SODAR Settings

SODAR contains a number of site-wide backend settings, which greatly affect the provided features and user experience. The settings are provided to the server as environment variables and they originate both from the SODAR Core platform and SODAR itself. Settings can be either mandatory or optional. Default values for all mandatory settings are provided by the SODAR Docker Compose deployment framework.

Hint

To easily see what values for SODAR site settings are currently in use, navigate to the Site Info admin application and select the Settings tab.

Note

In sodar-docker-compose environments, internal SODAR settings may be prefixed as SODAR_*.

SODAR Core Settings

Settings originating from SODAR Core are documented in the SODAR Core documentation. Documentation on settings is linked below.

Enabled Backend Plugins

The ENABLED_BACKEND_PLUGINS settings defines which backend applications are used in SODAR. These originate both SODAR Core and SODAR itself. The default configuration for running SODAR in production is a list of applications as follows:

appalerts_backend: Creation and management of user alerts.
omics_irods: iRODS backend for iRODS connections.
isatemplates_backend: Provide access to custom ISA-Tab templates in the Sample Sheets app.
ontologyaccess_backend: Provide ontology lookup for the Sample Sheets app.
sodar_cache: Enable the SODAR Cache.
taskflow: Provide complex iRODS transactions for project data.
timeline_backend: Creation events for the project timeline.

It is not recommended to modify this configuration except for special circumstances. If removed from the list, the functionality regarding a specific backend will be disabled in SODAR.

SODAR Settings

Settings from SODAR applications themselves are described below.

iRODS Settings

ENABLE_IRODS: Use iRODS except if set false (boolean).
IRODS_HOST: iRODS host (string).
IRODS_HOST_FQDN: Fully qualified domain name of iRODS host, for cases where IRODS_HOST is given as e.g. an internal docker network host (string).
IRODS_PORT: iRODS port (integer).
IRODS_ZONE: iRODS zone (string).
IRODS_ROOT_PATH: iRODS root path, without the zone. Used if the SODAR projects collection is not intended to be placed directly under IRODS_ZONE (string).
IRODS_USER: Name of iRODS admin user to be used by backend processes (string).
IRODS_PASS: Password of iRODS admin user (string).
IRODS_SAMPLE_COLL: Name of sample data collection under each project (string, default: sample_data).
IRODS_LANDING_ZONE_COLL: Name of landing zone collection under each project (string, default: landing_zones).
IRODS_ENV_DEFAULT: Default iRODS environment for backend and client connections (dict).
IRODS_ENV_BACKEND: iRODS environment overrides for backend connections (dict).
IRODS_ENV_CLIENT: iRODS environment overrides for client connections (dict).
IRODS_CERT_PATH: iRODS certificate path on server (string).
IRODS_SODAR_AUTH: Enable local basic auth endpoint for iRODS if an external LDAP/AD server is not used (boolean, default: False).

Warning

Changing path settings such as IRODS_ROOT_PATH, IRODS_SAMPLE_COLL and IRODS_LANDING_ZONE_COLL is not recommended on an existing SODAR installation. In that case, manual moving of existing iRODS collections is required or links to iRODS will not work as expected.

Taskflow Backend Settings

TASKFLOW_IRODS_CONN_TIMEOUT: Connection timeout for taskflows in seconds, other SODAR iRODS sessions are not affected (int, default: 480).
TASKFLOW_LOCK_RETRY_COUNT: Retry count for project lock retrieval for Taskflow operations (int, default: 2).
TASKFLOW_LOCK_RETRY_INTERVAL: Retry interval for project lock retrieval for Taskflow operations (int, default: 3).

iRODS WebDAV Settings

IRODS_WEBDAV_ENABLED: Enable WebDAV unless set false (boolean).
IRODS_WEBDAV_URL: URL for the iRODS WebDAV server (string).
IRODS_WEBDAV_URL_ANON: URL for anonymous WebDAV access, in case running on a different server than the general WebDAV (string, default: IRODS_WEBDAV_URL).
IRODS_WEBDAV_URL_ANON_TMPL: Template for anonymous ticket access via the anonymous WebDAV URL (regex).
IRODS_WEBDAV_USER_ANON: User name for anonymous WebDAV access (string, default: ticket).
IRODS_WEBDAV_IGV_PROXY: Enable the use of IGV proxy on the WebDAV server. This should be set True if the WebDAV is deployed on a different host than SODAR itself. This will avoid having to log in twice when opening a session file in IGV. If SODAR and the WebDAV are deployed on the same host, this should be set False (boolean, default: True).

iRODS Backend Settings

IRODSBACKEND_STATUS_INTERVAL: iRODS backend status query interval in seconds (integer).
IRODS_QUERY_BATCH_SIZE: Batch query size for improving sequential iRODS query performance (integer).

Sample Sheets Settings

SHEETS_ALLOW_CRITICAL: Allow critical altamISA warnings on import (boolean).
SHEETS_IRODS_LIMIT: iRODS file query limit (integer).
SHEETS_ENABLE_STUDY_TABLE_CACHE: Enable caching of study tables unless set false (boolean).
SHEETS_MIN_COLUMN_WIDTH: Minimum default column width in study/assay tables (integer).
SHEETS_MAX_COLUMN_WIDTH: Maximum default column width in study/assay tables (integer).
SHEETS_VERSION_PAGINATION: Version list pagination limit (integer).
SHEETS_IRODS_TICKET_PAGINATION: iRODS ticket list pagination limit (integer).
SHEETS_IRODS_TICKET_PAGINATION: iRODS deletion request list pagination limit (integer).
SHEETS_ONTOLOGY_URL_TEMPLATE: URL template for ontology lookup (string).
SHEETS_ONTOLOGY_URL_SKIP: Skip URL template modification if substring is found in the accession attribute (list).
SHEETS_EXTERNAL_LINK_PATH: Path for JSON file containing labels and other metadata for external link columns (dict, default={PROJECT_ROOT}/samplesheets/config/ext_links.json). Each item the JSON dictionary should contain an ID descriptor such as x-generic-remote as its key. The item should contain a label parameter containing a display-friendly description of the ID. If linking out to an external resource is needed, add a url parameter containing a URL pattern in form of https://example.com/{id}.
SHEETS_SYNC_INTERVAL: Interval for remote sheet synchronization in minutes (integer).
SHEETS_IGV_OMIT_BAM: BAM and CRAM file name suffixes to omit from study shortcuts and IGV session generation.
SHEETS_IGV_OMIT_VCF: VCF file name suffixes to omit from study shortcuts and IGV session generation.

Landing Zones Settings

LANDINGZONES_STATUS_INTERVAL: Zone status query interval in seconds (integer).
LANDINGZONES_TRIGGER_ENABLE: Enable automated move triggering (boolean).
LANDINGZONES_TRIGGER_MOVE_INTERVAL: Automated move file check interval in seconds (integer).
LANDINGZONES_TRIGGER_FILE: File name for automated move triggering (string, default: .sodar_validate_and_move).
LANDINGZONES_DISABLE_FOR_USERS: Disable non-superuser uploads via landing zones, useful for e.g. demo instances (boolean).
LZ_BIH_PROTEOMICS_SMB_EXPIRY_DAYS: BIH proteomics configuration SMB expiry days (integer).
LZ_BIH_PROTEOMICS_SMB_USER: BIH proteomics configuration SMB user (string).
LZ_BIH_PROTEOMICS_SMB_PASS: BIH proteomics configuration SMB password (string).

Ontology Access Settings

ONTOLOGYACCESS_BULK_CREATE: Bulk term creation limit for ontology import (integer).
ONTOLOGYACCESS_QUERY_LIMIT: Term query limit (integer).

ISA Templates Settings

ISATEMPLATES_ENABLE_CUBI_TEMPLATES: Enable templates from the cubi-isa-templates repository (boolean).

SODAR Docker Compose Settings

Settings specific to the sodar-docker-compose repository are described here.

SODAR_SERVER_VERSION: Version of the SODAR server. Should be the latest release tag (e.g. 0.12.0-0) or the latest development version dev-0. For production it is strongly recommended to use the latest tagged release.
IRODS_VERSION: Version of the CUBI irods-docker image to use. Corresponds to the iRODS package version, e.g. 4.2.11-1.
SSSD_VERSION: SSSD version if using LDAP logins.
IRODS_SSSD_AUTH: Enable SSSD-based logins for iRODS.
IRODS_SODAR_AUTH: Enable PAM logins via the SODAR server for iRODS.
IRODS_SODAR_API_HOST: SODAR server host for iRODS in case the previous setting is set true.