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

2. 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 or the UUID of that landing zone.

SODAR authentication

To use this command, which internally executes iRODS icommands, you need to authenticate with iRODS by running:

$ iinit

To be able to access the SODAR API (which is only required, if you specify a landing zone UUID instead of an iRODS path), you also need an API token. For token management for SODAR, the following docs can be used:

• https://sodar.bihealth.org/manual/ui_user_menu.html
• https://sodar.bihealth.org/manual/ui_api_tokens.html

There are three options how to supply the token. Only one is needed. The options are the following:

1. configure ~/.cubitkrc.toml.

   [global]
   
   sodar_server_url = "https://sodar.bihealth.org/"
   sodar_api_token = "<your API token here>"
   

2. pass via command line.

   $ cubi-tk sodar ingest-fastq --sodar-url "https://sodar.bihealth.org/" --sodar-api-token "<your API token here>"
   

3. set as environment variable.

   $ SODAR_API_TOKEN="<your API token here>"
   

More Information

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