Initial configurations for riboseq

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
   # <cache_dir>.
-  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.

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"

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']
 }