[BioRuby] SRA downloader

[Raoul Bonnal]

Next time a little bit of research  :-(


http://phylogenomics.blogspot.com/2011/02/though-i-generally-love-ncbi.html?showComment=1297359206321#c7246439301219289057

On 15/feb/2011, at 10.37, Raoul Bonnal wrote:

> 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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--
Ra