[emboss-dev] Commandline changes in EMBOSS applications

Peter Cock p.j.a.cock at googlemail.com
Mon Oct 3 13:55:52 UTC 2011

On Mon, Oct 3, 2011 at 8:16 AM, Jon Ison <jison at ebi.ac.uk> wrote:
> Morning
> I think it depends on what's most important, maintaining the richness of the EMBOSS command-line
> (dependencies in default values) or compatibility with the Galaxy or any interface that can't
> handle this.  That's a tough one!  I'm leaning towards the latter, but not if it makes many
> applications really messy.
> So I would add new options and remove old ones - bearing in mind that would need to be done for
> all apps.
> Cheers

Peter R,

Given Galaxy can handle this (even if it is a bit awkward to do),
what are the other interfaces / wrapper developers where
context dependent defaults may be an issue?

It isn't an issue for Biopython (although our wrappers are all
hand coded for now, rather than being generated from the
EMBOSS ACD files - a possible student project one day?)

Peter C.

More information about the emboss-dev mailing list