[EMBOSS] emma and clustalw2

[Peter Rice]

Dear Sebastien,

On 31/01/2013 16:04, Moretti Sébastien wrote:
> I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64.
> My environment contains both clustalw and clustalw2, that's why
> clustalw2 binary is called clustalw2.
> Accordingly I have changed this line in the emma.acd file (before
> compilation):
>      external: "clustalw2"
> instead of
>      external: "clustalw"

The name is fixed within emma source code in a call to ajAcdGetPathC, so 
changing it in the ACD file will not work.

You can define EMBOSS_CLUSTALW to point to clustalw2 in your 
emboss.default file (for all users), in your personal ~/.embossrc file 
(only for yourself), or as an environment variable for the current session.

> When I try to run emma, I get this error message:
>
> Multiple sequence alignment (ClustalW wrapper)
> Warning: Cannot find 'clustalw', no ACD external definition found

This is because emma is looking for "clustalw" explicitly in the path or 
defined as above.

The ACD parser has found an application called "clustalw2" so it 
completed successfully. However, when emma asks for the path to 
"clustalw" it is surprised to find that the ACD parser does not know the 
answer.

Hope that helps,

Peter Rice
EMBOSS Team