diff --git a/common_toolset/annotation.yml b/common_toolset/annotation.yml deleted file mode 100644 index 7e0411ae..00000000 --- a/common_toolset/annotation.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: Annotation -tools: -- name: prokka - owner: crs4 -- name: busco - owner: iuc -- name: mlst - owner: iuc -- name: abricate - owner: iuc -- name: hammock - owner: hammock -- name: roary - owner: iuc -- name: gubbins - owner: iuc -- name: probmetab - owner: mmonsoor -- name: lcmsmatching - owner: prog diff --git a/common_toolset/annotation.yml.lock b/common_toolset/annotation.yml.lock deleted file mode 100644 index 8782d430..00000000 --- a/common_toolset/annotation.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Annotation -tools: -- name: prokka - owner: crs4 - revisions: - - eaee459f3d69 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: busco - owner: iuc - revisions: - - 1440ae06552f - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: mlst - owner: iuc - revisions: - - 1f5641a52664 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: abricate - owner: iuc - revisions: - - 78c75f134c16 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: hammock - owner: hammock - revisions: - - afddbcbc8ee8 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: roary - owner: iuc - revisions: - - f1ccc8a6eb05 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: gubbins - owner: iuc - revisions: - - 637ec5d5368c - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: probmetab - owner: mmonsoor - revisions: - - 52b222a626b0 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: lcmsmatching - owner: prog - revisions: - - f86fec07f392 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation diff --git a/common_toolset/assembly.yml b/common_toolset/assembly.yml deleted file mode 100644 index 840bc09e..00000000 --- a/common_toolset/assembly.yml +++ /dev/null @@ -1,14 +0,0 @@ -tool_panel_section_label: Assembly -tools: -- name: unicycler - owner: iuc -- name: quast - owner: iuc -- name: spades - owner: nml -- name: shovill - owner: iuc -- name: velvetoptimiser - owner: simon-gladman -- name: pilon - owner: iuc diff --git a/common_toolset/assembly.yml.lock b/common_toolset/assembly.yml.lock deleted file mode 100644 index af625809..00000000 --- a/common_toolset/assembly.yml.lock +++ /dev/null @@ -1,41 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Assembly -tools: -- name: unicycler - owner: iuc - revisions: - - 0a3a602cd1e3 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: quast - owner: iuc - revisions: - - f30d03867854 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: spades - owner: nml - revisions: - - b8d633fbf5f5 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: shovill - owner: iuc - revisions: - - 865119fcb694 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: velvetoptimiser - owner: simon-gladman - revisions: - - 37d88f41c810 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: pilon - owner: iuc - revisions: - - 11e5408fd238 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly diff --git a/common_toolset/bed.yml b/common_toolset/bed.yml deleted file mode 100644 index a97a3e41..00000000 --- a/common_toolset/bed.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: BED -tools: -- name: bedtools - owner: iuc diff --git a/common_toolset/bed.yml.lock b/common_toolset/bed.yml.lock deleted file mode 100644 index b58e983f..00000000 --- a/common_toolset/bed.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: BED -tools: -- name: bedtools - owner: iuc - revisions: - - dde39ba9c031 - tool_panel_section_id: bed - tool_panel_section_label: BED diff --git a/common_toolset/chip_seq.yml b/common_toolset/chip_seq.yml deleted file mode 100644 index 3eb9692d..00000000 --- a/common_toolset/chip_seq.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: ChIP-seq -tools: -- name: chipseeker - owner: rnateam -- name: macs2 - owner: iuc -- name: sicer - owner: devteam -- name: ngsutils_bam_filter - owner: iuc -- name: diffbind - owner: bgruening -- name: tag_pileup_frequency - owner: iuc -- name: fasta_nucleotide_color_plot - owner: iuc -- name: resize_coordinate_window - owner: iuc -- name: macs - owner: devteam diff --git a/common_toolset/chip_seq.yml.lock b/common_toolset/chip_seq.yml.lock deleted file mode 100644 index eb26d727..00000000 --- a/common_toolset/chip_seq.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: ChIP-seq -tools: -- name: chipseeker - owner: rnateam - revisions: - - 1b9a9409831d - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: macs2 - owner: iuc - revisions: - - 424aefbd7777 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: sicer - owner: devteam - revisions: - - 74c9214cc8e6 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: ngsutils_bam_filter - owner: iuc - revisions: - - 2e957d4c4b95 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: diffbind - owner: bgruening - revisions: - - c97a786e8fb5 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: tag_pileup_frequency - owner: iuc - revisions: - - 6432735cdb22 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: fasta_nucleotide_color_plot - owner: iuc - revisions: - - e4b5401adcec - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: resize_coordinate_window - owner: iuc - revisions: - - 9ba78e8985dc - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: macs - owner: devteam - revisions: - - f6319b0b4391 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq diff --git a/common_toolset/chromosome_conformation.yml b/common_toolset/chromosome_conformation.yml deleted file mode 100644 index 3a0dd5e3..00000000 --- a/common_toolset/chromosome_conformation.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Chromosome Conformation -tools: -- name: hifive - owner: sauria diff --git a/common_toolset/chromosome_conformation.yml.lock b/common_toolset/chromosome_conformation.yml.lock deleted file mode 100644 index 30cd3d9e..00000000 --- a/common_toolset/chromosome_conformation.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Chromosome Conformation -tools: -- name: hifive - owner: sauria - revisions: - - cc95aa05f643 - tool_panel_section_id: chromosome_conformation - tool_panel_section_label: Chromosome Conformation diff --git a/common_toolset/collection_operations.yml b/common_toolset/collection_operations.yml deleted file mode 100644 index a6a37c4a..00000000 --- a/common_toolset/collection_operations.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Collection Operations -tools: -- name: collection_column_join - owner: iuc -- name: collapse_collections - owner: nml diff --git a/common_toolset/collection_operations.yml.lock b/common_toolset/collection_operations.yml.lock deleted file mode 100644 index cbb61c3b..00000000 --- a/common_toolset/collection_operations.yml.lock +++ /dev/null @@ -1,17 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Collection Operations -tools: -- name: collection_column_join - owner: iuc - revisions: - - 071084070619 - tool_panel_section_id: collection_operations - tool_panel_section_label: Collection Operations -- name: collapse_collections - owner: nml - revisions: - - 25136a2b0cfe - tool_panel_section_id: collection_operations - tool_panel_section_label: Collection Operations diff --git a/common_toolset/convert_formats.yml b/common_toolset/convert_formats.yml deleted file mode 100644 index 5b996965..00000000 --- a/common_toolset/convert_formats.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: Convert Formats -tools: -- name: tabular_to_fasta - owner: devteam -- name: fasta_to_tabular - owner: devteam -- name: intermine_galaxy_exchange - owner: iuc -- name: bam_to_scidx - owner: iuc -- name: fastq_to_fasta - owner: devteam -- name: tabular_to_fastq - owner: devteam -- name: fastqtofasta - owner: devteam -- name: fastq_to_tabular - owner: devteam -- name: idpquery - owner: galaxyp diff --git a/common_toolset/convert_formats.yml.lock b/common_toolset/convert_formats.yml.lock deleted file mode 100644 index db897873..00000000 --- a/common_toolset/convert_formats.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Convert Formats -tools: -- name: tabular_to_fasta - owner: devteam - revisions: - - 0b4e36026794 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: fasta_to_tabular - owner: devteam - revisions: - - 7e801ab2b70e - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: intermine_galaxy_exchange - owner: iuc - revisions: - - c24014d80001 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: bam_to_scidx - owner: iuc - revisions: - - 408520e1ae1a - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: fastq_to_fasta - owner: devteam - revisions: - - 02a5f43cd5d1 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: tabular_to_fastq - owner: devteam - revisions: - - b8cdc0507586 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: fastqtofasta - owner: devteam - revisions: - - 4844c1810c16 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: fastq_to_tabular - owner: devteam - revisions: - - ccf4e1d1fcbe - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: idpquery - owner: galaxyp - revisions: - - 66c38e74d1ae - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats diff --git a/common_toolset/datamash.yml b/common_toolset/datamash.yml deleted file mode 100644 index 662eb7df..00000000 --- a/common_toolset/datamash.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Datamash -tools: -- name: datamash_ops - owner: iuc -- name: datamash_transpose - owner: iuc -- name: datamash_reverse - owner: iuc diff --git a/common_toolset/datamash.yml.lock b/common_toolset/datamash.yml.lock deleted file mode 100644 index c70a8d8f..00000000 --- a/common_toolset/datamash.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Datamash -tools: -- name: datamash_ops - owner: iuc - revisions: - - 562f3c677828 - tool_panel_section_id: datamash - tool_panel_section_label: Datamash -- name: datamash_transpose - owner: iuc - revisions: - - 22c2a1ac7ae3 - tool_panel_section_id: datamash - tool_panel_section_label: Datamash -- name: datamash_reverse - owner: iuc - revisions: - - 0f1724dd59d2 - tool_panel_section_id: datamash - tool_panel_section_label: Datamash diff --git a/common_toolset/deeptools.yml b/common_toolset/deeptools.yml deleted file mode 100644 index 446f542a..00000000 --- a/common_toolset/deeptools.yml +++ /dev/null @@ -1,36 +0,0 @@ -tool_panel_section_label: deepTools -tools: -- name: deeptools_plot_profile - owner: bgruening -- name: deeptools_bam_coverage - owner: bgruening -- name: deeptools_plot_pca - owner: bgruening -- name: deeptools_plot_heatmap - owner: bgruening -- name: deeptools_plot_fingerprint - owner: bgruening -- name: deeptools_plot_enrichment - owner: bgruening -- name: deeptools_plot_coverage - owner: bgruening -- name: deeptools_plot_correlation - owner: bgruening -- name: deeptools_multi_bigwig_summary - owner: bgruening -- name: deeptools_multi_bam_summary - owner: bgruening -- name: deeptools_correct_gc_bias - owner: bgruening -- name: deeptools_compute_matrix - owner: bgruening -- name: deeptools_compute_gc_bias - owner: bgruening -- name: deeptools_bigwig_compare - owner: bgruening -- name: deeptools_bam_pe_fragmentsize - owner: bgruening -- name: deeptools_bam_compare - owner: bgruening -- name: deeptools_compute_matrix_operations - owner: bgruening diff --git a/common_toolset/deeptools.yml.lock b/common_toolset/deeptools.yml.lock deleted file mode 100644 index fee67610..00000000 --- a/common_toolset/deeptools.yml.lock +++ /dev/null @@ -1,107 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: deepTools -tools: -- name: deeptools_plot_profile - owner: bgruening - revisions: - - d806504e96d9 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_bam_coverage - owner: bgruening - revisions: - - 7a7fd0f5f15d - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_pca - owner: bgruening - revisions: - - aa200e4f3939 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_heatmap - owner: bgruening - revisions: - - a7849312d328 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_fingerprint - owner: bgruening - revisions: - - d57251071381 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_enrichment - owner: bgruening - revisions: - - d9114ef1c8a5 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_coverage - owner: bgruening - revisions: - - 4e12ea27f788 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_correlation - owner: bgruening - revisions: - - bd7db9e2f2cb - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_multi_bigwig_summary - owner: bgruening - revisions: - - 2f9e4843f480 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_multi_bam_summary - owner: bgruening - revisions: - - 69a8621ca2f0 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_correct_gc_bias - owner: bgruening - revisions: - - c34d11ea4ba6 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_compute_matrix - owner: bgruening - revisions: - - b73e213add0c - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_compute_gc_bias - owner: bgruening - revisions: - - b8858746dc1f - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_bigwig_compare - owner: bgruening - revisions: - - 71aa86af6762 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_bam_pe_fragmentsize - owner: bgruening - revisions: - - 1d848bc4585f - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_bam_compare - owner: bgruening - revisions: - - 268e91e540ee - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_compute_matrix_operations - owner: bgruening - revisions: - - c3e012dfe21f - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools diff --git a/common_toolset/emboss.yml b/common_toolset/emboss.yml deleted file mode 100644 index a6f95ed2..00000000 --- a/common_toolset/emboss.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: EMBOSS -tools: -- name: emboss_5 - owner: devteam diff --git a/common_toolset/emboss.yml.lock b/common_toolset/emboss.yml.lock deleted file mode 100644 index 04676c6d..00000000 --- a/common_toolset/emboss.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: EMBOSS -tools: -- name: emboss_5 - owner: devteam - revisions: - - dc492eb6a4fc - tool_panel_section_id: emboss - tool_panel_section_label: EMBOSS diff --git a/common_toolset/epigenetics.yml b/common_toolset/epigenetics.yml deleted file mode 100644 index 0335c7a4..00000000 --- a/common_toolset/epigenetics.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Epigenetics -tools: -- name: vcf_filter - owner: devteam -- name: hicup_deduplicator - owner: bgruening diff --git a/common_toolset/epigenetics.yml.lock b/common_toolset/epigenetics.yml.lock deleted file mode 100644 index de7b5503..00000000 --- a/common_toolset/epigenetics.yml.lock +++ /dev/null @@ -1,17 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Epigenetics -tools: -- name: vcf_filter - owner: devteam - revisions: - - da1a6f33b504 - tool_panel_section_id: epigenetics - tool_panel_section_label: Epigenetics -- name: hicup_deduplicator - owner: bgruening - revisions: - - 46e5b4782715 - tool_panel_section_id: epigenetics - tool_panel_section_label: Epigenetics diff --git a/common_toolset/evolution.yml b/common_toolset/evolution.yml deleted file mode 100644 index a19b0471..00000000 --- a/common_toolset/evolution.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Evolution -tools: -- name: iqtree - owner: iuc diff --git a/common_toolset/evolution.yml.lock b/common_toolset/evolution.yml.lock deleted file mode 100644 index 4ec72870..00000000 --- a/common_toolset/evolution.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Evolution -tools: -- name: iqtree - owner: iuc - revisions: - - d1c340a5664b - tool_panel_section_id: evolution - tool_panel_section_label: Evolution diff --git a/common_toolset/fastafastq.yml b/common_toolset/fastafastq.yml deleted file mode 100644 index df05370a..00000000 --- a/common_toolset/fastafastq.yml +++ /dev/null @@ -1,72 +0,0 @@ -tool_panel_section_label: FASTA/FASTQ -tools: -- name: find_subsequences - owner: bgruening -- name: cutadapt - owner: lparsons -- name: flash - owner: iuc -- name: fastx_trimmer - owner: devteam -- name: fastx_reverse_complement - owner: devteam -- name: fastx_clipper - owner: devteam -- name: fastq_quality_filter - owner: devteam -- name: length_and_gc_content - owner: iuc -- name: fastx_renamer - owner: devteam -- name: fastx_barcode_splitter - owner: devteam -- name: fastx_artifacts_filter - owner: devteam -- name: fastq_quality_converter - owner: devteam -- name: fastq_paired_end_joiner - owner: devteam -- name: fastq_paired_end_interlacer - owner: devteam -- name: fastq_paired_end_deinterlacer - owner: devteam -- name: fastq_join - owner: lparsons -- name: fastq_paired_end_splitter - owner: devteam -- name: fastq_masker_by_quality - owner: devteam -- name: fastq_manipulation - owner: devteam -- name: fastq_groomer - owner: devteam -- name: fastq_filter - owner: devteam -- name: fastq_combiner - owner: devteam -- name: trim_galore - owner: bgruening -- name: short_reads_trim_seq - owner: devteam -- name: short_reads_figure_score - owner: devteam -- name: fastx_collapser - owner: devteam -- name: fastq_trimmer - owner: devteam -- name: fastq_trimmer_by_quality - owner: devteam -- name: fasta_nucleotide_changer - owner: devteam -- name: fasta_formatter - owner: devteam -- name: fasta_filter_by_length - owner: devteam -- name: fasta_concatenate_by_species - owner: devteam -- name: fasta_compute_length - owner: devteam -- name: fastp - owner: iuc -- name: fasta_stats - owner: iuc diff --git a/common_toolset/fastafastq.yml.lock b/common_toolset/fastafastq.yml.lock deleted file mode 100644 index b2d9ad52..00000000 --- a/common_toolset/fastafastq.yml.lock +++ /dev/null @@ -1,215 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: FASTA/FASTQ -tools: -- name: find_subsequences - owner: bgruening - revisions: - - d882a0a75759 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: cutadapt - owner: lparsons - revisions: - - e4691e1589d3 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: flash - owner: iuc - revisions: - - a27654fc4270 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_trimmer - owner: devteam - revisions: - - 547e8d00f11c - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_reverse_complement - owner: devteam - revisions: - - 0c2907307ba4 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_clipper - owner: devteam - revisions: - - 736b8f6ee456 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_quality_filter - owner: devteam - revisions: - - 7b4468117008 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: length_and_gc_content - owner: iuc - revisions: - - f088370d2a3c - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_renamer - owner: devteam - revisions: - - 3599f5451ee2 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_barcode_splitter - owner: devteam - revisions: - - 4bedca26c133 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_artifacts_filter - owner: devteam - revisions: - - 567d5b3c52b1 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_quality_converter - owner: devteam - revisions: - - 54053ea6c77e - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_paired_end_joiner - owner: devteam - revisions: - - 822cc1e6274e - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_paired_end_interlacer - owner: devteam - revisions: - - ef49268ee579 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_paired_end_deinterlacer - owner: devteam - revisions: - - b7ce72b00e62 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_join - owner: lparsons - revisions: - - 8ec3dfde378b - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_paired_end_splitter - owner: devteam - revisions: - - 9bbe5b7ffa12 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_masker_by_quality - owner: devteam - revisions: - - eb592e9ec47a - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_manipulation - owner: devteam - revisions: - - 4ac14b275aca - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_groomer - owner: devteam - revisions: - - 71e5fa25b8a2 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_filter - owner: devteam - revisions: - - 06934412f56d - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_combiner - owner: devteam - revisions: - - 56389130cb63 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: trim_galore - owner: bgruening - revisions: - - 949f01671246 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: short_reads_trim_seq - owner: devteam - revisions: - - 25e6fe525306 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: short_reads_figure_score - owner: devteam - revisions: - - b52b9c7aabd9 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_collapser - owner: devteam - revisions: - - 7ce1891db6f5 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_trimmer - owner: devteam - revisions: - - 2d0d13b0b0f1 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_trimmer_by_quality - owner: devteam - revisions: - - c64d534a763c - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_nucleotide_changer - owner: devteam - revisions: - - 091ca73f5804 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_formatter - owner: devteam - revisions: - - 859422bcb689 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_filter_by_length - owner: devteam - revisions: - - 2fd6033d0e9c - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_concatenate_by_species - owner: devteam - revisions: - - 717aee069681 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_compute_length - owner: devteam - revisions: - - de2db1bdfbf8 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastp - owner: iuc - revisions: - - 1d8fe9bc4cb0 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_stats - owner: iuc - revisions: - - 9c620a950d3a - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ diff --git a/common_toolset/fastq_quality_control.yml b/common_toolset/fastq_quality_control.yml deleted file mode 100644 index 7262b15b..00000000 --- a/common_toolset/fastq_quality_control.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: FASTQ Quality Control -tools: -- name: fastqc - owner: devteam -- name: trimmomatic - owner: pjbriggs -- name: multiqc - owner: iuc -- name: fastq_stats - owner: devteam -- name: fastx_quality_statistics - owner: devteam -- name: fastx_nucleotides_distribution - owner: devteam -- name: fastq_quality_boxplot - owner: devteam diff --git a/common_toolset/fastq_quality_control.yml.lock b/common_toolset/fastq_quality_control.yml.lock deleted file mode 100644 index cdb752dc..00000000 --- a/common_toolset/fastq_quality_control.yml.lock +++ /dev/null @@ -1,47 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: FASTQ Quality Control -tools: -- name: fastqc - owner: devteam - revisions: - - e7b2202befea - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: trimmomatic - owner: pjbriggs - revisions: - - 51b771646466 - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: multiqc - owner: iuc - revisions: - - b2f1f75d49c4 - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: fastq_stats - owner: devteam - revisions: - - e2cf940128d5 - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: fastx_quality_statistics - owner: devteam - revisions: - - 59003d0543cd - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: fastx_nucleotides_distribution - owner: devteam - revisions: - - 21796f46e0ba - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: fastq_quality_boxplot - owner: devteam - revisions: - - 3987db70a4b0 - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control diff --git a/common_toolset/fetch_sequencesalignments.yml b/common_toolset/fetch_sequencesalignments.yml deleted file mode 100644 index 9ddda79a..00000000 --- a/common_toolset/fetch_sequencesalignments.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Fetch Sequences/Alignments -tools: -- name: extract_genomic_dna - owner: iuc diff --git a/common_toolset/fetch_sequencesalignments.yml.lock b/common_toolset/fetch_sequencesalignments.yml.lock deleted file mode 100644 index a8bd6870..00000000 --- a/common_toolset/fetch_sequencesalignments.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Fetch Sequences/Alignments -tools: -- name: extract_genomic_dna - owner: iuc - revisions: - - e400dcbc60d0 - tool_panel_section_id: fetch_sequences_alignments - tool_panel_section_label: Fetch Sequences/Alignments diff --git a/common_toolset/filter_and_sort.yml b/common_toolset/filter_and_sort.yml deleted file mode 100644 index 89ef7a6d..00000000 --- a/common_toolset/filter_and_sort.yml +++ /dev/null @@ -1,10 +0,0 @@ -tool_panel_section_label: Filter and Sort -tools: -- name: column_arrange_by_header - owner: bgruening -- name: sample_seqs - owner: peterjc -- name: sqlite_to_tabular - owner: jjohnson -- name: query_tabular - owner: jjohnson diff --git a/common_toolset/filter_and_sort.yml.lock b/common_toolset/filter_and_sort.yml.lock deleted file mode 100644 index 9137579d..00000000 --- a/common_toolset/filter_and_sort.yml.lock +++ /dev/null @@ -1,29 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Filter and Sort -tools: -- name: column_arrange_by_header - owner: bgruening - revisions: - - 6c6d26ff01ff - tool_panel_section_id: filter_and_sort - tool_panel_section_label: Filter and Sort -- name: sample_seqs - owner: peterjc - revisions: - - 7c40a1fbc82e - tool_panel_section_id: filter_and_sort - tool_panel_section_label: Filter and Sort -- name: sqlite_to_tabular - owner: jjohnson - revisions: - - 123b9ca5e26a - tool_panel_section_id: filter_and_sort - tool_panel_section_label: Filter and Sort -- name: query_tabular - owner: jjohnson - revisions: - - 5bb148ee644a - tool_panel_section_id: filter_and_sort - tool_panel_section_label: Filter and Sort diff --git a/common_toolset/gatk.yml b/common_toolset/gatk.yml deleted file mode 100644 index 9bc16af1..00000000 --- a/common_toolset/gatk.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: GATK -tools: -- name: count_covariates - owner: devteam diff --git a/common_toolset/gatk.yml.lock b/common_toolset/gatk.yml.lock deleted file mode 100644 index 6050d29d..00000000 --- a/common_toolset/gatk.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: GATK -tools: -- name: count_covariates - owner: devteam - revisions: - - 14e304b70425 - tool_panel_section_id: gatk - tool_panel_section_label: GATK diff --git a/common_toolset/gatk_tools.yml b/common_toolset/gatk_tools.yml deleted file mode 100644 index 1a5907fd..00000000 --- a/common_toolset/gatk_tools.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: GATK Tools -tools: -- name: gatk2 - owner: iuc diff --git a/common_toolset/gatk_tools.yml.lock b/common_toolset/gatk_tools.yml.lock deleted file mode 100644 index 839b4105..00000000 --- a/common_toolset/gatk_tools.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: GATK Tools -tools: -- name: gatk2 - owner: iuc - revisions: - - 35c00763cb5c - tool_panel_section_id: gatk_tools - tool_panel_section_label: GATK Tools diff --git a/common_toolset/gemini.yml b/common_toolset/gemini.yml deleted file mode 100644 index 0f8df51a..00000000 --- a/common_toolset/gemini.yml +++ /dev/null @@ -1,36 +0,0 @@ -tool_panel_section_label: Gemini -tools: -- name: gemini_load - owner: iuc -- name: gemini_db_info - owner: iuc -- name: gemini_windower - owner: iuc -- name: gemini_pathways - owner: iuc -- name: gemini_annotate - owner: iuc -- name: gemini_interactions - owner: iuc -- name: gemini_qc - owner: iuc -- name: gemini_set_somatic - owner: iuc -- name: gemini_roh - owner: iuc -- name: gemini_fusions - owner: iuc -- name: gemini_query - owner: iuc -- name: gemini_lof_sieve - owner: iuc -- name: gemini_actionable_mutations - owner: iuc -- name: gemini_amend - owner: iuc -- name: gemini_stats - owner: iuc -- name: gemini_gene_wise - owner: iuc -- name: gemini_burden - owner: iuc diff --git a/common_toolset/gemini.yml.lock b/common_toolset/gemini.yml.lock deleted file mode 100644 index 1969ba49..00000000 --- a/common_toolset/gemini.yml.lock +++ /dev/null @@ -1,107 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Gemini -tools: -- name: gemini_load - owner: iuc - revisions: - - b2c25142267e - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_db_info - owner: iuc - revisions: - - bc8b01d1b496 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_windower - owner: iuc - revisions: - - 3b5b1ebc8423 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_pathways - owner: iuc - revisions: - - c63b7eefb07a - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_annotate - owner: iuc - revisions: - - 0c8f7322f8fc - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_interactions - owner: iuc - revisions: - - 7028ca3cac1c - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_qc - owner: iuc - revisions: - - 8414eecc3828 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_set_somatic - owner: iuc - revisions: - - '991049484627' - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_roh - owner: iuc - revisions: - - d65ca2fa673b - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_fusions - owner: iuc - revisions: - - 6e3d2bd01a96 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_query - owner: iuc - revisions: - - cd00221d67cb - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_lof_sieve - owner: iuc - revisions: - - dda378a72430 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_actionable_mutations - owner: iuc - revisions: - - 643a9ad97f08 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_amend - owner: iuc - revisions: - - bff8fad3fb69 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_stats - owner: iuc - revisions: - - 86d4303cc3ca - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_gene_wise - owner: iuc - revisions: - - 4b26f6c99227 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_burden - owner: iuc - revisions: - - 699ce2631e79 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini diff --git a/common_toolset/genome_diversity.yml b/common_toolset/genome_diversity.yml deleted file mode 100644 index 62e10bfa..00000000 --- a/common_toolset/genome_diversity.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Genome Diversity -tools: -- name: genome_diversity - owner: miller-lab -- name: fasttree - owner: iuc diff --git a/common_toolset/genome_diversity.yml.lock b/common_toolset/genome_diversity.yml.lock deleted file mode 100644 index 87fb88f2..00000000 --- a/common_toolset/genome_diversity.yml.lock +++ /dev/null @@ -1,17 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Genome Diversity -tools: -- name: genome_diversity - owner: miller-lab - revisions: - - e56023008e36 - tool_panel_section_id: genome_diversity - tool_panel_section_label: Genome Diversity -- name: fasttree - owner: iuc - revisions: - - c7e73acfa3eb - tool_panel_section_id: genome_diversity - tool_panel_section_label: Genome Diversity diff --git a/common_toolset/get_data.yml b/common_toolset/get_data.yml deleted file mode 100644 index 325bbaac..00000000 --- a/common_toolset/get_data.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Get Data -tools: -- name: sra_tools - owner: iuc -- name: trinity_define_clusters_by_cutting_tree - owner: iuc diff --git a/common_toolset/get_data.yml.lock b/common_toolset/get_data.yml.lock deleted file mode 100644 index 00a67ad2..00000000 --- a/common_toolset/get_data.yml.lock +++ /dev/null @@ -1,17 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Get Data -tools: -- name: sra_tools - owner: iuc - revisions: - - 1790dcf3c32d - tool_panel_section_id: get_data - tool_panel_section_label: Get Data -- name: trinity_define_clusters_by_cutting_tree - owner: iuc - revisions: - - 6fa08f46db8c - tool_panel_section_id: get_data - tool_panel_section_label: Get Data diff --git a/common_toolset/graphdisplay_data.yml b/common_toolset/graphdisplay_data.yml deleted file mode 100644 index ad76b7fc..00000000 --- a/common_toolset/graphdisplay_data.yml +++ /dev/null @@ -1,28 +0,0 @@ -tool_panel_section_label: Graph/Display Data -tools: -- name: ggplot2_heatmap2 - owner: iuc -- name: xy_plot - owner: devteam -- name: circos - owner: iuc -- name: venn_list - owner: peterjc -- name: ucsc_custom_track - owner: devteam -- name: scatterplot - owner: devteam -- name: histogram - owner: devteam -- name: gmaj - owner: devteam -- name: bandage - owner: iuc -- name: jbrowse - owner: iuc -- name: ggplot2_heatmap - owner: iuc -- name: krona_text - owner: saskia-hiltemann -- name: mummer - owner: peterjc diff --git a/common_toolset/graphdisplay_data.yml.lock b/common_toolset/graphdisplay_data.yml.lock deleted file mode 100644 index f917348f..00000000 --- a/common_toolset/graphdisplay_data.yml.lock +++ /dev/null @@ -1,83 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Graph/Display Data -tools: -- name: ggplot2_heatmap2 - owner: iuc - revisions: - - ca7cb0eaad62 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: xy_plot - owner: devteam - revisions: - - ecb437f1d298 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: circos - owner: iuc - revisions: - - ae9994cf526f - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: venn_list - owner: peterjc - revisions: - - e13206029a72 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: ucsc_custom_track - owner: devteam - revisions: - - 760f588e8a26 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: scatterplot - owner: devteam - revisions: - - efda9a4a50e7 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: histogram - owner: devteam - revisions: - - cdb9e89e2970 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: gmaj - owner: devteam - revisions: - - 2cd5ee197ec7 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: bandage - owner: iuc - revisions: - - 58124285e462 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: jbrowse - owner: iuc - revisions: - - 2bb2e07a7a21 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: ggplot2_heatmap - owner: iuc - revisions: - - de002ba2b849 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: krona_text - owner: saskia-hiltemann - revisions: - - b14f1444e464 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: mummer - owner: peterjc - revisions: - - d9f3d4779507 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data diff --git a/common_toolset/iwtomics.yml b/common_toolset/iwtomics.yml deleted file mode 100644 index 11366df8..00000000 --- a/common_toolset/iwtomics.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: IWTomics -tools: -- name: iwtomics_loadandplot - owner: iuc -- name: iwtomics_testandplot - owner: iuc -- name: iwtomics_plotwithscale - owner: iuc diff --git a/common_toolset/iwtomics.yml.lock b/common_toolset/iwtomics.yml.lock deleted file mode 100644 index 8ac920a6..00000000 --- a/common_toolset/iwtomics.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: IWTomics -tools: -- name: iwtomics_loadandplot - owner: iuc - revisions: - - ce633cc8f5f9 - tool_panel_section_id: iwtomics - tool_panel_section_label: IWTomics -- name: iwtomics_testandplot - owner: iuc - revisions: - - 94965e369be4 - tool_panel_section_id: iwtomics - tool_panel_section_label: IWTomics -- name: iwtomics_plotwithscale - owner: iuc - revisions: - - 1bc9150ed125 - tool_panel_section_id: iwtomics - tool_panel_section_label: IWTomics diff --git a/common_toolset/join_subtract_and_group.yml b/common_toolset/join_subtract_and_group.yml deleted file mode 100644 index cedfb0cd..00000000 --- a/common_toolset/join_subtract_and_group.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Join, Subtract and Group -tools: -- name: subtract_query - owner: devteam diff --git a/common_toolset/join_subtract_and_group.yml.lock b/common_toolset/join_subtract_and_group.yml.lock deleted file mode 100644 index 9386136f..00000000 --- a/common_toolset/join_subtract_and_group.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Join, Subtract and Group -tools: -- name: subtract_query - owner: devteam - revisions: - - ff3901618482 - tool_panel_section_id: join__subtract_and_group - tool_panel_section_label: Join, Subtract and Group diff --git a/common_toolset/mapping.yml b/common_toolset/mapping.yml deleted file mode 100644 index fd7fc040..00000000 --- a/common_toolset/mapping.yml +++ /dev/null @@ -1,18 +0,0 @@ -tool_panel_section_label: Mapping -tools: -- name: bowtie2 - owner: devteam -- name: lastz - owner: devteam -- name: bwa - owner: devteam -- name: star_fusion - owner: iuc -- name: megablast_xml_parser - owner: devteam -- name: megablast_wrapper - owner: devteam -- name: bowtie_wrappers - owner: devteam -- name: lastz_paired_reads - owner: devteam diff --git a/common_toolset/mapping.yml.lock b/common_toolset/mapping.yml.lock deleted file mode 100644 index 1fd477ec..00000000 --- a/common_toolset/mapping.yml.lock +++ /dev/null @@ -1,53 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Mapping -tools: -- name: bowtie2 - owner: devteam - revisions: - - 017aba02828d - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: lastz - owner: devteam - revisions: - - e7f19d6a9af8 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: bwa - owner: devteam - revisions: - - 01ac0a5fedc3 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: star_fusion - owner: iuc - revisions: - - 04b73d626680 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: megablast_xml_parser - owner: devteam - revisions: - - 03ca082aeb2e - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: megablast_wrapper - owner: devteam - revisions: - - fb2e0e1dac89 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: bowtie_wrappers - owner: devteam - revisions: - - b46e7d48076a - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: lastz_paired_reads - owner: devteam - revisions: - - ecc974513241 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping diff --git a/common_toolset/metagenomic_analysis.yml b/common_toolset/metagenomic_analysis.yml deleted file mode 100644 index 6c44ba39..00000000 --- a/common_toolset/metagenomic_analysis.yml +++ /dev/null @@ -1,34 +0,0 @@ -tool_panel_section_label: Metagenomic Analysis -tools: -- name: diamond - owner: bgruening -- name: vsearch - owner: iuc -- name: vegan_rarefaction - owner: iuc -- name: vegan_fisher_alpha - owner: iuc -- name: vegan_diversity - owner: iuc -- name: kraken_report - owner: devteam -- name: kraken - owner: devteam -- name: taxonomy_krona_chart - owner: crs4 -- name: metagenomeseq_normalization - owner: iuc -- name: kraken_taxonomy_report - owner: iuc -- name: biom_add_metadata - owner: iuc -- name: biom_convert - owner: iuc -- name: kraken_translate - owner: devteam -- name: kraken_filter - owner: devteam -- name: kraken2tax - owner: devteam -- name: poisson2test - owner: devteam diff --git a/common_toolset/metagenomic_analysis.yml.lock b/common_toolset/metagenomic_analysis.yml.lock deleted file mode 100644 index faf2f050..00000000 --- a/common_toolset/metagenomic_analysis.yml.lock +++ /dev/null @@ -1,101 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Metagenomic Analysis -tools: -- name: diamond - owner: bgruening - revisions: - - 64be1ac21109 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: vsearch - owner: iuc - revisions: - - b3c7199d8786 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: vegan_rarefaction - owner: iuc - revisions: - - b0d5976540e3 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: vegan_fisher_alpha - owner: iuc - revisions: - - f9966e11885b - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: vegan_diversity - owner: iuc - revisions: - - a2c047a2c380 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken_report - owner: devteam - revisions: - - 6c09bed3444f - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken - owner: devteam - revisions: - - 8ba2174315aa - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: taxonomy_krona_chart - owner: crs4 - revisions: - - c9f8fef1df74 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: metagenomeseq_normalization - owner: iuc - revisions: - - d16f7cc26516 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken_taxonomy_report - owner: iuc - revisions: - - b11b3ac48bb9 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: biom_add_metadata - owner: iuc - revisions: - - 367b1ed91207 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: biom_convert - owner: iuc - revisions: - - 501c21cce614 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken_translate - owner: devteam - revisions: - - 9bdcba262627 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken_filter - owner: devteam - revisions: - - 5bee9adae474 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken2tax - owner: devteam - revisions: - - f03c7ba8d8bc - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: poisson2test - owner: devteam - revisions: - - 5ff18ec88181 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis diff --git a/common_toolset/mimodd.yml b/common_toolset/mimodd.yml deleted file mode 100644 index 50da3c14..00000000 --- a/common_toolset/mimodd.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: MiModD -tools: -- name: mimodd_main - owner: wolma diff --git a/common_toolset/mimodd.yml.lock b/common_toolset/mimodd.yml.lock deleted file mode 100644 index 90858eba..00000000 --- a/common_toolset/mimodd.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: MiModD -tools: -- name: mimodd_main - owner: wolma - revisions: - - bfcd121b99bf - tool_panel_section_id: mimodd - tool_panel_section_label: MiModD diff --git a/common_toolset/mothur.yml b/common_toolset/mothur.yml deleted file mode 100644 index ed3e970d..00000000 --- a/common_toolset/mothur.yml +++ /dev/null @@ -1,264 +0,0 @@ -tool_panel_section_label: Mothur -tools: -- name: mothur_taxonomy_to_krona - owner: iuc -- name: mothur_merge_count - owner: iuc -- name: mothur_chimera_vsearch - owner: iuc -- name: mothur_rename_seqs - owner: iuc -- name: mothur_biom_info - owner: iuc -- name: mothur_venn - owner: iuc -- name: mothur_unique_seqs - owner: iuc -- name: mothur_unifrac_weighted - owner: iuc -- name: mothur_unifrac_unweighted - owner: iuc -- name: mothur_trim_seqs - owner: iuc -- name: mothur_trim_flows - owner: iuc -- name: mothur_tree_shared - owner: iuc -- name: mothur_summary_tax - owner: iuc -- name: mothur_summary_single - owner: iuc -- name: mothur_summary_shared - owner: iuc -- name: mothur_summary_seqs - owner: iuc -- name: mothur_summary_qual - owner: iuc -- name: mothur_sub_sample - owner: iuc -- name: mothur_split_groups - owner: iuc -- name: mothur_split_abund - owner: iuc -- name: mothur_sort_seqs - owner: iuc -- name: mothur_shhh_seqs - owner: iuc -- name: mothur_shhh_flows - owner: iuc -- name: mothur_sffinfo - owner: iuc -- name: mothur_seq_error - owner: iuc -- name: mothur_sens_spec - owner: iuc -- name: mothur_screen_seqs - owner: iuc -- name: mothur_reverse_seqs - owner: iuc -- name: mothur_remove_seqs - owner: iuc -- name: mothur_remove_rare - owner: iuc -- name: mothur_remove_otus - owner: iuc -- name: mothur_remove_otulabels - owner: iuc -- name: mothur_remove_lineage - owner: iuc -- name: mothur_remove_groups - owner: iuc -- name: mothur_remove_dists - owner: iuc -- name: mothur_rarefaction_single - owner: iuc -- name: mothur_rarefaction_shared - owner: iuc -- name: mothur_primer_design - owner: iuc -- name: mothur_pre_cluster - owner: iuc -- name: mothur_phylotype - owner: iuc -- name: mothur_phylo_diversity - owner: iuc -- name: mothur_pcr_seqs - owner: iuc -- name: mothur_pcoa - owner: iuc -- name: mothur_pca - owner: iuc -- name: mothur_parsimony - owner: iuc -- name: mothur_parse_list - owner: iuc -- name: mothur_pairwise_seqs - owner: iuc -- name: mothur_otu_hierarchy - owner: iuc -- name: mothur_otu_association - owner: iuc -- name: mothur_normalize_shared - owner: iuc -- name: mothur_nmds - owner: iuc -- name: mothur_mimarks_attributes - owner: iuc -- name: mothur_metastats - owner: iuc -- name: mothur_merge_taxsummary - owner: iuc -- name: mothur_merge_sfffiles - owner: iuc -- name: mothur_merge_groups - owner: iuc -- name: mothur_merge_files - owner: iuc -- name: mothur_mantel - owner: iuc -- name: mothur_make_sra - owner: iuc -- name: mothur_make_shared - owner: iuc -- name: mothur_make_lookup - owner: iuc -- name: mothur_make_lefse - owner: iuc -- name: mothur_make_group - owner: iuc -- name: mothur_make_fastq - owner: iuc -- name: mothur_make_design - owner: iuc -- name: mothur_make_contigs - owner: iuc -- name: mothur_make_biom - owner: iuc -- name: mothur_list_seqs - owner: iuc -- name: mothur_list_otulabels - owner: iuc -- name: mothur_libshuff - owner: iuc -- name: mothur_lefse - owner: iuc -- name: mothur_indicator - owner: iuc -- name: mothur_homova - owner: iuc -- name: mothur_heatmap_sim - owner: iuc -- name: mothur_heatmap_bin - owner: iuc -- name: mothur_get_sharedseqs - owner: iuc -- name: mothur_get_seqs - owner: iuc -- name: mothur_get_sabund - owner: iuc -- name: mothur_get_relabund - owner: iuc -- name: mothur_get_rabund - owner: iuc -- name: mothur_get_otus - owner: iuc -- name: mothur_get_oturep - owner: iuc -- name: mothur_get_otulist - owner: iuc -- name: mothur_get_otulabels - owner: iuc -- name: mothur_get_mimarkspackage - owner: iuc -- name: mothur_get_lineage - owner: iuc -- name: mothur_get_label - owner: iuc -- name: mothur_get_group - owner: iuc -- name: mothur_get_groups - owner: iuc -- name: mothur_get_dists - owner: iuc -- name: mothur_get_coremicrobiome - owner: iuc -- name: mothur_get_communitytype - owner: iuc -- name: mothur_filter_shared - owner: iuc -- name: mothur_filter_seqs - owner: iuc -- name: mothur_fastq_info - owner: iuc -- name: mothur_dist_shared - owner: iuc -- name: mothur_dist_seqs - owner: iuc -- name: mothur_deunique_tree - owner: iuc -- name: mothur_deunique_seqs - owner: iuc -- name: mothur_degap_seqs - owner: iuc -- name: mothur_create_database - owner: iuc -- name: mothur_count_seqs - owner: iuc -- name: mothur_count_groups - owner: iuc -- name: mothur_corr_axes - owner: iuc -- name: mothur_cooccurrence - owner: iuc -- name: mothur_consensus_seqs - owner: iuc -- name: mothur_collect_single - owner: iuc -- name: mothur_collect_shared - owner: iuc -- name: mothur_cluster - owner: iuc -- name: mothur_cluster_split - owner: iuc -- name: mothur_cluster_fragments - owner: iuc -- name: mothur_cluster_classic - owner: iuc -- name: mothur_clearcut - owner: iuc -- name: mothur_classify_tree - owner: iuc -- name: mothur_classify_seqs - owner: iuc -- name: mothur_classify_otu - owner: iuc -- name: mothur_chop_seqs - owner: iuc -- name: mothur_chimera_uchime - owner: iuc -- name: mothur_chimera_slayer - owner: iuc -- name: mothur_chimera_pintail - owner: iuc -- name: mothur_chimera_perseus - owner: iuc -- name: mothur_chimera_check - owner: iuc -- name: mothur_chimera_ccode - owner: iuc -- name: mothur_chimera_bellerophon - owner: iuc -- name: mothur_bin_seqs - owner: iuc -- name: mothur_anosim - owner: iuc -- name: mothur_amova - owner: iuc -- name: mothur_align_seqs - owner: iuc -- name: mothur_align_check - owner: iuc -- name: mothur_hcluster - owner: iuc -- name: mothur_classify_rf - owner: iuc diff --git a/common_toolset/mothur.yml.lock b/common_toolset/mothur.yml.lock deleted file mode 100644 index be4da916..00000000 --- a/common_toolset/mothur.yml.lock +++ /dev/null @@ -1,791 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Mothur -tools: -- name: mothur_taxonomy_to_krona - owner: iuc - revisions: - - 71e7d93a593e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_merge_count - owner: iuc - revisions: - - ccba5bd49390 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_vsearch - owner: iuc - revisions: - - d531f28e8266 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_rename_seqs - owner: iuc - revisions: - - 03b326e1f6a1 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_biom_info - owner: iuc - revisions: - - 3b426f118175 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_venn - owner: iuc - revisions: - - e4f4c1c0d193 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_unique_seqs - owner: iuc - revisions: - - 7c3f9c0850ac - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_unifrac_weighted - owner: iuc - revisions: - - 136cb4f4b996 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_unifrac_unweighted - owner: iuc - revisions: - - 3597ca9089a5 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_trim_seqs - owner: iuc - revisions: - - c49a6454726c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_trim_flows - owner: iuc - revisions: - - 4d56c7e82ba6 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_tree_shared - owner: iuc - revisions: - - 40d8938eaa24 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_tax - owner: iuc - revisions: - - 5eb0f670aa35 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_single - owner: iuc - revisions: - - 2857a688a7e9 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_shared - owner: iuc - revisions: - - 74c8ebee088c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_seqs - owner: iuc - revisions: - - 411ddfefe041 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_qual - owner: iuc - revisions: - - d50fdfdc2a0c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_sub_sample - owner: iuc - revisions: - - 34e1fbd32a04 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_split_groups - owner: iuc - revisions: - - 68c20caae797 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_split_abund - owner: iuc - revisions: - - d850b4b9659d - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_sort_seqs - owner: iuc - revisions: - - cbe644faff63 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_shhh_seqs - owner: iuc - revisions: - - 6ee54b761c3c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_shhh_flows - owner: iuc - revisions: - - 7cca6773bc2a - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_sffinfo - owner: iuc - revisions: - - 12507ed33710 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_seq_error - owner: iuc - revisions: - - a03c9ebf1959 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_sens_spec - owner: iuc - revisions: - - ddda05cfccb4 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_screen_seqs - owner: iuc - revisions: - - 94d8dbac60d8 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_reverse_seqs - owner: iuc - revisions: - - 03450507aa98 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_seqs - owner: iuc - revisions: - - 2fa446f85b18 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_rare - owner: iuc - revisions: - - 196b1583580a - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_otus - owner: iuc - revisions: - - ce3c9cb04314 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_otulabels - owner: iuc - revisions: - - ba9df7320629 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_lineage - owner: iuc - revisions: - - 2f633c057c0d - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_groups - owner: iuc - revisions: - - 7c5b7dddd02e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_dists - owner: iuc - revisions: - - ea7b70e1a61b - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_rarefaction_single - owner: iuc - revisions: - - 8091da04fbac - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_rarefaction_shared - owner: iuc - revisions: - - 419266a5e29e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_primer_design - owner: iuc - revisions: - - 6e8cdd7e6825 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_pre_cluster - owner: iuc - revisions: - - fbbe2b081299 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_phylotype - owner: iuc - revisions: - - 58f143161d30 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_phylo_diversity - owner: iuc - revisions: - - 3868f54b097e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_pcr_seqs - owner: iuc - revisions: - - 2b8dce0751e5 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_pcoa - owner: iuc - revisions: - - c9fc98593dec - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_pca - owner: iuc - revisions: - - 7474b222205d - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_parsimony - owner: iuc - revisions: - - 65955ae23f29 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_parse_list - owner: iuc - revisions: - - 3b803b7f3388 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_pairwise_seqs - owner: iuc - revisions: - - c05906ab8c41 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_otu_hierarchy - owner: iuc - revisions: - - 7590f83a6419 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_otu_association - owner: iuc - revisions: - - 0fb08aeb215e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_normalize_shared - owner: iuc - revisions: - - ad80d646ed1c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_nmds - owner: iuc - revisions: - - 98f1cc2bc428 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_mimarks_attributes - owner: iuc - revisions: - - 247d1bacbefe - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_metastats - owner: iuc - revisions: - - 10866c1f8e06 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_merge_taxsummary - owner: iuc - revisions: - - 80bd73567a2c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_merge_sfffiles - owner: iuc - revisions: - - ec717c8dce9b - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_merge_groups - owner: iuc - revisions: - - 052bc33e134e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_merge_files - owner: iuc - revisions: - - 12b1bd17d614 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_mantel - owner: iuc - revisions: - - 17b471efdc40 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_sra - owner: iuc - revisions: - - 33a3f68dc34b - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_shared - owner: iuc - revisions: - - b5f98810181e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_lookup - owner: iuc - revisions: - - d56e5a7a9cef - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_lefse - owner: iuc - revisions: - - 678c90b43e17 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_group - owner: iuc - revisions: - - afc13b55ead3 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_fastq - owner: iuc - revisions: - - e9b12c5ad27f - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_design - owner: iuc - revisions: - - 5280cc8135eb - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_contigs - owner: iuc - revisions: - - 4b72b6c43327 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_make_biom - owner: iuc - revisions: - - 143cd841de28 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_list_seqs - owner: iuc - revisions: - - ea1a32c7927e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_list_otulabels - owner: iuc - revisions: - - 0c9eb32683bf - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_libshuff - owner: iuc - revisions: - - eefbe872fd04 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_lefse - owner: iuc - revisions: - - 772e6a5b7358 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_indicator - owner: iuc - revisions: - - 0232e2fe594c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_homova - owner: iuc - revisions: - - 68005ede9e6e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_heatmap_sim - owner: iuc - revisions: - - 0674bdcb3019 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_heatmap_bin - owner: iuc - revisions: - - 5e6fddbd1366 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_sharedseqs - owner: iuc - revisions: - - 75b80a4fa86d - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_seqs - owner: iuc - revisions: - - f31e3b8f2336 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_sabund - owner: iuc - revisions: - - c79ecbd31c44 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_relabund - owner: iuc - revisions: - - 7756edb68ddc - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_rabund - owner: iuc - revisions: - - 398973de93ab - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_otus - owner: iuc - revisions: - - 278a9f09614c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_oturep - owner: iuc - revisions: - - 648b3da84b07 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_otulist - owner: iuc - revisions: - - 2478fb777d97 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_otulabels - owner: iuc - revisions: - - 630ad54722c6 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_mimarkspackage - owner: iuc - revisions: - - 6c54b38dd0da - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_lineage - owner: iuc - revisions: - - b2b145255ece - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_label - owner: iuc - revisions: - - bb8b69e90604 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_group - owner: iuc - revisions: - - f2b626fe7082 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_groups - owner: iuc - revisions: - - b1c35f71607f - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_dists - owner: iuc - revisions: - - 6936b18e2a9e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_coremicrobiome - owner: iuc - revisions: - - ae1411cffbee - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_get_communitytype - owner: iuc - revisions: - - beb4e0832f3b - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_filter_shared - owner: iuc - revisions: - - e44c38a17c7a - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_filter_seqs - owner: iuc - revisions: - - a0ce9fb3f260 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_fastq_info - owner: iuc - revisions: - - f02f3ca6dfd1 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_dist_shared - owner: iuc - revisions: - - 5d6d9f0d0652 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_dist_seqs - owner: iuc - revisions: - - 57eb5df69242 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_deunique_tree - owner: iuc - revisions: - - 98083c5a4338 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_deunique_seqs - owner: iuc - revisions: - - 0369aff1be76 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_degap_seqs - owner: iuc - revisions: - - a7fced14ce99 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_create_database - owner: iuc - revisions: - - 34669a26ea47 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_count_seqs - owner: iuc - revisions: - - f00841c6fc14 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_count_groups - owner: iuc - revisions: - - dc02f3831a1a - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_corr_axes - owner: iuc - revisions: - - 0968daa9b52f - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_cooccurrence - owner: iuc - revisions: - - 57fe046c8fbe - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_consensus_seqs - owner: iuc - revisions: - - e432f17722c8 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_collect_single - owner: iuc - revisions: - - 7f212a2a4a3b - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_collect_shared - owner: iuc - revisions: - - 9c78c5ffa049 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_cluster - owner: iuc - revisions: - - 3bb756df109c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_cluster_split - owner: iuc - revisions: - - 2c02989afecb - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_cluster_fragments - owner: iuc - revisions: - - 881f9a4013a9 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_cluster_classic - owner: iuc - revisions: - - 6ba59950d95c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_clearcut - owner: iuc - revisions: - - 20e764494303 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_classify_tree - owner: iuc - revisions: - - 931e9b25e81d - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_classify_seqs - owner: iuc - revisions: - - 65b370206748 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_classify_otu - owner: iuc - revisions: - - 29882f4a1ef3 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chop_seqs - owner: iuc - revisions: - - 6e1047fa1a51 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_uchime - owner: iuc - revisions: - - 4e3780d096af - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_slayer - owner: iuc - revisions: - - a899cc1416bc - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_pintail - owner: iuc - revisions: - - cc3eef74fe31 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_perseus - owner: iuc - revisions: - - 128cbea05aeb - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_check - owner: iuc - revisions: - - 35c91da65b75 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_ccode - owner: iuc - revisions: - - 79255ca0b19a - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_bellerophon - owner: iuc - revisions: - - ad0df6ad0499 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_bin_seqs - owner: iuc - revisions: - - 3fc101a0498f - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_anosim - owner: iuc - revisions: - - 652d2803062c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_amova - owner: iuc - revisions: - - 5aa5d26efeea - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_align_seqs - owner: iuc - revisions: - - 5d134e0b31fd - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_align_check - owner: iuc - revisions: - - dd533a49feed - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_hcluster - owner: iuc - revisions: - - '989184322514' - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_classify_rf - owner: iuc - revisions: - - 010296966465 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur diff --git a/common_toolset/motif.yml b/common_toolset/motif.yml deleted file mode 100644 index 20f2d510..00000000 --- a/common_toolset/motif.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Motif -tools: -- name: meme_meme - owner: iuc -- name: meme_fimo - owner: iuc -- name: weblogo3 - owner: devteam diff --git a/common_toolset/motif.yml.lock b/common_toolset/motif.yml.lock deleted file mode 100644 index 77d1faa1..00000000 --- a/common_toolset/motif.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Motif -tools: -- name: meme_meme - owner: iuc - revisions: - - 57e5d9382f36 - tool_panel_section_id: motif - tool_panel_section_label: Motif -- name: meme_fimo - owner: iuc - revisions: - - c1a9a297ba8b - tool_panel_section_id: motif - tool_panel_section_label: Motif -- name: weblogo3 - owner: devteam - revisions: - - dc25a5169a91 - tool_panel_section_id: motif - tool_panel_section_label: Motif diff --git a/common_toolset/multiple_alignments.yml b/common_toolset/multiple_alignments.yml deleted file mode 100644 index e46f7ad0..00000000 --- a/common_toolset/multiple_alignments.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Multiple Alignments -tools: -- name: mafft - owner: rnateam -- name: clustalw - owner: devteam -- name: cdhit - owner: bebatut diff --git a/common_toolset/multiple_alignments.yml.lock b/common_toolset/multiple_alignments.yml.lock deleted file mode 100644 index 2b678693..00000000 --- a/common_toolset/multiple_alignments.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Multiple Alignments -tools: -- name: mafft - owner: rnateam - revisions: - - c5908940967d - tool_panel_section_id: multiple_alignments - tool_panel_section_label: Multiple Alignments -- name: clustalw - owner: devteam - revisions: - - d6694932c5e0 - tool_panel_section_id: multiple_alignments - tool_panel_section_label: Multiple Alignments -- name: cdhit - owner: bebatut - revisions: - - 93f25d52cfa5 - tool_panel_section_id: multiple_alignments - tool_panel_section_label: Multiple Alignments diff --git a/common_toolset/nanopore.yml b/common_toolset/nanopore.yml deleted file mode 100644 index 67cd9c30..00000000 --- a/common_toolset/nanopore.yml +++ /dev/null @@ -1,28 +0,0 @@ -tool_panel_section_label: Nanopore -tools: -- name: poretools_yield_plot - owner: iuc -- name: poretools_winner - owner: iuc -- name: poretools_times - owner: iuc -- name: poretools_tabular - owner: iuc -- name: poretools_stats - owner: iuc -- name: poretools_squiggle - owner: iuc -- name: poretools_qualpos - owner: iuc -- name: poretools_qualdist - owner: iuc -- name: poretools_occupancy - owner: iuc -- name: poretools_nucdist - owner: iuc -- name: poretools_hist - owner: iuc -- name: poretools_extract - owner: iuc -- name: poretools_events - owner: iuc diff --git a/common_toolset/nanopore.yml.lock b/common_toolset/nanopore.yml.lock deleted file mode 100644 index 95df9dc6..00000000 --- a/common_toolset/nanopore.yml.lock +++ /dev/null @@ -1,83 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Nanopore -tools: -- name: poretools_yield_plot - owner: iuc - revisions: - - 64a83664b814 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_winner - owner: iuc - revisions: - - 9d8f41103cc6 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_times - owner: iuc - revisions: - - e5072f0d3772 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_tabular - owner: iuc - revisions: - - 7f0b324de883 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_stats - owner: iuc - revisions: - - ae4c8446ce30 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_squiggle - owner: iuc - revisions: - - ce8af9373061 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_qualpos - owner: iuc - revisions: - - 2e22ebec211a - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_qualdist - owner: iuc - revisions: - - 44111014e7c1 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_occupancy - owner: iuc - revisions: - - 336791b5665f - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_nucdist - owner: iuc - revisions: - - 3ae7ccba16cf - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_hist - owner: iuc - revisions: - - 47936349f3e9 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_extract - owner: iuc - revisions: - - 7593f94691fb - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_events - owner: iuc - revisions: - - 1d835c691480 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore diff --git a/common_toolset/ncbi_blast.yml b/common_toolset/ncbi_blast.yml deleted file mode 100644 index b03bebe9..00000000 --- a/common_toolset/ncbi_blast.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: NCBI BLAST+ -tools: -- name: ncbi_blast_plus - owner: devteam diff --git a/common_toolset/ncbi_blast.yml.lock b/common_toolset/ncbi_blast.yml.lock deleted file mode 100644 index 58637735..00000000 --- a/common_toolset/ncbi_blast.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: NCBI BLAST+ -tools: -- name: ncbi_blast_plus - owner: devteam - revisions: - - e25d3acf6e68 - tool_panel_section_id: ncbi_blast_ - tool_panel_section_label: NCBI BLAST+ diff --git a/common_toolset/operate_on_genomic_intervals.yml b/common_toolset/operate_on_genomic_intervals.yml deleted file mode 100644 index ffab8d91..00000000 --- a/common_toolset/operate_on_genomic_intervals.yml +++ /dev/null @@ -1,26 +0,0 @@ -tool_panel_section_label: Operate on Genomic Intervals -tools: -- name: merge - owner: devteam -- name: concat - owner: devteam -- name: subtract - owner: devteam -- name: join - owner: devteam -- name: intersect - owner: devteam -- name: coverage - owner: devteam -- name: complement - owner: devteam -- name: cluster - owner: devteam -- name: basecoverage - owner: devteam -- name: annotation_profiler - owner: devteam -- name: flanking_features - owner: devteam -- name: get_flanks - owner: devteam diff --git a/common_toolset/operate_on_genomic_intervals.yml.lock b/common_toolset/operate_on_genomic_intervals.yml.lock deleted file mode 100644 index b7bf75aa..00000000 --- a/common_toolset/operate_on_genomic_intervals.yml.lock +++ /dev/null @@ -1,77 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Operate on Genomic Intervals -tools: -- name: merge - owner: devteam - revisions: - - 381cd27bf67a - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: concat - owner: devteam - revisions: - - 35a89f8cc96e - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: subtract - owner: devteam - revisions: - - 0145969324c4 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: join - owner: devteam - revisions: - - a10f49d9218a - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: intersect - owner: devteam - revisions: - - 33b3f3688db4 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: coverage - owner: devteam - revisions: - - 4ef9819dc7fb - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: complement - owner: devteam - revisions: - - 38c8bb402872 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: cluster - owner: devteam - revisions: - - 05696474ee89 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: basecoverage - owner: devteam - revisions: - - 2cedec3759e4 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: annotation_profiler - owner: devteam - revisions: - - 3b33da018e74 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: flanking_features - owner: devteam - revisions: - - a09d13b108fd - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: get_flanks - owner: devteam - revisions: - - 077f404ae1bb - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals diff --git a/common_toolset/phenotype_association.yml b/common_toolset/phenotype_association.yml deleted file mode 100644 index a21cf8b0..00000000 --- a/common_toolset/phenotype_association.yml +++ /dev/null @@ -1,12 +0,0 @@ -tool_panel_section_label: Phenotype Association -tools: -- name: vcf2pgsnp - owner: devteam -- name: snpfreq - owner: devteam -- name: divide_pg_snp - owner: devteam -- name: hgv_fundo - owner: devteam -- name: hgv_hilbertvis - owner: devteam diff --git a/common_toolset/phenotype_association.yml.lock b/common_toolset/phenotype_association.yml.lock deleted file mode 100644 index b42b82bb..00000000 --- a/common_toolset/phenotype_association.yml.lock +++ /dev/null @@ -1,35 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Phenotype Association -tools: -- name: vcf2pgsnp - owner: devteam - revisions: - - 5fca46616675 - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association -- name: snpfreq - owner: devteam - revisions: - - 5c3ac057608b - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association -- name: divide_pg_snp - owner: devteam - revisions: - - f74fdfc17143 - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association -- name: hgv_fundo - owner: devteam - revisions: - - ca3fcd18dc3e - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association -- name: hgv_hilbertvis - owner: devteam - revisions: - - e1a9ad05dced - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association diff --git a/common_toolset/phylogenetics.yml b/common_toolset/phylogenetics.yml deleted file mode 100644 index a29a8293..00000000 --- a/common_toolset/phylogenetics.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Phylogenetics -tools: -- name: phyml - owner: iuc diff --git a/common_toolset/phylogenetics.yml.lock b/common_toolset/phylogenetics.yml.lock deleted file mode 100644 index 9a65e8ab..00000000 --- a/common_toolset/phylogenetics.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Phylogenetics -tools: -- name: phyml - owner: iuc - revisions: - - 850e213bee26 - tool_panel_section_id: phylogenetics - tool_panel_section_label: Phylogenetics diff --git a/common_toolset/picard.yml b/common_toolset/picard.yml deleted file mode 100644 index 44fb2253..00000000 --- a/common_toolset/picard.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Picard -tools: -- name: picard - owner: devteam diff --git a/common_toolset/picard.yml.lock b/common_toolset/picard.yml.lock deleted file mode 100644 index ebb9051d..00000000 --- a/common_toolset/picard.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Picard -tools: -- name: picard - owner: devteam - revisions: - - 7d34178f2812 - tool_panel_section_id: picard - tool_panel_section_label: Picard diff --git a/common_toolset/presto.yml b/common_toolset/presto.yml deleted file mode 100644 index 8e73367c..00000000 --- a/common_toolset/presto.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: pRESTO -tools: -- name: migmap - owner: iuc diff --git a/common_toolset/presto.yml.lock b/common_toolset/presto.yml.lock deleted file mode 100644 index dadc1ab1..00000000 --- a/common_toolset/presto.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: pRESTO -tools: -- name: migmap - owner: iuc - revisions: - - 6ad9d48a512e - tool_panel_section_id: presto - tool_panel_section_label: pRESTO diff --git a/common_toolset/proteomics.yml b/common_toolset/proteomics.yml deleted file mode 100644 index fb0b4e91..00000000 --- a/common_toolset/proteomics.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Proteomics -tools: -- name: protease_prediction - owner: bgruening diff --git a/common_toolset/proteomics.yml.lock b/common_toolset/proteomics.yml.lock deleted file mode 100644 index ccb45409..00000000 --- a/common_toolset/proteomics.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Proteomics -tools: -- name: protease_prediction - owner: bgruening - revisions: - - c7a363d7ab26 - tool_panel_section_id: proteomics - tool_panel_section_label: Proteomics diff --git a/common_toolset/regional_variation.yml b/common_toolset/regional_variation.yml deleted file mode 100644 index 26a9f15c..00000000 --- a/common_toolset/regional_variation.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: Regional Variation -tools: -- name: substitution_rates - owner: devteam -- name: indels_3way - owner: devteam -- name: featurecounter - owner: devteam -- name: karyotype_plot - owner: guru-ananda -- name: heatmap - owner: guru-ananda -- name: draw_stacked_barplots - owner: devteam -- name: compute_motifs_frequency - owner: devteam -- name: compute_motif_frequencies_for_all_motifs - owner: devteam -- name: categorize_elements_satisfying_criteria - owner: devteam diff --git a/common_toolset/regional_variation.yml.lock b/common_toolset/regional_variation.yml.lock deleted file mode 100644 index eed4cfe0..00000000 --- a/common_toolset/regional_variation.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Regional Variation -tools: -- name: substitution_rates - owner: devteam - revisions: - - 3d9544198582 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: indels_3way - owner: devteam - revisions: - - 5ad24b81dd10 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: featurecounter - owner: devteam - revisions: - - ac6218e2b686 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: karyotype_plot - owner: guru-ananda - revisions: - - d810aa84ee6a - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: heatmap - owner: guru-ananda - revisions: - - dbd447fcd3e4 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: draw_stacked_barplots - owner: devteam - revisions: - - e997b710e38a - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: compute_motifs_frequency - owner: devteam - revisions: - - 1f8ee7f9701b - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: compute_motif_frequencies_for_all_motifs - owner: devteam - revisions: - - 5319efa51514 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: categorize_elements_satisfying_criteria - owner: devteam - revisions: - - 586c1f0e1515 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation diff --git a/common_toolset/rna_seq.yml b/common_toolset/rna_seq.yml deleted file mode 100644 index bca72b72..00000000 --- a/common_toolset/rna_seq.yml +++ /dev/null @@ -1,74 +0,0 @@ -tool_panel_section_label: RNA-seq -tools: -- name: limma_voom - owner: iuc -- name: edger - owner: iuc -- name: hisat2 - owner: iuc -- name: featurecounts - owner: iuc -- name: dexseq - owner: iuc -- name: stringtie - owner: iuc -- name: salmon - owner: bgruening -- name: kallisto_quant - owner: iuc -- name: kallisto_pseudo - owner: iuc -- name: sailfish - owner: bgruening -- name: goseq - owner: iuc -- name: deseq2 - owner: iuc -- name: rgrnastar - owner: iuc -- name: cummerbund - owner: devteam -- name: htseq_count - owner: lparsons -- name: gffcompare - owner: iuc -- name: cuffmerge - owner: devteam -- name: filter_transcripts_via_tracking - owner: devteam -- name: structurefold - owner: tyty -- name: express - owner: devteam -- name: trinotate - owner: iuc -- name: trinity_analyze_diff_expr - owner: iuc -- name: selectsequencesfrommsa - owner: rnateam -- name: trinity_gene_to_trans_map - owner: iuc -- name: trinity_samples_qccheck - owner: iuc -- name: describe_samples - owner: iuc -- name: trinity_run_de_analysis - owner: iuc -- name: trinity_filter_low_expr_transcripts - owner: iuc -- name: trinity_contig_exn50_statistic - owner: iuc -- name: trinity_abundance_estimates_to_matrix - owner: iuc -- name: trinity_align_and_estimate_abundance - owner: iuc -- name: trinity - owner: iuc -- name: transdecoder - owner: iuc -- name: infernal - owner: bgruening -- name: tophat_fusion_post - owner: devteam -- name: rsem - owner: jjohnson diff --git a/common_toolset/rna_seq.yml.lock b/common_toolset/rna_seq.yml.lock deleted file mode 100644 index aa9ffc40..00000000 --- a/common_toolset/rna_seq.yml.lock +++ /dev/null @@ -1,221 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: RNA-seq -tools: -- name: limma_voom - owner: iuc - revisions: - - 0921444c832d - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: edger - owner: iuc - revisions: - - 555659de7321 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: hisat2 - owner: iuc - revisions: - - 3fb01a8c902d - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: featurecounts - owner: iuc - revisions: - - 9301937c9037 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: dexseq - owner: iuc - revisions: - - 9fd8b69e6e68 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: stringtie - owner: iuc - revisions: - - eba36e001f45 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: salmon - owner: bgruening - revisions: - - 6b0ba6de1424 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: kallisto_quant - owner: iuc - revisions: - - 10c98fab6c5a - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: kallisto_pseudo - owner: iuc - revisions: - - 1c75aa5de15e - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: sailfish - owner: bgruening - revisions: - - a8f343909c17 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: goseq - owner: iuc - revisions: - - 67c29afac85f - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: deseq2 - owner: iuc - revisions: - - 0696db066a5b - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: rgrnastar - owner: iuc - revisions: - - 0a563fd2f22e - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: cummerbund - owner: devteam - revisions: - - 78fcfc04fcfe - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: htseq_count - owner: lparsons - revisions: - - 7f5a8d427b39 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: gffcompare - owner: iuc - revisions: - - 2bb86e2c417f - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: cuffmerge - owner: devteam - revisions: - - cf747d1bd79a - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: filter_transcripts_via_tracking - owner: devteam - revisions: - - 45f89dcf0b4c - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: structurefold - owner: tyty - revisions: - - 7bb98e9296e9 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: express - owner: devteam - revisions: - - 7b0708761d05 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinotate - owner: iuc - revisions: - - 6fd16fad465d - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_analyze_diff_expr - owner: iuc - revisions: - - dc0f01791c9b - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: selectsequencesfrommsa - owner: rnateam - revisions: - - 876c70c6ecad - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_gene_to_trans_map - owner: iuc - revisions: - - 37a1129c89d2 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_samples_qccheck - owner: iuc - revisions: - - 9871104ea630 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: describe_samples - owner: iuc - revisions: - - 0693ccd171c4 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_run_de_analysis - owner: iuc - revisions: - - 1d689e4e1caf - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_filter_low_expr_transcripts - owner: iuc - revisions: - - e406ac71165d - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_contig_exn50_statistic - owner: iuc - revisions: - - 34a018cbee9c - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_abundance_estimates_to_matrix - owner: iuc - revisions: - - d6a479fd4281 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_align_and_estimate_abundance - owner: iuc - revisions: - - 478f36effca1 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity - owner: iuc - revisions: - - c9cfec002f71 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: transdecoder - owner: iuc - revisions: - - 0db979fead3a - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: infernal - owner: bgruening - revisions: - - 477d829d3250 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: tophat_fusion_post - owner: devteam - revisions: - - f83394a2c2da - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: rsem - owner: jjohnson - revisions: - - 14267d364365 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq diff --git a/common_toolset/rseqc.yml b/common_toolset/rseqc.yml deleted file mode 100644 index d3d15522..00000000 --- a/common_toolset/rseqc.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: RSeQC -tools: -- name: rseqc - owner: nilesh diff --git a/common_toolset/rseqc.yml.lock b/common_toolset/rseqc.yml.lock deleted file mode 100644 index 35ccb93a..00000000 --- a/common_toolset/rseqc.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: RSeQC -tools: -- name: rseqc - owner: nilesh - revisions: - - f437057e46f1 - tool_panel_section_id: rseqc - tool_panel_section_label: RSeQC diff --git a/common_toolset/sambam.yml b/common_toolset/sambam.yml deleted file mode 100644 index db5117cd..00000000 --- a/common_toolset/sambam.yml +++ /dev/null @@ -1,50 +0,0 @@ -tool_panel_section_label: SAM/BAM -tools: -- name: samtools_sort - owner: devteam -- name: samtools_mpileup - owner: devteam -- name: samtools_flagstat - owner: devteam -- name: samtool_filter2 - owner: devteam -- name: bam_to_sam - owner: devteam -- name: samtools_idxstats - owner: devteam -- name: sam_to_bam - owner: devteam -- name: samtools_calmd - owner: devteam -- name: samtools_bedcov - owner: devteam -- name: samtools_split - owner: devteam -- name: samtools_stats - owner: devteam -- name: samtools_slice_bam - owner: devteam -- name: samtools_reheader - owner: devteam -- name: samtools_rmdup - owner: devteam -- name: sam_merge - owner: devteam -- name: pileup_interval - owner: devteam -- name: pileup_parser - owner: devteam -- name: sam2interval - owner: devteam -- name: sam_bitwise_flag_filter - owner: devteam -- name: sam_pileup - owner: devteam -- name: bamtools_split - owner: devteam -- name: bamtools - owner: devteam -- name: bamtools_filter - owner: devteam -- name: samtools_phase - owner: devteam diff --git a/common_toolset/sambam.yml.lock b/common_toolset/sambam.yml.lock deleted file mode 100644 index 7b30df0f..00000000 --- a/common_toolset/sambam.yml.lock +++ /dev/null @@ -1,149 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: SAM/BAM -tools: -- name: samtools_sort - owner: devteam - revisions: - - e613c1ad4c4c - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_mpileup - owner: devteam - revisions: - - fa7ad9b89f4a - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_flagstat - owner: devteam - revisions: - - 4e404acfafa6 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtool_filter2 - owner: devteam - revisions: - - 56c31114ad4a - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: bam_to_sam - owner: devteam - revisions: - - 88eedb4abea0 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_idxstats - owner: devteam - revisions: - - 04d5581db1f5 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam_to_bam - owner: devteam - revisions: - - f7a0d41036c7 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_calmd - owner: devteam - revisions: - - e65c2cd0964c - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_bedcov - owner: devteam - revisions: - - 12749212f61b - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_split - owner: devteam - revisions: - - b7f7826ef1cd - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_stats - owner: devteam - revisions: - - 793ad847121d - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_slice_bam - owner: devteam - revisions: - - a4a10c7924d1 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_reheader - owner: devteam - revisions: - - db000c6007a0 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_rmdup - owner: devteam - revisions: - - 9129584416e2 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam_merge - owner: devteam - revisions: - - 1977f1637890 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: pileup_interval - owner: devteam - revisions: - - ef11139d4545 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: pileup_parser - owner: devteam - revisions: - - 85bedbea8a12 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam2interval - owner: devteam - revisions: - - 8c737b8ddc45 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam_bitwise_flag_filter - owner: devteam - revisions: - - 0b2424a404d9 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam_pileup - owner: devteam - revisions: - - 890d97772e2a - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: bamtools_split - owner: devteam - revisions: - - e2c1b62e1db1 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: bamtools - owner: devteam - revisions: - - 04866f817daa - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: bamtools_filter - owner: devteam - revisions: - - 4fe8a75334c8 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_phase - owner: devteam - revisions: - - 6166013090c0 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM diff --git a/common_toolset/seqtk.yml b/common_toolset/seqtk.yml deleted file mode 100644 index a2885d11..00000000 --- a/common_toolset/seqtk.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Seqtk -tools: -- name: seqtk - owner: iuc diff --git a/common_toolset/seqtk.yml.lock b/common_toolset/seqtk.yml.lock deleted file mode 100644 index 2f182149..00000000 --- a/common_toolset/seqtk.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Seqtk -tools: -- name: seqtk - owner: iuc - revisions: - - a09586d5149a - tool_panel_section_id: seqtk - tool_panel_section_label: Seqtk diff --git a/common_toolset/statistics.yml b/common_toolset/statistics.yml deleted file mode 100644 index 91809ff3..00000000 --- a/common_toolset/statistics.yml +++ /dev/null @@ -1,28 +0,0 @@ -tool_panel_section_label: Statistics -tools: -- name: count_gff_features - owner: devteam -- name: t_test_two_samples - owner: devteam -- name: mine - owner: devteam -- name: plot_from_lda - owner: devteam -- name: lda_analysis - owner: devteam -- name: generate_pc_lda_matrix - owner: devteam -- name: correlation - owner: devteam -- name: best_regression_subsets - owner: devteam -- name: canonical_correlation_analysis - owner: devteam -- name: kernel_canonical_correlation_analysis - owner: devteam -- name: kernel_principal_component_analysis - owner: devteam -- name: principal_component_analysis - owner: devteam -- name: dwt_var_perfeature - owner: devteam diff --git a/common_toolset/statistics.yml.lock b/common_toolset/statistics.yml.lock deleted file mode 100644 index 875a6013..00000000 --- a/common_toolset/statistics.yml.lock +++ /dev/null @@ -1,83 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Statistics -tools: -- name: count_gff_features - owner: devteam - revisions: - - 188392a0d0a8 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: t_test_two_samples - owner: devteam - revisions: - - c2ffc9885b5a - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: mine - owner: devteam - revisions: - - 5e2c89443c44 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: plot_from_lda - owner: devteam - revisions: - - 08affc5d2aef - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: lda_analysis - owner: devteam - revisions: - - f0b6217f4a0c - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: generate_pc_lda_matrix - owner: devteam - revisions: - - 04cdbd00dcec - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: correlation - owner: devteam - revisions: - - 24e01abf9e34 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: best_regression_subsets - owner: devteam - revisions: - - 4f33ec73e445 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: canonical_correlation_analysis - owner: devteam - revisions: - - 9bc0c48a027f - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: kernel_canonical_correlation_analysis - owner: devteam - revisions: - - 5ce5a2adb875 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: kernel_principal_component_analysis - owner: devteam - revisions: - - 3d58aa83e4a3 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: principal_component_analysis - owner: devteam - revisions: - - f568051cdf2e - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: dwt_var_perfeature - owner: devteam - revisions: - - 7a15159140d1 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics diff --git a/common_toolset/text_manipulation.yml b/common_toolset/text_manipulation.yml deleted file mode 100644 index 78bf4d90..00000000 --- a/common_toolset/text_manipulation.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: Text Manipulation -tools: -- name: column_maker - owner: devteam -- name: annotatemyids - owner: iuc -- name: uniprot_rest_interface - owner: bgruening -- name: add_input_name_as_column - owner: mvdbeek -- name: replace_column_by_key_value_file - owner: bgruening -- name: text_processing - owner: bgruening -- name: regex_find_replace - owner: galaxyp diff --git a/common_toolset/text_manipulation.yml.lock b/common_toolset/text_manipulation.yml.lock deleted file mode 100644 index d7955877..00000000 --- a/common_toolset/text_manipulation.yml.lock +++ /dev/null @@ -1,47 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Text Manipulation -tools: -- name: column_maker - owner: devteam - revisions: - - 464b9305180e - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: annotatemyids - owner: iuc - revisions: - - 1aae04680c4b - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: uniprot_rest_interface - owner: bgruening - revisions: - - 054483e27a35 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: add_input_name_as_column - owner: mvdbeek - revisions: - - 06061aa49527 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: replace_column_by_key_value_file - owner: bgruening - revisions: - - d533e4b75800 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: text_processing - owner: bgruening - revisions: - - 0a8c6b61f0f4 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: regex_find_replace - owner: galaxyp - revisions: - - 209b7c5ee9d7 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation diff --git a/common_toolset/variant_calling.yml b/common_toolset/variant_calling.yml deleted file mode 100644 index 2136906b..00000000 --- a/common_toolset/variant_calling.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: Variant Calling -tools: -- name: varscan_version_2 - owner: devteam -- name: snpeff - owner: iuc -- name: naive_variant_caller - owner: blankenberg -- name: snpsift - owner: iuc -- name: freebayes - owner: devteam -- name: mutate_snp_codon - owner: devteam -- name: allele_counts - owner: nick diff --git a/common_toolset/variant_calling.yml.lock b/common_toolset/variant_calling.yml.lock deleted file mode 100644 index d9c63088..00000000 --- a/common_toolset/variant_calling.yml.lock +++ /dev/null @@ -1,47 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Variant Calling -tools: -- name: varscan_version_2 - owner: devteam - revisions: - - bc1e0cd41241 - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: snpeff - owner: iuc - revisions: - - 8f92c2b26e6d - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: naive_variant_caller - owner: blankenberg - revisions: - - 07e71cf6c8ef - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: snpsift - owner: iuc - revisions: - - 2b3e65a4252f - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: freebayes - owner: devteam - revisions: - - 156b60c1530f - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: mutate_snp_codon - owner: devteam - revisions: - - 8f0af7251167 - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: allele_counts - owner: nick - revisions: - - 411adeff1eec - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling diff --git a/common_toolset/vcfbcf.yml b/common_toolset/vcfbcf.yml deleted file mode 100644 index 68aa018b..00000000 --- a/common_toolset/vcfbcf.yml +++ /dev/null @@ -1,122 +0,0 @@ -tool_panel_section_label: VCF/BCF -tools: -- name: vcffilter - owner: devteam -- name: vcfdistance - owner: devteam -- name: vcfselectsamples - owner: devteam -- name: vcfvcfintersect - owner: devteam -- name: vcfsort - owner: devteam -- name: vcfrandomsample - owner: devteam -- name: vcfprimers - owner: devteam -- name: vcfleftalign - owner: devteam -- name: vcfhethom - owner: devteam -- name: vcfgenotypes - owner: devteam -- name: vcfgeno2haplo - owner: devteam -- name: vcfflatten - owner: devteam -- name: vcffixup - owner: devteam -- name: vcfcommonsamples - owner: devteam -- name: vcfcombine - owner: devteam -- name: vcfcheck - owner: devteam -- name: vcfbreakcreatemulti - owner: devteam -- name: vcfbedintersect - owner: devteam -- name: vcfannotategenotypes - owner: devteam -- name: vcfannotate - owner: devteam -- name: vcfallelicprimitives - owner: devteam -- name: vcfaddinfo - owner: devteam -- name: vcf2tsv - owner: devteam -- name: vcftools_annotate - owner: devteam -- name: vcftools_slice - owner: devteam -- name: bcftools_plugin_tag2tag - owner: iuc -- name: bcftools_query - owner: iuc -- name: bcftools_plugin_dosage - owner: iuc -- name: bcftools_annotate - owner: iuc -- name: bcftools_csq - owner: iuc -- name: bcftools_filter - owner: iuc -- name: bcftools_view - owner: iuc -- name: bcftools_call - owner: iuc -- name: bcftools_roh - owner: iuc -- name: bcftools_merge - owner: iuc -- name: bcftools_isec - owner: iuc -- name: bcftools_plugin_fill_tags - owner: iuc -- name: bcftools_plugin_fill_an_ac - owner: iuc -- name: bcftools_stats - owner: iuc -- name: bcftools_reheader - owner: iuc -- name: bcftools_plugin_impute_info - owner: iuc -- name: bcftools_convert_from_vcf - owner: iuc -- name: bcftools_consensus - owner: iuc -- name: bcftools_concat - owner: iuc -- name: bcftools_plugin_mendelian - owner: iuc -- name: bcftools_mpileup - owner: iuc -- name: bcftools_plugin_counts - owner: iuc -- name: bcftools_plugin_setgt - owner: iuc -- name: bcftools_cnv - owner: iuc -- name: bcftools_plugin_missing2ref - owner: iuc -- name: bcftools_query_list_samples - owner: iuc -- name: bcftools_norm - owner: iuc -- name: bcftools_convert_to_vcf - owner: iuc -- name: bcftools_plugin_fixploidy - owner: iuc -- name: bcftools_gtcheck - owner: iuc -- name: snippy - owner: iuc -- name: varscan_somatic - owner: iuc -- name: vcftools_merge - owner: devteam -- name: vcftools_isec - owner: devteam -- name: vcftools_subset - owner: devteam diff --git a/common_toolset/vcfbcf.yml.lock b/common_toolset/vcfbcf.yml.lock deleted file mode 100644 index e03801e1..00000000 --- a/common_toolset/vcfbcf.yml.lock +++ /dev/null @@ -1,365 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: VCF/BCF -tools: -- name: vcffilter - owner: devteam - revisions: - - 81972652519c - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfdistance - owner: devteam - revisions: - - 48e458c721b3 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfselectsamples - owner: devteam - revisions: - - 958b6484a7f1 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfvcfintersect - owner: devteam - revisions: - - 6f6bf10618d7 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfsort - owner: devteam - revisions: - - 5b7120c66efc - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfrandomsample - owner: devteam - revisions: - - 12b570dd0bc5 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfprimers - owner: devteam - revisions: - - d226a7327946 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfleftalign - owner: devteam - revisions: - - d2406f98a782 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfhethom - owner: devteam - revisions: - - b07ef36cf7e6 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfgenotypes - owner: devteam - revisions: - - f5653ed90dfd - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfgeno2haplo - owner: devteam - revisions: - - b890055e07bd - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfflatten - owner: devteam - revisions: - - b24e368ae7b1 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcffixup - owner: devteam - revisions: - - fc5a64fdd5b2 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfcommonsamples - owner: devteam - revisions: - - 254f285dbaaa - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfcombine - owner: devteam - revisions: - - 53edb91ed051 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfcheck - owner: devteam - revisions: - - 5e850c85ba32 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfbreakcreatemulti - owner: devteam - revisions: - - 690b1d846263 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfbedintersect - owner: devteam - revisions: - - 9edfe5145ba8 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfannotategenotypes - owner: devteam - revisions: - - 70bc6ced57f7 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfannotate - owner: devteam - revisions: - - 6faa2c4c71d2 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfallelicprimitives - owner: devteam - revisions: - - a8a4f94aa321 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfaddinfo - owner: devteam - revisions: - - afc0ba768690 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcf2tsv - owner: devteam - revisions: - - e92b3c0f9224 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_annotate - owner: devteam - revisions: - - 57a6550df582 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_slice - owner: devteam - revisions: - - 1363e5d4a8b8 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_tag2tag - owner: iuc - revisions: - - 2f8261ee0ea9 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_query - owner: iuc - revisions: - - 0770b1203e90 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_dosage - owner: iuc - revisions: - - 67bb9fcc0d96 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_annotate - owner: iuc - revisions: - - 2f09d9744e0b - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_csq - owner: iuc - revisions: - - 40388f544e5d - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_filter - owner: iuc - revisions: - - c01a175420f5 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_view - owner: iuc - revisions: - - ed94a3dccad0 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_call - owner: iuc - revisions: - - cb30a39055d0 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_roh - owner: iuc - revisions: - - f213f57dde66 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_merge - owner: iuc - revisions: - - beb87637bee3 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_isec - owner: iuc - revisions: - - 611f4cab1289 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_fill_tags - owner: iuc - revisions: - - 32f524fdc096 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_fill_an_ac - owner: iuc - revisions: - - d4a497619edf - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_stats - owner: iuc - revisions: - - e3c64225cbe6 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_reheader - owner: iuc - revisions: - - 3e9e03b3107a - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_impute_info - owner: iuc - revisions: - - 9b298d4d10c2 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_convert_from_vcf - owner: iuc - revisions: - - a7db83715075 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_consensus - owner: iuc - revisions: - - 70b8e9908ea8 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_concat - owner: iuc - revisions: - - 398d2ccc4233 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_mendelian - owner: iuc - revisions: - - 8c5c747e2bb4 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_mpileup - owner: iuc - revisions: - - 256e65e460b7 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_counts - owner: iuc - revisions: - - ed2ebaaded62 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_setgt - owner: iuc - revisions: - - 5ecd5f91b501 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_cnv - owner: iuc - revisions: - - 13fe14c56f6d - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_missing2ref - owner: iuc - revisions: - - ed003195e914 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_query_list_samples - owner: iuc - revisions: - - be337120b496 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_norm - owner: iuc - revisions: - - 76655fe2c70e - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_convert_to_vcf - owner: iuc - revisions: - - 843e008b15fd - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_fixploidy - owner: iuc - revisions: - - 2978f7d1f150 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_gtcheck - owner: iuc - revisions: - - 833ad3665419 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: snippy - owner: iuc - revisions: - - feb7e635c6af - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: varscan_somatic - owner: iuc - revisions: - - b79bb8b09822 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_merge - owner: devteam - revisions: - - 71e19ddf52f5 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_isec - owner: devteam - revisions: - - aa232e38338f - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_subset - owner: devteam - revisions: - - 23436d1d0fa1 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF diff --git a/scripts/fix-lockfile.py b/scripts/fix-lockfile.py index d79cb77a..63051567 100644 --- a/scripts/fix-lockfile.py +++ b/scripts/fix-lockfile.py @@ -96,7 +96,7 @@ def update_file(fn, install_repository_dependencies, install_resolver_dependenci parser = argparse.ArgumentParser() parser.add_argument('--no-install-repository-dependencies', action='store_true', default=False, help="Don't install TS repository dependencies") - parser.add_argument('--no-install-resolver-dependencies', action='store_true', default=False, + parser.add_argument('--no-install-resolver-dependencies', action='store_true', default=True, help="Don't install tool dependencies via Galaxy dependency resolver (e.g. conda)") parser.add_argument('fn', type=argparse.FileType('r'), help="Tool.yaml file") args = parser.parse_args() diff --git a/test.galaxyproject.org/annotation.yml.lock b/test.galaxyproject.org/annotation.yml.lock index 836d9129..119c725b 100644 --- a/test.galaxyproject.org/annotation.yml.lock +++ b/test.galaxyproject.org/annotation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Annotation tools: diff --git a/test.galaxyproject.org/assembly.yml.lock b/test.galaxyproject.org/assembly.yml.lock index ebd5587e..cffa8519 100644 --- a/test.galaxyproject.org/assembly.yml.lock +++ b/test.galaxyproject.org/assembly.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Assembly tools: diff --git a/test.galaxyproject.org/bed.yml.lock b/test.galaxyproject.org/bed.yml.lock index 648f1a77..2b045725 100644 --- a/test.galaxyproject.org/bed.yml.lock +++ b/test.galaxyproject.org/bed.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: BED tools: diff --git a/test.galaxyproject.org/collection_operations.yml.lock b/test.galaxyproject.org/collection_operations.yml.lock index 2a76162d..1599fe7f 100644 --- a/test.galaxyproject.org/collection_operations.yml.lock +++ b/test.galaxyproject.org/collection_operations.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Collection Operations tools: diff --git a/test.galaxyproject.org/convert_formats.yml.lock b/test.galaxyproject.org/convert_formats.yml.lock index af261da4..f133f56b 100644 --- a/test.galaxyproject.org/convert_formats.yml.lock +++ b/test.galaxyproject.org/convert_formats.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Convert Formats tools: diff --git a/test.galaxyproject.org/data_managers.yml.lock b/test.galaxyproject.org/data_managers.yml.lock index aba1bdf6..ed30aa35 100644 --- a/test.galaxyproject.org/data_managers.yml.lock +++ b/test.galaxyproject.org/data_managers.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Data Managers tools: diff --git a/test.galaxyproject.org/deeptools.yml.lock b/test.galaxyproject.org/deeptools.yml.lock index b3ee9723..f9a69ce2 100644 --- a/test.galaxyproject.org/deeptools.yml.lock +++ b/test.galaxyproject.org/deeptools.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: deepTools tools: diff --git a/test.galaxyproject.org/emboss.yml.lock b/test.galaxyproject.org/emboss.yml.lock index 04676c6d..323a0cf7 100644 --- a/test.galaxyproject.org/emboss.yml.lock +++ b/test.galaxyproject.org/emboss.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: EMBOSS tools: diff --git a/test.galaxyproject.org/evolution.yml.lock b/test.galaxyproject.org/evolution.yml.lock index 700d952e..220601d6 100644 --- a/test.galaxyproject.org/evolution.yml.lock +++ b/test.galaxyproject.org/evolution.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Evolution tools: diff --git a/test.galaxyproject.org/extract_features.yml.lock b/test.galaxyproject.org/extract_features.yml.lock index 6fad9885..edb56292 100644 --- a/test.galaxyproject.org/extract_features.yml.lock +++ b/test.galaxyproject.org/extract_features.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tools: - name: parse_mito_blast diff --git a/test.galaxyproject.org/fabio_tools.yml.lock b/test.galaxyproject.org/fabio_tools.yml.lock index f6c467a2..6979a697 100644 --- a/test.galaxyproject.org/fabio_tools.yml.lock +++ b/test.galaxyproject.org/fabio_tools.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Fabio Tools tools: diff --git a/test.galaxyproject.org/fasta_fastq.yml.lock b/test.galaxyproject.org/fasta_fastq.yml.lock index 8002c89c..23472ee7 100644 --- a/test.galaxyproject.org/fasta_fastq.yml.lock +++ b/test.galaxyproject.org/fasta_fastq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: FASTA/FASTQ tools: diff --git a/test.galaxyproject.org/fastq_quality_control.yml.lock b/test.galaxyproject.org/fastq_quality_control.yml.lock index cbaed337..cb10331b 100644 --- a/test.galaxyproject.org/fastq_quality_control.yml.lock +++ b/test.galaxyproject.org/fastq_quality_control.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: FASTQ Quality Control tools: diff --git a/test.galaxyproject.org/filter_and_sort.yml.lock b/test.galaxyproject.org/filter_and_sort.yml.lock index 22a70f5f..6965c92f 100644 --- a/test.galaxyproject.org/filter_and_sort.yml.lock +++ b/test.galaxyproject.org/filter_and_sort.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Filter and Sort tools: diff --git a/test.galaxyproject.org/gatk.yml.lock b/test.galaxyproject.org/gatk.yml.lock index cf99b7a2..5511f6f2 100644 --- a/test.galaxyproject.org/gatk.yml.lock +++ b/test.galaxyproject.org/gatk.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: GATK tools: diff --git a/test.galaxyproject.org/gemini.yml.lock b/test.galaxyproject.org/gemini.yml.lock index db7ccc4b..74d8e1e8 100644 --- a/test.galaxyproject.org/gemini.yml.lock +++ b/test.galaxyproject.org/gemini.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: GEMINI tools: diff --git a/test.galaxyproject.org/get_data.yml.lock b/test.galaxyproject.org/get_data.yml.lock index a9cc5175..17a4cfa8 100644 --- a/test.galaxyproject.org/get_data.yml.lock +++ b/test.galaxyproject.org/get_data.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Get Data tools: diff --git a/test.galaxyproject.org/graph_display_data.yml.lock b/test.galaxyproject.org/graph_display_data.yml.lock index 5266c497..4e648ede 100644 --- a/test.galaxyproject.org/graph_display_data.yml.lock +++ b/test.galaxyproject.org/graph_display_data.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Graph/Display Data tools: diff --git a/test.galaxyproject.org/hicexplorer.yml.lock b/test.galaxyproject.org/hicexplorer.yml.lock index ede80c6c..11aa49ac 100644 --- a/test.galaxyproject.org/hicexplorer.yml.lock +++ b/test.galaxyproject.org/hicexplorer.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: HiCExplorer tools: diff --git a/test.galaxyproject.org/hyphy_tools.yml.lock b/test.galaxyproject.org/hyphy_tools.yml.lock index c72b85b0..e4a713b0 100644 --- a/test.galaxyproject.org/hyphy_tools.yml.lock +++ b/test.galaxyproject.org/hyphy_tools.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: HyPhy Methods tools: diff --git a/test.galaxyproject.org/ideas.yml.lock b/test.galaxyproject.org/ideas.yml.lock index 77e69ac9..724904eb 100644 --- a/test.galaxyproject.org/ideas.yml.lock +++ b/test.galaxyproject.org/ideas.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: IDEAS tools: diff --git a/test.galaxyproject.org/join__subtract_and_group.yml.lock b/test.galaxyproject.org/join__subtract_and_group.yml.lock index 0bd6bf79..cfbfa100 100644 --- a/test.galaxyproject.org/join__subtract_and_group.yml.lock +++ b/test.galaxyproject.org/join__subtract_and_group.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Join, Subtract and Group tools: diff --git a/test.galaxyproject.org/machine_learning.yml.lock b/test.galaxyproject.org/machine_learning.yml.lock index 971d1e74..21aca19e 100644 --- a/test.galaxyproject.org/machine_learning.yml.lock +++ b/test.galaxyproject.org/machine_learning.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Machine Learning tools: diff --git a/test.galaxyproject.org/metagenomic_analysis.yml.lock b/test.galaxyproject.org/metagenomic_analysis.yml.lock index e6f28c13..f33cf365 100644 --- a/test.galaxyproject.org/metagenomic_analysis.yml.lock +++ b/test.galaxyproject.org/metagenomic_analysis.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Metagenomic Analysis tools: diff --git a/test.galaxyproject.org/metagenomic_analysis__deprecated_.yml.lock b/test.galaxyproject.org/metagenomic_analysis__deprecated_.yml.lock index 89834bcd..c8dd5650 100644 --- a/test.galaxyproject.org/metagenomic_analysis__deprecated_.yml.lock +++ b/test.galaxyproject.org/metagenomic_analysis__deprecated_.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Metagenomic Analysis (deprecated) tools: diff --git a/test.galaxyproject.org/mimodd.yml.lock b/test.galaxyproject.org/mimodd.yml.lock index 90858eba..4991ece2 100644 --- a/test.galaxyproject.org/mimodd.yml.lock +++ b/test.galaxyproject.org/mimodd.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: MiModD tools: diff --git a/test.galaxyproject.org/motifs.yml.lock b/test.galaxyproject.org/motifs.yml.lock index ebc47858..bde98c5e 100644 --- a/test.galaxyproject.org/motifs.yml.lock +++ b/test.galaxyproject.org/motifs.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Motifs tools: diff --git a/test.galaxyproject.org/multiple_alignments.yml.lock b/test.galaxyproject.org/multiple_alignments.yml.lock index 03876f8d..76ab2186 100644 --- a/test.galaxyproject.org/multiple_alignments.yml.lock +++ b/test.galaxyproject.org/multiple_alignments.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Multiple Alignments tools: diff --git a/test.galaxyproject.org/nanopore.yml.lock b/test.galaxyproject.org/nanopore.yml.lock index 5405c221..1b3eff8c 100644 --- a/test.galaxyproject.org/nanopore.yml.lock +++ b/test.galaxyproject.org/nanopore.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Nanopore tools: diff --git a/test.galaxyproject.org/ncbi_blast_.yml.lock b/test.galaxyproject.org/ncbi_blast_.yml.lock index 4e7227b4..a0fb1f85 100644 --- a/test.galaxyproject.org/ncbi_blast_.yml.lock +++ b/test.galaxyproject.org/ncbi_blast_.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: NCBI BLAST+ tools: diff --git a/test.galaxyproject.org/operate_on_genomic_intervals.yml.lock b/test.galaxyproject.org/operate_on_genomic_intervals.yml.lock index ae3f4a62..4d01979d 100644 --- a/test.galaxyproject.org/operate_on_genomic_intervals.yml.lock +++ b/test.galaxyproject.org/operate_on_genomic_intervals.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Operate on Genomic Intervals tools: diff --git a/test.galaxyproject.org/picard.yml.lock b/test.galaxyproject.org/picard.yml.lock index ebb9051d..dfd7e405 100644 --- a/test.galaxyproject.org/picard.yml.lock +++ b/test.galaxyproject.org/picard.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Picard tools: diff --git a/test.galaxyproject.org/planttribes.yml.lock b/test.galaxyproject.org/planttribes.yml.lock index c4667e66..6f691e42 100644 --- a/test.galaxyproject.org/planttribes.yml.lock +++ b/test.galaxyproject.org/planttribes.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: PlantTribes tools: diff --git a/test.galaxyproject.org/protein_modeling.yml.lock b/test.galaxyproject.org/protein_modeling.yml.lock index b8ac2d35..5d4b9275 100644 --- a/test.galaxyproject.org/protein_modeling.yml.lock +++ b/test.galaxyproject.org/protein_modeling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Protein Modeling tools: diff --git a/test.galaxyproject.org/regional_variation.yml.lock b/test.galaxyproject.org/regional_variation.yml.lock index aca56dd7..520ef635 100644 --- a/test.galaxyproject.org/regional_variation.yml.lock +++ b/test.galaxyproject.org/regional_variation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Regional Variation tools: diff --git a/test.galaxyproject.org/rna_seq.yml.lock b/test.galaxyproject.org/rna_seq.yml.lock index 289466fa..528d6b5c 100644 --- a/test.galaxyproject.org/rna_seq.yml.lock +++ b/test.galaxyproject.org/rna_seq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RNA-seq tools: diff --git a/test.galaxyproject.org/rseqc.yml.lock b/test.galaxyproject.org/rseqc.yml.lock index 35ccb93a..1ceafe2a 100644 --- a/test.galaxyproject.org/rseqc.yml.lock +++ b/test.galaxyproject.org/rseqc.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RSeQC tools: diff --git a/test.galaxyproject.org/sam_bam.yml.lock b/test.galaxyproject.org/sam_bam.yml.lock index e4f50af9..ead4bf41 100644 --- a/test.galaxyproject.org/sam_bam.yml.lock +++ b/test.galaxyproject.org/sam_bam.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: SAM/BAM tools: diff --git a/test.galaxyproject.org/statistics.yml.lock b/test.galaxyproject.org/statistics.yml.lock index 0cbbe849..4b4208dd 100644 --- a/test.galaxyproject.org/statistics.yml.lock +++ b/test.galaxyproject.org/statistics.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Statistics tools: diff --git a/test.galaxyproject.org/text_manipulation.yml.lock b/test.galaxyproject.org/text_manipulation.yml.lock index f53d8cd2..5aada8c8 100644 --- a/test.galaxyproject.org/text_manipulation.yml.lock +++ b/test.galaxyproject.org/text_manipulation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Text Manipulation tools: diff --git a/test.galaxyproject.org/transposon_insertion_sequencing.yml.lock b/test.galaxyproject.org/transposon_insertion_sequencing.yml.lock index 8487e26b..068030bc 100644 --- a/test.galaxyproject.org/transposon_insertion_sequencing.yml.lock +++ b/test.galaxyproject.org/transposon_insertion_sequencing.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Transposon Insertion Sequencing tools: diff --git a/test.galaxyproject.org/usegalaxy___common_tools_test.yml.lock b/test.galaxyproject.org/usegalaxy___common_tools_test.yml.lock index 8167b9cb..2f08daa9 100644 --- a/test.galaxyproject.org/usegalaxy___common_tools_test.yml.lock +++ b/test.galaxyproject.org/usegalaxy___common_tools_test.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: usegalaxy.* common tools test tools: diff --git a/test.galaxyproject.org/variant_calling.yml.lock b/test.galaxyproject.org/variant_calling.yml.lock index a3213c41..bf6d9480 100644 --- a/test.galaxyproject.org/variant_calling.yml.lock +++ b/test.galaxyproject.org/variant_calling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Variant Calling tools: diff --git a/test.galaxyproject.org/vcf_bcf.yml.lock b/test.galaxyproject.org/vcf_bcf.yml.lock index 4aae8a50..47223f0f 100644 --- a/test.galaxyproject.org/vcf_bcf.yml.lock +++ b/test.galaxyproject.org/vcf_bcf.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: VCF/BCF tools: diff --git a/usegalaxy.org/assembly.yml.lock b/usegalaxy.org/assembly.yml.lock index 363439bd..b026ce2c 100644 --- a/usegalaxy.org/assembly.yml.lock +++ b/usegalaxy.org/assembly.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Assembly tools: diff --git a/usegalaxy.org/bed.yml.lock b/usegalaxy.org/bed.yml.lock index 32c73cf1..539c871d 100644 --- a/usegalaxy.org/bed.yml.lock +++ b/usegalaxy.org/bed.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: BED tools: diff --git a/usegalaxy.org/chip_seq.yml.lock b/usegalaxy.org/chip_seq.yml.lock index d60e08e4..841abe18 100644 --- a/usegalaxy.org/chip_seq.yml.lock +++ b/usegalaxy.org/chip_seq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: ChIP-seq tools: diff --git a/usegalaxy.org/chromosome_conformation.yml.lock b/usegalaxy.org/chromosome_conformation.yml.lock index 30cd3d9e..5bbe2efa 100644 --- a/usegalaxy.org/chromosome_conformation.yml.lock +++ b/usegalaxy.org/chromosome_conformation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Chromosome Conformation tools: diff --git a/usegalaxy.org/climate_analysis.yml.lock b/usegalaxy.org/climate_analysis.yml.lock index 531767dc..6ccdd807 100644 --- a/usegalaxy.org/climate_analysis.yml.lock +++ b/usegalaxy.org/climate_analysis.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Climate Analysis tools: diff --git a/usegalaxy.org/cloudmap__deprecated_.yml.lock b/usegalaxy.org/cloudmap__deprecated_.yml.lock index bcb39a58..f6fde597 100644 --- a/usegalaxy.org/cloudmap__deprecated_.yml.lock +++ b/usegalaxy.org/cloudmap__deprecated_.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: CloudMap (deprecated) tools: diff --git a/usegalaxy.org/collection_operations.yml.lock b/usegalaxy.org/collection_operations.yml.lock index 4e89945f..c3a73f63 100644 --- a/usegalaxy.org/collection_operations.yml.lock +++ b/usegalaxy.org/collection_operations.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Collection Operations tools: diff --git a/usegalaxy.org/convert_formats.yml.lock b/usegalaxy.org/convert_formats.yml.lock index 61878ec6..691d8c22 100644 --- a/usegalaxy.org/convert_formats.yml.lock +++ b/usegalaxy.org/convert_formats.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Convert Formats tools: diff --git a/usegalaxy.org/datamash.yml.lock b/usegalaxy.org/datamash.yml.lock index 9a592b72..6de747f9 100644 --- a/usegalaxy.org/datamash.yml.lock +++ b/usegalaxy.org/datamash.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Datamash tools: diff --git a/usegalaxy.org/deeptools.yml.lock b/usegalaxy.org/deeptools.yml.lock index 5e4a87f4..eafb3a5b 100644 --- a/usegalaxy.org/deeptools.yml.lock +++ b/usegalaxy.org/deeptools.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: deepTools tools: diff --git a/usegalaxy.org/du_novo.yml.lock b/usegalaxy.org/du_novo.yml.lock index 159040ca..2a16f850 100644 --- a/usegalaxy.org/du_novo.yml.lock +++ b/usegalaxy.org/du_novo.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Du Novo tools: diff --git a/usegalaxy.org/emboss.yml.lock b/usegalaxy.org/emboss.yml.lock index 1e2a5405..9aa12101 100644 --- a/usegalaxy.org/emboss.yml.lock +++ b/usegalaxy.org/emboss.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: EMBOSS tools: diff --git a/usegalaxy.org/evolution.yml.lock b/usegalaxy.org/evolution.yml.lock index be5e1923..459d8b3f 100644 --- a/usegalaxy.org/evolution.yml.lock +++ b/usegalaxy.org/evolution.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Evolution tools: diff --git a/usegalaxy.org/extract_features.yml.lock b/usegalaxy.org/extract_features.yml.lock index 989bde8d..658cf455 100644 --- a/usegalaxy.org/extract_features.yml.lock +++ b/usegalaxy.org/extract_features.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tools: - name: parse_mito_blast diff --git a/usegalaxy.org/fasta_fastq.yml.lock b/usegalaxy.org/fasta_fastq.yml.lock index cdb35963..73f9812e 100644 --- a/usegalaxy.org/fasta_fastq.yml.lock +++ b/usegalaxy.org/fasta_fastq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: FASTA/FASTQ tools: diff --git a/usegalaxy.org/fastq_quality_control.yml.lock b/usegalaxy.org/fastq_quality_control.yml.lock index 960ea61e..5c596d77 100644 --- a/usegalaxy.org/fastq_quality_control.yml.lock +++ b/usegalaxy.org/fastq_quality_control.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: FASTQ Quality Control tools: diff --git a/usegalaxy.org/fetch_sequences_alignments.yml.lock b/usegalaxy.org/fetch_sequences_alignments.yml.lock index ad98bfb5..ccec6eba 100644 --- a/usegalaxy.org/fetch_sequences_alignments.yml.lock +++ b/usegalaxy.org/fetch_sequences_alignments.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Fetch Sequences/Alignments tools: diff --git a/usegalaxy.org/gatk.yml.lock b/usegalaxy.org/gatk.yml.lock index 2280854b..af5f9ef6 100644 --- a/usegalaxy.org/gatk.yml.lock +++ b/usegalaxy.org/gatk.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: GATK tools: diff --git a/usegalaxy.org/genome_diversity.yml.lock b/usegalaxy.org/genome_diversity.yml.lock index 12e0d8df..734f7b74 100644 --- a/usegalaxy.org/genome_diversity.yml.lock +++ b/usegalaxy.org/genome_diversity.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Genome Diversity tools: diff --git a/usegalaxy.org/get_data.yml.lock b/usegalaxy.org/get_data.yml.lock index 765b4293..ba573ec5 100644 --- a/usegalaxy.org/get_data.yml.lock +++ b/usegalaxy.org/get_data.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Get Data tools: diff --git a/usegalaxy.org/gis_data_handling.yml.lock b/usegalaxy.org/gis_data_handling.yml.lock index 514207dc..4341f50d 100644 --- a/usegalaxy.org/gis_data_handling.yml.lock +++ b/usegalaxy.org/gis_data_handling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: GIS Data Handling tools: diff --git a/usegalaxy.org/graph_display_data.yml.lock b/usegalaxy.org/graph_display_data.yml.lock index 9a450e36..d11c76ac 100644 --- a/usegalaxy.org/graph_display_data.yml.lock +++ b/usegalaxy.org/graph_display_data.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Graph/Display Data tools: diff --git a/usegalaxy.org/hyphy.yml.lock b/usegalaxy.org/hyphy.yml.lock index 2f0962c3..63dc4ed8 100644 --- a/usegalaxy.org/hyphy.yml.lock +++ b/usegalaxy.org/hyphy.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: HyPhy tools: diff --git a/usegalaxy.org/iwtomics.yml.lock b/usegalaxy.org/iwtomics.yml.lock index 8ac920a6..f6a460bb 100644 --- a/usegalaxy.org/iwtomics.yml.lock +++ b/usegalaxy.org/iwtomics.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: IWTomics tools: diff --git a/usegalaxy.org/join__subtract_and_group.yml.lock b/usegalaxy.org/join__subtract_and_group.yml.lock index 9386136f..6063a1fa 100644 --- a/usegalaxy.org/join__subtract_and_group.yml.lock +++ b/usegalaxy.org/join__subtract_and_group.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Join, Subtract and Group tools: diff --git a/usegalaxy.org/machine_learning.yml.lock b/usegalaxy.org/machine_learning.yml.lock index c8b1ac33..d2471584 100644 --- a/usegalaxy.org/machine_learning.yml.lock +++ b/usegalaxy.org/machine_learning.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Machine Learning tools: diff --git a/usegalaxy.org/mapping.yml.lock b/usegalaxy.org/mapping.yml.lock index fae4850e..025e5f06 100644 --- a/usegalaxy.org/mapping.yml.lock +++ b/usegalaxy.org/mapping.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Mapping tools: diff --git a/usegalaxy.org/metagenomic_analysis.yml.lock b/usegalaxy.org/metagenomic_analysis.yml.lock index 97680133..a108140a 100644 --- a/usegalaxy.org/metagenomic_analysis.yml.lock +++ b/usegalaxy.org/metagenomic_analysis.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Metagenomic Analysis tools: diff --git a/usegalaxy.org/mimodd.yml.lock b/usegalaxy.org/mimodd.yml.lock index d3a388b6..1fb25ad7 100644 --- a/usegalaxy.org/mimodd.yml.lock +++ b/usegalaxy.org/mimodd.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: MiModD tools: diff --git a/usegalaxy.org/mothur.yml.lock b/usegalaxy.org/mothur.yml.lock index a71f3fd5..5384ff69 100644 --- a/usegalaxy.org/mothur.yml.lock +++ b/usegalaxy.org/mothur.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Mothur tools: diff --git a/usegalaxy.org/motif.yml.lock b/usegalaxy.org/motif.yml.lock index 996883a5..c6b8051e 100644 --- a/usegalaxy.org/motif.yml.lock +++ b/usegalaxy.org/motif.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Motif tools: diff --git a/usegalaxy.org/multiple_alignments.yml.lock b/usegalaxy.org/multiple_alignments.yml.lock index f9e0ca1b..60234e61 100644 --- a/usegalaxy.org/multiple_alignments.yml.lock +++ b/usegalaxy.org/multiple_alignments.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Multiple Alignments tools: diff --git a/usegalaxy.org/nanopore.yml.lock b/usegalaxy.org/nanopore.yml.lock index 657db944..998ccf50 100644 --- a/usegalaxy.org/nanopore.yml.lock +++ b/usegalaxy.org/nanopore.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Nanopore tools: diff --git a/usegalaxy.org/ncbi_blast_.yml.lock b/usegalaxy.org/ncbi_blast_.yml.lock index c4390865..6573dd8a 100644 --- a/usegalaxy.org/ncbi_blast_.yml.lock +++ b/usegalaxy.org/ncbi_blast_.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: NCBI BLAST+ tools: diff --git a/usegalaxy.org/operate_on_genomic_intervals.yml.lock b/usegalaxy.org/operate_on_genomic_intervals.yml.lock index ab774079..20c2ef62 100644 --- a/usegalaxy.org/operate_on_genomic_intervals.yml.lock +++ b/usegalaxy.org/operate_on_genomic_intervals.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Operate on Genomic Intervals tools: diff --git a/usegalaxy.org/pharmacology.yml.lock b/usegalaxy.org/pharmacology.yml.lock index ceb13498..bfbc68c4 100644 --- a/usegalaxy.org/pharmacology.yml.lock +++ b/usegalaxy.org/pharmacology.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Pharmacology tools: diff --git a/usegalaxy.org/phenotype_association.yml.lock b/usegalaxy.org/phenotype_association.yml.lock index b42b82bb..c77eec1e 100644 --- a/usegalaxy.org/phenotype_association.yml.lock +++ b/usegalaxy.org/phenotype_association.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Phenotype Association tools: diff --git a/usegalaxy.org/picard.yml.lock b/usegalaxy.org/picard.yml.lock index 8630fccf..78adef3f 100644 --- a/usegalaxy.org/picard.yml.lock +++ b/usegalaxy.org/picard.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Picard tools: diff --git a/usegalaxy.org/planttribes.yml.lock b/usegalaxy.org/planttribes.yml.lock index 6045d3ee..1909fd37 100644 --- a/usegalaxy.org/planttribes.yml.lock +++ b/usegalaxy.org/planttribes.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: PlantTribes tools: diff --git a/usegalaxy.org/presto.yml.lock b/usegalaxy.org/presto.yml.lock index 6946f115..d8241a32 100644 --- a/usegalaxy.org/presto.yml.lock +++ b/usegalaxy.org/presto.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: pRESTO tools: diff --git a/usegalaxy.org/protein_modeling.yml.lock b/usegalaxy.org/protein_modeling.yml.lock index a413ce1c..d652d039 100644 --- a/usegalaxy.org/protein_modeling.yml.lock +++ b/usegalaxy.org/protein_modeling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Protein Modeling tools: diff --git a/usegalaxy.org/proteomics.yml.lock b/usegalaxy.org/proteomics.yml.lock index 4b8dd539..a24e2d05 100644 --- a/usegalaxy.org/proteomics.yml.lock +++ b/usegalaxy.org/proteomics.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Proteomics tools: diff --git a/usegalaxy.org/regional_variation.yml.lock b/usegalaxy.org/regional_variation.yml.lock index 9f60f2c8..ca77f86e 100644 --- a/usegalaxy.org/regional_variation.yml.lock +++ b/usegalaxy.org/regional_variation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Regional Variation tools: diff --git a/usegalaxy.org/rna_analysis__deprecated_.yml.lock b/usegalaxy.org/rna_analysis__deprecated_.yml.lock index d344e87d..32a436f5 100644 --- a/usegalaxy.org/rna_analysis__deprecated_.yml.lock +++ b/usegalaxy.org/rna_analysis__deprecated_.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RNA Analysis (deprecated) tools: diff --git a/usegalaxy.org/rna_seq.yml.lock b/usegalaxy.org/rna_seq.yml.lock index 0f2ed34c..63b5970e 100644 --- a/usegalaxy.org/rna_seq.yml.lock +++ b/usegalaxy.org/rna_seq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RNA-seq tools: diff --git a/usegalaxy.org/rseqc.yml.lock b/usegalaxy.org/rseqc.yml.lock index 01a2e76e..3d6fed4a 100644 --- a/usegalaxy.org/rseqc.yml.lock +++ b/usegalaxy.org/rseqc.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RSeQC tools: diff --git a/usegalaxy.org/sam_bam.yml.lock b/usegalaxy.org/sam_bam.yml.lock index e7f26e30..a318d97d 100644 --- a/usegalaxy.org/sam_bam.yml.lock +++ b/usegalaxy.org/sam_bam.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: SAM/BAM tools: diff --git a/usegalaxy.org/seqtk.yml.lock b/usegalaxy.org/seqtk.yml.lock index f6a459a2..37de0340 100644 --- a/usegalaxy.org/seqtk.yml.lock +++ b/usegalaxy.org/seqtk.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Seqtk tools: diff --git a/usegalaxy.org/single_cell.yml.lock b/usegalaxy.org/single_cell.yml.lock index 773df7a9..71ae4106 100644 --- a/usegalaxy.org/single_cell.yml.lock +++ b/usegalaxy.org/single_cell.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Single-cell tools: diff --git a/usegalaxy.org/statistics.yml.lock b/usegalaxy.org/statistics.yml.lock index 0cf680ac..6d2d102d 100644 --- a/usegalaxy.org/statistics.yml.lock +++ b/usegalaxy.org/statistics.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Statistics tools: diff --git a/usegalaxy.org/str_fm__microsatellite_analysis.yml.lock b/usegalaxy.org/str_fm__microsatellite_analysis.yml.lock index 02252916..2cc65c14 100644 --- a/usegalaxy.org/str_fm__microsatellite_analysis.yml.lock +++ b/usegalaxy.org/str_fm__microsatellite_analysis.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: 'STR-FM: Microsatellite Analysis' tools: diff --git a/usegalaxy.org/text_manipulation.yml.lock b/usegalaxy.org/text_manipulation.yml.lock index 2960b0e1..289c931c 100644 --- a/usegalaxy.org/text_manipulation.yml.lock +++ b/usegalaxy.org/text_manipulation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Text Manipulation tools: diff --git a/usegalaxy.org/transposon_insertion_sequencing.yml.lock b/usegalaxy.org/transposon_insertion_sequencing.yml.lock index 71bdbfff..64418250 100644 --- a/usegalaxy.org/transposon_insertion_sequencing.yml.lock +++ b/usegalaxy.org/transposon_insertion_sequencing.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Transposon Insertion Sequencing tools: diff --git a/usegalaxy.org/vcf_bcf.yml.lock b/usegalaxy.org/vcf_bcf.yml.lock index b24ef687..fee26fa2 100644 --- a/usegalaxy.org/vcf_bcf.yml.lock +++ b/usegalaxy.org/vcf_bcf.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: VCF/BCF tools: diff --git a/usegalaxy.org/virology.yml.lock b/usegalaxy.org/virology.yml.lock index f267c01f..163fe8b8 100644 --- a/usegalaxy.org/virology.yml.lock +++ b/usegalaxy.org/virology.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Virology tools: