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Re: https://github.com/nf-core/covid19 - nextflow pipeline



Hi Andreas,

Wrt package lists I know you need this for the blends structure. I don't
have these lists, What I have is a small list of lists:

https://github.com/nanoporetech/ - the nanopore is a prime tool for
covid-19
https://github.com/nf-core

I am not sure about the amont of energy I want to continue to invest
into bcbio at the very moment, I must admit.

https://salsa.debian.org/med-team/bcbio/-/blob/master/debian/TODO
and there is another RNAseq library that is _almost_ there, i.e. we have
all the packages, but
https://salsa.debian.org/med-team/pigx-rnaseq/-/blob/master/debian/TODO
describes issues about getting the css files into the R packages to have
nicer reports, without which the tests of pigx-rnaseq fail. Also, this
runs into the missing bits of the popular r-cran-locfit package.

In the new queue is

vienna-rna - and we are talking about a virus with single RNA strand as
a genome, also a dependency of a dependency for bcbio
dnapi - another RNA-one, dependency for bcbio
python-numpy-groupies - forgot what this was for - some dependency for
something in nf-core?
minimap2 - reupload of something already in Debian, added a -dev package
as requested by nanopolish - for the nanopore

I must admit that I thought there were more, still. Some have been
rejected that were kindly adopted by Andreas, others have been rejected
and I have not reuploaded. pizzly (another indirect bcbio dependency)
was accepted - very nice, many thanks, missed that one.

The acceptance of vienna-rna or minimap2 will trigger other uploads. The
first nim-packages have recently been accepted - will have a look into
uploading what we have prepared on salsa.debian.org/nim-team.

Steffen


On 24.03.20 17:12, Andreas Tille wrote:

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





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