[EMBOSS] using emma: where to put clustalw

[Peter Rice]

Robin Colgrove wrote:
> I was trying to use emma for a multiple sequence alignment of dna 
> sequencing reads, but it complained that it could not find clustalw. I 
> could not find any mention of clustalw on the EMBOSS page, so I got a 
> copy from the clustalw homepage and -not knowing where to place it- 
> tried the /usr/local/share/ EMBOSS/acd directory. That didn't work, and 
> emma gives the error:
> 
>    EMBOSS An error in ajsys.c at line 398:
> cannot find program 'clustalw'
> 
> Looking in the emma.acd and ajsys.c files, I can't find any guidance.
> 
> Does anyone know how this is supposed to work?

Option 1: Install clustalw in your path so that you (and the emma program) can 
run it from the commandline. The directory where you installed EMBOSS is one 
possible place you can put it.

Option 2: Emma will look for a variable EMBOSS_CLUSTALW (an environment 
variable or a variable defined inemboss.defaults or .embossrc) that has the 
full path for clustalw.

Now ... we should document this ... and perhaps update the emma documentation 
which looks rather old and has too much old clustal information in it.

Hope this helps,

Peter