galaxy.yml

@@ -14,6 +14,8 @@
       become: true
       become_user: postgres
     - geerlingguy.pip
+    - gantsign.golang
+    - cyverse-ansible.singularity
     - galaxyproject.galaxy
     - role: uchida.miniconda
       become: true

group_vars/galaxyservers.yml

@@ -29,6 +29,8 @@ miniconda_manage_dependencies: false
 
 galaxy_config:
   galaxy:
+    dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml"
+    containers_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.xml"
     brand: "🧬🔬🚀"
     admin_users: admin@example.org
     database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
@@ -89,6 +91,10 @@ galaxy_config:
 galaxy_config_templates:
   - src: templates/galaxy/config/job_conf.xml.j2
     dest: "{{ galaxy_config.galaxy.job_config_file }}"
+  - src: templates/galaxy/config/container_resolvers_conf.xml.j2
+    dest: "{{ galaxy_config.galaxy.containers_resolvers_config_file }}"
+  - src: templates/galaxy/config/dependency_resolvers_conf.xml
+    dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}"
 
 # systemd
 galaxy_manage_systemd: yes
@@ -122,3 +128,9 @@ nginx_conf_http:
 nginx_ssl_role: usegalaxy_eu.certbot
 nginx_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem
 nginx_conf_ssl_certificate_key: /etc/ssl/user/privkey-nginx.pem
+
+# Golang
+golang_gopath: '/opt/workspace-go'
+# Singularity target version
+singularity_version: "3.7.4"
+singularity_go_path: "{{ golang_install_dir }}"

requirements.yml

@@ -12,3 +12,7 @@
   version: 0.3.0
 - src: usegalaxy_eu.certbot
   version: 0.1.5
+- src: cyverse-ansible.singularity
+  version: 048c4f178077d05c1e67ae8d9893809aac9ab3b7
+- src: gantsign.golang
+  version: 2.6.3

templates/galaxy/config/container_resolvers_conf.xml.j2

@@ -0,0 +1,6 @@
+<containers_resolvers>
+  <explicit_singularity />
+  <cached_mulled_singularity cache_directory="{{ galaxy_mutable_data_dir }}/cache/singularity" />
+  <mulled_singularity auto_install="False" cache_directory="{{ galaxy_mutable_data_dir }}/cache/singularity" />
+  <build_mulled_singularity auto_install="False" cache_directory="{{ galaxy_mutable_data_dir }}/cache/singularity" />
+</containers_resolvers>

templates/galaxy/config/dependency_resolvers_conf.xml

@@ -0,0 +1,2 @@
+<dependency_resolvers>
+</dependency_resolvers>

templates/galaxy/config/job_conf.xml.j2

@@ -2,8 +2,17 @@
     <plugins workers="4">
         <plugin id="local_plugin" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
     </plugins>
-    <destinations default="local_destination">
+    <destinations default="singularity">
         <destination id="local_destination" runner="local_plugin"/>
+        <destination id="singularity" runner="local_plugin">
+            <param id="singularity_enabled">true</param>
+            <!-- Ensuring a consistent collation environment is good for reproducibility. -->
+            <env id="LC_ALL">C</env>
+            <!-- The cache directory holds the docker containers that get converted. -->
+            <env id="SINGULARITY_CACHEDIR">/tmp/singularity</env>
+            <!-- Singularity uses a temporary directory to build the squashfs filesystem. -->
+            <env id="SINGULARITY_TMPDIR">/tmp</env>
+        </destination>
     </destinations>
     <tools>
     </tools>