Re: https://github.com/nf-core/covid19 - nextflow pipeline
[@Charles, please read below]
Hi Steffen,
On Tue, Mar 24, 2020 at 11:07:38PM +0100, Steffen Möller wrote:
> Wrt package lists I know you need this for the blends structure.
Well, not for the structure. We need to mention packaging tasks
and links to useful software could be put on our todo list. The
tool I currently prefer is the blends structure (until we have
something more practical).
> 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
Hmmm, that github directory lists several tools but none with this
description neither the name nanopore. I've found a software named
nanopore on Github here:
https://github.com/mitenjain/nanopore
Which one do you mean?
> https://github.com/nf-core
That's also a directory. I've got a previous hint to
https://salsa.debian.org/med-team/chip-seq
which is close to ready for uploading (should be listed on the covid-19
task soon). What else besided chip-seq would be most relevant.
> 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
I'll re-check your list.
> 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.
I can have a look. It needs multiqc which in turn has a non-free
dependency[1]. I might try to follow the hint that we simply drop
Highcharts and document in README.Debian that the functionality is
restricted. This might help the dependencies of multiqc. What do you
think about this?
> Also, this
> runs into the missing bits of the popular r-cran-locfit package.
Charles, are you reading here? We really need to push this issue
forward.
> 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'll send you a private mail about this.
> 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.
Again, make a list. I'll re-check.
> 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.
Let me know if you need help. I'd currently lower my constant bug
hunting effort (and would be **really** happy if anybody could at least
squash a few here) and will prefer COVID-19 relevant packages over it.
Kind regards
Andreas.
[1] https://github.com/ewels/MultiQC/issues/800
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