[EMBOSS] question about emma

[David.Bauer at SCHERING.DE]

That's correct but I think Jan is looking for something different.
The current configuration options (.embossrc etc.) control mostly functions
which are common to all programs (output format, stdout, auto etc.)
But if one wants to change the default behaviour of a particular program
the only way I see now is to creat an alternative set of acd files with
these settings.
Let's say I want to have matcher output always with -aformat markx2 and 3
alternatives.
It would be convenient to have some kind of sections in .embossrc for
programs similar to the DB sections:

PROG matcher [
      aformat: markx2
      alternatives: 3
]

Cheers,
David.




On 12/8/03 11:01 am, "Jan T. Kim" <kim at inb.uni-luebeck.de> wrote:

> However, I've been thinking from time to time that it would sometimes
> be handy to have a way to specify defaults for the EMBOSS programs,
> e.g. by means of an environment variable or a dotfile. Have I overlooked
> this? For example, it might be very convenient at times to change the
> default format for sequence output from FASTA to something which
> can accomodate more annotation information.

If you read the administration guide, such default settings and how to
override them are clearly documented. This has been in EMBOSS since 1.0.0
or
earlier.

The admin guide can be found on the emboss web site under the admin and
setup section.

..d




--
David Martin PhD
Bioinformatics Scientific Officer
Post-Genomics and Molecular Interactions Centre
University of Dundee