[EMBOSS] newbie emma (clustalw) question

[Peter Rice]

On 08/12/09 21:08, Tom Keller wrote:
> On Dec 8, 2009, at 12:13 PM, Tom Keller wrote:
>> This is an ongoing frustration. I use EMBOSS only occasionally, and
>> I can never find a good guide for setting environmental variables.
>> For example, I wanted to use emma with a new install of clustalw2.
>> I made a link to it in /usr/local/bin, but emma can't find it. How
>> do I fix this in a easy to maintain manner?

You got there first.

The simple answer is that emma will look for clustalw (not clustalw2) in
your path. This should include a link. If you can run clustalw from the
command line then it should also run from within emma.

> I finally found the answer. It's simple, but if you don't know it,
> your only guessing, and that is really not a good approach.
>
> The environmental variable to set is EMBOSS_CLUSTALW in whatever dot
> shell control file you use for setting env.
> for the bash shell, I edited .bashrc with:
> export EMBOSS_CLUSTALW=/usr/local/bin/clustalw

This was a feature we added so that clustalw could be launched from a
local installation, or to run an executable called clustalw2 (or
clustalw183)

> How would one go about requesting that this sort of info be added as
> a comment to the application tfm page? So instead of reading
> COMMENT
> none
>
> it read: Set env variable EMBOSS_CLUSTALW=<path to local clustalw executalble>

You just did :-)

We will go through the external programs and add more information.

There is a paragraph in the emma documentation (diagnostic error
messages) but it is not easy to find (and probably has not been read by
many users - I just found a typo in it).

We plan for a future release to call all external applications in a
common way, and to issue a standard error message describing the path
and environment variable options.

We will also add a reference to external programs in the ACD files for
interface developers to identify dependencies on other packages.

We will also look into adding messages to the EMBOSS configure script to
warn about required third party packages.

Thanks for the suggestions

regards,

Peter Rice