From a2a9f722aa60896c8d22339bebe15b46df4aa348 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 13 Feb 2026 12:23:32 +0100 Subject: [PATCH 1/5] add initial state of regalaxy tool installations --- .../assembly_annotation_tools.yml | 4 + .../assembly_annotation_tools.yml.lock | 9 ++ repeatexplorer-elixir.cerit-sc.cz/bed.yml | 6 + .../bed.yml.lock | 15 ++ repeatexplorer-elixir.cerit-sc.cz/dante.yml | 4 + .../dante.yml.lock | 12 ++ .../dante_ltr.yml | 4 + .../dante_ltr.yml.lock | 12 ++ .../dante_tir.yml | 4 + .../dante_tir.yml.lock | 8 ++ .../fasta_fastq_manipulation.yml | 38 ++++++ .../fasta_fastq_manipulation.yml.lock | 128 ++++++++++++++++++ .../genomic_file_utilities.yml | 4 + .../genomic_file_utilities.yml.lock | 8 ++ .../get_data.yml | 4 + .../get_data.yml.lock | 8 ++ repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml | 4 + .../jbrowse.yml.lock | 8 ++ .../ngs__qc_and_manipulation.yml | 26 ++++ .../ngs__qc_and_manipulation.yml.lock | 85 ++++++++++++ .../repeatexplorer.yml | 4 + .../repeatexplorer.yml.lock | 13 ++ .../repeatexplorer_utilities.yml | 6 + .../repeatexplorer_utilities.yml.lock | 15 ++ .../text_manipulation.yml | 4 + .../text_manipulation.yml.lock | 8 ++ .../tidecluster.yml | 4 + .../tidecluster.yml.lock | 11 ++ .../visualisation.yml | 16 +++ .../visualisation.yml.lock | 50 +++++++ 30 files changed, 522 insertions(+) create mode 100644 repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/bed.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/dante.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/get_data.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml.lock create mode 100644 repeatexplorer-elixir.cerit-sc.cz/visualisation.yml create mode 100644 repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock diff --git a/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml b/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml new file mode 100644 index 0000000..62016fe --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Assembly annotation tools +tools: +- name: repeat_annotation_pipeline3 + owner: petr-novak diff --git a/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock new file mode 100644 index 0000000..f19d657 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock @@ -0,0 +1,9 @@ +tools: +- name: repeat_annotation_pipeline3 + owner: petr-novak + revisions: + - 5366d5ea04bc + - 755a4d643184 + tool_panel_section_id: assembly_annotation_tools + tool_panel_section_label: Assembly annotation tools + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/bed.yml b/repeatexplorer-elixir.cerit-sc.cz/bed.yml new file mode 100644 index 0000000..8a8058e --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/bed.yml @@ -0,0 +1,6 @@ +tool_panel_section_label: BED +tools: +- name: gffread + owner: devteam +- name: bedtools + owner: iuc diff --git a/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock new file mode 100644 index 0000000..71c404e --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock @@ -0,0 +1,15 @@ +tools: +- name: gffread + owner: devteam + revisions: + - 3e436657dcd0 + tool_panel_section_id: bed + tool_panel_section_label: BED + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bedtools + owner: iuc + revisions: + - a1a923cd89e8 + tool_panel_section_id: bed + tool_panel_section_label: BED + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante.yml b/repeatexplorer-elixir.cerit-sc.cz/dante.yml new file mode 100644 index 0000000..1de29ed --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/dante.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: DANTE +tools: +- name: dante + owner: petr-novak diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock new file mode 100644 index 0000000..6992bcf --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock @@ -0,0 +1,12 @@ +tools: +- name: dante + owner: petr-novak + revisions: + - f0663cdbae66 + - 8f2bd3cae2de + - a9d7ebf988f9 + - 5210db15a5fa + - 726b8447eb09 + tool_panel_section_id: dante + tool_panel_section_label: DANTE + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml b/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml new file mode 100644 index 0000000..65ab988 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: DANTE_LTR +tools: +- name: dante_ltr + owner: petr-novak diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock new file mode 100644 index 0000000..4ba423f --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock @@ -0,0 +1,12 @@ +tools: +- name: dante_ltr + owner: petr-novak + revisions: + - e61f06df42b9 + - 27e5f58763f2 + - 08b5e23859ed + - d5508ce50c49 + - 8224e3d7b03a + tool_panel_section_id: dante_ltr + tool_panel_section_label: DANTE_LTR + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml b/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml new file mode 100644 index 0000000..19c6e68 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: DANTE_TIR +tools: +- name: dante_tir + owner: petr-novak diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock new file mode 100644 index 0000000..fbed942 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock @@ -0,0 +1,8 @@ +tools: +- name: dante_tir + owner: petr-novak + revisions: + - ce4d06c72092 + tool_panel_section_id: dante_tir + tool_panel_section_label: DANTE_TIR + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml b/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml new file mode 100644 index 0000000..90260d4 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml @@ -0,0 +1,38 @@ +tool_panel_section_label: FASTA/FASTQ manipulation +tools: +- name: fasta_compute_length + owner: devteam +- name: fasta_to_tabular + owner: devteam +- name: fasta_formatter + owner: devteam +- name: fastx_reverse_complement + owner: devteam +- name: fastx_trimmer + owner: devteam +- name: fastx_renamer + owner: devteam +- name: tabular_to_fasta + owner: devteam +- name: tabular_to_fastq + owner: devteam +- name: fastq_to_tabular + owner: devteam +- name: fastqtofasta + owner: devteam +- name: fastq_paired_end_deinterlacer + owner: devteam +- name: fastq_paired_end_interlacer + owner: devteam +- name: fasta_filter_by_length + owner: devteam +- name: ucsc_fasplit + owner: iuc +- name: trimmomatic + owner: pjbriggs +- name: trim_galore + owner: bgruening +- name: seqkit_stats + owner: iuc +- name: seqtk + owner: iuc diff --git a/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock new file mode 100644 index 0000000..740eaee --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock @@ -0,0 +1,128 @@ +tools: +- name: fasta_compute_length + owner: devteam + revisions: + - 7d37cfda8e00 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_to_tabular + owner: devteam + revisions: + - e7ed3c310b74 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_formatter + owner: devteam + revisions: + - 516b97a23d7e + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_reverse_complement + owner: devteam + revisions: + - 177f0621c266 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_trimmer + owner: devteam + revisions: + - 73194cdd4f57 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_renamer + owner: devteam + revisions: + - f984bb114520 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tabular_to_fasta + owner: devteam + revisions: + - 0a7799698fe5 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tabular_to_fastq + owner: devteam + revisions: + - 2dcfbbf9071a + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_to_tabular + owner: devteam + revisions: + - 4b347702c4aa + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastqtofasta + owner: devteam + revisions: + - 297962e79f39 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_deinterlacer + owner: devteam + revisions: + - f3936d0632cb + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_interlacer + owner: devteam + revisions: + - 2ccb8dcabddc + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_filter_by_length + owner: devteam + revisions: + - 8cacfcf96a52 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ucsc_fasplit + owner: iuc + revisions: + - bf04bd405d5b + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: trimmomatic + owner: pjbriggs + revisions: + - b9aaed85cbd1 + - 32f1f56bd970 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: trim_galore + owner: bgruening + revisions: + - cd7e644cae1d + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqkit_stats + owner: iuc + revisions: + - 54a954ee64d4 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqtk + owner: iuc + revisions: + - 4b494533146a + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml b/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml new file mode 100644 index 0000000..c94eb5a --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Genomic file utilities +tools: +- name: various_galaxy_tools + owner: petr-novak diff --git a/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock new file mode 100644 index 0000000..1f00ab2 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock @@ -0,0 +1,8 @@ +tools: +- name: various_galaxy_tools + owner: petr-novak + revisions: + - 1069776f7ae2 + tool_panel_section_id: genomic_file_utilities + tool_panel_section_label: Genomic file utilities + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/get_data.yml b/repeatexplorer-elixir.cerit-sc.cz/get_data.yml new file mode 100644 index 0000000..0780992 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/get_data.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Get Data +tools: +- name: ncbi_datasets + owner: iuc diff --git a/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock new file mode 100644 index 0000000..7e7806a --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock @@ -0,0 +1,8 @@ +tools: +- name: ncbi_datasets + owner: iuc + revisions: + - 198c75abbf55 + tool_panel_section_id: getext + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml b/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml new file mode 100644 index 0000000..417b44c --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Jbrowse +tools: +- name: jbrowse + owner: iuc diff --git a/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock new file mode 100644 index 0000000..7a800f2 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock @@ -0,0 +1,8 @@ +tools: +- name: jbrowse + owner: iuc + revisions: + - a6e57ff585c0 + tool_panel_section_id: jbrowse + tool_panel_section_label: Jbrowse + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml b/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml new file mode 100644 index 0000000..c6a5879 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml @@ -0,0 +1,26 @@ +tool_panel_section_label: 'NGS: QC and manipulation' +tools: +- name: fastqc + owner: devteam +- name: fastq_groomer + owner: devteam +- name: fastq_paired_end_splitter + owner: devteam +- name: fastq_stats + owner: devteam +- name: fastx_barcode_splitter + owner: devteam +- name: fastx_artifacts_filter + owner: devteam +- name: fastx_nucleotides_distribution + owner: devteam +- name: fastx_quality_statistics + owner: devteam +- name: fastq_quality_boxplot + owner: devteam +- name: fastq_quality_converter + owner: devteam +- name: fastq_quality_filter + owner: devteam +- name: multiqc + owner: iuc diff --git a/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock new file mode 100644 index 0000000..4fca8e5 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock @@ -0,0 +1,85 @@ +tools: +- name: fastqc + owner: devteam + revisions: + - 5ec9f6bceaee + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_groomer + owner: devteam + revisions: + - 47e5dbc3e790 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_splitter + owner: devteam + revisions: + - e39cc71d3ed6 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_stats + owner: devteam + revisions: + - f0e7deab6518 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_barcode_splitter + owner: devteam + revisions: + - 0b7ec11b3c7c + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_artifacts_filter + owner: devteam + revisions: + - 529bccd5e4a1 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_nucleotides_distribution + owner: devteam + revisions: + - b6b54ba71bd8 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_quality_statistics + owner: devteam + revisions: + - cc0fd298cc17 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_boxplot + owner: devteam + revisions: + - 867ab348287d + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_converter + owner: devteam + revisions: + - 045f0e1043f7 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_filter + owner: devteam + revisions: + - 64e9a6afdd0c + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: multiqc + owner: iuc + revisions: + - abfd8a6544d7 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml new file mode 100644 index 0000000..3691531 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: RepeatExplorer +tools: +- name: repeatexplorer2_testing + owner: petr-novak diff --git a/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml.lock new file mode 100644 index 0000000..066157a --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml.lock @@ -0,0 +1,13 @@ +tools: +- name: repeatexplorer2_testing + owner: petr-novak + revisions: + - a27646c27090 + - 3d0ba5734776 + - 792914356c37 + - 4308d3e572ee + - 5cca2c9aa4ad + - 20ef42e81eeb + tool_panel_section_id: repeatexplorer + tool_panel_section_label: RepeatExplorer + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml new file mode 100644 index 0000000..78fe0fc --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml @@ -0,0 +1,6 @@ +tool_panel_section_label: RepeatExplorer utilities +tools: +- name: re_utils + owner: petr-novak +- name: long_reads_sampling + owner: petr-novak diff --git a/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml.lock new file mode 100644 index 0000000..e52e5c8 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml.lock @@ -0,0 +1,15 @@ +tools: +- name: re_utils + owner: petr-novak + revisions: + - 91996b991991 + tool_panel_section_id: repeatexplorer_utilities + tool_panel_section_label: RepeatExplorer utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: long_reads_sampling + owner: petr-novak + revisions: + - 060fc04af21c + tool_panel_section_id: repeatexplorer_utilities + tool_panel_section_label: RepeatExplorer utilities + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml b/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml new file mode 100644 index 0000000..f3db33f --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Text manipulation +tools: +- name: text_processing + owner: bgruening diff --git a/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock new file mode 100644 index 0000000..a6de32c --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock @@ -0,0 +1,8 @@ +tools: +- name: text_processing + owner: bgruening + revisions: + - d698c222f354 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text manipulation + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml b/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml new file mode 100644 index 0000000..ee081a1 --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: TideCluster +tools: +- name: tidecluster + owner: petr-novak diff --git a/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml.lock new file mode 100644 index 0000000..a0f42fd --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml.lock @@ -0,0 +1,11 @@ +tools: +- name: tidecluster + owner: petr-novak + revisions: + - 30a8a954dd93 + - 440796be7576 + - 971dbc97e607 + - a0f57cfa1bb7 + tool_panel_section_id: tidecluster + tool_panel_section_label: TideCluster + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml b/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml new file mode 100644 index 0000000..7f77f2c --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml @@ -0,0 +1,16 @@ +tool_panel_section_label: Visualisation +tools: +- name: krona_text + owner: petr-novak +- name: histogram + owner: devteam +- name: ggplot2_point + owner: iuc +- name: ggplot2_histogram + owner: iuc +- name: ggplot2_violin + owner: iuc +- name: ggplot2_pca + owner: iuc +- name: ggplot2_heatmap + owner: iuc diff --git a/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock new file mode 100644 index 0000000..1cba60b --- /dev/null +++ b/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock @@ -0,0 +1,50 @@ +tools: +- name: krona_text + owner: petr-novak + revisions: + - 04021cfd5170 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: histogram + owner: devteam + revisions: + - 6f134426c2b0 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_point + owner: iuc + revisions: + - 3b12bf9b4b87 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_histogram + owner: iuc + revisions: + - b0d96516e6a5 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_violin + owner: iuc + revisions: + - 0e7290688b50 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_pca + owner: iuc + revisions: + - b1268b7544d3 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_heatmap + owner: iuc + revisions: + - 10515715c940 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu From 88480935448d29c45d4e797a96ea75268c67e33e Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 13 Feb 2026 12:25:39 +0100 Subject: [PATCH 2/5] mts is the default, no need to dupe --- .../assembly_annotation_tools.yml.lock | 4 +- .../bed.yml.lock | 5 +- .../dante.yml.lock | 10 ++-- .../dante_ltr.yml.lock | 10 ++-- .../dante_tir.yml.lock | 4 +- .../fasta_fastq_manipulation.yml.lock | 59 +++++++------------ .../genomic_file_utilities.yml.lock | 4 +- .../get_data.yml.lock | 6 +- .../jbrowse.yml.lock | 4 +- .../ngs__qc_and_manipulation.yml.lock | 39 +++++------- .../repeatexplorer.yml.lock | 10 ++-- .../repeatexplorer_utilities.yml.lock | 5 +- .../text_manipulation.yml.lock | 4 +- .../tidecluster.yml.lock | 4 +- .../visualisation.yml.lock | 10 +--- 15 files changed, 86 insertions(+), 92 deletions(-) diff --git a/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock index f19d657..4571a5e 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: repeat_annotation_pipeline3 owner: petr-novak @@ -6,4 +9,3 @@ tools: - 755a4d643184 tool_panel_section_id: assembly_annotation_tools tool_panel_section_label: Assembly annotation tools - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock index 71c404e..93b1930 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: gffread owner: devteam @@ -5,11 +8,9 @@ tools: - 3e436657dcd0 tool_panel_section_id: bed tool_panel_section_label: BED - tool_shed_url: toolshed.g2.bx.psu.edu - name: bedtools owner: iuc revisions: - a1a923cd89e8 tool_panel_section_id: bed tool_panel_section_label: BED - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock index 6992bcf..02e061d 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock @@ -1,12 +1,14 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: dante owner: petr-novak revisions: - - f0663cdbae66 - - 8f2bd3cae2de - - a9d7ebf988f9 - 5210db15a5fa - 726b8447eb09 + - 8f2bd3cae2de + - a9d7ebf988f9 + - f0663cdbae66 tool_panel_section_id: dante tool_panel_section_label: DANTE - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock index 4ba423f..e8f933d 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock @@ -1,12 +1,14 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: dante_ltr owner: petr-novak revisions: - - e61f06df42b9 - - 27e5f58763f2 - 08b5e23859ed - - d5508ce50c49 + - 27e5f58763f2 - 8224e3d7b03a + - d5508ce50c49 + - e61f06df42b9 tool_panel_section_id: dante_ltr tool_panel_section_label: DANTE_LTR - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock index fbed942..f7597fe 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: dante_tir owner: petr-novak @@ -5,4 +8,3 @@ tools: - ce4d06c72092 tool_panel_section_id: dante_tir tool_panel_section_label: DANTE_TIR - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock index 740eaee..f47dc5c 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock @@ -1,128 +1,113 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: fasta_compute_length owner: devteam revisions: - 7d37cfda8e00 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_to_tabular owner: devteam revisions: - e7ed3c310b74 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - 516b97a23d7e - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - 177f0621c266 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - 73194cdd4f57 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - f984bb114520 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta owner: devteam revisions: - 0a7799698fe5 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - 2dcfbbf9071a - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - 4b347702c4aa - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: - 297962e79f39 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - f3936d0632cb - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - 2ccb8dcabddc - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_filter_by_length owner: devteam revisions: - 8cacfcf96a52 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - bf04bd405d5b - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic owner: pjbriggs revisions: - - b9aaed85cbd1 - 32f1f56bd970 - tool_panel_section_id: fasta/fastq_manipulation + - b9aaed85cbd1 + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - cd7e644cae1d - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - 54a954ee64d4 - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - 4b494533146a - tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock index 1f00ab2..ff81cb7 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: various_galaxy_tools owner: petr-novak @@ -5,4 +8,3 @@ tools: - 1069776f7ae2 tool_panel_section_id: genomic_file_utilities tool_panel_section_label: Genomic file utilities - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock index 7e7806a..805e6f3 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock @@ -1,8 +1,10 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: ncbi_datasets owner: iuc revisions: - 198c75abbf55 - tool_panel_section_id: getext + tool_panel_section_id: get_data tool_panel_section_label: Get Data - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock index 7a800f2..85e837f 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: jbrowse owner: iuc @@ -5,4 +8,3 @@ tools: - a6e57ff585c0 tool_panel_section_id: jbrowse tool_panel_section_label: Jbrowse - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock index 4fca8e5..d2350b1 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock @@ -1,85 +1,76 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: fastqc owner: devteam revisions: - 5ec9f6bceaee - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - 47e5dbc3e790 - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - e39cc71d3ed6 - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - f0e7deab6518 - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - 0b7ec11b3c7c - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - 529bccd5e4a1 - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - b6b54ba71bd8 - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - cc0fd298cc17 - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_boxplot owner: devteam revisions: - 867ab348287d - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - 045f0e1043f7 - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_filter owner: devteam revisions: - 64e9a6afdd0c - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - abfd8a6544d7 - tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml.lock index 066157a..0d76ed8 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer.yml.lock @@ -1,13 +1,15 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: repeatexplorer2_testing owner: petr-novak revisions: - - a27646c27090 + - 20ef42e81eeb - 3d0ba5734776 - - 792914356c37 - 4308d3e572ee - 5cca2c9aa4ad - - 20ef42e81eeb + - 792914356c37 + - a27646c27090 tool_panel_section_id: repeatexplorer tool_panel_section_label: RepeatExplorer - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml.lock index e52e5c8..e438346 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/repeatexplorer_utilities.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: re_utils owner: petr-novak @@ -5,11 +8,9 @@ tools: - 91996b991991 tool_panel_section_id: repeatexplorer_utilities tool_panel_section_label: RepeatExplorer utilities - tool_shed_url: toolshed.g2.bx.psu.edu - name: long_reads_sampling owner: petr-novak revisions: - 060fc04af21c tool_panel_section_id: repeatexplorer_utilities tool_panel_section_label: RepeatExplorer utilities - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock index a6de32c..c562c63 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: text_processing owner: bgruening @@ -5,4 +8,3 @@ tools: - d698c222f354 tool_panel_section_id: text_manipulation tool_panel_section_label: Text manipulation - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml.lock index a0f42fd..1a713a9 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/tidecluster.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: tidecluster owner: petr-novak @@ -8,4 +11,3 @@ tools: - a0f57cfa1bb7 tool_panel_section_id: tidecluster tool_panel_section_label: TideCluster - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock index 1cba60b..22123d9 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock @@ -1,3 +1,6 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false tools: - name: krona_text owner: petr-novak @@ -5,46 +8,39 @@ tools: - 04021cfd5170 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram owner: devteam revisions: - 6f134426c2b0 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - 3b12bf9b4b87 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - b0d96516e6a5 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - 0e7290688b50 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca owner: iuc revisions: - b1268b7544d3 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - 10515715c940 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - tool_shed_url: toolshed.g2.bx.psu.edu From 9a49803dd9268bac657428590cd206c34a86593b Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 13 Feb 2026 13:10:34 +0100 Subject: [PATCH 3/5] fix makefile installation script --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 2aee74b..4b3609a 100644 --- a/Makefile +++ b/Makefile @@ -25,6 +25,6 @@ update-all: ## Run the update script for all repos find ./$(INSTANCE) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P $(NPROC) python scripts/update_tool.py install: ## Run the Ephemeris command to install all repos and revisions that are missing from a given INSTANCE - find ./$(INSTANCE) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 1 -I {} shed-tools install --toolsfile {} --galaxy $(INSTANCE) --api_key $(GALAXY_API_KEY) --skip_install_resolver_dependencies + find ./$(INSTANCE) -name '*.yml.lock' | grep '^\./[^/]*/' | xargs -n 1 -P 1 -I {} shed-tools install --toolsfile {} --galaxy $(INSTANCE) --api_key $(GALAXY_API_KEY) --skip_install_resolver_dependencies .PHONY: fix lint help update-owner update-all install From e41615532f4e76b29b0867db2c0dde40ab7aaf43 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 13 Feb 2026 13:10:42 +0100 Subject: [PATCH 4/5] update all tools on regalaxy --- repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock | 1 + .../fasta_fastq_manipulation.yml.lock | 14 ++++++++++++++ .../get_data.yml.lock | 1 + .../ngs__qc_and_manipulation.yml.lock | 12 ++++++++++++ .../text_manipulation.yml.lock | 1 + .../visualisation.yml.lock | 6 ++++++ 6 files changed, 35 insertions(+) diff --git a/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock index 93b1930..cc0c156 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock @@ -11,6 +11,7 @@ tools: - name: bedtools owner: iuc revisions: + - 2892111d91f8 - a1a923cd89e8 tool_panel_section_id: bed tool_panel_section_label: BED diff --git a/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock index f47dc5c..d975448 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock @@ -5,6 +5,7 @@ tools: - name: fasta_compute_length owner: devteam revisions: + - 5cbde03c1103 - 7d37cfda8e00 tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation @@ -18,23 +19,27 @@ tools: owner: devteam revisions: - 516b97a23d7e + - e773f1eb16cf tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - name: fastx_reverse_complement owner: devteam revisions: - 177f0621c266 + - 7566b751e769 tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - name: fastx_trimmer owner: devteam revisions: + - 1ea2ae5afb28 - 73194cdd4f57 tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - name: fastx_renamer owner: devteam revisions: + - 0ffae348abae - f984bb114520 tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation @@ -48,11 +53,13 @@ tools: owner: devteam revisions: - 2dcfbbf9071a + - 78fb18899c99 tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - name: fastq_to_tabular owner: devteam revisions: + - 43807a65369f - 4b347702c4aa tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation @@ -60,11 +67,13 @@ tools: owner: devteam revisions: - 297962e79f39 + - 4a3e93647a4e tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - name: fastq_paired_end_deinterlacer owner: devteam revisions: + - c48cf4699be7 - f3936d0632cb tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation @@ -72,6 +81,7 @@ tools: owner: devteam revisions: - 2ccb8dcabddc + - acb5090e281f tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - name: fasta_filter_by_length @@ -83,6 +93,7 @@ tools: - name: ucsc_fasplit owner: iuc revisions: + - 1add611a6018 - bf04bd405d5b tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation @@ -96,12 +107,14 @@ tools: - name: trim_galore owner: bgruening revisions: + - b94789823aad - cd7e644cae1d tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation - name: seqkit_stats owner: iuc revisions: + - 24107542edff - 54a954ee64d4 tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation @@ -109,5 +122,6 @@ tools: owner: iuc revisions: - 4b494533146a + - 8511b6d85fc7 tool_panel_section_id: fasta_fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation diff --git a/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock index 805e6f3..984667a 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock @@ -6,5 +6,6 @@ tools: owner: iuc revisions: - 198c75abbf55 + - bc18e25d4204 tool_panel_section_id: get_data tool_panel_section_label: Get Data diff --git a/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock index d2350b1..60fcfb1 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/ngs__qc_and_manipulation.yml.lock @@ -5,18 +5,21 @@ tools: - name: fastqc owner: devteam revisions: + - 2c64fded1286 - 5ec9f6bceaee tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: fastq_groomer owner: devteam revisions: + - 10d4df6a9d94 - 47e5dbc3e790 tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: fastq_paired_end_splitter owner: devteam revisions: + - 7fafac615aa1 - e39cc71d3ed6 tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' @@ -24,35 +27,41 @@ tools: owner: devteam revisions: - f0e7deab6518 + - f86c27295151 tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: fastx_barcode_splitter owner: devteam revisions: - 0b7ec11b3c7c + - 229caeddb2df tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: fastx_artifacts_filter owner: devteam revisions: + - 34edfa69c149 - 529bccd5e4a1 tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: fastx_nucleotides_distribution owner: devteam revisions: + - 751878fa37e5 - b6b54ba71bd8 tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: fastx_quality_statistics owner: devteam revisions: + - 48c943a0290a - cc0fd298cc17 tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: fastq_quality_boxplot owner: devteam revisions: + - 47df89f900a4 - 867ab348287d tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' @@ -60,17 +69,20 @@ tools: owner: devteam revisions: - 045f0e1043f7 + - 86713dc416ec tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: fastq_quality_filter owner: devteam revisions: - 64e9a6afdd0c + - b1e332a385f1 tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' - name: multiqc owner: iuc revisions: + - 26ee5e11ecbe - abfd8a6544d7 tool_panel_section_id: ngs__qc_and_manipulation tool_panel_section_label: 'NGS: QC and manipulation' diff --git a/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock index c562c63..0d87cce 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/text_manipulation.yml.lock @@ -5,6 +5,7 @@ tools: - name: text_processing owner: bgruening revisions: + - ab83aa685821 - d698c222f354 tool_panel_section_id: text_manipulation tool_panel_section_label: Text manipulation diff --git a/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock b/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock index 22123d9..d1f3366 100644 --- a/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock +++ b/repeatexplorer-elixir.cerit-sc.cz/visualisation.yml.lock @@ -12,17 +12,20 @@ tools: owner: devteam revisions: - 6f134426c2b0 + - d0b9dd19e919 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - name: ggplot2_point owner: iuc revisions: - 3b12bf9b4b87 + - f87634b12749 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - name: ggplot2_histogram owner: iuc revisions: + - 6b9816a913de - b0d96516e6a5 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation @@ -30,11 +33,13 @@ tools: owner: iuc revisions: - 0e7290688b50 + - 63d211052ffb tool_panel_section_id: visualisation tool_panel_section_label: Visualisation - name: ggplot2_pca owner: iuc revisions: + - 1df3b30325dd - b1268b7544d3 tool_panel_section_id: visualisation tool_panel_section_label: Visualisation @@ -42,5 +47,6 @@ tools: owner: iuc revisions: - 10515715c940 + - 15cebddc6dba tool_panel_section_id: visualisation tool_panel_section_label: Visualisation From b862e20a7d8097b063d3a825a13897a5610434bb Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 13 Feb 2026 13:15:08 +0100 Subject: [PATCH 5/5] bring regalaxy to CI --- .github/workflows/cron_update.yml | 2 +- .github/workflows/dispatch_lint.yml | 1 + .github/workflows/dispatch_update.yml | 1 + .github/workflows/fix.yml | 2 ++ .github/workflows/lint.yml | 1 + 5 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/cron_update.yml b/.github/workflows/cron_update.yml index 48429a9..0283cde 100644 --- a/.github/workflows/cron_update.yml +++ b/.github/workflows/cron_update.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - instance: [usegalaxy.cz, galaxy-umsa.grid.cesnet.cz] + instance: [usegalaxy.cz, galaxy-umsa.grid.cesnet.cz, repeatexplorer-elixir.cerit-sc.cz] python-version: [3.11] steps: - uses: actions/checkout@v4 diff --git a/.github/workflows/dispatch_lint.yml b/.github/workflows/dispatch_lint.yml index ccca7ee..df3a047 100644 --- a/.github/workflows/dispatch_lint.yml +++ b/.github/workflows/dispatch_lint.yml @@ -11,6 +11,7 @@ on: - galaxy-qa1.galaxy.cloud.e-infra.cz - usegalaxy.cz - galaxy-umsa.grid.cesnet.cz + - repeatexplorer-elixir.cerit-sc.cz jobs: build: diff --git a/.github/workflows/dispatch_update.yml b/.github/workflows/dispatch_update.yml index 6aa58c6..492e320 100644 --- a/.github/workflows/dispatch_update.yml +++ b/.github/workflows/dispatch_update.yml @@ -15,6 +15,7 @@ on: - galaxy-qa1.galaxy.cloud.e-infra.cz - usegalaxy.cz - galaxy-umsa.grid.cesnet.cz + - repeatexplorer-elixir.cerit-sc.cz permissions: contents: write diff --git a/.github/workflows/fix.yml b/.github/workflows/fix.yml index d1032b7..c55db0d 100644 --- a/.github/workflows/fix.yml +++ b/.github/workflows/fix.yml @@ -35,6 +35,8 @@ jobs: make INSTANCE=usegalaxy.cz fix make INSTANCE=galaxy-umsa.grid.cesnet.cz lint make INSTANCE=galaxy-umsa.grid.cesnet.cz fix + make INSTANCE=repeatexplorer-elixir.cerit-sc.cz lint + make INSTANCE=repeatexplorer-elixir.cerit-sc.cz fix - name: Create Pull Request uses: peter-evans/create-pull-request@v7 with: diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 111febe..4036835 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -32,3 +32,4 @@ jobs: make INSTANCE=galaxy-qa1.galaxy.cloud.e-infra.cz lint make INSTANCE=usegalaxy.cz lint make INSTANCE=galaxy-umsa.grid.cesnet.cz lint + make INSTANCE=repeatexplorer-elixir.cerit-sc.cz lint