Try adding singularity

UtrechtUniversity · Oct 1, 2024 · 974471c · 974471c
1 parent 1936fce
commit 974471c
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Showing 6 changed files with 34 additions and 2 deletions.
diff --git a/galaxysrv.yml b/galaxysrv.yml
@@ -27,6 +27,8 @@
   roles:
     - role: geerlingguy.docker
       when: not _molecule_active and _galaxy_jobs_docker
+    - role: usegalaxy_eu.apptainer
+      when: 
     - role: uusrc.general.nginx_reverse_proxy
       vars:
         nginx_reverse_proxy_locations: "{{ galaxy_nginx_vhost_config }}"

diff --git a/requirements.yml b/requirements.yml
@@ -9,6 +9,8 @@ roles:
     version: 1.1.2
   - src: galaxyproject.postgresql_objects
     version: 1.2.0
+  - src: usegalaxy_eu.apptainer
+    version: 0.0.2
   - src: geerlingguy.docker
     version: 6.1.0
 

diff --git a/templates/galaxy/config/container_resolvers_conf.yml.j2 b/templates/galaxy/config/container_resolvers_conf.yml.j2
@@ -0,0 +1,10 @@
+- 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/"
diff --git a/templates/galaxy/config/job_conf.xml.j2 b/templates/galaxy/config/job_conf.xml.j2
@@ -6,8 +6,17 @@
             <param id="pulsar_config">/srv/galaxy/config/pulsar_app.yml</param>
         </plugin>
     </plugins>
-    <destinations default="{{ 'docker_dispatch' if _galaxy_jobs_docker else 'local' }}">
+    <destinations default="{{ _galaxy_jobs_default }}">
         <destination id="local" runner="local"/>
+        {% if _galaxy_jobs_singularity %}
+        <destination id="singularity" runner="local">
+            <param id="singularity_volumes">$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$job_directory:rw,{{ galaxy_data_dir }}:rw</param>
+            <param id="singularity_enabled">true</param>
+            <env id="LC_ALL">C</env>
+            <env id="APPTAINER_CACHEDIR">/tmp/singularity</env>
+            <env id="APPTAINER_TMPDIR">/tmp</env>
+        </destination>
+        {% endif %}
         {% if _galaxy_jobs_docker %}
         <destination id="docker_local" runner="{{ 'pulsar' if _galaxy_jobs_pulsar_embedded else 'local'  }}">
             <param id="docker_enabled">true</param>
@@ -22,11 +31,14 @@
             <env id="REQUESTS_CA_BUNDLE">/etc/ssl/certs/ca-certificates.crt</env>
             {% endif %}
         </destination>
+        {% endif %}
         <destination id="docker_dispatch" runner="dynamic">
             <param id="type">docker_dispatch</param>
             <param id="docker_destination_id">docker_local</param>
             <param id="default_destination_id">local</param>
         </destination>
-        {% endif %}
     </destinations>
+    <tools>
+        <tool class="local" destination="local" />
+    </tools>
 </job_conf>
diff --git a/vars/galaxy_vars.yml b/vars/galaxy_vars.yml
@@ -25,6 +25,8 @@ galaxy_config_templates:
     dest: "{{ galaxy_config_dir }}/job_conf.xml"
   - src: templates/galaxy/config/pulsar_app.yml.j2
     dest: "{{ galaxy_config_dir }}/pulsar_app.yml"
+  - src: templates/galaxy/config/container_resolvers_conf.yml.j2
+    dest: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
 postgresql_objects_users:
   - name: galaxy
     password: null
@@ -43,6 +45,7 @@ galaxy_configuration:
     job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
     tool_config_file: "{{ galaxy_config_dir }}/tool_conf.xml"
     user_preferences_extra_conf_path: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml"
+    container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
     interactivetools_enable: "{{ _galaxy_use_interactive_tools }}"
     interactivetools_map: "{{ _galaxy_use_interactive_tools | ternary(gie_proxy_sessions_path, omit) }}"
     galaxy_infrastructure_url: "{{ _galaxy_local_address }}"

diff --git a/vars/src_galaxy_vars.yml b/vars/src_galaxy_vars.yml
@@ -14,6 +14,9 @@ _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_default: "{{ src_galaxy_jobs_default | default('local', true) }}"
+_galaxy_jobs_singularity: "{{ src_galaxy_jobs_singularity | default(true, 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 }}"