Differences between revisions 31 and 32
Revision 31 as of 2019-01-15 13:52:58
Size: 6960
Comment: +coinciding festivities on March 11
Revision 32 as of 2019-01-15 14:08:54
Size: 6957
Comment: booked a room for Matus
Deletions are marked like this. Additions are marked like this.
Line 54: Line 54:
|| 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

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.

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

https://www.vilnius-airport.lt/s/docs/2018_skrydziu_zemelapis_en.pdf

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# )

https://www.kaunas-airport.lt/images/pdf/2018_skrydziu_zemelapis_en.pdf

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

Email

confirmed

booked accom.

Organisation

Living in

Arrival at

Departure at

1

Michael R. Crusoe

mrc@commonwl.org

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

andrius.merkys@gmail.com

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

chuprikovalv@gmail.com

Yes

booked

UAM

ES

2019-03-09 14:40

2019-03-12 19:20

8

Matus Kalas

matus.kalas@uib.no

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:

  1. Generate a CTD description for each binary using the hidden --write-ctd option combined
  2. Convert that CTD to CWL with https://github.com/WorkflowConversion/CTDConverter

  3. 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:

  1. Setup pbuilder chroot / lxc container
  2. install Debian package / install program via ?BioConda

  3. Record:
    1. Time to install package/program
    2. 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:


CategorySprint