[EMBOSS] emma and clustalw2

[Moretti Sébastien]

Hi Mahmut,

Thanks it works nicely this way.
So, move back to   external: "clustalw"   and use EMBOSS_CLUSTALW variable.

> Hi Sebastien,
>
> It looks if I set EMBOSS_CLUSTALW environment variable to point to
> clustalw2 executable, as in the following example, i don't need to
> modify the emma.acd file.
>
>    export EMBOSS_CLUSTALW=~/esbin/clustalw-2.1/bin/clustalw2
>
> Regards,
> Mahmut
>
>> 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"
>>
>>
>> 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
>> Error: Failed to open filename '00011120B'
>> Problem writing out EMBOSS alignment file
>> Error: File 'msf::00011120B' remove failed, error:2 'No such file or
>> directory'

-- 
Sébastien Moretti
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://www.vital-it.ch/ http://myhits.vital-it.ch/