Management Commands

This section briefly lists the management commands available for SODAR administrators with shell access, in addition to the built-in commands in Django and used third party components. For more details on their usage, use the -h or --help argument.

SODAR Core Commands

These commands originate in SODAR Core. More information can be found in the SODAR Core documentation.

addremotesite

Add remote site for remote project synchronization.

batchupdateroles

Batch update project roles and send invites.

cleanappsettings

Clean up unused application settings.

deletecache

Delete SODAR Cache entries.

geticons

Download and install the latest versions of iconify icon sets. Must be followed by collectstatic to take effect.

synccache

Synchronize the SODAR Cache.

syncgroups

Synchronize user groups.

syncmodifyapi

Synchronize project metadata and user access in iRODS. Generally should only be used in development.

syncremote

Synchronize project and user data from a remote site if remote project sync is enabled.

SODAR Commands

These commands originate from the SODAR applications and are specific to operations regarding sample sheets, landing zones, iRODS data and ontologies.

busyzones

Return list of currently busy landing zones.

importobo

Import OBO format ontology. See Ontology Access Application.

importomimm

Import OMIM catalog as an ontology. See Ontology Access Application.

inactivezones

Return list of landing zones last modified over two weeks ago.

irodsorphans

Find orphans in iRODS project collections.

normalizesheets

Clean up and normalize previously imported sample sheets for non-standard data or other issues. Also updates render tables and creates a backup ISA-Tab version of the normalized sheets.

syncnames

Synchronize alternative names for sample sheet material search.

syncstudytables

Build study render tables in cache for all study tables. These will be automatically built when accessing sample sheets if existing cache is not up-to-date, but this can be used to e.g. regenerate the cache if something has been changed in study table rendering.