Site 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.
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.
ontologyaccess_backend
Provide ontology lookup for the Sample Sheets app.
sodar_cache
Enable the SODAR Cache.
taskflow
Enable use of the SODAR Taskflow service for iRODS transactions.
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, if something else than
/{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
).
Taskflow Backend Settings
TASKFLOW_BACKEND_HOST
SODAR Taskflow service host (string).
TASKFLOW_BACKEND_PORT
SODAR Taskflow service port (integer).
TASKFLOW_SODAR_SECRET
Shared secret between SODAR and SODAR Taskflow (string).
TASKFLOW_TEST_MODE
Run SODAR Tasflow in test mode. Should always be set false unless running tests in development (boolean).
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 setFalse
(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_TABLE_HEIGHT
Default study/assay table height.
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_LABELS
Labels for external link columns (dict).
SHEETS_SYNC_INTERVAL
Interval for remote sheet synchronization in minutes (integer).
Landing Zones Settings
LANDINGZONES_STATUS_INTERVAL
Zone status query interval in seconds (integer).
LANDINGZONES_TRIGGER_MOVE_INVERVAL
Automated move file check interval in seconds (integer).
LANDINGZONES_TRIGGER_FILE
File name for automated move triggering (string, default:
.sodar_validate_and_move
).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).