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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit b05c45b7b2a6a7c9cace195707f0609b1a1ed20a |
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modified:
ega_download_streamer.xml |
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added:
README.rst |
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| diff -r a1f6611f0533 -r 42fbce72bc07 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Jun 21 09:51:55 2016 -0400 |
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| @@ -0,0 +1,36 @@ +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/ega_client_galaxy_wrapper |
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| diff -r a1f6611f0533 -r 42fbce72bc07 ega_download_streamer.xml --- a/ega_download_streamer.xml Tue Mar 29 07:44:25 2016 -0400 +++ b/ega_download_streamer.xml Tue Jun 21 09:51:55 2016 -0400 |
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| @@ -113,13 +113,15 @@ <help> **What it does** -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. +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 shall be decrypted using the streamer after downloading has completed. -To download a given dataset, the user should provide the corresponding EGA file identifier (e.g. EGAF00001059069). +**How to use** + +When you load the tool in galaxy, the user should provide the corresponding EGA file identifier (e.g. EGAF00001059069). **Configuration** -The admin has to configure the server such that the environment variables $user and $pass are exported and reflect the credentials of the EGA account. The user and password shall not be visible to users. This can also be done in the config/jobs_conf.xml file. +The admin has to configure a generic account, further described in the README: https://raw.githubusercontent.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper/master/README.rst https://www.ebi.ac.uk/ega/about/your_EGA_account/download_streaming_client </help> |