Re: Is pigx-rnaseq ready to be uploaded?
On 13.09.21 20:36, Nilesh Patra wrote:
On 9/13/21 11:07 PM, Steffen Möller wrote:
On 13.09.21 18:27, Nilesh Patra wrote:
...
However, I see that you've added this line in d/ch: "hisat2 - upstream changed default genomic aligner"
What would this mean? There's no upstream release for hisat2, as I saw, what needs to be done to get this in then?
The package already ships in Debian. This was just that d/changelog is
also meant to summarize what is new in the respective release.
OK, so this was for summary, and not for any TODO, right?
Yes.
d/control
put it as
hisat2|rna-star <!nocheck>,
which is not perfectly correct, I tend to think, since one would need to
adjust the testing for rna-star if I get this right.
I don't know about the software myself, if you could take a look and push what
you deem sensible, that'd be very cool.
Done. Also eliminated some lintian warnings. All dependencies have been
transitioned, so it cowbuilds now. Good to go imho.
...
Would you object it's removal?
Also, @Andreas, what d'you think?
r-cran-gprofiler should not make it into the next release. But I do not
see a point into removing it from testing. I suggest to file an RC bug
against it, so we do not forget about it.
But do not immediately ask for
its removal.
Filed #994212
Thank you!
I'll contact the pigx-rnaseq upstream group once this transitioned to
testing. They should love this but I also know they are using guix on
their side (so am I when using pigx-rnaseq on our cluster). So, my next
two personal milestones are
* Qiime update/upload (which implies an update of scikit-learn) and
the automated testing with a qiime-tutorials package
* Singularity as part of my routine workflows on our cluster
To link this more to our Covid trigger,
https://www.nature.com/articles/s41522-021-00232-5 and other work
describe the effect that Covid has on the microbiome. Dunning-Kruger
here, any such analysis I do not expect to be much more complicated than
what we already show in the tutorials. It may be an interesting
experiment to see if we as a community could jointly come up with a
meta-analysis of these data sets. The meta^2-experiment is how we
interact between ourselves and the outside world to get there.
Best,
Steffen
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