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[hg] galaxy 3764: Add 'filter transcripts via tracking' tool to ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4e5ca6c44804 changeset: 3764:4e5ca6c44804 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon May 10 12:42:05 2010 -0400 description: Add 'filter transcripts via tracking' tool to RNA-seq tools. This tool is useful for operating on output files from cufftools suite. diffstat: tool_conf.xml.sample | 1 + tools/ngs_rna/filter_transcripts_via_tracking.py | 70 +++++++++++++++++++++++ tools/ngs_rna/filter_transcripts_via_tracking.xml | 32 ++++++++++ 3 files changed, 103 insertions(+), 0 deletions(-) diffs (121 lines): diff -r 1110a91888e2 -r 4e5ca6c44804 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon May 10 11:55:08 2010 -0400 +++ b/tool_conf.xml.sample Mon May 10 12:42:05 2010 -0400 @@ -239,6 +239,7 @@ <tool file="ngs_rna/cufflinks_wrapper.xml" /> <tool file="ngs_rna/cuffcompare_wrapper.xml" /> <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> </section> <section name="NGS: SAM Tools" id="samtools"> <tool file="samtools/sam_bitwise_flag_filter.xml" /> diff -r 1110a91888e2 -r 4e5ca6c44804 tools/ngs_rna/filter_transcripts_via_tracking.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ngs_rna/filter_transcripts_via_tracking.py Mon May 10 12:42:05 2010 -0400 @@ -0,0 +1,70 @@ +#!/usr/bin/env python +import os, sys, tempfile + +assert sys.version_info[:2] >= ( 2, 4 ) + +def __main__(): + """ + Utility script for analyzing Cufflinks data: uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts + produced by cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the GTF so that the output GTF contains only + transcript found in the tracking file. Because a tracking file has multiple samples, a sample number is used to filter transcripts for + a particular sample. + """ + # Read parms. + tracking_file_name = sys.argv[1] + transcripts_file_name = sys.argv[2] + output_file_name = sys.argv[3] + sample_number = int ( sys.argv[4] ) + + # Open files. + transcripts_file = open( transcripts_file_name, 'r' ) + output_file = open( output_file_name, 'w' ) + + # Read transcript IDs from tracking file. + transcript_ids = {} + for i, line in enumerate( file( tracking_file_name ) ) : + # Split line into elements. Line format is + # [Transfrag ID] [Locus ID] [Ref Gene ID] [Ref Transcript ID] [Class code] [qJ:<gene_id>|<transcript_id>|<FMI>|<FPKM>|<conf_lo>|<conf_hi>] + line = line.rstrip( '\r\n' ) + elems = line.split( '\t' ) + + # Get transcript info. + if sample_number == 1: + transcript_info = elems[4] + elif sample_number == 2: + transcript_info = elems[5] + if not transcript_info.startswith('q'): + # No transcript for this sample. + continue + + # Get and store transcript id. + transcript_id = transcript_info.split('|')[1] + transcript_id = transcript_id.strip('"') + transcript_ids[transcript_id] = "" + + # Filter transcripts file using transcript_ids + for i, line in enumerate( file( transcripts_file_name ) ): + # GTF format: chrom source, name, chromStart, chromEnd, score, strand, frame, attributes. + elems = line.split( '\t' ) + + # Get attributes. + attributes_list = elems[8].split(";") + attributes = {} + for name_value_pair in attributes_list: + pair = name_value_pair.strip().split(" ") + name = pair[0].strip() + if name == '': + continue + # Need to strip double quote from values + value = pair[1].strip(" \"") + attributes[name] = value + + # Get element's transcript id. + transcript_id = attributes['transcript_id'] + if transcript_id in transcript_ids: + output_file.write(line) + + # Clean up. + output_file.close() + +if __name__ == "__main__": __main__() diff -r 1110a91888e2 -r 4e5ca6c44804 tools/ngs_rna/filter_transcripts_via_tracking.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ngs_rna/filter_transcripts_via_tracking.xml Mon May 10 12:42:05 2010 -0400 @@ -0,0 +1,32 @@ +<tool id="filter_combined_via_tracking" name="Filter Combined Transcripts" version="0.1"> + <description>using tracking file</description> + <command interpreter="python"> + filter_transcripts_via_tracking.py + $tracking_file + $transcripts_file + $filtered_transcripts + $sample_num + </command> + <inputs> + <param format="gtf" name="transcripts_file" type="data" label="Cufflinks assembled transcripts" help=""/> + <param format="tabular" name="tracking_file" type="data" label="Cuffcompare tracking file" help=""/> + <param name="sample_num" type="select" label="Sample Number"> + <option value="1">1</option> + <option value="2">2</option> + </param> + </inputs> + + <outputs> + <data format="gtf" name="filtered_transcripts"/> + </outputs> + + <tests> + </tests> + + <help> + Uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts produced by + cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the + GTF so that the output GTF contains only transcript found in the tracking file. Because a tracking file has multiple + samples, a sample number is used to filter transcripts for a particular sample. + </help> +</tool>

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[hg] galaxy 3763: right welcome.html at last
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1110a91888e2 changeset: 3763:1110a91888e2 user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 11:55:08 2010 -0400 description: right welcome.html at last diffstat: static/welcome.html | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (15 lines): diff -r df72c7a8d5cf -r 1110a91888e2 static/welcome.html --- a/static/welcome.html Mon May 10 11:49:25 2010 -0400 +++ b/static/welcome.html Mon May 10 11:55:08 2010 -0400 @@ -8,9 +8,9 @@ <body> <div class="document"> <div class="warningmessagelarge"> - <strong>Welcome to Galaxy at the Channing Laboratory</strong> + <strong>Hello world! It's running...</strong> <hr> - Your jobs will run under SGE on the cluster. + To customize this page edit <code>static/welcome.html</code> </div> <br/> <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" />

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[hg] galaxy 3762: Revert inadvertantly updated tool_conf.xml.sam...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/df72c7a8d5cf changeset: 3762:df72c7a8d5cf user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 11:49:25 2010 -0400 description: Revert inadvertantly updated tool_conf.xml.sample and welcome.html diffstat: static/welcome.html | 3 +- tool_conf.xml.sample | 231 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 233 insertions(+), 1 deletions(-) diffs (256 lines): diff -r ecbd01636a92 -r df72c7a8d5cf static/welcome.html --- a/static/welcome.html Mon May 10 11:22:50 2010 -0400 +++ b/static/welcome.html Mon May 10 11:49:25 2010 -0400 @@ -10,9 +10,10 @@ <div class="warningmessagelarge"> <strong>Welcome to Galaxy at the Channing Laboratory</strong> <hr> + Your jobs will run under SGE on the cluster. </div> <br/> - <img src="images/Armitagep_manhattan.png" alt="manhattan plot" style="display: block; margin-left: auto; margin-right: auto;" /> + <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> <hr/> This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. </div> diff -r ecbd01636a92 -r df72c7a8d5cf tool_conf.xml.sample --- a/tool_conf.xml.sample Mon May 10 11:22:50 2010 -0400 +++ b/tool_conf.xml.sample Mon May 10 11:49:25 2010 -0400 @@ -23,6 +23,237 @@ <tool file="data_source/hbvar.xml" /> <tool file="validation/fix_errors.xml" /> </section> + <section name="Send Data" id="send"> + <tool file="data_destination/epigraph.xml" /> + <tool file="data_destination/epigraph_test.xml" /> + </section> + <section name="ENCODE Tools" id="EncodeTools"> + <tool file="encode/gencode_partition.xml" /> + <tool file="encode/random_intervals.xml" /> + </section> + <section name="Lift-Over" id="liftOver"> + <tool file="extract/liftOver_wrapper.xml" /> + </section> + <section name="Text Manipulation" id="textutil"> + <tool file="filters/fixedValueColumn.xml" /> + <tool file="stats/column_maker.xml" /> + <tool file="filters/catWrapper.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/mergeCols.xml" /> + <tool file="filters/convert_characters.xml" /> + <tool file="filters/CreateInterval.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/changeCase.xml" /> + <tool file="filters/pasteWrapper.xml" /> + <tool file="filters/remove_beginning.xml" /> + <tool file="filters/randomlines.xml" /> + <tool file="filters/headWrapper.xml" /> + <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /> + <tool file="stats/dna_filtering.xml" /> + <tool file="new_operations/tables_arithmetic_operations.xml" /> + </section> + <section name="Filter and Sort" id="filter"> + <tool file="stats/filtering.xml" /> + <tool file="filters/sorter.xml" /> + <tool file="filters/grep.xml" /> + </section> + <section name="Join, Subtract and Group" id="group"> + <tool file="filters/joiner.xml" /> + <tool file="filters/compare.xml"/> + <tool file="new_operations/subtract_query.xml"/> + <tool file="stats/grouping.xml" /> + <tool file="new_operations/column_join.xml" /> + </section> + <section name="Convert Formats" id="convert"> + <tool file="filters/axt_to_concat_fasta.xml" /> + <tool file="filters/axt_to_fasta.xml" /> + <tool file="filters/axt_to_lav.xml" /> + <tool file="filters/bed2gff.xml" /> + <tool file="fasta_tools/fasta_to_tabular.xml" /> + <tool file="filters/gff2bed.xml" /> + <tool file="filters/lav_to_bed.xml" /> + <tool file="maf/maf_to_bed.xml" /> + <tool file="maf/maf_to_interval.xml" /> + <tool file="maf/maf_to_fasta.xml" /> + <tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="filters/wiggle_to_simple.xml" /> + <tool file="filters/sff_extractor.xml" /> + <tool file="filters/gtf2bedgraph.xml" /> + </section> + <section name="Extract Features" id="features"> + <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> + <tool file="extract/extract_GFF_Features.xml" /> + </section> + <section name="Fetch Sequences" id="fetchSeq"> + <tool file="extract/extract_genomic_dna.xml" /> + </section> + <section name="Fetch Alignments" id="fetchAlign"> + <tool file="maf/interval2maf_pairwise.xml" /> + <tool file="maf/interval2maf.xml" /> + <tool file="maf/maf_split_by_species.xml"/> + <tool file="maf/interval_maf_to_merged_fasta.xml" /> + <tool file="maf/genebed_maf_to_fasta.xml"/> + <tool file="maf/maf_stats.xml"/> + <tool file="maf/maf_thread_for_species.xml"/> + <tool file="maf/maf_limit_to_species.xml"/> + <tool file="maf/maf_limit_size.xml"/> + <tool file="maf/maf_by_block_number.xml"/> + <tool file="maf/maf_reverse_complement.xml"/> + <tool file="maf/maf_filter.xml"/> + </section> + <section name="Get Genomic Scores" id="scores"> + <tool file="stats/wiggle_to_simple.xml" /> + <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> + <tool file="extract/phastOdds/phastOdds_tool.xml" /> + </section> + <section name="Operate on Genomic Intervals" id="bxops"> + <tool file="new_operations/intersect.xml" /> + <tool file="new_operations/subtract.xml" /> + <tool file="new_operations/merge.xml" /> + <tool file="new_operations/concat.xml" /> + <tool file="new_operations/basecoverage.xml" /> + <tool file="new_operations/coverage.xml" /> + <tool file="new_operations/complement.xml" /> + <tool file="new_operations/cluster.xml" id="cluster" /> + <tool file="new_operations/join.xml" /> + <tool file="new_operations/get_flanks.xml" /> + <tool file="new_operations/flanking_features.xml" /> + <tool file="annotation_profiler/annotation_profiler.xml" /> + </section> + <section name="Statistics" id="stats"> + <tool file="stats/gsummary.xml" /> + <tool file="filters/uniq.xml" /> + <tool file="stats/cor.xml" /> + <tool file="regVariation/t_test_two_samples.xml" /> + <tool file="regVariation/compute_q_values.xml" /> + </section> + <section name="Graph/Display Data" id="plots"> + <tool file="plotting/histogram2.xml" /> + <tool file="plotting/scatterplot.xml" /> + <tool file="plotting/bar_chart.xml" /> + <tool file="plotting/xy_plot.xml" /> + <tool file="plotting/boxplot.xml" /> + <tool file="visualization/GMAJ.xml" /> + <tool file="visualization/LAJ.xml" /> + <tool file="visualization/build_ucsc_custom_track.xml" /> + </section> + <section name="Regional Variation" id="regVar"> + <tool file="regVariation/windowSplitter.xml" /> + <tool file="regVariation/featureCounter.xml" /> + <tool file="regVariation/quality_filter.xml" /> + <tool file="regVariation/maf_cpg_filter.xml" /> + <tool file="regVariation/getIndels_2way.xml" /> + <tool file="regVariation/getIndels_3way.xml" /> + <tool file="regVariation/getIndelRates_3way.xml" /> + <tool file="regVariation/substitutions.xml" /> + <tool file="regVariation/substitution_rates.xml" /> + <tool file="regVariation/microsats_alignment_level.xml" /> + <tool file="regVariation/microsats_mutability.xml" /> + <tool file="regVariation/delete_overlapping_indels.xml" /> + <tool file="regVariation/compute_motifs_frequency.xml" /> + <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /> + <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s + <tool file="regVariation/draw_stacked_barplots.xml" /> + </section> + <section name="Multiple regression" id="multReg"> + <tool file="regVariation/linear_regression.xml" /> + <tool file="regVariation/best_regression_subsets.xml" /> + <tool file="regVariation/rcve.xml" /> + </section> + <section name="Multivariate Analysis" id="multVar"> + <tool file="multivariate_stats/pca.xml" /> + <tool file="multivariate_stats/cca.xml" /> + <tool file="multivariate_stats/kpca.xml" /> + <tool file="multivariate_stats/kcca.xml" /> + </section> + <section name="Evolution" id="hyphy"> + <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> + <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> + <tool file="hyphy/hyphy_dnds_wrapper.xml" /> + <tool file="evolution/mutate_snp_codon.xml" /> + <tool file="evolution/codingSnps.xml" /> + <tool file="evolution/add_scores.xml" /> + </section> + <section name="Metagenomic analyses" id="tax_manipulation"> + <tool file="taxonomy/gi2taxonomy.xml" /> + <tool file="taxonomy/t2t_report.xml" /> + <tool file="taxonomy/t2ps_wrapper.xml" /> + <tool file="taxonomy/find_diag_hits.xml" /> + <tool file="taxonomy/lca.xml" /> + <tool file="taxonomy/poisson2test.xml" /> + </section> + <section name="FASTA manipulation" id="fasta_manipulation"> + <tool file="fasta_tools/fasta_compute_length.xml" /> + <tool file="fasta_tools/fasta_filter_by_length.xml" /> + <tool file="fasta_tools/fasta_concatenate_by_species.xml" /> + <tool file="fasta_tools/fasta_to_tabular.xml" /> + <tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastx_toolkit/fasta_formatter.xml" /> + <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> + <tool file="fastx_toolkit/fastx_collapser.xml" /> + </section> + <section name="NGS: QC and manipulation" id="cshl_library_information"> + <label text="Illumina data" id="illumina" /> + <tool file="fastq/fastq_groomer.xml" /> + <tool file="fastq/fastq_paired_end_splitter.xml" /> + <tool file="fastq/fastq_paired_end_joiner.xml" /> + <tool file="fastq/fastq_stats.xml" /> +  + <label text="Roche-454 data" id="454" /> + <tool file="metag_tools/short_reads_figure_score.xml" /> + <tool file="metag_tools/short_reads_trim_seq.xml" /> + <tool file="fastq/fastq_combiner.xml" /> + <label text="AB-SOLiD data" id="solid" /> + <tool file="next_gen_conversion/solid2fastq.xml" /> + <tool file="solid_tools/solid_qual_stats.xml" /> + <tool file="solid_tools/solid_qual_boxplot.xml" /> + <label text="Generic FASTQ manipulation" id="generic_fastq" /> + <tool file="fastq/fastq_filter.xml" /> + <tool file="fastq/fastq_trimmer.xml" /> + <tool file="fastq/fastq_trimmer_by_quality.xml" /> + <tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /> + <tool file="fastq/fastq_to_tabular.xml" /> + <tool file="fastq/tabular_to_fastq.xml" /> + </section> + <section name="NGS: Mapping" id="solexa_tools"> + <tool file="sr_mapping/lastz_wrapper.xml" /> + <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" /> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bowtie_color_wrapper.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + <tool file="sr_mapping/PerM.xml" /> + </section> + <section name="NGS: Expression Analysis" id="ngs-rna-tools"> + <tool file="ngs_rna/tophat_wrapper.xml" /> + <tool file="ngs_rna/cufflinks_wrapper.xml" /> + <tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + </section> + <section name="NGS: SAM Tools" id="samtools"> + <tool file="samtools/sam_bitwise_flag_filter.xml" /> + <tool file="samtools/sam2interval.xml" /> + <tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/sam_merge.xml" /> + <tool file="samtools/sam_pileup.xml" /> + <tool file="samtools/pileup_parser.xml" /> + <tool file="samtools/pileup_interval.xml" /> + </section> + <section name="NGS: Peak Calling" id="peak_calling"> + <tool file="peak_calling/macs_wrapper.xml" /> + <tool file="genetrack/genetrack_indexer.xml" /> + <tool file="genetrack/genetrack_peak_prediction.xml" /> + </section> <section name="SNP/WGA: Data; Filters" id="rgdat"> <label text="Data: Import and upload" id="rgimport" /> <tool file="data_source/upload.xml"/>

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[hg] galaxy 3761: Bug in SGE external metadata
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ecbd01636a92 changeset: 3761:ecbd01636a92 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon May 10 11:22:50 2010 -0400 description: Bug in SGE external metadata diffstat: lib/galaxy/jobs/runners/sge.py | 3 +-- 1 files changed, 1 insertions(+), 2 deletions(-) diffs (17 lines): diff -r f53d06cf2f93 -r ecbd01636a92 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Mon May 10 11:13:51 2010 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Mon May 10 11:22:50 2010 -0400 @@ -166,12 +166,11 @@ script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) if self.app.config.set_metadata_externally: - output_fnames = [ str( o ) for o in job_wrapper.get_output_fnames() ] script += "cd %s\n" % os.path.abspath( os.getcwd() ) script += "%s\n" % job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), tmp_dir = self.app.config.new_file_path, dataset_files_path = self.app.model.Dataset.file_path, - output_fnames = output_fnames, + output_fnames = job_wrapper.get_output_fnames(), set_extension = False, kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior fh = file( jt.remoteCommand, "w" )

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[hg] galaxy 3760: Add external metadata to SGE
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f53d06cf2f93 changeset: 3760:f53d06cf2f93 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon May 10 11:13:51 2010 -0400 description: Add external metadata to SGE diffstat: lib/galaxy/jobs/runners/sge.py | 9 +++++++++ 1 files changed, 9 insertions(+), 0 deletions(-) diffs (19 lines): diff -r 6aa1379d35e0 -r f53d06cf2f93 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Mon May 10 10:17:11 2010 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Mon May 10 11:13:51 2010 -0400 @@ -165,6 +165,15 @@ jt.nativeSpecification = ' '.join(nativeSpec) script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) + if self.app.config.set_metadata_externally: + output_fnames = [ str( o ) for o in job_wrapper.get_output_fnames() ] + script += "cd %s\n" % os.path.abspath( os.getcwd() ) + script += "%s\n" % job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), + tmp_dir = self.app.config.new_file_path, + dataset_files_path = self.app.model.Dataset.file_path, + output_fnames = output_fnames, + set_extension = False, + kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior fh = file( jt.remoteCommand, "w" ) fh.write( script ) fh.close()

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[hg] galaxy 3759: SNP/WGA tool changes only
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6aa1379d35e0 changeset: 3759:6aa1379d35e0 user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 10:17:11 2010 -0400 description: SNP/WGA tool changes only Updates to functional test outputs Minor tweaks to some tests All now pass when run using -sid but there's something busted when a full functional test is run diffstat: static/welcome.html | 5 +- test-data/rgCaCotest1_CaCo_log.txt | 20 +- test-data/rgGLMtest1_GLM_log.txt | 28 +- test-data/rgQQtest1.pdf | 52 +- test-data/rgTDTtest1_TDT_log.txt | 18 +- test-data/rgtestouts/rgClean/rgCleantest1.log | 28 +- test-data/rgtestouts/rgEigPCA/Rplots.pdf | 46 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R | 2 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html | 35 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf | 50 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt | 6 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls | 80 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par | 6 +- test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 8 +- test-data/rgtestouts/rgGRR/rgGRRtest1.html | 14 +- test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 118 +- test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 1560 +++++----- test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf | 0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png | 0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG | 0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt | 16 +- test-data/rgtestouts/rgHaploView/alljoin.pdf | 0 test-data/rgtestouts/rgHaploView/allnup.pdf | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html | 16 +- test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS | 14 +- test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS | 10 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed | 2 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log | 96 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped | 80 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out | 4 +- test-data/rgtestouts/rgManQQ/Allelep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R | 4 +- test-data/rgtestouts/rgManQQ/rgManQQtest1.html | 4 +- test-data/rgtestouts/rgPedSub/rgPedSubtest1.log | 8 +- test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf | 182 +- test-data/rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls | 36 +- test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls | 72 +- test-data/rgtestouts/rgQC/ldp_tinywga.bed | 2 +- test-data/rgtestouts/rgQC/ldp_tinywga.bim | 10 +- test-data/rgtestouts/rgQC/ldp_tinywga.log | 18 +- test-data/rgtestouts/rgQC/rgQCtest1.html | 208 +- test-data/rgtestouts/rgQC/tinywga.het | 80 +- test-data/rgtestouts/rgQC/tinywga.log | 6 +- test-data/rgtestouts/rgQC/tinywga.prune.in | 10 +- test-data/rgtestouts/rgQC/tinywga.prune.out | 10 +- test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf | 50 +- test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf | 52 +- test-data/rgtestouts/rgQC/tinywga_s_het.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het.pdf | 343 +- test-data/rgtestouts/rgQC/tinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf | 182 +- test-data/rgtestouts/rgfakePed/rgfakePedtest1.lped | 2 +- test-data/rgtestouts/rgfakePed/rgfakePedtest1.ped | 80 +- test-data/rgtestouts/rgfakePhe/rgfakePhetest1.pphe | 80 +- tool-data/annotation_profiler_options.xml.sample | 2 +- tool_conf.xml.sample | 231 - tools/rgenetics/rgGRR.py | 12 +- tools/rgenetics/rgGRR.xml | 10 +- tools/rgenetics/rgHaploView.xml | 4 +- tools/rgenetics/rgQC.xml | 2 +- tools/rgenetics/rgtest.sh | 6 +- tools/rgenetics/rgutils.py | 20 +- 81 files changed, 2045 insertions(+), 2007 deletions(-) diffs (truncated from 5750 to 3000 lines): diff -r acaf971320bd -r 6aa1379d35e0 static/welcome.html --- a/static/welcome.html Mon May 10 10:03:00 2010 -0400 +++ b/static/welcome.html Mon May 10 10:17:11 2010 -0400 @@ -8,12 +8,11 @@ <body> <div class="document"> <div class="warningmessagelarge"> - <strong>Hello world! It's running...</strong> + <strong>Welcome to Galaxy at the Channing Laboratory</strong> <hr> - To customize this page edit <code>static/welcome.html</code> </div> <br/> - <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> + <img src="images/Armitagep_manhattan.png" alt="manhattan plot" style="display: block; margin-left: auto; margin-right: auto;" /> <hr/> This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. </div> diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgCaCotest1_CaCo_log.txt --- a/test-data/rgCaCotest1_CaCo_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgCaCotest1_CaCo_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,6 +1,6 @@ @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,24 +10,24 @@ Skipping web check... [ --noweb ] Writing this text to log file [ rgCaCotest1.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --out rgCaCotest1 --model -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -40,7 +40,7 @@ Full-model association tests, minimum genotype count: --cell 5 Writing full model association results to [ rgCaCotest1.model ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 ###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772 -Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 25/03/2010 21:01:31 +Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 09/05/2010 21:23:49 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgGLMtest1_GLM_log.txt --- a/test-data/rgGLMtest1_GLM_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgGLMtest1_GLM_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,11 +1,11 @@ -rgGLM.py called with ['/opt/galaxy/tools/rgenetics/rgGLM.py', '/opt/galaxy/test-data/tinywga', '/opt/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/opt/galaxy/test-data/rgGLMtest1_GLM.xls', '/opt/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/opt/galaxy/test-data/rgGLM_GLM_topTable.gff'] -vcl=['plink', '--noweb', '--bfile', '/opt/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/opt/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] -xformQassoc got resf=/tmp/tmpCB6CwWrgGLM/tinywga.assoc.linear, outfname=/opt/galaxy/test-data/rgGLMtest1_GLM.xls +rgGLM.py called with ['/share/shared/galaxy/tools/rgenetics/rgGLM.py', '/share/shared/galaxy/test-data/tinywga', '/share/shared/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_topTable.gff'] +vcl=['plink', '--noweb', '--bfile', '/share/shared/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/share/shared/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] +xformQassoc got resf=/tmp/tmpXKEn_LrgGLM/tinywga.assoc.linear, outfname=/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls ###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -15,31 +15,31 @@ Skipping web check... [ --noweb ] Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --pheno-name c1 - --pheno /opt/galaxy/test-data/tinywga.pphe + --pheno /share/shared/galaxy/test-data/tinywga.pphe --out tinywga --mind 1 --geno 1 --maf 0 --linear -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode -Reading alternate phenotype from [ /opt/galaxy/test-data/tinywga.pphe ] +Reading alternate phenotype from [ /share/shared/galaxy/test-data/tinywga.pphe ] 40 individuals with non-missing alternate phenotype Assuming a quantitative trait Missing phenotype value is -9 @@ -54,5 +54,5 @@ Converting data to Individual-major format Writing linear model association results to [ tinywga.assoc.linear ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgQQtest1.pdf --- a/test-data/rgQQtest1.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgQQtest1.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210132) -/ModDate (D:20100325210132) +/CreationDate (D:20100509212350) +/ModDate (D:20100509212350) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -331,10 +331,42 @@ 8 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +/BaseEncoding /PDFDocEncoding +/Differences [ + 0/.notdef 1/.notdef 2/.notdef 3/.notdef 4/.notdef 5/.notdef 6/.notdef 7/.notdef + 8/.notdef 9/.notdef 10/.notdef 11/.notdef 12/.notdef 13/.notdef 14/.notdef 15/.notdef + 16/.notdef 17/.notdef 18/.notdef 19/.notdef 20/.notdef 21/.notdef 22/.notdef 23/.notdef + 24/.notdef 25/.notdef 26/.notdef 27/.notdef 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142/.notdef 143/.notdef + 144/dotlessi 145/grave 146/acute 147/circumflex 148/tilde 149/macron 150/breve 151/dotaccent + 152/dieresis 153/.notdef 154/ring 155/cedilla 156/.notdef 157/hungarumlaut 158/ogonek 159/caron + 160/space 161/exclamdown 162/cent 163/sterling 164/Euro 165/yen 166/Scaron 167/section + 168/scaron 169/copyright 170/ordfeminine 171/guillemotleft 172/logicalnot 173/hyphen 174/registered 175/macron + 176/degree 177/plusminus 178/twosuperior 179/threesuperior 180/Zcaron 181/mu 182/paragraph 183/periodcentered + 184/zcaron 185/onesuperior 186/ordmasculine 187/guillemotright 188/OE 189/oe 190/Ydieresis 191/questiondown + 192/Agrave 193/Aacute 194/Acircumflex 195/Atilde 196/Adieresis 197/Aring 198/AE 199/Ccedilla + 200/Egrave 201/Eacute 202/Ecircumflex 203/Edieresis 204/Igrave 205/Iacute 206/Icircumflex 207/Idieresis + 208/Eth 209/Ntilde 210/Ograve 211/Oacute 212/Ocircumflex 213/Otilde 214/Odieresis 215/multiply + 216/Oslash 217/Ugrave 218/Uacute 219/Ucircumflex 220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] >> endobj 9 0 obj @@ -370,9 +402,9 @@ 0000000293 00000 n 0000006405 00000 n 0000006612 00000 n -0000006869 00000 n -0000006952 00000 n -0000007049 00000 n +0000009405 00000 n +0000009488 00000 n +0000009585 00000 n trailer << /Size 12 @@ -380,5 +412,5 @@ /Root 2 0 R >> startxref -7151 +9687 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgTDTtest1_TDT_log.txt --- a/test-data/rgTDTtest1_TDT_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgTDTtest1_TDT_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,6 +1,6 @@ @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,25 +10,25 @@ Skipping web check... [ --noweb ] Writing this text to log file [ rgTDTtest1.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --out rgTDTtest1 --mind 0.5 --tdt -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -48,6 +48,6 @@ 0 Mendel errors detected in total Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 ###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgClean/rgCleantest1.log --- a/test-data/rgtestouts/rgClean/rgCleantest1.log Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.log Mon May 10 10:17:11 2010 -0400 @@ -1,7 +1,7 @@ -rgClean.py started, called as /opt/galaxy/tools/rgenetics/rgClean.py /opt/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /opt/galaxy/test-data/rgtestouts/rgClean 0 0 0 0 +rgClean.py started, called as /share/shared/galaxy/tools/rgenetics/rgClean.py /share/shared/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /share/shared/galaxy/test-data/rgtestouts/rgClean 0 0 0 0 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,14 +10,14 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] +Analysis started: Sun May 9 21:23:43 2010 Options in effect: --noweb ---bfile /opt/galaxy/test-data/tinywga +--bfile /share/shared/galaxy/test-data/tinywga --make-bed ---out /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 +--out /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 --set-hh-missing --mind 1 --geno 1 @@ -25,16 +25,16 @@ --hwe 0 --me 1 1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -57,10 +57,10 @@ 0 Mendel errors detected in total 0 families ( 0 individuals ) removed due to Mendel errors 0 markers removed due to Mendel errors, 25 remaining -Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] -Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] -Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] +Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] +Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] +Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] Using (default) SNP-major mode Converting data to SNP-major format -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:43 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/Rplots.pdf --- a/test-data/rgtestouts/rgEigPCA/Rplots.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/Rplots.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210125) -/ModDate (D:20100325210125) +/CreationDate (D:20100509212343) +/ModDate (D:20100509212343) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -34,10 +34,42 @@ 5 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +/BaseEncoding /PDFDocEncoding +/Differences [ + 0/.notdef 1/.notdef 2/.notdef 3/.notdef 4/.notdef 5/.notdef 6/.notdef 7/.notdef + 8/.notdef 9/.notdef 10/.notdef 11/.notdef 12/.notdef 13/.notdef 14/.notdef 15/.notdef + 16/.notdef 17/.notdef 18/.notdef 19/.notdef 20/.notdef 21/.notdef 22/.notdef 23/.notdef + 24/.notdef 25/.notdef 26/.notdef 27/.notdef 28/.notdef 29/.notdef 30/.notdef 31/.notdef + 32/space 33/exclam 34/quotedbl 35/numbersign 36/dollar 37/percent 38/ampersand 39/quoteright + 40/parenleft 41/parenright 42/asterisk 43/plus 44/comma 45/minus 46/period 47/slash + 48/zero 49/one 50/two 51/three 52/four 53/five 54/six 55/seven + 56/eight 57/nine 58/colon 59/semicolon 60/less 61/equal 62/greater 63/question + 64/at 65/A 66/B 67/C 68/D 69/E 70/F 71/G + 72/H 73/I 74/J 75/K 76/L 77/M 78/N 79/O + 80/P 81/Q 82/R 83/S 84/T 85/U 86/V 87/W + 88/X 89/Y 90/Z 91/bracketleft 92/backslash 93/bracketright 94/asciicircum 95/underscore + 96/quoteleft 97/a 98/b 99/c 100/d 101/e 102/f 103/g + 104/h 105/i 106/j 107/k 108/l 109/m 110/n 111/o + 112/p 113/q 114/r 115/s 116/t 117/u 118/v 119/w + 120/x 121/y 122/z 123/braceleft 124/bar 125/braceright 126/asciitilde 127/.notdef + 128/.notdef 129/.notdef 130/.notdef 131/.notdef 132/.notdef 133/.notdef 134/.notdef 135/.notdef + 136/.notdef 137/.notdef 138/.notdef 139/.notdef 140/.notdef 141/.notdef 142/.notdef 143/.notdef + 144/dotlessi 145/grave 146/acute 147/circumflex 148/tilde 149/macron 150/breve 151/dotaccent + 152/dieresis 153/.notdef 154/ring 155/cedilla 156/.notdef 157/hungarumlaut 158/ogonek 159/caron + 160/space 161/exclamdown 162/cent 163/sterling 164/Euro 165/yen 166/Scaron 167/section + 168/scaron 169/copyright 170/ordfeminine 171/guillemotleft 172/logicalnot 173/hyphen 174/registered 175/macron + 176/degree 177/plusminus 178/twosuperior 179/threesuperior 180/Zcaron 181/mu 182/paragraph 183/periodcentered + 184/zcaron 185/onesuperior 186/ordmasculine 187/guillemotright 188/OE 189/oe 190/Ydieresis 191/questiondown + 192/Agrave 193/Aacute 194/Acircumflex 195/Atilde 196/Adieresis 197/Aring 198/AE 199/Ccedilla + 200/Egrave 201/Eacute 202/Ecircumflex 203/Edieresis 204/Igrave 205/Iacute 206/Icircumflex 207/Idieresis + 208/Eth 209/Ntilde 210/Ograve 211/Oacute 212/Ocircumflex 213/Otilde 214/Odieresis 215/multiply + 216/Oslash 217/Ugrave 218/Uacute 219/Ucircumflex 220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] >> endobj xref @@ -55,5 +87,5 @@ /Root 2 0 R >> startxref -618 +3154 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Mon May 10 10:17:11 2010 -0400 @@ -16,4 +16,4 @@ legend("top",legend=llist,pch=glist,col=glist,title="Sample") grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") dev.off() -#R script autogenerated by rgenetics/rgutils.py on 25/03/2010 21:01:25 +#R script autogenerated by rgenetics/rgutils.py on 09/05/2010 21:23:43 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Mon May 10 10:17:11 2010 -0400 @@ -9,30 +9,27 @@ </head> <body> <div class="document"> -<h4>Output from rgEigPCA.py run at 25/03/2010 21:01:25<br/> +<h4>Output from rgEigPCA.py run at 09/05/2010 21:23:43<br/> </h4> -newfilepath=/opt/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td> +newfilepath=/share/shared/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td> <a href="rgEigPCAtest1_PCAPlot.pdf"><img src="rgEigPCAtest1_PCAPlot.pdf.png" alt="Samples plotted in first 2 eigenvector space" hspace="10" align="left" /></a></td></tr></table><br/> -<div class="document">All Files:<ol><li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li> -<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (311 B)</a></li> +<div class="document">All Files:<ol><li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li> +<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (338 B)</a></li> +<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.1 KB)</a></li> +<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (10.4 KB)</a></li> +<li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li> +<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.2 KB)</a></li> +<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li> +<li><a href="Rplots.pdf">Rplots.pdf (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li> <li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png (27.1 KB)</a></li> -<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.0 KB)</a></li> -<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt (257 B)</a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps (13.6 KB)</a></li> -<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li> -<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.3 KB)</a></li> -<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (7.9 KB)</a></li> -<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf (2.1 KB)</a></li> -<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li> -<li><a href="Rplots.pdf">Rplots.pdf (813 B)</a></li> </ol></div><div class="document">Log rgEigPCAtest1_log.txt contents follow below<p/><pre>parameter file: rgEigPCAtest1_pca.xls.par ### THE INPUT PARAMETERS ##PARAMETER NAME: VALUE -genotypename: /opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO @@ -156,5 +153,5 @@ Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069 </pre></div>If you need to rerun this analysis, the command line used was -smartpca.perl -i /opt/galaxy/test-data/tinywga.ped -a /opt/galaxy/test-data/tinywga.map -b /opt/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2 +smartpca.perl -i /share/shared/galaxy/test-data/tinywga.ped -a /share/shared/galaxy/test-data/tinywga.map -b /share/shared/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2 <p/></div></body></html> diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210125) -/ModDate (D:20100325210125) +/CreationDate (D:20100509212343) +/ModDate (D:20100509212343) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -410,10 +410,42 @@ 8 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis 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95/underscore + 96/quoteleft 97/a 98/b 99/c 100/d 101/e 102/f 103/g + 104/h 105/i 106/j 107/k 108/l 109/m 110/n 111/o + 112/p 113/q 114/r 115/s 116/t 117/u 118/v 119/w + 120/x 121/y 122/z 123/braceleft 124/bar 125/braceright 126/asciitilde 127/.notdef + 128/.notdef 129/.notdef 130/.notdef 131/.notdef 132/.notdef 133/.notdef 134/.notdef 135/.notdef + 136/.notdef 137/.notdef 138/.notdef 139/.notdef 140/.notdef 141/.notdef 142/.notdef 143/.notdef + 144/dotlessi 145/grave 146/acute 147/circumflex 148/tilde 149/macron 150/breve 151/dotaccent + 152/dieresis 153/.notdef 154/ring 155/cedilla 156/.notdef 157/hungarumlaut 158/ogonek 159/caron + 160/space 161/exclamdown 162/cent 163/sterling 164/Euro 165/yen 166/Scaron 167/section + 168/scaron 169/copyright 170/ordfeminine 171/guillemotleft 172/logicalnot 173/hyphen 174/registered 175/macron + 176/degree 177/plusminus 178/twosuperior 179/threesuperior 180/Zcaron 181/mu 182/paragraph 183/periodcentered + 184/zcaron 185/onesuperior 186/ordmasculine 187/guillemotright 188/OE 189/oe 190/Ydieresis 191/questiondown + 192/Agrave 193/Aacute 194/Acircumflex 195/Atilde 196/Adieresis 197/Aring 198/AE 199/Ccedilla + 200/Egrave 201/Eacute 202/Ecircumflex 203/Edieresis 204/Igrave 205/Iacute 206/Icircumflex 207/Idieresis + 208/Eth 209/Ntilde 210/Ograve 211/Oacute 212/Ocircumflex 213/Otilde 214/Odieresis 215/multiply + 216/Oslash 217/Ugrave 218/Uacute 219/Ucircumflex 220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] >> endobj 9 0 obj << @@ -441,8 +473,8 @@ 0000000293 00000 n 0000007168 00000 n 0000007363 00000 n -0000007620 00000 n -0000007716 00000 n +0000010156 00000 n +0000010252 00000 n trailer << /Size 11 @@ -450,5 +482,5 @@ /Root 2 0 R >> startxref -7818 +10354 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@ parameter file: rgEigPCAtest1_pca.xls.par ### THE INPUT PARAMETERS ##PARAMETER NAME: VALUE -genotypename: /opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Mon May 10 10:17:11 2010 -0400 @@ -3,43 +3,43 @@ 7.7400 7.2550 4.2710 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.1608 -0.0349 0.0222 0.1244 - -0.1027 0.2939 -0.1091 -0.1832 - 0.2593 -0.1916 -0.2862 -0.1609 - 0.0302 0.2348 0.0136 0.1216 - -0.2453 -0.0165 -0.0856 0.0221 - 0.3015 0.2159 0.0173 0.3393 - -0.1608 -0.0349 0.0222 0.1244 - -0.1027 0.2939 -0.1091 -0.1832 - 0.2593 -0.1916 -0.2862 -0.1609 - -0.2453 -0.0165 -0.0856 0.0221 - -0.2493 -0.2867 -0.1811 0.1404 - 0.3015 0.2159 0.0173 0.3393 - -0.1027 0.2939 -0.1091 -0.1832 - 0.2593 -0.1916 -0.2862 -0.1609 - 0.0302 0.2348 0.0136 0.1216 - -0.2453 -0.0165 -0.0856 0.0221 - -0.2453 -0.0165 -0.0856 0.0221 - 0.3015 0.2159 0.0173 0.3393 - 0.2593 -0.1916 -0.2862 -0.1609 - 0.0302 0.2348 0.0136 0.1216 - 0.2593 -0.1916 -0.2862 -0.1609 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 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/opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt --- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Mon May 10 10:17:11 2010 -0400 @@ -1,13 +1,13 @@ Reading genotypes for 40 subjects and 5 markers Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00482821464539 T2: 0.0623338222504 T3: 0.000771522521973 TOT: 0.0691449642181 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 +Relstate parentchild: mean(mean)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 -Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 +Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22 +Relstate unrelated: mean(mean)=1.55 sdev(mean)=0.24, mean(sdev)=0.59 sdev(sdev)=0.24 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 780 pairs are available of 780 Outliers: 0 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/rgGRRtest1.html --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Mon May 10 10:17:11 2010 -0400 @@ -9,34 +9,34 @@ </head> <body> <div class="document"> -<h4><div>Output from rgGRR.py run at 15/04/2010 13:12:45<br> +<h4><div>Output from rgGRR.py run at 09/05/2010 21:23:42<br> </h4> If you need to rerun this analysis, the command line was -<pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre> +<pre>'/share/shared/galaxy/tools/rgenetics/rgGRR.py' '/share/shared/galaxy/test-data/tinywga' 'tinywga' '/share/shared/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/share/shared/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6' 'true'</pre> </div> <embed src="rgGRRtest1.svg" type="image/svg+xml" width="1150" height="600" /><div><h4>Click the links below to save output files and plots</h4><br><ol> <li><a href="rgGRRtest1.svg" type="image/svg+xml" >rgGRR Plot (requires SVG)</a></li> <li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li> +<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> <li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li> -<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> </ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 5 markers Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00482821464539 T2: 0.0623338222504 T3: 0.000771522521973 TOT: 0.0691449642181 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 +Relstate parentchild: mean(mean)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 +Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22 -Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 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1.023277 5 5 +1340_9 1344_13 1.400000 0.894427 -1.469163 1.023277 5 5 +1340_9 1345_12 1.400000 0.894427 1.029902 -0.619941 5 5 +1341_1 1341_11 1.400000 0.894427 -0.642422 0.715736 5 5 +1341_1 1341_12 1.400000 0.894427 0.354770 0.285726 5 5 +1341_1 1341_13 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_1 1341_14 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_1 1341_2 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_1 1344_1 1.400000 0.894427 -1.469163 1.023277 5 5 +1341_1 1344_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_1 1344_13 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_1 1345_12 1.400000 0.894427 1.029902 -0.619941 5 5 +1341_11 1341_12 1.400000 0.894427 -1.140216 1.652064 5 5 +1341_11 1341_13 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_11 1341_14 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_11 1341_2 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_11 1344_1 1.400000 0.894427 -1.469163 2.115187 5 5 +1341_11 1344_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_11 1344_13 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_11 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5 +1341_12 1341_13 1.400000 0.894427 -0.132290 0.048238 5 5 +1341_12 1341_14 1.400000 0.894427 -0.132290 0.048238 5 5 +1341_12 1341_2 1.400000 0.894427 -0.132290 0.048238 5 5 +1341_12 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_12 1344_12 1.400000 0.894427 -0.636142 1.267018 5 5 +1341_12 1344_13 1.400000 0.894427 -0.636142 1.267018 5 5 +1341_12 1345_12 1.400000 0.894427 1.862924 -2.506901 5 5 +1341_13 1341_14 1.400000 0.894427 1.883560 -2.485480 5 5 +1341_13 1341_2 1.400000 0.894427 1.351962 -1.627597 5 5 +1341_13 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_13 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_13 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_13 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_14 1341_2 1.400000 0.894427 1.351962 -1.627597 5 5 +1341_14 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_14 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_14 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_14 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_2 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_2 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_2 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_2 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1344_1 1344_12 1.400000 0.894427 -0.642422 0.715735 5 5 +1344_1 1344_13 1.400000 0.894427 -0.642422 0.715735 5 5 +1344_1 1345_12 1.400000 0.894427 -2.302185 1.712469 5 5 +1344_12 1344_13 1.400000 0.894427 1.883560 -2.485480 5 5 +1344_12 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5 +1344_13 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG Binary file test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt --- a/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt Mon May 10 10:17:11 2010 -0400 @@ -1,7 +1,7 @@ -PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin +PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region -## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 +## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 ## executing mogrify -resize 800x400! *.PNG returned 0 ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0 ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0 @@ -12,16 +12,16 @@ ## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0 ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0 ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** -Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 +Arguments: -n -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 Max LD comparison distance = 200000kb -Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info +Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped +Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info 10 out of 10 markers passed the MAF threshold. 10 out of 10 markers passed the Mendel threshold. 10 out of 10 markers passed the genotyping threshold. @@ -33,11 +33,11 @@ Writing output to rgHaploViewtest1.ped.TESTS Writing output to rgHaploViewtest1.ped.CHAPS ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** -Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng +Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng Max LD comparison distance = 200000kb diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/alljoin.pdf Binary file test-data/rgtestouts/rgHaploView/alljoin.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/allnup.pdf Binary file test-data/rgtestouts/rgHaploView/allnup.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html Mon May 10 10:17:11 2010 -0400 @@ -23,13 +23,13 @@ <li><a href="rgHaploViewtest1.ped.LD.PNG">rgHaploViewtest1.ped.LD.PNG - rgHaploViewtest1.ped.LD.PNG</a></li> <li><a href="rgHaploViewtest1.ped.TAGS">rgHaploViewtest1.ped.TAGS - rgHaploViewtest1.ped.TAGS Tagger output</a></li> <li><a href="rgHaploViewtest1.ped.TESTS">rgHaploViewtest1.ped.TESTS - rgHaploViewtest1.ped.TESTS Tagger output</a></li> -</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin +</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region -## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 +## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 ## executing mogrify -resize 800x400! *.PNG returned 0 @@ -51,7 +51,7 @@ ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** @@ -59,7 +59,7 @@ -Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 +Arguments: -n -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 @@ -67,9 +67,9 @@ Max LD comparison distance = 200000kb -Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped +Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info +Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info 10 out of 10 markers passed the MAF threshold. @@ -93,7 +93,7 @@ ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** @@ -101,7 +101,7 @@ -Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng +Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG Binary file test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS Mon May 10 10:17:11 2010 -0400 @@ -9,17 +9,17 @@ rs3788347 rs3788347 1.0 rs756632 rs756632 1.0 rs4820539 rs4820539 1.0 -rs2283804 rs2267006 1.0 -rs2267006 rs2267006 1.0 +rs2283804 rs2283804 1.0 +rs2267006 rs2283804 1.0 rs4822363 rs4822363 1.0 Test Alleles Captured -rs2267006 rs2267006,rs2283804 -rs4820539 rs4820539 -rs3788347 rs3788347 +rs2283804 rs2267006,rs2283804 rs756632 rs756632 +rs2283802 rs2283802 +rs4820537 rs4820537 rs2267000 rs2267000 rs4822363 rs4822363 -rs2283802 rs2283802 -rs4820537 rs4820537 rs16997606 rs16997606 +rs3788347 rs3788347 +rs4820539 rs4820539 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@ -rs2267006 -rs4820539 -rs3788347 +rs2283804 rs756632 +rs2283802 +rs4820537 rs2267000 rs4822363 -rs2283802 -rs4820537 rs16997606 +rs3788347 +rs4820539 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed Mon May 10 10:17:11 2010 -0400 @@ -1,1 +1,1 @@ -lÿÿÿÿûÿúÿÿÿmÿÿÿýÿÿÿÿÿ:ú¢ÿ¿«¯ü( \ No newline at end of file +lú £ïªîþ¨:*»ïêìª,«Àÿÿÿÿûÿúÿÿÿ \ No newline at end of file diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +22 rs3788347 0 21797804 3 1 +22 rs5759608 0 21832708 2 4 22 rs2267010 0 21864366 3 1 -22 rs12160770 0 21892925 1 3 -22 rs4822375 0 21905642 1 3 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@ -## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 25/03/2010 21:01:24 +## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42 ## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 +## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -12,30 +12,30 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -60,20 +60,20 @@ 0 markers removed due to Mendel errors, 25 remaining Converting data to SNP-major format Performing LD-based pruning... -Writing pruned-in SNPs to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] -Writing pruned-out SNPs to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] +Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] +Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] Scanning from chromosome 22 to 22 Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ] For chromosome 22, 22 SNPs pruned out, 3 remaining -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/tinywga --extract /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 +## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -82,48 +82,48 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga - --extract /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in + --bfile /share/shared/galaxy/test-data/tinywga + --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode -Reading list of SNPs to extract [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read +Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read Before frequency and genotyping pruning, there are 3 SNPs 27 founders and 13 non-founders found -Total genotyping rate in remaining individuals is 0.975 +Total genotyping rate in remaining individuals is 1 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 3 SNPs After filtering, 10 cases, 30 controls and 0 missing After filtering, 21 males, 19 females, and 0 of unspecified sex -Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] -Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] +Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] Using (default) SNP-major mode -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 +## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -132,38 +132,38 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 -Reading map (extended format) from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -3 markers to be included from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] -40 individuals read from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +3 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 3 SNPs 27 founders and 13 non-founders found -Total genotyping rate in remaining individuals is 0.975 +Total genotyping rate in remaining individuals is 1 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 3 SNPs After filtering, 10 cases, 30 controls and 0 missing After filtering, 21 males, 19 females, and 0 of unspecified sex -Writing recoded ped file to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] -Writing new map file to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] +Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] +Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +22 rs3788347 0 21797804 +22 rs5759608 0 21832708 22 rs2267010 0 21864366 -22 rs12160770 0 21892925 -22 rs4822375 0 21905642 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped Mon May 10 10:17:11 2010 -0400 @@ -1,40 +1,40 @@ -101 1 3 2 2 2 1 1 0 0 1 3 -101 2 0 0 2 1 1 1 3 3 1 3 -101 3 0 0 1 1 1 1 1 3 3 3 -105 1 3 2 2 2 1 1 0 0 1 1 -105 2 0 0 2 1 1 1 3 3 1 3 -105 3 0 0 1 1 1 1 3 3 1 3 -112 1 3 2 1 2 1 1 3 3 3 3 -112 2 0 0 2 1 1 1 3 3 3 3 -112 3 0 0 1 1 1 1 3 3 1 3 -117 1 3 2 2 2 1 1 3 3 1 1 -117 2 0 0 2 1 1 1 3 3 1 3 -117 3 0 0 1 1 1 1 3 3 1 3 -12 1 3 2 1 2 1 1 3 3 3 3 -12 2 0 0 2 1 1 1 3 3 3 3 -12 3 0 0 1 1 1 1 3 3 3 3 -13 1 3 2 1 2 1 1 3 3 3 3 -13 2 0 0 2 1 1 1 0 0 3 3 -13 3 0 0 1 1 3 1 3 3 3 3 -1334 1 10 11 1 2 1 1 3 3 3 3 -1334 10 0 0 1 1 1 1 3 3 1 3 -1334 11 0 0 2 1 1 1 3 3 3 3 -1334 12 0 0 1 1 1 1 3 3 1 3 -1334 13 0 0 2 1 1 1 3 3 1 3 -1334 2 12 13 2 2 1 1 3 3 1 3 -1340 1 9 10 1 2 3 1 3 3 3 3 -1340 10 0 0 2 1 3 1 3 3 3 3 -1340 11 0 0 1 1 1 1 3 3 1 3 -1340 12 0 0 2 1 1 1 3 3 1 3 -1340 2 11 12 2 2 1 1 3 3 1 3 -1340 9 0 0 1 1 1 1 3 3 3 3 -1341 1 11 12 1 1 1 1 3 3 1 1 -1341 11 0 0 1 1 1 1 3 3 1 3 -1341 12 0 0 2 1 1 1 3 3 1 1 -1341 13 0 0 1 1 1 1 3 3 3 3 -1341 14 0 0 2 1 1 1 3 3 3 3 -1341 2 13 14 2 1 1 1 3 3 3 3 -1344 1 12 13 1 1 1 1 3 3 1 1 -1344 12 0 0 1 1 1 1 3 3 1 3 -1344 13 0 0 2 1 1 1 3 3 1 3 -1345 12 0 0 1 1 1 1 3 3 1 1 +101 1 3 2 2 2 3 3 2 4 1 1 +101 2 0 0 2 1 3 3 2 4 1 1 +101 3 0 0 1 1 3 3 4 4 1 1 +105 1 3 2 2 2 3 1 2 2 1 1 +105 2 0 0 2 1 3 1 2 4 1 1 +105 3 0 0 1 1 3 1 2 4 1 1 +112 1 3 2 1 2 1 1 2 4 1 1 +112 2 0 0 2 1 1 1 2 2 1 1 +112 3 0 0 1 1 3 1 4 4 1 1 +117 1 3 2 2 2 3 3 2 4 1 1 +117 2 0 0 2 1 3 3 4 4 1 1 +117 3 0 0 1 1 3 3 2 4 1 1 +12 1 3 2 1 2 3 3 4 4 1 1 +12 2 0 0 2 1 3 3 4 4 1 1 +12 3 0 0 1 1 3 1 2 4 1 1 +13 1 3 2 1 2 3 1 4 4 1 1 +13 2 0 0 2 1 1 1 2 4 1 1 +13 3 0 0 1 1 3 3 2 4 3 1 +1334 1 10 11 1 2 3 1 2 4 1 1 +1334 10 0 0 1 1 3 1 4 4 1 1 +1334 11 0 0 2 1 1 1 2 2 1 1 +1334 12 0 0 1 1 1 1 4 4 1 1 +1334 13 0 0 2 1 3 1 2 4 1 1 +1334 2 12 13 2 2 1 1 4 4 1 1 +1340 1 9 10 1 2 3 1 2 4 3 1 +1340 10 0 0 2 1 3 1 2 4 3 1 +1340 11 0 0 1 1 3 1 2 4 1 1 +1340 12 0 0 2 1 3 1 2 4 1 1 +1340 2 11 12 2 2 3 1 2 2 1 1 +1340 9 0 0 1 1 1 1 4 4 1 1 +1341 1 11 12 1 1 3 1 2 4 1 1 +1341 11 0 0 1 1 1 1 2 2 1 1 +1341 12 0 0 2 1 3 1 4 4 1 1 +1341 13 0 0 1 1 1 1 2 4 1 1 +1341 14 0 0 2 1 1 1 2 4 1 1 +1341 2 13 14 2 1 1 1 2 4 1 1 +1344 1 12 13 1 1 3 3 2 2 1 1 +1344 12 0 0 1 1 3 1 2 2 1 1 +1344 13 0 0 2 1 3 1 2 2 1 1 +1345 12 0 0 1 1 3 1 4 4 1 1 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +rs3788347 +rs5759608 rs2267010 -rs12160770 -rs4822375 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out Mon May 10 10:17:11 2010 -0400 @@ -2,14 +2,12 @@ rs2267000 rs16997606 rs4820537 -rs3788347 rs756632 rs4820539 rs2283804 rs2267006 rs4822363 rs5751592 -rs5759608 rs5759612 rs2267009 rs5759636 @@ -17,6 +15,8 @@ rs2267013 rs6003566 rs2256725 +rs12160770 rs5751611 rs762601 rs2156921 +rs4822375 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Allelep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Allelep_manhattan.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Mon May 10 10:17:11 2010 -0400 @@ -108,7 +108,7 @@ if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) plot } -rgqqMan = function(infile="/opt/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), +rgqqMan = function(infile="/share/shared/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), title="rgManQQtest1",grey=0) { rawd = read.table(infile,head=T,sep=' ')

1 0

[hg] galaxy 3757: Clean up annotation display for workflow steps.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/42de27d4215f changeset: 3757:42de27d4215f user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sun May 09 22:37:50 2010 -0400 description: Clean up annotation display for workflow steps. diffstat: templates/workflow/display.mako | 6 +++++- 1 files changed, 5 insertions(+), 1 deletions(-) diffs (16 lines): diff -r 8094d8531fb2 -r 42de27d4215f templates/workflow/display.mako --- a/templates/workflow/display.mako Fri May 07 18:25:29 2010 -0400 +++ b/templates/workflow/display.mako Sun May 09 22:37:50 2010 -0400 @@ -108,7 +108,11 @@ </div> %endif </td> - <td class="annotation">${step.annotation}</td> + <td class="annotation"> + %if hasattr( step, "annotation") and step.annotation is not None: + ${step.annotation} + %endif + </td> </tr> %endfor </table>

1 0

[hg] galaxy 3758: lims:
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/acaf971320bd changeset: 3758:acaf971320bd user: rc date: Mon May 10 10:03:00 2010 -0400 description: lims: default view of requests page now shows requests belonging to any state diffstat: lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diffs (44 lines): diff -r 42de27d4215f -r acaf971320bd lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Sun May 09 22:37:50 2010 -0400 +++ b/lib/galaxy/web/controllers/requests.py Mon May 10 10:03:00 2010 -0400 @@ -79,7 +79,7 @@ num_rows_per_page = 50 preserve_state = True use_paging = True - default_filter = dict( deleted="False", state=model.Request.states.NEW) + default_filter = dict( deleted="False") columns = [ NameColumn( "Name", key="name", diff -r 42de27d4215f -r acaf971320bd lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Sun May 09 22:37:50 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon May 10 10:03:00 2010 -0400 @@ -90,7 +90,7 @@ num_rows_per_page = 50 preserve_state = True use_paging = True - default_filter = dict( deleted="False", state=model.Request.states.SUBMITTED) + default_filter = dict( deleted="False") columns = [ NameColumn( "Name", key="name", @@ -259,7 +259,7 @@ ''' List all request made by the current user ''' - #self.__sample_datasets(trans, **kwd) + self.__sample_datasets(trans, **kwd) if 'operation' in kwd: operation = kwd['operation'].lower() if not kwd.get( 'id', None ): @@ -1774,7 +1774,9 @@ status=status) def __sample_datasets(self, trans, **kwd): - samples = trans.sa_session.query( trans.app.model.Sample ).all() + samples = trans.sa_session.query( trans.app.model.Sample )\ + .filter( trans.app.model.Sample.table.c.deleted==False)\ + .all() for s in samples: if s.dataset_files: newdf = []

1 0

[hg] galaxy 3756: trackster: fix track saving
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8094d8531fb2 changeset: 3756:8094d8531fb2 user: Kanwei Li <kanwei(a)gmail.com> date: Fri May 07 18:25:29 2010 -0400 description: trackster: fix track saving diffstat: static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 6 +++--- templates/tracks/browser.mako | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diffs (50 lines): diff -r 4aec0992748e -r 8094d8531fb2 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Fri May 07 10:28:28 2010 -0400 +++ b/static/scripts/packed/trackster.js Fri May 07 18:25:29 2010 -0400 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern! (right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.! max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;t his.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks.splice(this.tracks.indexOf(a))},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_fa! ctor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.high-this.low)+this.low}! this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high ===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").a! ttr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'>! </div>"),l=this.content_div.width()/f,h;this.content_div.children(":fi rst").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-! c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=unde! fined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null ,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=! true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1]! ;if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h =g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mo! de),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100! ;this.container_div.addClass("feature-track");this.dataset_id=a;this.z o_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=tr! ue;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by! _tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by _tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.vi! ew.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=a! c&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min( a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math! .min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label! >").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id ",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_det! ail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file +var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern! (right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.! max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;t his.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor! ,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.high-this.lo! w)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(t his.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0! );'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position:! relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.c hildren(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.vi! ew,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertica! l_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:nu ll,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.da! ta_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;! h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}els e{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":t! his.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.h! eight_px=100;this.container_div.addClass("feature-track");this.dataset _id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data! _queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u! =this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if (this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_s! lots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L! [3];if(ag<=ac&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ce il(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Ma! th.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<l! abel></label>").attr("for",e).text("Block color:"),l=$("<input></input >").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.! vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file diff -r 4aec0992748e -r 8094d8531fb2 static/scripts/trackster.js --- a/static/scripts/trackster.js Fri May 07 10:28:28 2010 -0400 +++ b/static/scripts/trackster.js Fri May 07 18:25:29 2010 -0400 @@ -118,7 +118,7 @@ }, remove_track: function( track ) { track.container_div.fadeOut('slow', function() { $(this).remove(); }); - delete this.tracks.splice(this.tracks.indexOf(track)); + delete this.tracks[this.tracks.indexOf(track)]; }, update_options: function() { var sorted = $("ul#sortable-ul").sortable('toArray'); @@ -129,7 +129,7 @@ for (var track_id in view.tracks) { var track = view.tracks[track_id]; - if (track.update_options) { + if (track && track.update_options) { track.update_options(track_id); } } @@ -173,7 +173,7 @@ $("#high").val( commatize(this.high) ); if (!nodraw) { for ( var i = 0, len = this.tracks.length; i < len; i++ ) { - if (this.tracks[i].enabled) { + if (this.tracks[i] && this.tracks[i].enabled) { this.tracks[i].draw(); } } diff -r 4aec0992748e -r 8094d8531fb2 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri May 07 10:28:28 2010 -0400 +++ b/templates/tracks/browser.mako Fri May 07 18:25:29 2010 -0400 @@ -239,7 +239,7 @@ var sorted = $("ul#sortable-ul").sortable('toArray'); var payload = []; for (var i in sorted) { - var track_id = parseInt(sorted[i].split("track_")[1]), + var track_id = parseInt(sorted[i].split("track_")[1].split("_li")[0]), track = view.tracks[track_id]; payload.push( {

1 0

[hg] galaxy 3755: Another update to search+select: pack script a...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4aec0992748e changeset: 3755:4aec0992748e user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri May 07 10:28:28 2010 -0400 description: Another update to search+select: pack script and replace icon. diffstat: static/images/fugue/control-270.png | 0 static/images/fugue/plus-white.png | 0 static/june_2007_style/blue/base.css | 2 +- static/scripts/packed/galaxy.base.js | 2 +- 4 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r f550290ed5ad -r 4aec0992748e static/images/fugue/control-270.png Binary file static/images/fugue/control-270.png has changed diff -r f550290ed5ad -r 4aec0992748e static/images/fugue/plus-white.png Binary file static/images/fugue/plus-white.png has changed diff -r f550290ed5ad -r 4aec0992748e static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri May 07 09:16:51 2010 -0400 +++ b/static/june_2007_style/blue/base.css Fri May 07 10:28:28 2010 -0400 @@ -147,4 +147,4 @@ .tipsy-west{background-position:left center;} .editable-text{cursor:pointer;} .editable-text:hover{cursor: text;border: dotted #999999 1px;} -.text-and-autocomplete-select{background-image:url(/static/images/fugue/plus-white.png);background-repeat: no-repeat;background-position:top right;} +.text-and-autocomplete-select{background-image:url(/static/images/fugue/control-270.png);background-repeat: no-repeat;background-position:right;} diff -r f550290ed5ad -r 4aec0992748e static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri May 07 09:16:51 2010 -0400 +++ b/static/scripts/packed/galaxy.base.js Fri May 07 10:28:28 2010 -0400 @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen! 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u(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString()! .toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).sp lit(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a){if(a===undefined){a=20}$('select[refresh_on_change!="true"]').each(function(){var b=$(this);if(b.find("option").length<a){return}var c=b.attr("value");var d=$("<input type='text' class='text-and-autocomplete-select'></input>");d.attr("size",40);d.attr("name",b.attr("name"));d.attr("id",b.attr("id"));d.click(function(){var i=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",i);$(this).select()});var h=[];var g={};b.children("option").each(function(){var j=$(this).text();var i=$(this).attr("value");if(i=="?"){return}h.push(j);g[j]=i;g[i]=i;if(i==c){d.attr("value",j! 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(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyC ode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){l.text(o);if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete! k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()}); \ No newline at end of file

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