Repository ega_download_streamer
Owner: yhoogstrate
Synopsis: European Genome-phenome Archive (EGA) download client
Individual files or whole datasets may be downloaded from European Genome-phenome Archive (EGA) in a secure manner by first placing a download request and then downloading the file/s associated with the request. All files are automatically encrypted prior to streaming and must be decrypted using the streamer after download is complete. 
https://www.ebi.ac.uk/ega/about/your_EGA_account/download_streaming_client#about
Type: unrestricted
Revision: 5:3e2cccf08053
This revision can be installed: True
Times cloned / installed: 124

Repository README files - may contain important installation or license information

ega_client_galaxy_wrapper

Bio-molecular high throughput data is privacy sensitive and can not easily made accessible to the entire outside world. To manage access to long term-archival of such data the European Genome-phenome Archive (EGA) project was initiated to facilitate data access and management to funded projects after completion to enable continued access to these data. Strict protocols govern how information is managed, stored, transferred and distributed and each data provider is responsible for ensuring a Data Access Committee is in place to grant access to the data. Obtaining such data is achieved with the EGA download streamer.

License

This embeds access to the EGA download streamer into Galaxy (16.07+). The EGA download streamer (https://www.ebi.ac.uk/ega/about/your_EGA_account/download_streaming_client) is free software released under the GNU GPL 3 license. By installating this tool you automatically agree with the terms of this license.

Installation

The galaxy wrapper is available in the public tool sheds under the name ega_download_streamer and can be viewed at the following url: https://toolshed.g2.bx.psu.edu/view/yhoogstrate/ega_download_streamer

The galaxy web administrator can install this wrapper in the admin menu, under the tabs Tools and Tool Shed: Search Tool Shed. In here, the admin needs to go to the Galaxy main tool shed where the search term ega_download_streamer should show the tool installer maintained by yhoogstrate. By pressing on it, a new page will open. This page will indicate that it will automatically install the tool dependencies and shows this README, including the LICENSE, and a button that will install the entire package into the galaxy server.

Because currently galaxy does not (yet?) support a password input type, the tool has to be configured by setting up 1 generic account. This is done by adding lines, setting up the proper environment variables, to a destination (computer node) in galaxy's ./config/job_conf.xml:

<destination id="local_dest" runner="local">

<env id="user">email</env>

<env id="pass">Secret12456...blabla</env>

</destination>

The runner="local" should correspond to the runner that runs the ega_download_streamer (only for complex setups, local is default).

Maintainance

The galaxy repository is maintained by Youri Hoogstrate and was written for an ELIXIR/EGA project.

Bugs and other contributions to the galaxy wrapper are more than welcome at: https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc

Dependencies of this repository

Repository package_ega_download_streamer_2_1_6 revision 04fdd0070044 owned by yhoogstrate

Name Version Type
EGA_download_streamer 2.1.6 package

Contents of this repository

Name Description Version Minimum Galaxy Version
data from the European Genome-phenome Archive in a secure manner 2.1.6.g0 any

Categories
Data Source - Tools for retrieving data from external data sources
Web Services - Tools enabling access to web services