From d00c80286677a074a09a5bc169090e16251ce755 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 5 Jun 2025 10:40:15 +0200 Subject: [PATCH] drop all cpt tools they generally do not have containers, are often pulsar-incompatible, or outright broken --- .../annotation.yml | 14 -- .../annotation.yml.lock | 43 ------ .../fasta_fastq.yml | 2 - .../fasta_fastq.yml.lock | 6 - .../phylogenetics.yml | 4 - .../phylogenetics.yml.lock | 13 +- usegalaxy.cz/annotation.yml | 38 ------ usegalaxy.cz/annotation.yml.lock | 124 ------------------ usegalaxy.cz/convert_formats.yml | 12 -- usegalaxy.cz/convert_formats.yml.lock | 44 +------ usegalaxy.cz/fasta_fastq.yml | 2 - usegalaxy.cz/fasta_fastq.yml.lock | 6 - usegalaxy.cz/graph_display_data.yml | 2 - usegalaxy.cz/graph_display_data.yml.lock | 7 - usegalaxy.cz/phylogenetics.yml | 8 +- usegalaxy.cz/phylogenetics.yml.lock | 18 --- 16 files changed, 3 insertions(+), 340 deletions(-) diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml index f17807a..4fe2308 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml @@ -124,24 +124,10 @@ tools: owner: bgruening - name: pfamscan owner: bgruening -- name: cpt_phageqc_annotations - owner: cpt -- name: cpt_intron_detection - owner: cpt -- name: cpt_gbk_renumber - owner: cpt -- name: cpt_require_shine - owner: cpt - name: tb_variant_filter owner: iuc - name: pharokka owner: iuc -- name: cpt_gff_add_parents - owner: cpt -- name: cpt_remove_annotations - owner: cpt -- name: cpt_prep_for_apollo - owner: cpt - name: funannotate_predict owner: iuc - name: funannotate_compare diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock index ac227cf..1e3f765 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock @@ -384,30 +384,6 @@ tools: - 15cff34c2005 tool_panel_section_id: annotation tool_panel_section_label: Annotation -- name: cpt_phageqc_annotations - owner: cpt - revisions: - - c3140b08d703 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_intron_detection - owner: cpt - revisions: - - 0a98d5259ef0 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_gbk_renumber - owner: cpt - revisions: - - 8cac332dbc77 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_require_shine - owner: cpt - revisions: - - a6dc48930318 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation - name: tb_variant_filter owner: iuc revisions: @@ -420,25 +396,6 @@ tools: - 2f40d2ccb0eb tool_panel_section_id: annotation tool_panel_section_label: Annotation -- name: cpt_gff_add_parents - owner: cpt - revisions: - - d839cfd1c3a6 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_remove_annotations - owner: cpt - revisions: - - 49f50c55a9f8 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_prep_for_apollo - owner: cpt - revisions: - - 6901154b1003 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: funannotate_predict owner: iuc revisions: - 3cc3ef448854 diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml index 1c23328..44b26d0 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml @@ -96,5 +96,3 @@ tools: owner: devteam - name: fastx_barcode_splitter owner: devteam -- name: cpt_fasta_remove_id - owner: cpt diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock index 8be8012..9680d52 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock @@ -302,9 +302,3 @@ tools: - 0b7ec11b3c7c tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ -- name: cpt_fasta_remove_id - owner: cpt - revisions: - - 78222649a59a - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml index 4d141db..cad879f 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml @@ -54,7 +54,3 @@ tools: owner: iuc - name: snp_dists owner: iuc -- name: cpt_related_genomes_nuc - owner: cpt -- name: cpt_xmfa_to_table - owner: cpt diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock index dac77c1..dd146f9 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock @@ -178,15 +178,4 @@ tools: - f78492521996 tool_panel_section_id: phylogenetics tool_panel_section_label: Phylogenetics -- name: cpt_related_genomes_nuc - owner: cpt - revisions: - - 5a5fe0a6f78d - tool_panel_section_id: phylogenetics - tool_panel_section_label: Phylogenetics -- name: cpt_xmfa_to_table - owner: cpt - revisions: - - 06d8e28d0bd7 - tool_panel_section_id: phylogenetics - tool_panel_section_label: Phylogenetics + diff --git a/usegalaxy.cz/annotation.yml b/usegalaxy.cz/annotation.yml index 2ee6047..8c4f63c 100644 --- a/usegalaxy.cz/annotation.yml +++ b/usegalaxy.cz/annotation.yml @@ -240,50 +240,12 @@ tools: owner: iuc - name: braker3 owner: genouest -- name: cpt_phageqc_annotations - owner: cpt -- name: cpt_gff_extract_seq - owner: cpt -- name: cpt_intron_detection - owner: cpt -- name: cpt_lipory - owner: cpt -- name: cpt_gbk_renumber - owner: cpt -- name: cpt_genome_editor - owner: cpt -- name: cpt_annotation_table - owner: cpt -- name: cpt_gff_rebase - owner: cpt -- name: cpt_require_shine - owner: cpt -- name: cpt_get_orfs - owner: cpt -- name: cpt_gff_add_parents - owner: cpt -- name: cpt_fix_sixpack - owner: cpt -- name: cpt_shinefind - owner: cpt -- name: cpt_type_filter - owner: cpt -- name: cpt_req_phage_start - owner: cpt -- name: cpt_remove_annotations - owner: cpt -- name: cpt_prep_for_apollo - owner: cpt -- name: cpt_convert_glimmer - owner: cpt - name: agat owner: bgruening - name: helixer owner: genouest - name: hmmer3 owner: iuc -- name: cpt_intersect_adjacent - owner: cpt - name: blast2go owner: peterjc - name: funannotate_predict diff --git a/usegalaxy.cz/annotation.yml.lock b/usegalaxy.cz/annotation.yml.lock index e12dfb6..1ba1d94 100644 --- a/usegalaxy.cz/annotation.yml.lock +++ b/usegalaxy.cz/annotation.yml.lock @@ -824,124 +824,6 @@ tools: - bd103884a09c tool_panel_section_id: annotation tool_panel_section_label: Annotation -- name: cpt_phageqc_annotations - owner: cpt - revisions: - - c3140b08d703 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_gff_extract_seq - owner: cpt - revisions: - - 3d9f283ff09d - - ab40380424c9 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_intron_detection - owner: cpt - revisions: - - 0a98d5259ef0 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_lipory - owner: cpt - revisions: - - 2654bcd9b14d - - b79df4966ebb - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_gbk_renumber - owner: cpt - revisions: - - 8cac332dbc77 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_genome_editor - owner: cpt - revisions: - - 0e8079ac24f8 - - 78ce8a1a8fd1 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_annotation_table - owner: cpt - revisions: - - 6998c2570145 - - 848dd74f4382 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_gff_rebase - owner: cpt - revisions: - - 4f4b413056f6 - - d0b52c1d6b25 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_require_shine - owner: cpt - revisions: - - a6dc48930318 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_get_orfs - owner: cpt - revisions: - - f56389d8abda - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_gff_add_parents - owner: cpt - revisions: - - d839cfd1c3a6 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_fix_sixpack - owner: cpt - revisions: - - 326429ea1d33 - - e23a13d56fce - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_shinefind - owner: cpt - revisions: - - 6a5aac2a4c89 - - 75f99d20c2a2 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_type_filter - owner: cpt - revisions: - - a77124b86382 - - d40c9632250f - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_req_phage_start - owner: cpt - revisions: - - 33b5403e0357 - - 4962f275bcaa - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_remove_annotations - owner: cpt - revisions: - - 49f50c55a9f8 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_prep_for_apollo - owner: cpt - revisions: - - 6901154b1003 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: cpt_convert_glimmer - owner: cpt - revisions: - - 746e52d94b49 - - faff58a642fb - tool_panel_section_id: annotation - tool_panel_section_label: Annotation - name: agat owner: bgruening revisions: @@ -963,12 +845,6 @@ tools: - b5066aa77fea tool_panel_section_id: annotation tool_panel_section_label: Annotation -- name: cpt_intersect_adjacent - owner: cpt - revisions: - - 7e393668b4b9 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation - name: blast2go owner: peterjc revisions: diff --git a/usegalaxy.cz/convert_formats.yml b/usegalaxy.cz/convert_formats.yml index ace72d2..6b280aa 100644 --- a/usegalaxy.cz/convert_formats.yml +++ b/usegalaxy.cz/convert_formats.yml @@ -80,15 +80,3 @@ tools: owner: iuc - name: xmlstarlet owner: ecology -- name: cpt_gff_split - owner: cpt -- name: cpt_gbk_to_5col - owner: cpt -- name: cpt_gff_to_gbk - owner: cpt -- name: cpt_gbk_to_gff - owner: cpt -- name: cpt_convert_mga - owner: cpt -- name: cpt_fix_aragorn - owner: cpt diff --git a/usegalaxy.cz/convert_formats.yml.lock b/usegalaxy.cz/convert_formats.yml.lock index 32d5c5d..e3c39b6 100644 --- a/usegalaxy.cz/convert_formats.yml.lock +++ b/usegalaxy.cz/convert_formats.yml.lock @@ -279,46 +279,4 @@ tools: revisions: - 4a9ac1df3278 tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: cpt_gff_split - owner: cpt - revisions: - - 8bd03ba8510a - - ba8b6a5ffd9e - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: cpt_gbk_to_5col - owner: cpt - revisions: - - 1bdd481d5c25 - - 8f5f2142fc2b - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: cpt_gff_to_gbk - owner: cpt - revisions: - - 03384dbb511d - - 35a6c466e270 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: cpt_gbk_to_gff - owner: cpt - revisions: - - a921d6148d88 - - bb6332a85aa6 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: cpt_convert_mga - owner: cpt - revisions: - - 1bf722ba06e3 - - 2c83f55438c9 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: cpt_fix_aragorn - owner: cpt - revisions: - - 733cb0807083 - - 8da37080e35f - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats + tool_panel_section_label: Convert Formats \ No newline at end of file diff --git a/usegalaxy.cz/fasta_fastq.yml b/usegalaxy.cz/fasta_fastq.yml index 5086cb4..b0e7e2d 100644 --- a/usegalaxy.cz/fasta_fastq.yml +++ b/usegalaxy.cz/fasta_fastq.yml @@ -168,7 +168,5 @@ tools: owner: iuc - name: bbtools_bbmerge owner: iuc -- name: cpt_fasta_remove_id - owner: cpt - name: prinseq owner: iuc diff --git a/usegalaxy.cz/fasta_fastq.yml.lock b/usegalaxy.cz/fasta_fastq.yml.lock index 43ea478..a8c814c 100644 --- a/usegalaxy.cz/fasta_fastq.yml.lock +++ b/usegalaxy.cz/fasta_fastq.yml.lock @@ -621,12 +621,6 @@ tools: - c9e516d65a3d tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ -- name: cpt_fasta_remove_id - owner: cpt - revisions: - - 78222649a59a - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ - name: prinseq owner: iuc revisions: diff --git a/usegalaxy.cz/graph_display_data.yml b/usegalaxy.cz/graph_display_data.yml index 549db50..0b4082d 100644 --- a/usegalaxy.cz/graph_display_data.yml +++ b/usegalaxy.cz/graph_display_data.yml @@ -72,7 +72,5 @@ tools: owner: iuc - name: pathifier owner: artbio -- name: cpt_linear_genome_plot - owner: cpt - name: geneiobio owner: iuc diff --git a/usegalaxy.cz/graph_display_data.yml.lock b/usegalaxy.cz/graph_display_data.yml.lock index a72e7ae..525c00d 100644 --- a/usegalaxy.cz/graph_display_data.yml.lock +++ b/usegalaxy.cz/graph_display_data.yml.lock @@ -251,13 +251,6 @@ tools: - fec313f5c889 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data -- name: cpt_linear_genome_plot - owner: cpt - revisions: - - e2449c8659be - - e923c686ead9 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data - name: geneiobio owner: iuc revisions: diff --git a/usegalaxy.cz/phylogenetics.yml b/usegalaxy.cz/phylogenetics.yml index ca1034a..8ed5b20 100644 --- a/usegalaxy.cz/phylogenetics.yml +++ b/usegalaxy.cz/phylogenetics.yml @@ -83,10 +83,4 @@ tools: - name: picrust2_place_seqs owner: iuc - name: picrust2_shuffle_predictions - owner: iuc -- name: cpt_related_genomes_nuc - owner: cpt -- name: cpt_related_genomes_prot - owner: cpt -- name: cpt_xmfa_to_table - owner: cpt + owner: iuc \ No newline at end of file diff --git a/usegalaxy.cz/phylogenetics.yml.lock b/usegalaxy.cz/phylogenetics.yml.lock index 8dd5544..3dbe4b7 100644 --- a/usegalaxy.cz/phylogenetics.yml.lock +++ b/usegalaxy.cz/phylogenetics.yml.lock @@ -308,21 +308,3 @@ tools: - 881f2faa5fe7 tool_panel_section_id: phylogenetics tool_panel_section_label: Phylogenetics -- name: cpt_related_genomes_nuc - owner: cpt - revisions: - - 5a5fe0a6f78d - tool_panel_section_id: phylogenetics - tool_panel_section_label: Phylogenetics -- name: cpt_related_genomes_prot - owner: cpt - revisions: - - ebcc87a27f9c - tool_panel_section_id: phylogenetics - tool_panel_section_label: Phylogenetics -- name: cpt_xmfa_to_table - owner: cpt - revisions: - - 06d8e28d0bd7 - tool_panel_section_id: phylogenetics - tool_panel_section_label: Phylogenetics