Support singularity

galaxysrv.yml

@@ -27,6 +27,8 @@
   roles:
     - role: geerlingguy.docker
       when: not _molecule_active and _galaxy_jobs_docker
+    - role: usegalaxy_eu.apptainer
+      when: _galaxy_jobs_singularity
     - role: uusrc.general.nginx_reverse_proxy
       vars:
         nginx_reverse_proxy_locations: "{{ galaxy_nginx_vhost_config }}"

requirements.yml

@@ -11,6 +11,8 @@ roles:
     version: 1.2.0
   - src: geerlingguy.docker
     version: 6.1.0
+  - src: usegalaxy_eu.apptainer
+    version: 0.0.2
 
 collections:
   - name: community.general

templates/galaxy/config/job_conf.yml.j2

@@ -21,6 +21,32 @@ execution:
       docker_destination_id: docker_local
       default_destination_id: local
 
+    singularity:
+      singularity_volumes: "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$job_directory:rw,{{ galaxy_mutable_data_dir }}:rw"
+      runner: local_runner
+      singularity_enabled: true
+      container_resolvers:
+        - type: cached_explicit_singularity
+          cache_directory: "{{ galaxy_mutable_data_dir }}/cache/singularity/explicit/"
+        - type: cached_mulled_singularity
+          cache_directory: "{{ galaxy_mutable_data_dir }}/cache/singularity/mulled/"
+        - type: mulled_singularity
+          auto_install: False
+          cache_directory: "{{ galaxy_mutable_data_dir }}/cache/singularity/mulled/"
+        - type: build_mulled_singularity
+          auto_install: False
+          cache_directory: "{{ galaxy_mutable_data_dir }}/cache/singularity/built/"
+      env:
+        # Ensuring a consistent collation environment is good for reproducibility.
+        - name: LC_ALL
+          value: C
+        # The cache directory holds the docker containers that get converted
+        - name: APPTAINER_CACHEDIR
+          value: /tmp/singularity
+        # Apptainer uses a temporary directory to build the squashfs filesystem
+        - name: APPTAINER_TMPDIR
+          value: /tmp
+
 tools:
   - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
     environment: local_env

vars/src_galaxy_vars.yml

@@ -12,8 +12,8 @@ _galaxy_custom_repo_branch: "{{ src_galaxy_custom_repo_branch | default('main',
 _galaxy_api_exposed: "{{ src_galaxy_api_exposed | default(true, true) }}"
 _galaxy_use_interactive_tools: "{{ src_galaxy_interactive_tools | default(true, true) | bool }}"
 _galaxy_server_fqdn: "{{ workspace_fqdn | default('localhost', true) }}"
+_galaxy_jobs_singularity: "{{ src_galaxy_jobs_singularity | default(false, false) | bool  }}"
 _galaxy_jobs_docker: "{{ _galaxy_use_interactive_tools or (src_galaxy_jobs_docker | default(true, false) | bool )  }}"
-_galaxy_jobs_pulsar_embedded: "{{ src_galaxy_pulsar_embedded | default(_galaxy_use_interactive_tools, true) | bool }}"
 
 # Build the final lists of tool and workflow installation files
 _galaxy_tool_files: "{{ src_galaxy_tool_files | default('', true) | split(',') | select() + _galaxy_default_tool_files_list }}"  # select() necessary because split on the default '' yields ['']