diff --git a/templates/galaxy/config/job_conf.yml.j2 b/templates/galaxy/config/job_conf.yml.j2 index c510035..d76f5b6 100644 --- a/templates/galaxy/config/job_conf.yml.j2 +++ b/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 + environment: local_env diff --git a/vars/galaxy_vars.yml b/vars/galaxy_vars.yml index d0b468c..a6fb7dc 100644 --- a/vars/galaxy_vars.yml +++ b/vars/galaxy_vars.yml @@ -7,7 +7,7 @@ galaxy_manage_systemd: false galaxy_venv_dir: "{{ _galaxy_root }}/venv" galaxy_config_dir: "{{ _galaxy_root }}/config" galaxy_mutable_data_dir: "{{ src_galaxy_storage_path | default(_galaxy_root+'/datadir', true) }}" # component variable src_galaxy_storage_path -galaxy_commit_id: "release_{{ src_galaxy_version | default('23.2', true) }}" # component variable src_galaxy_version +galaxy_commit_id: "release_{{ src_galaxy_version | default('24.0', true) }}" # component variable src_galaxy_version galaxy_separate_privileges: true galaxy_create_user: true galaxy_manage_paths: true @@ -18,13 +18,22 @@ galaxy_group: galaxy galaxy_client_use_prebuilt: true galaxy_systemd_root: true galaxy_backup_configfiles: false + +#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" +pulsar_config_file: "{{ galaxy_config_dir }}/pulsar_app.yml" +container_resolvers_config_file: "{{galaxy_config_dir }}/container_resolvers_conf.yml" + galaxy_config_templates: - src: templates/galaxy/config/user_preferences_extra_conf.yml.j2 - dest: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml" + dest: "{{ user_preference_config_file }}" - src: templates/galaxy/config/job_conf.yml.j2 - dest: "{{ galaxy_config_dir }}/job_conf.yml" + dest: "{{ job_config_file }}" - src: templates/galaxy/config/pulsar_app.yml.j2 - dest: "{{ galaxy_config_dir }}/pulsar_app.yml" + dest: "{{ pulsar_config_file }}" + - src: templates/galaxy/config/container_resolvers_conf.yml.j2" + dest: "{{ container_resolvers_config_file }}" postgresql_objects_users: - name: galaxy password: null @@ -81,7 +90,7 @@ galaxy_configuration: remote_user_maildomain: "{{ _galaxy_remote_user_maildomain }}" database_connection: "postgresql:///galaxy?host=/var/run/postgresql" file_path: "{{ galaxy_mutable_data_dir }}/datasets" - job_config_file: "{{ galaxy_config_dir }}/job_conf.yml" + job_config_file: "{{ job_config_file }}" tool_config_file: "{{ galaxy_config_dir }}/tool_conf.xml" user_preferences_extra_conf_path: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml" interactivetools_enable: "{{ _galaxy_use_interactive_tools }}" @@ -124,8 +133,8 @@ galaxy_configuration: gx_it_proxy: enable: "{{ _galaxy_use_interactive_tools }}" port: "{{ gie_proxy_port }}" -galaxy_config_templates: +#galaxy_config_templates: # - src: templates/galaxy/config/container_resolvers_conf.yml.j2 # dest: "{{ galaxy_config.galaxy.container_resolvers_config_file }}" - - src: templates/galaxy/config/dependency_resolvers_conf.xml - dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}" +# - src: templates/galaxy/config/dependency_resolvers_conf.xml +# dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}"