Hi Andreas, it is completely clear to me that one should use as many packaged libraries as possible. I'm simply not sure if it works with the older SeqAn package apart from modifications. I would have to test this first, and for reasons of consistency I would then go back to this release also on sourceforge. Since I know that a lot changes were introduced in the recent year, especially in the align module and the argument parser, this could cause problems and I also prefer to rely on the recent implementations.
Therefore, I propose to wait for the next SeqAn package release. I will then use it also for the Flexbar version on sourceforge and will try to come along without modifications. Since I applied only very slight modifications, I am optimistic that it works out and I will discuss it with SeqAn developers. I definitely prefer to use an official and unmodified release, and see it as an aim for coming versions. Besides from cleaner sources and packaging, it would then also become obsolete to adjust new SeqAn libs to modifications for inclusion in Flexbar. However, I am not sure how fast a new packaged release will be provided. Best regards Johannes On Jan 25, 2013, at 11:08 PM, Andreas Tille <ti...@debian.org> wrote: > Hi Johannes, > > many thanks for getting involved. > > On Fri, Jan 25, 2013 at 03:11:23PM +0100, Johannes Röhr wrote: >> Tony asked me to join discussion on Flexbar packaging. I'm not sure if the >> stable SeqAn 1.3.1 package release misses functionality that I rely on, or >> if the behaviour of functions changed even if it compiles with this release. >> For example the new ArgumentParser has been added rather recently and I >> would not be surprised if its functionality changed in the time between the >> SeqAn package release and the revision that I incorporated. >> >> However, I think the question is not only if it compiles somehow using this >> package. It should be exacly the same behaviour for one version of Flexbar. >> This isn't clear if the seqan sources differ in version, not to talk about >> slight modifications I made. > > Thanks for the clarifications. I'd take this for some veto to not use > the Debian packaged seqan library. The question is whether the > modifications you made might be incorporated into upstream seqan. If > this would be feasible we could package a seqan version that would fit > flexbar (and most probably other applications.) Do you think this is > possible? > >> Thank you for the interest to include Flexbar! > > Sure. We try to fit the needs of all bioinformatics tasks. > > Kind regards and thanks again for joining here > > Andreas. > > -- > http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1de0773-19d4-48db-ad6a-e66e83a39...@users.sourceforge.net
