2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e9fc9e7adc63/ Changeset: e9fc9e7adc63 User: inithello Date: 2014-01-27 15:53:14 Summary: Migrate 43 tools from the distribution to the tool shed. Affected #: 296 files diff -r 04bce95d8fd21ae597ba839936dd644870450051 -r e9fc9e7adc63554b6f8a5604bce8be6b37d35d55 lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py @@ -0,0 +1,103 @@ +""" +The following tools have been eliminated from the distribution: + +1: Bowtie2 +2: Control-based ChIP-seq Analysis Tool +3: ClustalW multiple sequence alignment program for DNA or proteins +4: Compute P-values and Correlation Coefficients for Feature Occurrences +5: Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features +6: Compute P-values and Second Moments for Feature Occurrences +7: Compute P-values and Max Variances for Feature Occurrences +8: Wavelet variance using Discrete Wavelet Transfoms +9: Quantify the abundances of a set of target sequences from sampled subsequences +10: Read QC reports using FastQC +11: Combine FASTA and QUAL into FASTQ. +12: Filter FASTQ reads by quality score and length +13: Convert between various FASTQ quality formats. +14: Manipulate FASTQ reads on various attributes. +15: FASTQ Masker by quality score +16: FASTQ de-interlacer on paired end reads. +17: FASTQ interlacer on paired end reads +18: FASTQ joiner on paired end reads +19: FASTQ splitter on joined paired end reads +20: FASTQ Summary Statistics by column +21: FASTQ to FASTA converter +22: FASTQ to Tabular converter +23: FASTQ Trimmer by quality +24: FASTQ Quality Trimmer by sliding window +25: Filter Combined Transcripts +26: find_diag_hits +27: Call SNPS with Freebayes +28: Fetch taxonomic representation +29: GMAJ Multiple Alignment Viewer +30: Find lowest diagnostic rank +31: Model-based Analysis of ChIP-Seq +32: Poisson two-sample test +33: Statistical approach for the Identification of ChIP-Enriched Regions +34: Draw phylogeny +35: Summarize taxonomy +36: Tabular to FASTQ converter +37: Find splice junctions using RNA-seq data +38: Gapped-read mapper for RNA-seq data +39: Annotate a VCF file (dbSNP, hapmap) +40: Extract reads from a specified region +41: Filter a VCF file +42: Generate the intersection of two VCF files +43: Sequence Logo generator for fasta (eg Clustal alignments) + +The tools are now available in the repositories respectively: + +1: bowtie2 +2: ccat +3: clustalw +4: dwt_cor_ava_perclass +5: dwt_cor_avb_all +6: dwt_ivc_all +7: dwt_var_perclass +8: dwt_var_perfeature +9: express +10: fastqc +11: fastq_combiner +12: fastq_filter +13: fastq_groomer +14: fastq_manipulation +15: fastq_masker_by_quality +16: fastq_paired_end_deinterlacer +17: fastq_paired_end_interlacer +18: fastq_paired_end_joiner +19: fastq_paired_end_splitter +20: fastq_stats +21: fastqtofasta +22: fastq_to_tabular +23: fastq_trimmer +24: fastq_trimmer_by_quality +25: filter_transcripts_via_tracking +26: find_diag_hits +27: freebayes_wrapper +28: gi2taxonomy +29: gmaj +30: lca_wrapper +31: macs +32: poisson2test +33: sicer +34: t2ps +35: t2t_report +36: tabular_to_fastq +37: tophat +38: tophat2 +39: vcf_annotate +40: vcf_extract +41: vcf_filter +42: vcf_intersect +43: weblogo3 + +from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu +and will be installed into your local Galaxy instance at the +location discussed above by running the following command. +""" + +def upgrade( migrate_engine ): + print __doc__ + +def downgrade( migrate_engine ): + pass diff -r 04bce95d8fd21ae597ba839936dd644870450051 -r e9fc9e7adc63554b6f8a5604bce8be6b37d35d55 scripts/migrate_tools/0009_tools.sh --- /dev/null +++ b/scripts/migrate_tools/0009_tools.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml $@ diff -r 04bce95d8fd21ae597ba839936dd644870450051 -r e9fc9e7adc63554b6f8a5604bce8be6b37d35d55 scripts/migrate_tools/0009_tools.xml --- /dev/null +++ b/scripts/migrate_tools/0009_tools.xml @@ -0,0 +1,132 @@ +<?xml version="1.0"?> +<toolshed name="toolshed.g2.bx.psu.edu"> + <repository owner="devteam" changeset_revision="96d2e31a3938" name="bowtie2" description="Bowtie2"> + <tool id="bowtie2" version="0.2" file="bowtie2_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="a0c8dc671a23" name="ccat" description="Control-based ChIP-seq Analysis Tool"> + <tool id="peakcalling_ccat" version="0.0.1" file="ccat_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="7cc64024fe92" name="clustalw" description="ClustalW multiple sequence alignment program for DNA or proteins"> + <tool id="clustalw" version="0.1" file="rgClustalw.xml" /> + </repository> + <repository owner="devteam" changeset_revision="6708501767b6" name="dwt_cor_ava_perclass" description="Compute P-values and Correlation Coefficients for Feature Occurrences"> + <tool id="compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_cor_aVa_perClass.xml" /> + </repository> + <repository owner="devteam" changeset_revision="0f2eda4ea8dc" name="dwt_cor_avb_all" description="Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features"> + <tool id="compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_cor_aVb_all.xml" /> + </repository> + <repository owner="devteam" changeset_revision="0b89b03ad760" name="dwt_ivc_all" description="Compute P-values and Second Moments for Feature Occurrences"> + <tool id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_IvC_all.xml" /> + </repository> + <repository owner="devteam" changeset_revision="cb422b6f49d2" name="dwt_var_perclass" description="Compute P-values and Max Variances for Feature Occurrences"> + <tool id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_var_perClass.xml" /> + </repository> + <repository owner="devteam" changeset_revision="d56c5d2e1a29" name="dwt_var_perfeature" description="Wavelet variance using Discrete Wavelet Transfoms"> + <tool id="dwt_var1" version="1.0.0" file="execute_dwt_var_perFeature.xml" /> + </repository> + <repository owner="devteam" changeset_revision="7b0708761d05" name="express" description="Quantify the abundances of a set of target sequences from sampled subsequences"> + <tool id="express" version="1.1.1" file="express_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="e28c965eeed4" name="fastqc" description="Read QC reports using FastQC"> + <tool id="fastqc" version="1.0.0" file="rgFastQC.xml" /> + </repository> + <repository owner="devteam" changeset_revision="94306bdd58f7" name="fastq_combiner" description="Combine FASTA and QUAL into FASTQ."> + <tool id="fastq_combiner" version="1.0.1" file="fastq_combiner.xml" /> + </repository> + <repository owner="devteam" changeset_revision="30d9ece6c752" name="fastq_filter" description="Filter FASTQ reads by quality score and length"> + <tool id="fastq_filter" version="1.0.0" file="fastq_filter.xml" /> + </repository> + <repository owner="devteam" changeset_revision="1298445c852b" name="fastq_groomer" description="Convert between various FASTQ quality formats."> + <tool id="fastq_groomer" version="1.0.4" file="fastq_groomer.xml" /> + </repository> + <repository owner="devteam" changeset_revision="5d1e9e13e8db" name="fastq_manipulation" description="Manipulate FASTQ reads on various attributes."> + <tool id="fastq_manipulation" version="1.0.1" file="fastq_manipulation.xml" /> + </repository> + <repository owner="devteam" changeset_revision="5a7b5751617b" name="fastq_masker_by_quality" description="FASTQ Masker by quality score"> + <tool id="fastq_masker_by_quality" version="1.0.0" file="fastq_masker_by_quality.xml" /> + </repository> + <repository owner="devteam" changeset_revision="f0949bc49926" name="fastq_paired_end_deinterlacer" description="FASTQ de-interlacer on paired end reads."> + <tool id="fastq_paired_end_deinterlacer" version="1.1" file="fastq_paired_end_deinterlacer.xml" /> + </repository> + <repository owner="devteam" changeset_revision="b89bdf6acb6c" name="fastq_paired_end_interlacer" description="FASTQ interlacer on paired end reads"> + <tool id="fastq_paired_end_interlacer" version="1.1" file="fastq_paired_end_interlacer.xml" /> + </repository> + <repository owner="devteam" changeset_revision="2793d1d765b9" name="fastq_paired_end_joiner" description="FASTQ joiner on paired end reads"> + <tool id="fastq_paired_end_joiner" version="1.0.0" file="fastq_paired_end_joiner.xml" /> + </repository> + <repository owner="devteam" changeset_revision="c549e99026db" name="fastq_paired_end_splitter" description="FASTQ splitter on joined paired end reads"> + <tool id="fastq_paired_end_splitter" version="1.0.0" file="fastq_paired_end_splitter.xml" /> + </repository> + <repository owner="devteam" changeset_revision="9b7b4e0ca9db" name="fastq_stats" description="FASTQ Summary Statistics by column"> + <tool id="fastq_stats" version="1.0.0" file="fastq_stats.xml" /> + </repository> + <repository owner="devteam" changeset_revision="3571553aeb20" name="fastqtofasta" description="FASTQ to FASTA converter"> + <tool id="fastq_to_fasta_python" version="1.0.0" file="fastq_to_fasta.xml" /> + </repository> + <repository owner="devteam" changeset_revision="bc9269529e88" name="fastq_to_tabular" description="FASTQ to Tabular converter"> + <tool id="fastq_to_tabular" version="1.1.0" file="fastq_to_tabular.xml" /> + </repository> + <repository owner="devteam" changeset_revision="0b9feb0ed628" name="fastq_trimmer" description="FASTQ Trimmer by quality"> + <tool id="fastq_trimmer" version="1.0.0" file="fastq_trimmer.xml" /> + </repository> + <repository owner="devteam" changeset_revision="1cdcaf5fc1da" name="fastq_trimmer_by_quality" description="FASTQ Quality Trimmer by sliding window"> + <tool id="fastq_quality_trimmer" version="1.0.0" file="fastq_trimmer_by_quality.xml" /> + </repository> + <repository owner="devteam" changeset_revision="31154ff9f5e1" name="filter_transcripts_via_tracking" description="Filter Combined Transcripts"> + <tool id="filter_combined_via_tracking" version="0.1" file="filter_transcripts_via_tracking.xml" /> + </repository> + <repository owner="devteam" changeset_revision="acf51ff24c7d" name="find_diag_hits" description="find_diag_hits"> + <tool id="find_diag_hits" version="1.0.0" file="find_diag_hits.xml" /> + </repository> + <repository owner="devteam" changeset_revision="33a0e6aca936" name="freebayes_wrapper" description="Call SNPS with Freebayes"> + <tool id="freebayes_wrapper" version="0.5.0" file="freebayes.xml" /> + </repository> + <repository owner="devteam" changeset_revision="7b1b03c4465d" name="gi2taxonomy" description="Fetch taxonomic representation"> + <tool id="Fetch Taxonomic Ranks" version="1.1.0" file="gi2taxonomy.xml" /> + </repository> + <repository owner="devteam" changeset_revision="2cd5ee197ec7" name="gmaj" description="GMAJ Multiple Alignment Viewer"> + <tool id="gmaj_1" version="2.0.1" file="GMAJ.xml" /> + </repository> + <repository owner="devteam" changeset_revision="33e8ed5a4601" name="lca_wrapper" description="Find lowest diagnostic rank"> + <tool id="lca1" version="1.0.1" file="lca.xml" /> + </repository> + <repository owner="devteam" changeset_revision="ae2ec275332a" name="macs" description="Model-based Analysis of ChIP-Seq"> + <tool id="peakcalling_macs" version="1.0.1" file="macs_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="8cd5945559b8" name="poisson2test" description="Poisson two-sample test"> + <tool id="poisson2test" version="1.0.0" file="poisson2test.xml" /> + </repository> + <repository owner="devteam" changeset_revision="82a8234e03f2" name="sicer" description="Statistical approach for the Identification of ChIP-Enriched Regions"> + <tool id="peakcalling_sicer" version="0.0.1" file="sicer_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="9e2b9ca7f33a" name="t2ps" description="Draw phylogeny"> + <tool id="Draw_phylogram" version="1.0.0" file="t2ps_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="592acb9505fc" name="t2t_report" description="Summarize taxonomy"> + <tool id="t2t_report" version="1.0.0" file="t2t_report.xml" /> + </repository> + <repository owner="devteam" changeset_revision="b334cd1095ea" name="tabular_to_fastq" description="Tabular to FASTQ converter"> + <tool id="tabular_to_fastq" version="1.0.0" file="tabular_to_fastq.xml" /> + </repository> + <repository owner="devteam" changeset_revision="1030acbecce6" name="tophat" description="Find splice junctions using RNA-seq data"> + <tool id="tophat" version="1.5.0" file="tophat_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="ffa30bedbee3" name="tophat2" description="Gapped-read mapper for RNA-seq data"> + <tool id="tophat2" version="0.6" file="tophat2_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="b001b50f2009" name="vcf_annotate" description="Annotate a VCF file (dbSNP, hapmap)"> + <tool id="vcf_annotate" version="1.0.0" file="annotate.xml" /> + </repository> + <repository owner="devteam" changeset_revision="76ad0b7865b9" name="vcf_extract" description="Extract reads from a specified region"> + <tool id="vcf_extract" version="1.0.0" file="extract.xml" /> + </repository> + <repository owner="devteam" changeset_revision="da1a6f33b504" name="vcf_filter" description="Filter a VCF file"> + <tool id="vcf_filter" version="1.0.0" file="filter.xml" /> + </repository> + <repository owner="devteam" changeset_revision="9d162bde4113" name="vcf_intersect" description="Generate the intersection of two VCF files"> + <tool id="vcf_intersect" version="1.0.0" file="vcf_tools/intersect.xml" /> + </repository> + <repository owner="devteam" changeset_revision="66253fc0a69b" name="weblogo3" description="Sequence Logo generator for fasta (eg Clustal alignments)"> + <tool id="rgweblogo3" version="0.4" file="rgWebLogo3.xml" /> + </repository> +</toolshed> \ No newline at end of file This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/8207135c2509/ Changeset: 8207135c2509 User: inithello Date: 2014-01-27 15:53:51 Summary: Remove migrated tools from tool_conf.xml.main Affected #: 1 file diff -r e9fc9e7adc63554b6f8a5604bce8be6b37d35d55 -r 8207135c2509db9d875becf0fded05212b3d87e0 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -55,7 +55,6 @@ <section id="convert" name="Convert Formats"><tool file="filters/bed2gff.xml" /><tool file="fasta_tools/fasta_to_tabular.xml" /> - <tool file="fastq/fastq_to_fasta.xml" /><tool file="filters/gff2bed.xml" /><tool file="maf/maf_to_bed.xml" /><tool file="maf/maf_to_interval.xml" /> @@ -182,14 +181,6 @@ <section id="clustal" name="Multiple Alignments"><tool file="rgenetics/rgClustalw.xml" /></section> - <section id="tax_manipulation" name="Metagenomic analyses"> - <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 id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /> @@ -202,41 +193,26 @@ <tool file="phenotype_association/gpass.xml" /><tool file="phenotype_association/beam.xml" /><tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/freebayes.xml" /><tool file="phenotype_association/master2pg.xml" /><tool file="phenotype_association/vcf2pgSnp.xml" /></section><label id="ngs" text="NGS Toolbox Beta" /><section id="cshl_library_information" name="NGS: QC and manipulation"><label id="illumina" text="Illumina data" /> - <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 id="454" text="Roche-454 data" /><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 id="solid" text="AB-SOLiD data" /><tool file="next_gen_conversion/solid2fastq.xml" /><tool file="solid_tools/solid_qual_stats.xml" /><tool file="solid_tools/solid_qual_boxplot.xml" /><label id="generic_fastq" text="Generic FASTQ manipulation" /> - <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 id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" /><label id="fastq_qc" text="FASTQ QC" /><tool file="rgenetics/rgFastQC.xml" /></section><section id="ngs_mapping" name="NGS: Mapping"><label id="illumina" text="Illumina" /> - <tool file="sr_mapping/bowtie2_wrapper.xml" /><label id="roche_454" text="Roche-454" /><tool file="metag_tools/megablast_wrapper.xml" /><tool file="metag_tools/megablast_xml_parser.xml" /> @@ -283,10 +259,6 @@ </section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> - <tool file="ngs_rna/tophat_wrapper.xml" /> - <tool file="ngs_rna/tophat2_wrapper.xml" /> - <tool file="ngs_rna/express_wrapper.xml" /><label id="filtering" text="Filtering" /> - <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section></toolbox> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.