[BioC] BSgenome package - add the bos taurus genome

[Herve Pages]

Hi João,

Sorry I forgot to mention that the package is only available as a source
package. The Windows and Mac OS X binaries will come later.
In the mean time, if your Windows box is configured to install from
source, you can do:

  > options(pkgType="source")
  > library(BSgenome)
  > available.genomes()   # now you should see it!
  > source("http://bioconductor.org/biocLite.R")
  > biocLite("BSgenome.Btaurus.UCSC.bosTau3")

Cheers,
H.


João Fadista wrote:
> Dear Herve,
> 
> I Installed the R devel and the BioC devel (I suppose) but I was not able to get the package:
> 
>> library(BSgenome)
>> available.genomes()
>  [1] "BSgenome.Amellifera.UCSC.apiMel2"    
>  [2] "BSgenome.Athaliana.TAIR.01222004"    
>  [3] "BSgenome.Celegans.UCSC.ce2"          
>  [4] "BSgenome.Dmelanogaster.BDGP.Release5"
>  [5] "BSgenome.Dmelanogaster.FlyBase.r51"  
>  [6] "BSgenome.Dmelanogaster.UCSC.dm2"     
>  [7] "BSgenome.Ggallus.UCSC.galGal3"       
>  [8] "BSgenome.Hsapiens.UCSC.hg16"         
>  [9] "BSgenome.Hsapiens.UCSC.hg17"         
> [10] "BSgenome.Hsapiens.UCSC.hg18"         
> [11] "BSgenome.Mmusculus.UCSC.mm6"         
> [12] "BSgenome.Mmusculus.UCSC.mm7"         
> [13] "BSgenome.Mmusculus.UCSC.mm8"         
> [14] "BSgenome.Mmusculus.UCSC.mm9"         
> [15] "BSgenome.Scerevisiae.UCSC.sacCer1"   
> 
>> source("http://bioconductor.org/biocLite.R")
> Warning messages:
> 1: In safeSource() : Redefining 'biocinstall'
> 2: In safeSource() : Redefining 'biocinstallPkgGroups'
> 3: In safeSource() : Redefining 'biocinstallRepos'
> 
>> biocLite("BSgenome.Btaurus.UCSC.bosTau3")
> Running biocinstall version 2.2.2 with R version 2.7.0 (under development)
> Your version of R requires version 2.2 of Bioconductor.
> Warning message:
> package 'BSgenome.Btaurus.UCSC.bosTau3' is not available  
> 
>> sessionInfo()
> R version 2.7.0 Under development (unstable) (2008-03-11 r44737) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] BSgenome_1.7.4    Biostrings_2.7.32 Biobase_1.99.2
> 
> 
> 
> Did I make something wrong?
> 
> 
> Best regards,
> João
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -----Original Message-----
> From: Herve Pages [mailto:hpages at fhcrc.org] 
> Sent: Wednesday, March 12, 2008 4:21 AM
> To: João Fadista
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] BSgenome package - add the bos taurus genome
> 
> Hi João,
> 
> João Fadista wrote:
>> Yes, it´s that version. Thanks a lot. When you add the package please let me know.
> 
> I've just added BSgenome.Btaurus.UCSC.bosTau3 to our public repository (for BioC devel only). From R 2.7.0:
> 
>   > library(BSgenome)
>   > available.genomes()
>    [1] "BSgenome.Amellifera.UCSC.apiMel2"
>    [2] "BSgenome.Athaliana.TAIR.01222004"
>    [3] "BSgenome.Btaurus.UCSC.bosTau3"
>    [4] "BSgenome.Celegans.UCSC.ce2"
>    [5] "BSgenome.Dmelanogaster.BDGP.Release5"
>    [6] "BSgenome.Dmelanogaster.FlyBase.r51"
>    [7] "BSgenome.Dmelanogaster.UCSC.dm2"
>    [8] "BSgenome.Ggallus.UCSC.galGal3"
>    [9] "BSgenome.Hsapiens.UCSC.hg16"
>   [10] "BSgenome.Hsapiens.UCSC.hg17"
>   [11] "BSgenome.Hsapiens.UCSC.hg18"
>   [12] "BSgenome.Mmusculus.UCSC.mm6"
>   [13] "BSgenome.Mmusculus.UCSC.mm7"
>   [14] "BSgenome.Mmusculus.UCSC.mm8"
>   [15] "BSgenome.Mmusculus.UCSC.mm9"
>   [16] "BSgenome.Scerevisiae.UCSC.sacCer1"
> 
> Install as usual with biocLite():
> 
>   > source("http://bioconductor.org/biocLite.R")
>   > biocLite("BSgenome.Btaurus.UCSC.bosTau3")
> 
> It's big (736.7 Mb) so depending on your connection it might take a while.
> Let me know in case of problems.
> 
> Cheers,
> H.