PyEGA3

After setting up your EGA download account, you can proceed to download using the EGA download client – PyEGA3. The pyEGA3 download client is a python-based tool for viewing and downloading files from authorised EGA datasets. This download client is continuously being developed for more user-friendly download experiences.

No, the download client cannot be used to download metadata. Registered EGA users can download metadata of an authorised dataset by logging into the EGA webpage and navigating to the dataset of choice. Approximately two thirds down the page you will find the option to download the metadata as a zip file.

The main EGA download client is pyEGA3 download client, a python-based tool for viewing and downloading files from authorised EGA datasets.We could exceptionally consider the option of an Aspera download for users experiencing very slow download rates or facing particular issues.Contact the EGA Helpdesk for further information.

The PyEGA3 client is compatible with any OS with Python 3.6+ installed. The client requires a connection to the internet, sufficient space on the destination drive, and the EGA download account credentials.

We strongly recommend checking our video tutorial demonstrating the usage of PyEGA3 from installation to file download. More detailed information is available at PyEGA3 GitHub.

PyEGA3 makes HTTPS calls to the EGA Data API (https://ega.ebi.ac.uk:8443). This port 8443 must be reachable from the location where PyEGA3 is executed to avoid timeouts.

Updating the client to the latest version can be achieved by running the following command:

pip3 install pyega3 --upgrade

An EGA download test account (ega-test-data@ebi.ac.uk) has been created for troubleshooting and training purposes. The test account does not require an EGA username and password because it contains publicly accessible files from the 1000 Genomes Project. More information about the use of this account and log in details are available at pyEGA3.

The PyEGA3 download client supports automatic resumption of downloads. To enable quicker download speeds, the API breaks files into up to four segments and downloads them in parallel. With the resume feature, downloads will automatically resume if you encounter any errors or if the connection is interrupted.

Download speeds can be optimised using the --connections parameter which will parallelise download at the file level. If the --connections parameter is provided, all files >100Mb will be downloaded using the specified number of parallel connections.

Using a very high number of connections will introduce overhead that can slow the download of the file. It is important to note that files are still downloaded sequentially, so using multiple connections does not mean downloading multiple files in parallel. We recommend trying with 30 connections initially and adjusting from there to get maximum throughput.

Please note that when a file is being saved, it goes through two processes. First, the downloaded file "chunks" are pieced back together to reconstruct the original file. Secondly, PyEGA3 calculates the checksum of the file to confirm that the file was downloaded successfully. Larger files will take more time to reconstruct and validate the checksum.

PyEGA3 implements the GA4GH-compliant htsget protocol for supporting requests over genomic ranges. This exciting new feature means that for data files with accompanying index files (e.g. .crai for CRAM files) users can download specific regions of interest rather than the entire file, saving both time and storage space. Please note that in order for the genomic range requests to work for a BAM, CRAM or VCF file there must be an associated BAI, CRAI or TBI file, respectively. If the dataset does not contain these index files then genomic range requests cannot be performed.

Files are transferred over secure HTTPS connections and received unencrypted, thus there is no need for decryption after data download.

After the download completes, file integrity is verified using checksums. The PyEGA3 download client automatically verifies each file’s unencrypted md5 after download to ensure that the file was downloaded correctly from the EGA.

Ensure that your credentials are formatted correctly. Please contact the EGA Helpdesk if you are unsure about your account’s username (i.e. your email address).

500 server errors are internal server errors from EGA’s end. Retry after some time and, if the 500 error persists:

1. check our homepage or Twitter for any outage information or
2. report it to EGA Helpdesk.

This type of error occurs when one slice download was prematurely interrupted. Please re-start the same download. The download client will pick up any partial download and download any missing slices.

Please note that the data access was given to the email (username) provided to the Data Access Committee (DAC) in your official request. Therefore, you shall check that the account that you are using is the same one that you sent to the DAC.

This might mean that the connection ports are blocked. Check that the port 8443 is reachable.

In case the port is reachable and the error persists, please try to modify the file pyega3.py on line 44 in the python module installation:

Replace

endpoint = 'https://ipinfo.io/json'

with

endpoint = 'https://api.myip.com'

Make sure that you are using the correct credentials (username and password) and there is no typo. Contact EGA Helpdesk if the problem persists.