[Bioc-sig-seq] Rsamtools

[Vincent Carey]

On Tue, Mar 16, 2010 at 2:28 PM, Tillinghast, Guy, M.D.
<Guy.Tillinghast at rivhs.com> wrote:
> Vincent,
>
> After I have used Subversion to download Rsamtools onto my hard drive, is it possible to use install.packages() within R to install Rsamtools?
> (Or, do I have to use Rtools?)

if you have run an appropriate version of Rtools.exe for an R 2.11
installation, it should be possible to use install.packages to get
Rsamtools installed.  you will have to indicate type="source",
repos=NULL in addition to the path of the .tar.gz archive that you
will need to make from the subversion repository.  (for that you'll
have to do Rcmd build on top of the Rsamtools folder, and you will
need Rtools for that to work.)

forwarding to sequencing list where others may be interested (and may
correct me if i am mistaken!)


>
> Guy
>
> -----Original Message-----
> From: Vincent Carey [mailto:stvjc at channing.harvard.edu]
> Sent: Tuesday, March 09, 2010 9:30 PM
> To: Tillinghast, Guy, M.D.
> Subject: Re: Rsamtools
>
> Hi Guy -- Rsamtools has never been on the web site, but is accessible via subversion.  It will be in the next release.  You can get a copy of the source using
>
> svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools
>
> with username/passwd "readonly" when prompted.
>
> On Tue, Mar 9, 2010 at 8:19 PM, Tillinghast, Guy, M.D.
> <Guy.Tillinghast at rivhs.com> wrote:
>>  Dear Vincent,
>>
>> I hope all is well.
>>
>> I am having difficulities in downloading Rsamtools, as it does not
>> appear on the bioconductor web site anymore.  Should I be using
>> another package to import bam files into R?  (i.e. is scanbam() now in
>> another
>> package?)
>>
>> Thanks in advance,
>> Guy
>>
>>
>>
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>
>
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