From f9f12751ea19c6699e87d2e1205edd8520e93076 Mon Sep 17 00:00:00 2001 From: codemeleon Date: Mon, 17 Jun 2024 17:26:34 +0100 Subject: [PATCH] Initial configurations for riboseq --- group_vars/gxconfig.yml | 82 +++++++++---------- group_vars/sn06.yml | 7 +- .../galaxy/config/global_host_filters.py.j2 | 1 + 3 files changed, 45 insertions(+), 45 deletions(-) diff --git a/group_vars/gxconfig.yml b/group_vars/gxconfig.yml index 7c2dc94e7..99685a93d 100644 --- a/group_vars/gxconfig.yml +++ b/group_vars/gxconfig.yml @@ -338,7 +338,7 @@ base_app_main: &BASE_APP_MAIN # external tooling. # The value of this option will be resolved with respect to # . - short_term_storage_dir: '/data/jwd04/short_term_web_storage' + short_term_storage_dir: "/data/jwd04/short_term_web_storage" # Default duration before short term web storage files will be cleaned # up by Galaxy tasks (in seconds). The default duration is 1 day. @@ -566,7 +566,7 @@ base_app_main: &BASE_APP_MAIN # Point Galaxy at a repository consisting of a copy of the bio.tools # database (e.g. https://github.com/bio-tools/content/) to resolve # bio.tools data for tool metadata. - biotools_content_directory: '/opt/galaxy/mutable-data/cache/biotools/content' + biotools_content_directory: "/opt/galaxy/mutable-data/cache/biotools/content" # Set this to true to attempt to resolve bio.tools metadata for tools # for tool not resovled via biotools_content_directory. @@ -991,45 +991,45 @@ base_app_main: &BASE_APP_MAIN # Append "{brand}" text to the masthead. brand_by_host: - 'usegalaxy.eu': Europe - 'assembly.usegalaxy.eu': Genome Assembly - 'nanopore': Nanopore - 'erasmusmc': ErasmusMC - 'climate.usegalaxy.eu': Climate - 'hicexplorer.usegalaxy.eu': HiCExplorer - 'annotation.usegalaxy.eu': Genome Annotation - 'metabolomics.usegalaxy.eu': Metabolomics - 'metagenomics.usegalaxy.eu': Metagenomics - 'microbiome.usegalaxy.eu': Microbiome - 'microgalaxy.usegalaxy.eu': microGalaxy - 'rna.usegalaxy.eu': RNA - 'graphclust.usegalaxy.eu': GraphClust - 'ecology.usegalaxy.eu': Ecology - 'proteomics.usegalaxy.eu': Proteomics - 'clipseq.usegalaxy.eu': CLIP-Explorer - 'cheminformatics.usegalaxy.eu': Cheminformatics - 'imaging.usegalaxy.eu': Imaging - 'test.usegalaxy.eu': Testing - 'beta.usegalaxy.eu': beta - 'streetscience.usegalaxy.eu': StreetScienceCommunity - 'singlecell.usegalaxy.eu': Single Cell Omics - 'humancellatlas.usegalaxy.eu': Human Cell Atlas - 'ml.usegalaxy.eu': Machine Learning - 'live.usegalaxy.eu': Live - 'plants.usegalaxy.eu': Plants - 'virology.usegalaxy.eu': Virology - 'lite.usegalaxy.eu': Lite - 'covid19.usegalaxy.eu': COVID-19 - 'africa.usegalaxy.eu': Africa - 'india.usegalaxy.eu': India - 'spatialomics.usegalaxy.eu': Spatial Omics - 'materials.usegalaxy.eu': Materials - 'phage.usegalaxy.eu': Phage - 'earth-system.usegalaxy.eu': Earth System - 'cancer.usegalaxy.eu': Cancer - 'aqua.usegalaxy.eu': Aqua - 'eirene.usegalaxy.eu': EIRENE - + "usegalaxy.eu": Europe + "assembly.usegalaxy.eu": Genome Assembly + "nanopore": Nanopore + "erasmusmc": ErasmusMC + "climate.usegalaxy.eu": Climate + "hicexplorer.usegalaxy.eu": HiCExplorer + "annotation.usegalaxy.eu": Genome Annotation + "metabolomics.usegalaxy.eu": Metabolomics + "metagenomics.usegalaxy.eu": Metagenomics + "microbiome.usegalaxy.eu": Microbiome + "microgalaxy.usegalaxy.eu": microGalaxy + "rna.usegalaxy.eu": RNA + "graphclust.usegalaxy.eu": GraphClust + "ecology.usegalaxy.eu": Ecology + "proteomics.usegalaxy.eu": Proteomics + "clipseq.usegalaxy.eu": CLIP-Explorer + "cheminformatics.usegalaxy.eu": Cheminformatics + "imaging.usegalaxy.eu": Imaging + "test.usegalaxy.eu": Testing + "beta.usegalaxy.eu": beta + "streetscience.usegalaxy.eu": StreetScienceCommunity + "singlecell.usegalaxy.eu": Single Cell Omics + "humancellatlas.usegalaxy.eu": Human Cell Atlas + "ml.usegalaxy.eu": Machine Learning + "live.usegalaxy.eu": Live + "plants.usegalaxy.eu": Plants + "virology.usegalaxy.eu": Virology + "lite.usegalaxy.eu": Lite + "covid19.usegalaxy.eu": COVID-19 + "africa.usegalaxy.eu": Africa + "india.usegalaxy.eu": India + "spatialomics.usegalaxy.eu": Spatial Omics + "materials.usegalaxy.eu": Materials + "phage.usegalaxy.eu": Phage + "earth-system.usegalaxy.eu": Earth System + "cancer.usegalaxy.eu": Cancer + "aqua.usegalaxy.eu": Aqua + "eirene.usegalaxy.eu": EIRENE + "riboseq.usegalaxy.eu": Ribo-seq # This option has been deprecated, use the `logo_src` instead to # change the default logo including the galaxy brand title. diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml index 58de5f569..681a16843 100644 --- a/group_vars/sn06.yml +++ b/group_vars/sn06.yml @@ -298,7 +298,6 @@ galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv galaxy_nonrepro_tools: "{{ galaxy_root }}/custom-tools" galaxy_nonrepro_commit: master - # Custom override # Our galaxy_tool_dependency_dir is on NFS, and permissions are set in such a # way that they cannot be changed by the ansible connected user. @@ -373,7 +372,7 @@ galaxy_themes_subdomains: - name: cancer - name: aqua - name: eirene - + - name: riboseq galaxy_config_file_src_dir: files/galaxy galaxy_config_files: @@ -465,5 +464,5 @@ galaxy_config_templates: dest: "{{ galaxy_config['galaxy']['object_store_config_file'] }}" - src: "{{ galaxy_config_file_src_dir }}/tpv/destinations.yml.j2" dest: "{{ tpv_mutable_dir }}/destinations.yml" - - src: '{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2' - dest: '{{ galaxy_config_dir }}/vault_conf.yml' + - src: "{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2" + dest: "{{ galaxy_config_dir }}/vault_conf.yml" diff --git a/templates/galaxy/config/global_host_filters.py.j2 b/templates/galaxy/config/global_host_filters.py.j2 index c92073eb4..4972466d8 100644 --- a/templates/galaxy/config/global_host_filters.py.j2 +++ b/templates/galaxy/config/global_host_filters.py.j2 @@ -145,6 +145,7 @@ DOMAIN_SECTIONS = { "biodiversity_data_exploration" ], 'eirene': ['chemicaltoolbox','metabolomics','interactivetools'] + 'riboseq': ['transcriptomics','rna_seq','ribo_seq','rna_analysis', 'gene_regulation','interactivetools'] }