Re: COVID-19 Biohackathon April 5-11 2020

[Steffen Möller <steffen_moeller@gmx.de>]

On 16.03.20 10:05, Andreas Tille wrote:
> Hi Michael,
>
> On Mon, Mar 16, 2020 at 09:19:29AM +0100, Michael Crusoe wrote:
> > There is one planned for the week starting April 5th
> >
> > https://github.com/virtual-biohackathons/covid-19-bh20
> > https://github.com/virtual-biohackathons/covid-19-bh20/wiki
> >
> > We should propose Debian-Med related projects, like
> I like this idea and I hope my involvement in the issue in my day job
> will not block me to much to contribute here.

Is there a chance we can get hold of some daytime colleagues of yours?

> > 1) Tag all COVID-19 related software that is packages or our on wishlist.
> > This should include medical imaging, molecular dynamics modelers,
> > epidemiological tracking and statistics, hospital management, and more
> Pretty good idea.  However, we need to trust the readers of this list
> (may be the readers of debian-devel-announce or some social media) to
> complete that tagging and the list of stuff that needs packaging.  I
> can only do technical work.

Doesn't that mean we need something to circumvent the New Queue?

And maybe do some functional but dirty packaging as in "not get all
embedded JavaScript libraries out of the way prior of putting the
package up for use"?

> > 2) Also tag supporting libraries / tools for the above. Should it be the
> > same tag or a different tag?
> I'd vote for same tag.
>
> > 3) Use these tags to highlight related bugs in Debian
> +1

> > 4) Make versions of published workflows available using the Common Workflow
> > Language and biocontainers.pro software containers (which uses Debian &
> > Conda)
> >
> > What else am I missing?
> >
> > I've created
> > https://salsa.debian.org/med-team/community/2020-covid19-hackathon as a
> > place to store notes and other planning materials.
> Good! Should we add a list of software to package and once it is done
> point ftpmaster to that list to rank it with higher preference?
>
> Is something in the new queue a potential candidate for fast-processing?

You know, I am after bcbio for two years now. It is deeply frustrating.
It is not much better for other sequencing pipelines. How many packages
will we be talking about? 20? 30? 50? 100?

If we are after working packages quickly and this involves the new queue
then I am afraid I would need some extra encouragement.


> > Sylvestre Ledru has encouraged us to post something to debian-announce@ as
> > well, but I want to have a plan from this group first. My draft
> > announcement is at
> > https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/debian-announce_draft
> > so please help me refine the text.
> I hope to be able to do this in the next couple of hours.
>
> > Hope all of you are well,
> I'm perfectly fine - hope the same for you.
>
> Thanks a lot for this effort

I want to thank you both, too.

Steffen