Dear Debian Community,
Debian Med joined the virtual (online) [COVID-19 Biohackathon] from
April 5-11 2020. We considered the outcome a great success in terms of
the approached tasks, the new members we gained and the support of
Debian infrastructure teams (namely the ftpmaster team). We tried to
tie up to this success in a [second Debian Med hackathon] since
COVID-19 is not over. The Debian Med team wants to do another week of
hackathon as kind of "DebCamp effort". Thus our third sprint will
be held from August 16th to August 22th 2020.
A [recently shared pre-publication draft paper] highlights which
software tools are considered useful "to Accelerate SARS-CoV-2 and
Coronavirus Research". Many of these tools would benefit from being
packaged in Debian and all the advantages that Debian brings for both
users and upstream alike.
As in the previous sprints most tasks do not require any knowledge of
biology or medicine, and all types of contributions are welcome: bug
triage, testing, documentation, CI, translations, packaging, and code
contributions.
1. [Debian related bugs in COVID-19 related packages]
2. [COVID-19 related software that is awaiting packaging]
please respond to the RFP with your intent so we don't duplicate work
We also maintain some rough spreadsheet to assemble preconditions
for [some frequently used workflows].
3. You can also contribute directly to the upstream packages, linked
from the [Debian Med COVID-19 task page]. Note: many biomedical
software packages are quite resource limited, even compared to a
typical FOSS project. Please be kind to the upstream author/maintainers
and realize that they may have limited resources to review your
contribution. Triaging open issues and opening pull requests to fix
problems is likely to be more useful than nitpicking their coding
style.
4. Architectures/porting: Please focus on amd64, as it is the primary
architecture for biomedical software. A secondary tier would be arm64 /
ppc64el / s390x (but beware the endian-related issues on s390x). From a
free/open hardware perspective it would be great to see more riscv64
support, but that is not a priority right now
5. Python developers: The Debian Med team is also trying to [improve the
availability of automated biomedical pipelines/workflows] using the
Common Workflow Language open standard. The reference implementation of
CWL is written in Python and there are many [open issues ready for work
that don't require any biomedical background].
6. It is very easy to contribute to Debian Med team. We have a lowNMU
policy for all our packages. Merge requests on Salsa are usually
processed quickly (but please ping some of the latest Uploaders of the
package to make sure it will be noticed). Even better if you ask for
membership to the team and push directly to the salsa repository.
7. The [debian-med-team-policy] should answer all questions how to contribute.
8. There is a [work-needed wiki] that will help keep track of who is
working on which projects.
9. There is also a [NEW requests wiki] where we can request expedited
NEW processing to support this effort. In the last sprint ftpmaster
was picking from here with high priority. Thanks again for this.
During the hackathon we will coordinate ourselves via the the Salsa
coordination page, Debian Med mailing list and IRC:
* https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/Covid-19-hackathon
* https://lists.debian.org/debian-med/
* https://wiki.debian.org/IRC
* irc://irc.debian.org/debian-med
* https://jitsi.debian.social/DebianMedCovid19
on Monday 2020-08-17 and Friday 2020-08-21 as well as ad-hoc
meetings if needed (in former sprints we did daily video
meetings but it seems some kind of starting and ending
meeting might be sufficient).
Thanks in advance for considering to join our sprint.
Sincerely
Andreas Tille on behalf of the Debian Med team.
[COVID-19 Biohackathon] https://github.com/virtual-biohackathons/covid-19-bh20
[second Debian Med hackathon] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/2nd-Covid-19-Hackathon
[recently shared pre-publication draft paper] https://doi.org/10.20944/preprints202005.0376.v1
[Debian related bugs in COVID-19 related packages] https://blends.debian.org/med/bugs/covid-19.html
[COVID-19 related software that is awaiting packaging] https://blends.debian.org/med/tasks/covid-19
[some frequently used workflows] https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
[Debian Med COVID-19 task page] https://blends.debian.org/med/tasks/covid-19
[improve the availability of automated biomedical pipelines/workflows] https://doi.org/10.1007/s41019-017-0050-4
[open issues ready for work that don't require any biomedical background] https://github.com/common-workflow-language/cwltool/issues
[debian-med-team-policy] https://med-team.pages.debian.net/policy/
[work-needed wiki] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work
[NEW requests wiki] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/NEW-Requests
--
http://fam-tille.de
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