1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0d4ece99a476/ changeset: r5462:0d4ece99a476 user: fubar date: 2011-04-27 23:06:14 summary: uncommented new tools in tool_conf.xml.sample so buildbot can find them and explanation when insertsizemetrics fails affected #: 2 files (556 bytes) --- a/tool_conf.xml.sample Wed Apr 27 15:41:25 2011 -0400 +++ b/tool_conf.xml.sample Wed Apr 27 17:06:14 2011 -0400 @@ -236,44 +236,57 @@ <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /><tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /></section> - <section name="NGS: QC and manipulation" id="cshl_library_information"> - <label text="Illumina fastq" 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_masker_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" /> - <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" /> - <tool file="fastx_toolkit/fastq_quality_converter.xml" /> - <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> - <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> - <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastq_quality_filter.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> - <tool file="fastx_toolkit/fastx_barcode_splitter.xml" /> - <tool file="fastx_toolkit/fastx_clipper.xml" /> - <tool file="fastx_toolkit/fastx_collapser.xml" /> - <tool file="fastx_toolkit/fastx_renamer.xml" /> - <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> - <tool file="fastx_toolkit/fastx_trimmer.xml" /> + <section name="NGS: QC and manipulation" id="NGS_QC"> + <label text="FastQC: fastq/sam/bam" id="fastqcsambam" /> + <tool file="rgenetics/rgFastQC.xml" /> + <label text="QC/Metrics for sam/bam" id="qcsambam"/> + <tool file="picard/picard_BamIndexStats.xml" /> + <tool file="picard/rgPicardASMetrics.xml" /> + <tool file="picard/rgPicardGCBiasMetrics.xml" /> + <tool file="picard/rgPicardInsertSize.xml" /> + <label text=="bam/sam Cleaning" id="picard-tools"> + <tool file="picard/picard_AddOrReplaceReadGroups.xml" /> + <tool file="picard/picard_ReorderSam.xml" /> + <tool file="picard/picard_ReplaceSamHeader.xml" /> + <tool file="picard/rgPicardFixMate.xml" /> + <tool file="picard/rgPicardMarkDups.xml" /> + <label text="Illumina fastq" 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_masker_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" /> + <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" /> + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> + <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> + <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> + <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="fastx_toolkit/fastq_quality_filter.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> + <tool file="fastx_toolkit/fastx_barcode_splitter.xml" /> + <tool file="fastx_toolkit/fastx_clipper.xml" /> + <tool file="fastx_toolkit/fastx_collapser.xml" /> + <tool file="fastx_toolkit/fastx_renamer.xml" /> + <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> + <tool file="fastx_toolkit/fastx_trimmer.xml" /></section><!-- Keep this section commented until it includes tools that @@ -384,24 +397,8 @@ This section can be uncommented on test, but the tools are not ready for main. --> + <!-- - <section name="NGS: QC and manipulation" id="cshl_library_information"> - <label text="FastQC: fastq/sam/bam" /> - <tool file="rgenetics/rgFastQC.xml" /> - <label text="QC/Metrics for sam/bam" /> - <tool file="picard/picard_BamIndexStats.xml" /> - <tool file="picard/rgPicardASMetrics.xml" /> - <tool file="picard/rgPicardGCBiasMetrics.xml" /> - <tool file="picard/rgPicardInsertSize.xml" /> - </section> - <section name="NGS: bam/sam Cleaning" id="picard-tools"> - <tool file="picard/picard_AddOrReplaceReadGroups.xml" /> - <tool file="picard/picard_ReorderSam.xml" /> - <tool file="picard/picard_ReplaceSamHeader.xml" /> - <tool file="picard/rgPicardFixMate.xml" /> - <tool file="picard/rgPicardMarkDups.xml" /> - </section> - <section name="Genome Diversity" id="gd"><tool file="genome_diversity/extract_primers.xml" /> --- a/tools/picard/picard_wrapper.py Wed Apr 27 15:41:25 2011 -0400 +++ b/tools/picard/picard_wrapper.py Wed Apr 27 17:06:14 2011 -0400 @@ -526,7 +526,10 @@ cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir) else: - s = 'Unable to find expected pdf file %s\n' % pdfpath + s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath + s += This <b>always happens if single ended data was provided</b> to this tool,\n' + s += 'so please double check that your input data really is paired-end NGS data.<br/>\n' + s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>' stdouts = '' lf = open(pic.log_filename,'a') lf.write(s) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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