Hello, Over the past months/weeks I have invested some energy into an overhaul of the ViennaRNA package. It is needed as a testing-dependency of seqcluster which in turn is needed for bcbio. Sadly, it is of a "commercial redistribution only if not charging more than media costs" non-free type of software. There is something in me that wants to just not test seqcluster properly, so we do not need to install the ViennaRNA package and then have a free RNA sequencing pipeline. But then that sequencing pipeline would not be complete. This "freeness" vs "completeness" problem is somewhat interesting: It was well-intended by the developer and it is affecting only a side-application of an otherwise completely free pipeline. I suggest to collect some thoughts on this.
2.4.14 has done a few changes on how the documentation is built, which had me just not building the documentation as a quick hack. The perl and python interfaces I have not checked. Autotests are fine. The package could use some help to get platform-specific(?) optimisations in (simd?). And I was not really sure about the floating-point precision. So, anyway, please give this package a spin. And if someone finds this to be good enough for non-free, then please just go and upload. Best, Steffen
