[EMBOSS] emma/clustalw PATH problems
golharam at umdnj.edu
Thu Aug 18 19:10:52 UTC 2005
I ran into the same problem. I simply moved clustalw into a directory
in my path and everything works okay...
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
> "cannot find program 'clustalw'" - means that the ClustalW program
> 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
> 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
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
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