[BioC] AnnBuilder: Where to find which files are needed from AnnBuilder:::getSrcUrl("all", <ORGANISM>) locations?

[Marc Carlson]

Hi Johannes,

Since you are making packages for mouse I think you might want to use 
our newer SQLForge functions (found inside of the AnnotationDbi package) 
to make these.  Anbuilder is really being "phased out" except for those 
rare niche organisms that we have not been able to make databases for.  
There is a vignette online here for SQLForge:

http://www.bioconductor.org/packages/2.2/bioc/html/AnnotationDbi.html

SQLForge will make the newer .db style annotation packages as long as 
you are using a supported organism (and it looks like you are).  Let me 
know if you have questions about SQLForge.


    Marc



Johannes Graumann wrote:
> Hi,
>
> I'm using ABPkgBuilder to build some custom annotation packages, but can't
> use its downloading functionalities due to firewall policies only
> circumventable by "download.file"s "wget" option.
> So I basically call "AnnBuilder:::getSrcUrl("all", <ORGANISM>)" to get the
> targets and then loop over them, retrieving the files, storing them locally
> and rewriting the srcUrl to that location. My problem now is that some of
> the URLs refer not to files but directories and I'm unclear whether I need
> all of the content or just some files/directories.
> Can Anyone point out how to find that out?
>
> BTW: "AnnBuilder:::getSrcUrl("all", "Mus musculus")" returns this pair
>
>         HG      "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp"
>
> Which is wrong (?). Shouldn't that point
> at "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current"?
>
> Cheers, Joh
>
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