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 -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
