Manual for sea-snap itransfer-results

The cubi-tk sea-snap itransfer-results command lets you upload results of the Seasnap pipeline to SODAR. It relies on running the export function of Seasnap first. This export function allows to select which result files of the pipeline shall be uploaded into what folder structure, which can be configured via the Seasnap config file. It outputs a blueprint file with file paths and commands to use for the upload. For more information see the Seasnap documentation The itransfer-results function parallelizes the upload of these files.

The basic usage is:

  1. create blueprint

$ ./sea-snap mapping l export

  1. upload to SODAR

$ cubi-tk sea-snap itransfer-results BLUEPRINT DESTINATION

where each BLUEPRINT is the blueprint file mentioned above (probably „SODAR_export_blueprint.txt“) and DESTINATION is either an iRODS path to a landing zone in SODAR, the UUID of that landing zone or a SODAR project UUID.

More Information

Also see cubi-tk sea-snap itransfer-results CLI documentation and cubi-tk sea-snap itransfer-results --help for more information.