[BioC] unexpected behaviour of pairwiseAlignment() in Biostrings

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Jul 12 17:08:47 CEST 2010


Hi Avril

On Mon, Jul 12, 2010 at 10:53 AM, Coghlan, Avril <A.Coghlan at ucc.ie> wrote:
> Dear Patrick,
>
> I've updated my copy of the Biostrings() library but the pairwiseAlignment() function doesn't seem to have been fixed yet - I wonder could you send me the patch directly please?

You could actually grab the source changes yourself if they haven't
propagated to the release/package servers.

If you're using R 2.11 (and bioc 2.6), the subversion repository can
be found here:

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/

You could "check out" the Biostrings package via svn and install it from source.

Assuming you're using a *unix-esque OS (linux, os x, etc.), you could
do this from teh command line:

$ svn --username readonly co
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/Biostrings
Biostrings
## The password is also: readonly

$ R CMD INSTALL Biostrings

and voila ... you would have installed the latest package from source.

Hope that helps,

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact



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