forked from UtrechtUniversity/src-component-galaxy
-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
conf files copied, attempt to connect to localhost failed
- Loading branch information
1 parent
a33087c
commit ca7e33f
Showing
2 changed files
with
169 additions
and
28 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| # Variables for the galaxyproject.galaxy role | ||
| galaxy_config_style: yaml | ||
| galaxy_layout: custom | ||
| galaxy_server_dir: "{{ _galaxy_root }}/server" | ||
| galaxy_root: "{{ galaxy_server_dir }}" # workaround https://github.com/galaxyproject/ansible-galaxy/issues/138 | ||
| 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('24.0', true) }}" # component variable src_galaxy_version | ||
| galaxy_separate_privileges: true | ||
| galaxy_create_user: true | ||
| galaxy_manage_paths: true | ||
| galaxy_clone_depth: 1 | ||
| galaxy_user: galaxy | ||
| galaxy_privsep_user: gxpriv | ||
| 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: "{{ user_preference_config_file }}" | ||
| - src: templates/galaxy/config/job_conf.yml.j2 | ||
| dest: "{{ job_config_file }}" | ||
| - src: templates/galaxy/config/pulsar_app.yml.j2 | ||
| 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 | ||
| postgresql_objects_databases: | ||
| - name: galaxy | ||
| owner: galaxy | ||
| #Job config singularity and cvmfs | ||
| galaxy_job_config: | ||
| runners: | ||
| local_runner: | ||
| load: galaxy.jobs.runners.local:LocalJobRunner | ||
| workers: 4 | ||
| handling: | ||
| assign: ['db-skip-locked'] | ||
| execution: | ||
| default: singularity | ||
| environments: | ||
| local_env: | ||
| runner: local_runner | ||
| tmp_dir: true | ||
| singularity: | ||
| singularity_volumes: "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$job_directory:rw,{{ galaxy_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 | ||
|
|
||
| galaxy_configuration: | ||
| galaxy: | ||
| brand: "SURF Research Cloud" | ||
| use_remote_user: true | ||
| allow_user_creation: true | ||
| allow_user_deletion: true | ||
| admin_users: "{{ _galaxy_admins }}" | ||
| 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: "{{ 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 }}" | ||
| interactivetools_map: "{{ _galaxy_use_interactive_tools | ternary(gie_proxy_sessions_path, omit) }}" | ||
| galaxy_infrastructure_url: "{{ _galaxy_local_address }}" | ||
| outputs_to_working_directory: "{{ _galaxy_use_interactive_tools }}" | ||
| bootstrap_admin_api_key: "{{ _galaxy_bootstrap_api_key | default(omit) }}" | ||
| # CVMFS | ||
| tool_data_table_config_path: /cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml | ||
| # Tool Dependencies | ||
| dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml" | ||
| container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml" | ||
|
|
||
| gravity: | ||
| galaxy_root: "{{ galaxy_server_dir }}" | ||
| galaxy_user: "{{ galaxy_user }}" | ||
| virtualenv: "{{ galaxy_venv_dir }}" | ||
| process_manager: systemd | ||
|
|
||
| gunicorn: | ||
| # listening options | ||
| bind: "{{ _galaxy_local_address }}" | ||
| # performance options | ||
| workers: 2 | ||
| # Other options that will be passed to gunicorn | ||
| # This permits setting of 'secure' headers like REMOTE_USER (and friends) | ||
| # https://docs.gunicorn.org/en/stable/settings.html#forwarded-allow-ips | ||
| extra_args: '--forwarded-allow-ips="*"' | ||
| # This lets Gunicorn start Galaxy completely before forking which is faster. | ||
| # https://docs.gunicorn.org/en/stable/settings.html#preload-app | ||
| preload: true | ||
| celery: | ||
| concurrency: 2 | ||
| enable_beat: true | ||
| enable: true | ||
| queues: celery,galaxy.internal,galaxy.external | ||
| pool: threads | ||
| memory_limit: 2 | ||
| loglevel: DEBUG | ||
| gx_it_proxy: | ||
| enable: "{{ _galaxy_use_interactive_tools }}" | ||
| port: "{{ gie_proxy_port }}" | ||
| #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 }}" |