automate regalaxy toolset management

.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

.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:

.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

.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:

.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

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

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

repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock

@@ -0,0 +1,11 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+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

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

repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock

@@ -0,0 +1,17 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: gffread
+  owner: devteam
+  revisions:
+  - 3e436657dcd0
+  tool_panel_section_id: bed
+  tool_panel_section_label: BED
+- name: bedtools
+  owner: iuc
+  revisions:
+  - 2892111d91f8
+  - a1a923cd89e8
+  tool_panel_section_id: bed
+  tool_panel_section_label: BED

repeatexplorer-elixir.cerit-sc.cz/dante.yml

@@ -0,0 +1,4 @@
+tool_panel_section_label: DANTE
+tools:
+- name: dante
+  owner: petr-novak

repeatexplorer-elixir.cerit-sc.cz/dante.yml.lock

@@ -0,0 +1,14 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: dante
+  owner: petr-novak
+  revisions:
+  - 5210db15a5fa
+  - 726b8447eb09
+  - 8f2bd3cae2de
+  - a9d7ebf988f9
+  - f0663cdbae66
+  tool_panel_section_id: dante
+  tool_panel_section_label: DANTE

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

repeatexplorer-elixir.cerit-sc.cz/dante_ltr.yml.lock

@@ -0,0 +1,14 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: dante_ltr
+  owner: petr-novak
+  revisions:
+  - 08b5e23859ed
+  - 27e5f58763f2
+  - 8224e3d7b03a
+  - d5508ce50c49
+  - e61f06df42b9
+  tool_panel_section_id: dante_ltr
+  tool_panel_section_label: DANTE_LTR

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

repeatexplorer-elixir.cerit-sc.cz/dante_tir.yml.lock

@@ -0,0 +1,10 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: dante_tir
+  owner: petr-novak
+  revisions:
+  - ce4d06c72092
+  tool_panel_section_id: dante_tir
+  tool_panel_section_label: DANTE_TIR

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

repeatexplorer-elixir.cerit-sc.cz/fasta_fastq_manipulation.yml.lock

@@ -0,0 +1,127 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: fasta_compute_length
+  owner: devteam
+  revisions:
+  - 5cbde03c1103
+  - 7d37cfda8e00
+  tool_panel_section_id: fasta_fastq_manipulation
+  tool_panel_section_label: FASTA/FASTQ manipulation
+- name: fasta_to_tabular
+  owner: devteam
+  revisions:
+  - e7ed3c310b74
+  tool_panel_section_id: fasta_fastq_manipulation
+  tool_panel_section_label: FASTA/FASTQ manipulation
+- name: fasta_formatter
+  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
+- name: tabular_to_fasta
+  owner: devteam
+  revisions:
+  - 0a7799698fe5
+  tool_panel_section_id: fasta_fastq_manipulation
+  tool_panel_section_label: FASTA/FASTQ manipulation
+- name: tabular_to_fastq
+  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
+- name: fastqtofasta
+  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
+- name: fastq_paired_end_interlacer
+  owner: devteam
+  revisions:
+  - 2ccb8dcabddc
+  - acb5090e281f
+  tool_panel_section_id: fasta_fastq_manipulation
+  tool_panel_section_label: FASTA/FASTQ manipulation
+- name: fasta_filter_by_length
+  owner: devteam
+  revisions:
+  - 8cacfcf96a52
+  tool_panel_section_id: fasta_fastq_manipulation
+  tool_panel_section_label: FASTA/FASTQ manipulation
+- name: ucsc_fasplit
+  owner: iuc
+  revisions:
+  - 1add611a6018
+  - bf04bd405d5b
+  tool_panel_section_id: fasta_fastq_manipulation
+  tool_panel_section_label: FASTA/FASTQ manipulation
+- name: trimmomatic
+  owner: pjbriggs
+  revisions:
+  - 32f1f56bd970
+  - b9aaed85cbd1
+  tool_panel_section_id: fasta_fastq_manipulation
+  tool_panel_section_label: FASTA/FASTQ manipulation
+- 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
+- name: seqtk
+  owner: iuc
+  revisions:
+  - 4b494533146a
+  - 8511b6d85fc7
+  tool_panel_section_id: fasta_fastq_manipulation
+  tool_panel_section_label: FASTA/FASTQ manipulation

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

repeatexplorer-elixir.cerit-sc.cz/genomic_file_utilities.yml.lock

@@ -0,0 +1,10 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: various_galaxy_tools
+  owner: petr-novak
+  revisions:
+  - 1069776f7ae2
+  tool_panel_section_id: genomic_file_utilities
+  tool_panel_section_label: Genomic file utilities

repeatexplorer-elixir.cerit-sc.cz/get_data.yml

@@ -0,0 +1,4 @@
+tool_panel_section_label: Get Data
+tools:
+- name: ncbi_datasets
+  owner: iuc

repeatexplorer-elixir.cerit-sc.cz/get_data.yml.lock

@@ -0,0 +1,11 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: ncbi_datasets
+  owner: iuc
+  revisions:
+  - 198c75abbf55
+  - bc18e25d4204
+  tool_panel_section_id: get_data
+  tool_panel_section_label: Get Data

repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml

@@ -0,0 +1,4 @@
+tool_panel_section_label: Jbrowse
+tools:
+- name: jbrowse
+  owner: iuc

repeatexplorer-elixir.cerit-sc.cz/jbrowse.yml.lock

@@ -0,0 +1,10 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: jbrowse
+  owner: iuc
+  revisions:
+  - a6e57ff585c0
+  tool_panel_section_id: jbrowse
+  tool_panel_section_label: Jbrowse

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