I would recommend getting as many components of http://covid19.genenetwork.org/ packaged for Debian as possible.
Workflows are at https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate Maybe someone can start by identifying the software used and seeing which is already packaged for Debian? Currently the workflows are run on Arvados. How is the packaging of Arvados coming along? -- Michael R. Crusoe On Fri, Nov 6, 2020, 17:50 Steffen Möller <[email protected]> wrote: > Dear all, > > We have multiple aims. Here are mine: > > a) do something good > b) show to the world that our infrastructure is usable > c) do something that is not redundant > d) be educational > e) come up with findings that can be reproduced > f) have it all automated, preferably in a way that it can be adapted for > other diseases/symptoms/whatever. > > Idea: We do not go for a single paper that we want to reanalyse (would > be redundant at best) but get _all_ RNA-seq raw data on Covid-19. I > thought about using PiGx-rnaseq (bcbio is not ready) to get us read > counts and the typical gene set enrichment analyses. With that many > samples, we should also have options for downstream analyses for which > earlier efforts possibly lacked the statistical power. > > How do you feel about this? Should we prepare a Virtual Sprint for it? > > Best, > > Steffen > >
