Here is how the data files contained in this package were produced:

1) Download the following files from UCSC to a DOWNLOAD dir:

   ftp://hgdownload.cse.ucsc.edu/goldenPath/mm8/bigZips/
     chromFa.tar.gz (803M)
     upstream1000.fa.gz (5.4M)
     upstream2000.fa.gz (11M)
     upstream5000.fa.gz (25M)

2) Shell commands:

   cd DOWNLOAD
   for i in *.gz ; do gunzip $i ; done
   for i in *.tar ; do tar xvf $i ; done
   find . -type f -path './*/*.fa' -exec mv {} . \;
   rmdir *
   R CMD INSTALL BSgenome.Mmusculus.UCSC.mm8

3) R commands:

   library(BSgenome.Mmusculus.UCSC.mm8)
   file <- system.file("scripts", "comments.R", package="BSgenome.Mmusculus.UCSC.mm8")
   source(file)
   buildDataFiles("DOWNLOAD", "DATA", seqnames(Mmusculus), "", ".fa", seqcomments)
   buildDataFiles("DOWNLOAD", "DATA", mseqnames(Mmusculus), "", ".fa", mseqcomments, FALSE)

