Manual for sodar ingest-collection
The cubi-tk sodar ingest command can be used to upload an arbitrary set of data files to SODAR.
It facilitates transfer of one or multiple sources into a single SODAR landing zone collection,
while optionally recursively matching and preserving the sub-folder structure.
Basic usage
$ cubi-tk sodar ingest [OPTION]... SOURCE [SOURCE ...] DESTINATION
Where each SOURCE is a path to a folder containing files and DESTINATION is either a SODAR iRODS path,
a landing zone UUID, or a SODAR project UUID.
For seamless usage ~/.irods/irods_environment.json and ~/.cubitkrc.toml should be present.
Parameters
-r, --recursive: Recursively find files in subdirectories and create iRODS sub-collections to match directory structure.-e, --exclude: Exclude files matching the given pattern.-s, --sync: Skip upload of files that already exist in iRODS.-K, --remote-checksums: Instruct iRODS to compute MD5 checksums of uploaded files for SODAR validation step.-y, --yes: Don’t stop for user permission. Enables scripting with this command.--collection: Set target iRODS collection in landing zone. Skips user input for this selection.
More Information
Also see cubi-tk sodar ingest-collection CLI documentation and cubi-tk sodar ingest-collection --help for more information.