[EMBOSS] emma/clustalw PATH problems

[Ryan Golhar]

I ran into the same problem.  I simply moved clustalw into a directory
in my path and everything works okay...



-----Original Message-----
From: emboss-bounces at emboss.open-bio.org
[mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Peter Rice
Sent: Thursday, August 18, 2005 1:13 PM
To: Anders Nistér
Cc: emboss at emboss.open-bio.org
Subject: Re: [EMBOSS] emma/clustalw PATH problems


Anders Nistér wrote:

> Looking through the manual for emma there is a mention of 
> EMBOSS_CLUSTALW:
> 
>    "cannot find program 'clustalw'" - means that the ClustalW program
has
>    not been set up on your site or is not in your environment (i.e. is
>    not on your path). The solutions are to (1) install clustalw in the
>    path so that emma can find it with the command "clustalw", or (2)
>    define a variable (an environment variable of in emboss.defaults or
>    your .embossrc file) called EMBOSS_CLUSTALW containing the command
>    (program name or full path) to run clustalw if you have it
elsewhere
>    on your system.
> 
> So I'm supposed to be able to specify the full path to clustalw 
> through EMBOSS_CLUSTALW....
> 

> Is the documentation wrong or is this a bug ?

Ouch. It is a bug.

The variable was originally set to allow older or newer versions of
clustalw 
to be called. We have not tested programs that are not in the path.

I am sure we can find a workaround for a fully specified path to the
program.

regards,

Peter

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