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booked a room for Matus
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|| 8 || Matus Kalas || matus.kalas@uib.no || Yes || requested || Uni Bergen, EDAM || NO || 2019-03-08T22:47 || 2019-03-11T18:50 || | || 8 || Matus Kalas || matus.kalas@uib.no || Yes || booked || Uni Bergen, EDAM || NO || 2019-03-08T22:47 || 2019-03-11T18:50 || |
Debian Med 2019 Sprint
Location, Date
- March 9 (Saturday) - 11 (Monday), 2019 **
Location: Vilnius, Lithuania, NVO Avilys coworking space Tauro g. 12, Vilnius LT-01114, Lithuania https://goo.gl/maps/125dEvYMtBS2
This is an informal co-working and co-learning event, participants are welcome to attend on the days that work for their schedule. There is a possibility to arrive or depart a day earlier or later, ask on the mailing list if this interests you.
IRC: #debian-med on irc.debian.org (OFTC)
?Sprints/2019/DebianMed2019Notes
Getting there
Use this link to get travel recommendations: https://www.rome2rio.com/map/My-hometown/Tauro-g-12-Vilnius-01114-Lituania
Travel wise you can fly into the VNO airport with many low cost flights. Travel time from the airport to the venue is 7 minutes by taxi, 20 minutes by city bus (1 EUR, pay on the bus)
For a local taxi, one can use invite code 9GVRN and get a free ride up to -4€. Redeem it at https://invite.taxify.eu/9GVRN
Lithuania's second city, Kaunas, also has an airport (KUN) and is 1.5 hours away by train or bus. (The KUN to Vilnius bus schedule is linked to the RyanAir flight schedule: https://www.ollex.lt/en/express/Kaunas-airport/buy-a-ticket# )
Accomodations proposal
Vilnius University apartments offer single rooms for 24-32 EUR). They're located 15 minutes walk from the venue. Breakfast is not included, but there are plenty of places to eat around.
Payments are to be made at the reception, all sorts of cards should be accepted.
To reserve your room, indicate "requested" in the "booked accom." column below.
The venue has free coffee, espresso, and tea prepared on demand.
Participants
(tentative/final list of participants here before/after the sprint)
No |
Name |
confirmed |
booked accom. |
Organisation |
Living in |
Arrival at |
Departure at |
|
1 |
Michael R. Crusoe |
Yes |
N/A |
CWL/VšĮ "Darbo eigos" |
LT |
2019-03-09T08:00 |
2019-03-11T21:00 |
|
2 |
Andreas Tille |
tille |
Yes |
booked |
Debian |
DE |
2019-03-08 18:15 |
2019-03-11 14:25 |
3 |
Andrius Merkys |
Yes |
N/A |
Vilnius University |
LT |
2019-03-09T08:00 |
2019-03-11T21:00 |
|
4 |
Olivier Sallou |
osallou |
Yes |
booked |
Debian |
FR |
2019-03-08 |
2019-03-11 |
5 |
Steffen Möller |
moeller |
Yes |
requested |
Debian |
DE |
early |
|
6 |
Sascha Steinbiss |
satta |
Yes |
booked |
Debian |
DE |
2019-03-08 18:15 |
2019-03-11 14:25 |
7 |
Liubov Chuprikova |
Yes |
booked |
UAM |
ES |
2019-03-09 14:40 |
2019-03-12 19:20 |
|
8 |
Matus Kalas |
Yes |
booked |
Uni Bergen, EDAM |
NO |
2019-03-08T22:47 |
2019-03-11T18:50 |
Please use ISO 3166 two-letter country codes and YYYY-MM-DDTHH:MM format.
Agenda
Michael R. Crusoe
Synchronize our metadata with wikidata; include their identifiers in debian/upstream/metadata. Write this up in a blog post to encourage other (bio.tools, ?OntoTools, etc.) to do the same.
Ship more CWL descriptions in /usr/share/commonwl/ http://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem
For app that use <seqan/arg_parse.h> and that lack a curated CWL description:
- Generate a CTD description for each binary using the hidden --write-ctd option combined
Convert that CTD to CWL with https://github.com/WorkflowConversion/CTDConverter
- Install that CWL description to /usr/share/commonwl as part of the package
Continue the packaging of popular CWL executors with full CWL v1.0.x support like toil-cwl-runner and Arvados. Assist packaging of Galaxy in anticipation of their CWL support.
Bring CWL workflows to Debian in their own right with automated testing.
Write up Google Summer of Code proposal about benchmarking of auto-vectorization and per CPU optimization to produce "fat" binaries for bioinformatics software: https://twitter.com/kloetzl/status/1076082255481720832
Steffen Möller
Revisit ?AutoDockTools
- bcbio workflow and its dependencies + Python 3 ports
- preparation for booth at upcoming conference(s)
Andrius Merkys
- Contribute to packaging and bug squashing for Debian Med
- Keysigning
Any takers???
Benchmark test between Debian Med and ?BioConda.
We have several packages featuring an autopkgtest. We take those package to automate the following benchmark:
- Setup pbuilder chroot / lxc container
install Debian package / install program via ?BioConda
- Record:
- Time to install package/program
- Time to run test
Finally graph the compared results.
Matus Kalas
Add & update EDAM annotations and catalogue IDs for Debian Med src packages
Discuss news in Bio.Tools strategy (more open) & more streamlined collaboration with Debian Med ++ then contribute our common ideas|recommendations|requirements to the shaping new Bio.Tools dev & curation model
Reports
Coinciding events
March 11 is celebrated as Day of Restoration of Lithuanian Independence. There usually are various festivities on this day in the Old Town.
Acknowledgements
the sprint has been possible thanks to:
donations to the Debian project [confirmation pending]
http://www.nvoavilys.lt/ NVO Avilys for donation of the work space, WiFi, and coffee!