File upload

The ena-utils upload command.

Uploading files to a Webin user file upload area is needed prior to files submission. See the associated ENA documentation for details.

Example

$ ena-utils upload --file_path <path/to/sequences/files.gz>

Submissions

The ena-utils submit command.

The ena-utils submit command has specific sub-commands for each type of object:

• Study (ex: ena-utils submit study)

• Sample (ex: ena-utils submit sample)

• Experiment (ex: ena-utils submit experiment)

• Run (ex: ena-utils submit run)

In addition, all these sub-commands come in two flavors:

• Unique object submission (ex: ena-utils submit study).

• Multiple objects submission using a submission file (ex: ena-utils submit study-set).

The ena-utils submit sub-commands allow to define some submission metadata. The possible metadata fields and values are specified in the ENA schema (also available in this documentation here). Check the sub-commands specific documentation to see which metadata fields are supported by your ena-utils version.

Template files for multiple objects submission can be created using the ena-utils create-template command, then edited to the specific needs of each submission.

By default, ena-utils submit sub-commands submit objects to the ENA test server (https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/).

Any data submission to ENA first requires the registration of a study object. See the associated ENA documentation for details.

Example

$ ena-utils submit study -a <alias> test_alias -t <title> -d <description>