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Re: BioCocoa

On Oct 13, 2008, at 1:21 AM, Charles Plessy wrote:

Le Sun, Oct 12, 2008 at 11:40:11PM -0700, Scott Christley a écrit :

The sequence converter code doesn't seem to compile with version 2.X,
so I think it needs to either be rewritten or maybe functionality is
missing from 2.X, I'm not sure which.  But I guess if we split the
old/new biococoa into two packages, we can still provide the old
application until its working in the new version.

As you renamed both the source and binary packages 'biococoa', removing the '.app' part, the current 'biococoa.app' package will stay in Debian
after we upload your work. If building SequenceConverter with BioCocoa
2.X is not possible, then I propose to rename the current biococoa.app
package "sequenceconverter.app", to avoid further confusions. I created a sequenceconverter.app directory in our repository, in which we can do
further work on this package an prepare a renaming if needed (actually
much of the renaming was already prepared a few weeks ago but was
reverted because it would have been too intrusive for a last-minute
upload to our next release). From now on you can erase legacy files
related to SequenceConverter in the 'biococoa' package.

Ok, great, let me add some more detail. SequenceConverter is actually a demo or example application, there are two others, one being a sequence viewer and the other a translator (dna -> aa). As examples, they really aren't suppose to be full blown applications, but just show off the API. Of course, I can see how a simple GUI file format converter would be useful!

Now there are some real applications within BioCocoa, one is a set of command line programs for doing ultraconserved analysis for genomes, actually that's the only one right now but there are others in development. I think the usefulness of a sequence converter warrants that its made a full blown application.

Anyways, so thinking ahead, if we start getting more applications in BioCocoa, maybe we don't want a separate package for each application? How about having just three main packages?


The disadvantage to this is that you might be getting more than you want if you just want a single application, but it certainly makes it easier than managing lots of packages. The applications may have their own release cycle, so biococoa-apps would really be gathering the latest version of a set of applications and packaging them together. Of course this is all theoretical right now, but good to think about the overall structure ahead of time.

By the way, for the write access to our repository, please create a
guest account on http://alioth.debian.org, and apply to the debian-med
group: http://alioth.debian.org/project/request.php?group_id=30063

Thanks, done!


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