Re: Thoughts on the Vienna RNA package
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.
>
> - 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.
> - 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.
> - 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 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.
> - 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
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