Re: bcbio - about where we are
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
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