From 00226711f06faf8af6b5ff9bf89cf98e739ba21e Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 19 Jun 2024 13:00:26 +0200 Subject: [PATCH 1/2] adding missing tools which are on European server but not on the main org server, needed for Foodborne workflow PathoGFAIR to be publically avaiable on the org server --- usegalaxy.org/metagenomic_analysis.yml | 2 ++ usegalaxy.org/metagenomic_analysis.yml.lock | 6 ++++++ usegalaxy.org/sam_bam.yml | 3 +++ usegalaxy.org/sam_bam.yml.lock | 6 ++++++ usegalaxy.org/variant_calling.yml | 2 ++ usegalaxy.org/variant_calling.yml.lock | 6 ++++++ 6 files changed, 25 insertions(+) diff --git a/usegalaxy.org/metagenomic_analysis.yml b/usegalaxy.org/metagenomic_analysis.yml index 784ca3fa..499c03e0 100644 --- a/usegalaxy.org/metagenomic_analysis.yml +++ b/usegalaxy.org/metagenomic_analysis.yml @@ -1,5 +1,7 @@ tool_panel_section_label: Metagenomic Analysis tools: +- name: krakentools_extract_kraken_reads + owner: iuc - name: kraken2 owner: iuc - name: diamond diff --git a/usegalaxy.org/metagenomic_analysis.yml.lock b/usegalaxy.org/metagenomic_analysis.yml.lock index 2945ba18..4f372e33 100644 --- a/usegalaxy.org/metagenomic_analysis.yml.lock +++ b/usegalaxy.org/metagenomic_analysis.yml.lock @@ -3,6 +3,12 @@ install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Metagenomic Analysis tools: +- name: krakentools_extract_kraken_reads + owner: iuc + revisions: + - f329328da134 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis - name: kraken2 owner: iuc revisions: diff --git a/usegalaxy.org/sam_bam.yml b/usegalaxy.org/sam_bam.yml index 4fdab5ee..b2c11a02 100644 --- a/usegalaxy.org/sam_bam.yml +++ b/usegalaxy.org/sam_bam.yml @@ -1,5 +1,8 @@ tool_panel_section_label: SAM/BAM tools: + +- name: samtools_coverage + owner: iuc - name: samtools_sort owner: devteam - name: samtools_mpileup diff --git a/usegalaxy.org/sam_bam.yml.lock b/usegalaxy.org/sam_bam.yml.lock index af7fadd4..a4d8333a 100644 --- a/usegalaxy.org/sam_bam.yml.lock +++ b/usegalaxy.org/sam_bam.yml.lock @@ -3,6 +3,12 @@ install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: SAM/BAM tools: +- name: samtools_coverage + owner: iuc + revisions: + - c4ff13d2aab3 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM - name: samtools_sort owner: devteam revisions: diff --git a/usegalaxy.org/variant_calling.yml b/usegalaxy.org/variant_calling.yml index b5fe4853..d3adb8d8 100644 --- a/usegalaxy.org/variant_calling.yml +++ b/usegalaxy.org/variant_calling.yml @@ -1,5 +1,7 @@ tool_panel_section_label: Variant Calling tools: +- name: clair3 + owner: iuc - name: snpfreqplot owner: iuc - name: varscan_version_2 diff --git a/usegalaxy.org/variant_calling.yml.lock b/usegalaxy.org/variant_calling.yml.lock index 33d58b7a..cf05dde5 100644 --- a/usegalaxy.org/variant_calling.yml.lock +++ b/usegalaxy.org/variant_calling.yml.lock @@ -3,6 +3,12 @@ install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Variant Calling tools: +- name: clair3 + owner: iuc + revisions: + - 63e02ef6e153 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling - name: snpfreqplot owner: iuc revisions: From 6707f73bbb9a8252417cff8469f84c1f009bb893 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 19 Jun 2024 13:14:42 +0200 Subject: [PATCH 2/2] updating fastp --- usegalaxy.org/fasta_fastq.yml.lock | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/usegalaxy.org/fasta_fastq.yml.lock b/usegalaxy.org/fasta_fastq.yml.lock index 8bf67c02..1cc1b18d 100644 --- a/usegalaxy.org/fasta_fastq.yml.lock +++ b/usegalaxy.org/fasta_fastq.yml.lock @@ -42,7 +42,12 @@ tools: owner: iuc revisions: - 1d8fe9bc4cb0 + - 3e2551a37201 + - 415fd81b85d3 - 65b93b623c77 + - 6c2351178f8d + - 988729b728f0 + - a935cbdf1c0e - c59d48774d03 - dbf9c561ef29 tool_panel_section_id: fasta_fastq