[BioC] BSgenome packages for new UCSC rn5 and galGal4 assemblies

[Kasper Daniel Hansen]

I would prefer sacCer1 to be kept around; we have packaged data that
was mapped to this version.  And it is small.

I would suggest keeping mm8 around as well, but I am not working in
mouse myself.  I don't know what the situation is in mouse, but plenty
of people are still using hg18.  Perhaps it is the same for mouse.

Kasper

On Thu, Jun 21, 2012 at 4:37 PM, Hervé Pagès <hpages at fhcrc.org> wrote:
> Hi there,
>
> Just packaged BSgenome.Rnorvegicus.UCSC.rn5 (Rat) and
> BSgenome.Ggallus.UCSC.galGal4 (Chicken), and dropped them
> into our BioC 2.11 (devel) repository. They should become
> available via biocLite() within the next hour or so. Note
> that only the source tarballs will be available for the moment
> so Windows and Mac users will need to install with:
>
>  install.packages(..., type="source")
>
> BTW, if nobody still needs them, I'd like to stop supporting mm8
> (from Feb. 2006) and sacCer1 (Oct. 2003) at some point. They've
> both been superseded by newer assemblies: by mm9 and sacCer2 for
> a while, and more recently by mm10 and sacCer3. The current plan
> is that they will be part of the next release (Bioc 2.11, October
> 2012) but will be removed from Bioc 2.12 (if nobody says anything
> in the meantime).
>
> Thanks,
> H.
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor