Hi Steffen, thanks for the update and all your efforts.
On Sat, Aug 03, 2019 at 04:53:36PM +0200, Steffen Möller wrote: > Hello, > > bcbio (https://github.com/bcbio/bcbio-nextgen) references a set of > gold-standard packages for the interpretation of next-generation > sequencing data. The actual set of packages required varies with the > exact data at hand and the workflow run on it, but Debian Med should > show that it can run this. For the moment we are still missing quite > some bits and, frankly, it does not look too good: > > * The new queue has a serious bandwidth problem. Some movement has happened in new recently. > * Much work: Many packages come with embedded external packages that > DFSG requires to be separate packages and needs to adapt upstream's > build scripts. More of concern is that it is at times uncertain if > upstream has fiddled with the embedded source tree, so the DFSG version > may have inadvertent scientific consequences. > * bcbio has 2nd degree dependencies like Vienna-RNA in non-free. And > the testing of these packages also make these non-free bits part of the > build dependencies. I have not seen any entry in https://wiki.debian.org/DebianMed/SoftwareLiberation for Vienna-RNA. IMHO we should always try to convince upstream - possibly with arguments like given at the bottom of that page from kallisto - and record our attempts on that Wiki page. I agree that not the most fun part of our maintenance work to nag authors of non-free software but tit belongs to our maintenance task anyway. > Details on how far we got is stated on > https://salsa.debian.org/med-team/bcbio/blob/master/debian/TODO . That > document was never finished since with every package one looks in detail > there are more dependencies uncovered that should also be listed. It is > not exactly sure about where to go from here. Emerging ideas are: > > * a repository outside Debian main to harbor packages that have not > yet made it into the distribution (evolving on > http://med.functional.domains) It might be some temporary solution to overcome some bottleneck but I personally do not see any long term persistance for this idea. > * maybe not package what is needed for autotests only when this is not > invoked by the bcbio workflows (ouch! - a very pragmatic approach, isn't?) That's something which does not make me and others here really happy. > * just don't ignore the DFSG and get stuff functional (have used all > words for that in the line above already - speechless) I'm not sure whether some typo slipped in here since I don't get it. > We just took one big hurdle, which was seqcluster. The next shall be > mosdepth with its many "nim" dependencies already prepared on > https://salsa.debian.org/nim-team. I'll then send an update on how the > bcbio tests go. Thanks again, Andreas. -- http://fam-tille.de
