Re: Thoughts on the Vienna RNA package
On Wed, Nov 14, 2007 at 02:02:03PM +0100, Steffen Moeller wrote :
> On Wednesday 14 November 2007 12:02:04 Charles Plessy wrote:
> > Hi all,
> >
> > I had a look at the Vienna package, and here are a few thoughts about
> > the work to be done.
Cool, that one of my day to day libraries....
> > - It uses a patched version of Readseq. Maybe we should consider to
> > build Vienna on Debian's readseq, possibly by adopting its patches if
> > they are not disruptive. By the way, we could incorporate the Debian
> > package for readseq in our repository, if its current maintainer
> > agrees.
> I do not have any preference. Redundancy should be avoided. This is also why I
> decided for the Vienna RNA package to include the RNAforest application from
> Bielefeld rather than packaging the Bielefeld version.
I will be also for packaging the application in one apt-get
(rnavienna-all).
> > - The Vienna package provides libraries that other programs use. For
> > instance, MiRanda, a sofware to discover targets of micro RNAs uses
> > Vienna's RNAlib.
> yip, it is an essential package. I did not have a look at the libraries yet.
> Their "make install" needs some fiddling.
Well, the source code also....
I have a series of patch that I am going to submit to the mainstream as
the code is not compiling without gcc. (Yeah, I know, but some time on
cluster you need to use icc or equivalent).
> > - Emboss provides some wrappers so we shoud probably package them as
> > well.
> Nice.
>
> > - There are some build issues such as the Makefile in the Kinfold
> > directory that has no distclean rule. Probably some autoconf mastery
> > can solve the problem.
> Which is beyond me. There are some static libraries being produced, which is
> also just slightly disturbing.
The RNA Vienna Libraries is a static only lib. So you will need some
more polishing for also providing the dynamic lib as a Debian policy compliant
package.
> > - The vienna-rna source package should probably be split into multiple
> > binary packages, for instance RNAforester which is a distinct work.
> Right. It comes from the authors auf RNAhybrid.
Hum, in this case, took the RNAlib v1.4 as a base (rnavienna-base), and
add a package for each stuff added inside (rnavienna-forester,
rnavienna-kinfold, ...) and the mandatory rnavienna-lib, rnavienna-dev.
> > - I do not have the impression that some commercial licences are sold,
> > so maybe we have a chance of obtaining a relicencing ?
> The license is kind of the same as with ClustalW, IIRC.
>
> Many thanks for your feedback, Charles. Please feel free to get a go at
> whatever you feel being most important.
>
> Cheers,
>
> Steffen
>
Just my 2 cents,
Cheers,
David
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