[BioC] AnnBuilder: Where to find which files are needed from AnnBuilder:::getSrcUrl("all", <ORGANISM>) locations?
mcarlson at fhcrc.org
Wed May 7 20:23:11 CEST 2008
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:
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.
Johannes Graumann wrote:
> 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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