Hi Steffen, thanks a lot for your clarification.
Can we expect a list of links pointing to packages that are needed? As I wrote in my other mail ftpmaster seems to be motivated. Currently its us who need to deliver. Kind regards Andreas. On Tue, Mar 24, 2020 at 03:37:22PM +0100, Steffen Möller wrote: > Hi Tony, > > On 23.03.20 17:04, Tony Travis wrote: > > On 23/03/2020 14:38, Steffen Möller wrote: > > > Dear all, > > > > > > With the enormous difficulties to get bcbio into our distribution (a > > > considderable list of sequential dependencies for nim, java libraries, > > > golang-bio, ....sigh) I also had an eye on nf-core and their > > > nextflow-based workflows. I think I uploaded the one or other package > > > from their dependencies but, well, treated it more like an inspiration > > > than a project. From what I oversee it is far easier to address than > > > bcbio. > > > [...] > > > > Hi, Steffen. > > > > I've just had a look at the "nf-core" repo and read this: > > > > "please only use Conda as a last resort" > ;) You read something else elsewhere. > > > > They recommend running "nf-core" under Docker or Singularity, which I > > believe would make it unsuitable for packaging as part of "med-bio". > No, not at all. We get the packages into our distribution and there will > be an additional recommendation. We just need to show that our packages > are functional and they have done a nice job with their collection of > test data. I (once upon a time) had an email exchange with upstream - > they are very Debian friendly. And so are the folks behind conda and bcbio. > > > > I'm currently running "bcbio_nextgen" under Ubuntu-MATE 18.04 + > > med-bio, but the developers advised me NOT to use the 'external' > > versions of tools like "bwa" or "bowtie2" from Debian-Med but install > > everything isolated from the 'system'. > This avoid confusion. I'd recommend the same. > > > > I think this sort of application is more effort than it's worth to > > package for "med-bio". However, I think that a bare-bones package > > equivalent to bootstrapping "bioconda" using "miniconda" would be > > worthwhile to provide a ready-to-use "bioconda" within Debian-Med. > > I concur. And this will happen. > > Anybody who is packaging for Debian is very likely to come up with > patches for upstream. This is what also makes upstream stronger. The > benefit of packaging after aims set by the nf-core community is that we > get our act together towards something tangible (a set of proven > workflows with test data with relevance for the ongoing pandemia) and to > improve the packages upstream. > > Steffen > > > -- http://fam-tille.de