[EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary

Peter biopython at maubp.freeserve.co.uk
Thu Aug 12 09:19:33 UTC 2010

On Thu, Aug 12, 2010 at 9:17 AM, Nigel Binns <n.binns at ed.ac.uk> wrote:
>  Hi Peter,
> Many thanks for your reply. I have ClustalW v2 installed (v2.0.12 - the
> latest release). The binary is named clustalw2. However, as I understand it,
> when running the Jemboss installation script, you are asked to provide the
> root directory that contains the clustalw binary rather than the name of the
> actual binary i.e /path/to/clustal/root/ rather than
> /path/to/clustal/root/clustalw2 or have I got that wrong?

I was suggesting the problem could be EMBOSS only looks for clustalw
and not clustalw2.

> The same issue applies to my installation of Primer3 ( latest release -
> 3-2.2.2-beta). The binary name is primer3_core. I get this error when I try
> to run eprimer3.
> Error   application terminated
>    Died: eprimer3 uses external program 'primer3_core' which is not in the
> PATH or defined as EMBOSS_PRIMER3_CORE
>         Part of the 'primer3' package, version 3.0, available from the
>         Whitehead Institute. See: http://primer3.sourceforge.net/
> Please can you tell me what file I should set the EMBOSS_CLUSTALW and
> EMBOSS_PRIMER3_CORE variables in.

They are just environment variables (set up in the OS), but I haven't
ever used Jemboss so don't know how it would handle this.

> Many thanks for your help.
> Nigel

Peter C.

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