Hello, your ENA-upload Galaxy container is running!

This container is optimized to clean human reads from raw reads and to upload them to ENA, this in only a few steps. The ENA uploading is based on the tool ena-upload-cli while the reads cleaning tool is based on Metagen-FastQC workflow.

ENA submission quick-start

Note: For more detailed information on the container and the ENA submission process read the documentation found on ELIXIR Belgium’s Data management hub

1. Log in to Galaxy and load your ENA credentials:

Login to Galaxy using admin as username and password as password. This will give you full access to the galaxy instance.
Go to User > Preferences in the top navigation
Click on Manage Information
Fill in the Your ENA Webin account details (If you do not have one, get your ENA Webin account here)
Click Save

2. Upload Data

Upload your raw data using Galaxy’s upload tool found at the top right of the Tools panel or using Upload File from your computer under Upload Data tool group.

3. Filter human reads out of the raw reads

Filter human traces from your raw data using Clean human reads from raw data from the Preprocessing Tools on the left panel.

Select human h38 reference genome
Choose single or paired-end
Select the files to clean
Click on ‘Execute’

4. Upload metadata and submit to ENA

The ENA Upload tool under Submission tools is used to generate the metadata in the right format, associate it with the sequence data files and submit everything to ENA. It is advisable to first test your submissions using the Webin test service where changes are not permanent and are erased every 24 hours.

The tool offers three ways of entering metadata for submission:

Complete the metadata spreadsheet template and upload it as in step 2 or;
Interactively generate the metadata structure or;
Complete the 4 tsv templates and upload as in step 2.

After uploading or completing the metadata, select the corresponding (human traces removed) data files, fill in your affiliation and click on ‘Execute’.

5. Check for a valid submission

Visit Webin online to check on your submissions or dev Webin to check on test submissions. If everything looks fine, publish the data by changing the “Release Date” of the study to a day later than the current day. It can take several days for ENA to index the data and to let it appear in a correct manner. Covid-19 data will also be indexed by the COVID-19 Data Portal

Galaxy is an open platform for supporting data intensive research. Galaxy is developed by The Galaxy Team with the support of many contributors. The Galaxy Docker project is supported by the University of Freiburg, part of de.NBI.

The Galaxy Project is supported in part by NHGRI, NSF, The Huck Institutes of the Life Sciences, The Institute for CyberScience at Penn State, and Johns Hopkins University.