[BioC] QuasR: how to use an indexed reference genome?

[Martin Morgan]

On 05/16/2013 11:41 PM, Michael Stadler wrote:
> If more people would prefer to use pre-built indices, and if the BioC
> agrees to host such big packages, it would also be conceivable to
> provide index packages corresponding to the BSgenome packages for download.

We've been experimenting with AnnotationHub (the package, and the cloud resource 
-- http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html) as a 
way to provide large(r) data without having to go through the full formalism of 
creating packages; perhaps the indexes are a good case for this? The user or 
software would then

   library(AnnotationHub)
   hub = AnnotationHub()
   hub$<tab>
   ## the preceeding works, now for hypothetical...!
   hub$bioconductor.QuasR.BSgenome<tab>

and when hitting <return> on a complete name the AnnotationHub would do the 
right thing, downloading and installing the index in an appropriate place 
(including, e.g., caching in the AnnotationHub cache, if that's appropriate...)

Martin

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