[BioRuby] SRA downloader
Raoul Bonnal
bonnalraoul at ingm.it
Tue Feb 15 09:37:36 UTC 2011
Hey Guys,
this is a new plugin to download sra archives in an easy way, I hope :-)
Why ? because I need to download some file from SRA and I don't want to type the wget/curl command and I want to explore the ftp from command line, then because I need to start the downloads in background on a remote server.
Where ? https://github.com/helios/bioruby-sradl
as usual is experimental so, please be careful. I'm quite lazy so test section doesn't exist and the code needs some refactoring; I know I'll add it soon.
The DSL needs to be improved.
The procedure is recursive so you can download a bunch of reads at the same time.
By default the reads downloaded are the LITE. In the read me there is an example of looking for a regular archive: it's also an example of using optional parameters in thor' scripts.
To post process SRA format you need the sra tools kit
http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.3_Installing_the_Too
This plugin has also the purpose to be demonstrative for a Thor application.
This could be added to our NGS ngs section.
Any suggestion is welcome.
Ciao.
--
Ra
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