[EMBOSS] needle standalone

[pmr at ebi.ac.uk]

Hi Igor,

> I work for the C. elegans genomic database WormBase (www.wormbase.org) and
> would like to be able to run needle locally. I found it as a part of the
> EMBOSS package, but I'd really prefer not to install other programs that
> the package contains. I'm wondering if there is a place where I can get
> just needle?

You will need to install EMBOSS, and keep various parts installed, for
needle to work.

I have successfully installed single EMBOSS applications standalone, and
can provide details if needed, but it is "not supported" ... and not
recommended.

For needle, for example, you need to provide the comparison matrix files
in a suitable directory, and point your copy of needle to the needle.acd
file and database definitions. This can be done through the
emboss.defaults file (which has to be somewhere needle will find it) or in
.embossrc (for one user only). A non-tivial undertaking.

Hope this helps,

Peter Rice