fix singularity with cvmfs: only conditinally add /cvmfs to container…

… mounts
UtrechtUniversity · Jan 14, 2025 · f15c13a · f15c13a
1 parent 853aac1
commit f15c13a
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Showing 3 changed files with 13 additions and 10 deletions.
diff --git a/tasks/set_config.yml b/tasks/set_config.yml
@@ -59,3 +59,15 @@
 - name: Save _galaxy_config
   ansible.builtin.set_fact:
     _galaxy_config: "{{ galaxy_configuration }}"
+
+- name: Set AppTainer volume mounts variable
+  ansible.builtin.set_fact:
+    apptainer_volumes: "{{ apptainer_volumes | default([]) | union([item]) }}"
+  when: item != omit
+  loop:
+    - "$galaxy_root:ro"
+    - "$tool_directory:ro"
+    - "$working_directory:rw"
+    - "$job_directory:rw"
+    - "{{ galaxy_mutable_data_dir }}:rw"
+    - "{% if _galaxy_enable_cvmfs %}/cvmfs{% else %}{{ omit }}{% endif %}" # Conditionally add the /cvmfs dir to volume mounts
diff --git a/templates/galaxy/config/job_conf.yml.j2 b/templates/galaxy/config/job_conf.yml.j2
@@ -26,7 +26,7 @@ execution:
 {% endif %}
 
     singularity:
-      singularity_volumes: "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$job_directory:rw,{{ galaxy_mutable_data_dir }}:rw"
+      singularity_volumes: {{ apptainer_volumes | join(',') }}
       runner: local
       singularity_enabled: true
       container_resolvers:

diff --git a/vars/galaxy_vars.yml b/vars/galaxy_vars.yml
@@ -21,15 +21,6 @@ galaxy_client_use_prebuilt: true
 galaxy_systemd_root: true
 galaxy_backup_configfiles: false
 
-# Defining volume mounts for AppTainer containers
-apptainer_volumes:
-  - "$galaxy_root:ro"
-  - "$tool_directory:ro"
-  - "$working_directory:rw"
-  - "$job_directory:rw"
-  - "{{ galaxy_mutable_data_dir }}:rw"
-  - "{{ _galaxy_enable_cvmfs | ternary(',/cvmfs', omit) }}"
-
 # Defining the variables for galaxy/config
 user_preference_config_file: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml"
 job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"