[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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