EGA Download Client - Quick Guide

*** Prior to starting your download, please check that your dataset is available to download using the client by following this link : Datasets currently not present in the download Client . Please email EGA Helpdesk to request an Aspera download account for any datasets that are unavailable in the client. ***

Background to download

The EgaDemoClient.jar application can be used as command line client, or as interactive shell. Both ways provide the same functionality.

It is important to remember that every downloading process consists of four parts, they are:

Decrypt the file or dataset
Files ready to use
  • At this point your files should be ready to use . Please contact the EGA Helpdesk for further queries

Decrypt the file or dataset
Files ready to use
  • At this point your files should be ready to use . Please contact the EGA Helpdesk for further queries


Using the Command Line Using the Interactive Shell


Red fields below need to be changed accordingly

  • Email (the email address under which your EGA account is held)
  • Password (the password you have set upon account creation)
  • Encryption/Decryption key (are the same entity and chosen by yourself;"abc")
  • Dataset (the dataset you wish to download) e.g., EGAD00010000498
  • File (the file you wish to download) e.g., EGAF00000000001

Using the Interactive Shell

Running the command “java -jar EgaDemoClient.jar” starts the interactive shell. This opens the EGA shell:

Welcome to the EGA Secure Data Shell Demo.
Type 'help' for help, and 'exit' to quit.
Ega Demo Download Client  Version: 2.2.2

EGA > login email Password: password

How do I find out what commands are available?

EGA > instructions

How do I list what datasets I have access to?

EGA > datasets

How do I find out what files are in a dataset?

EGA > files dataset EGAD00010000498

Once you identified the dataset or file you wish to download, it is time to request it. Requests require 4 parts:

  • (1) the type of the request: "dataset" or "file".
  • (2) The ID: the dataset ID or the file ID.
  • (3) The en/decryption key for received data.
  • (4) a request label - this label is later used to download the requested data. You should pick a label by which you can identify your request.

How do I request a whole dataset (all files within a dataset)?

EGA > request dataset EGAD00010000498 abc request_EGAD00010000498   

In this request all files in dataset EGAD00010000498 is requested. The data is going to be encrypted with the key "abc". And the request label is "request_EGAD00010000498".

How do I request only one file from a dataset?

EGA > request file EGAF00000000001 abc request_EGAF00000000001 

How do I find out what requests I’ve made?

EGA > requests

How do I download a request?

EGA > download request_EGAD00010000650

How do I download a request to a specific directory?

Requests are downloaded by default to the current path. This can be changed by using the command "path”, to set a new path. Command "pwd" displays the current path. The request itself is then downloaded using the "download" command, for example :

 EGA > download request_EGAD00010000650 path_to_directory

The default is to download three parallel streams. The number of streams can be adjusted by specifying a number, for example:

EGA > download request_EGAD00010000650 7

- uses 7 parallel streams

Can I download multiple files at once?

The easiest way to do this is to list the files within a dataset and filter them for all files with extension e.g., “.vcf.cip” or “.vcf.gpg”, and store the file stable IDs for these files (the EGAF numbers) . Then these files can be requested individually. If all requests are made with the same request name, then this will appear as one single request in the downloader and can be downloaded just like all other requests streams.

How do I decrypt the dataset?

The whole dataset cannot be decrypted at once; instead this has to be done on a file by file basis.

How do I decrypt the file

EGA > decrypt /Users/kerryg/Downloads/EgaDemoClient_2.1.7/_Bai_RNA-Expression-Microarray_9256760088_H_Grn.idat.cip abc 

This will decrypt the file specified using {key} as decryption key. Upon decryption the encrypted file is deleted. In case of the ‘decryptkeep’ command the encrypted file is not deleted.

Metadata for some datasets are now available in the download client these can be requested using the following command, and will download unencrypted.

How do I download metadata?

Metadata for some datasets are now available in the download client these can be requested using the following command, and will download unencrypted.

EGA > download metadata EGAD00010000498

Troubleshooting

There are several options to explore how to better use the download system.

EGA > tutorial
EGA > help 
the help command outputs the readme file content

If you are experiencing trouble in downloading please use the following link. Downloader Troubleshooting


Should you need further assistance please contact ega-helpdesk@ebi.ac.uk

Using the Command mode


How do I log in

To log in and use the client:

java -jar EgaDemoClient.jar -p email password –help  

(adding -help gives the option to view all commands available).

How do I list what datasets I have access to?

java -jar EgaDemoClient.jar -p email password -ld

How do I find out what files are in a dataset?

java -jar EgaDemoClient.jar -p email password -lfd EGAD00010000212

How do I request a file?

java -jar EgaDemoClient.jar -p email password -rf EGAF00000584907 -re abc -label request_EGAF00000584907

How do I request a whole dataset (all files)?

java -jar EgaDemoClient.jar -p email password -rfd EGAD00010000212 -re abc -label request_EGAD00010000212 

Can I download multiple files at once?

The easiest way to do this is to list the files within a dataset and filter them for all files with extension e.g., “.vcf.cip” or “.vcf.gpg”, and store the file stable IDs for these files (the EGAF numbers) . Then these files can be requested individually. If all requests are made with the same request name, then this will appear as one single request in the downloader and can be downloaded just like all other requests streams

How do I list what requests I have made?

java -jar EgaDemoClient.jar -p email password -lr 

How do I download a request?

java -jar EgaDemoClient.jar -p email password -dr request_EGAD00010000212 -nt 7 

(7 uses 7 parallel streams (there is a maximum of 15 streams), please note default is 3 if not specified)

How do I download a request to a specific directory?

java -jar EgaDemoClient.jar -p email password -dr request_EGAD00010000212 -nt 7 –path_to_directory

How do I decrypt the file?

java -jar EgaDemoClient.jar -p email password -dc path_to_file_1 -dck abc

How do I decrypt multiple files at once?

java -jar EgaDemoClient.jar -p email password -dc path_to_file_1  path_to_file_2  path_to_file_3 -dck abc

Troubleshooting

If you are experiencing trouble in downloading please use the following link. Downloader Troubleshooting

Should you need further assistance please contact ega-helpdesk@ebi.ac.uk