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job_conf.xml debug
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mirelaminkova committed Oct 14, 2024
1 parent 4b55be7 commit a33087c
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Showing 2 changed files with 44 additions and 9 deletions.
28 changes: 27 additions & 1 deletion templates/galaxy/config/job_conf.yml.j2
Original file line number Diff line number Diff line change
Expand Up @@ -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
25 changes: 17 additions & 8 deletions vars/galaxy_vars.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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 }}"
Expand Down Expand Up @@ -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 }}"

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