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

Johannes Graumann johannes_graumann at web.de
Wed May 7 17:03:39 CEST 2008


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

More information about the Bioconductor mailing list