_option_max_overflow = '20', file_path = file_path, new_file_path = new_file_path, tool_path = tool_path, 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.

1 0

Jump to page:

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

galaxy-commits February 2011