[emboss-dev] Commandline changes in EMBOSS applications

Guy Bottu gbottu at vub.ac.be
Wed Oct 5 18:33:17 UTC 2011

Jon Ison wrote:
> 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.

I think that you should anyway not reduce the richness of ACD language. 
After all, there are people that use the EMBOSS libraries to develop 
applications for their local use, without using Galaxy or any other 
particular tool.

As for prettyplot, making the changes suggested by Peter is OK since the 
functionality is fully preserved and it does not become significantly 
more difficult from the viewpoint of the user. There might however be 
problems with some other programs where eliminating dependencies cannot 
be done without making the interface messy...

	Guy Bottu

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