Debian Med Sprint 2020

Location, Date

Venue

We will have access to one large (~15 people) and one small (~ 5 people) meeting room, so working in separate groups from time to time is definitely possible. A comfortable open space with coffee machine for socialising and relaxing is available.

Network and Wifi

There will be only public WiFi provided by DCSO. Sorry, no wired ethernet unless someone brings an access point and switch.

Getting there

Berlin can be easily reached from within Germany using the DB train system (Berlin Hbf or Berlin-Südkreuz) or Flixbus long-distance bus service (Berlin ZOB or Alexanderplatz). There are also two main international airports: Berlin Tegel (TXL) and Schönefeld (SXF). Both have good public transport connections to the rest of the city for typically <5 EUR per trip (TXL bus or S-Bahn S9 and S45 for SXF).

The venue is easily reachable by S-Bahn (S1, Ringbahn S41/S42/S46) via Schöneberg station. There are also a couple of buses running (M46, 248). See https://sbahn.berlin/liniennetz/station/235/ for more details. Südkreuz station would also be an alternative with a bit of walking.

Please avoid coming by car in favour of the environment and limited parking.

Accommodation

There are a variety of hotels and hostels just a couple of S-Bahn stations from the venue, e.g. near Potsdamer Platz or Anhalter Bahnhof: https://www.google.com/maps/search/hotels+near+euref-campus/@52.4884989,13.3415758,14z/data=!3m1!4b1!4m5!2m4!5m3!5m2!4m1!1i2

Examples:

Food

The venue is located in the "Rote Insel" district of Berlin (https://en.wikipedia.org/wiki/Rote_Insel) with many suitable and affordable lunch spots, e.g. good Korean and Indian restaurants, a South German Wirtshaus within very short walking distance, and various fast food options (with vegetarian menu items).

Bring

Please consider bringing the following items:

Participants

Please add yourself to the list below if you wish to attend. There will be space for ~15 participants.

No

Name

Email

confirmed

booked accom.

Affiliation

Country

Arrival at

Departure at

1

Sascha Steinbiss

satta

Yes

Debian

DE

2020-02-08T09:00

2020-02-09T19:00

2

Andreas Tille

tille

Yes

Debian

DE

2020-02-07T18:00

2020-02-09T19:00

3

Olivier Sallou

osallou

Yes

Yes

Debian

FR

2020-02-07T??:00

2020-02-10T??:00

4

Steffen Möller

moeller

Yes

No

Debian

DE

2020-02-07T??:00

2020-02-10T??:00

5

Michael R. Crusoe

mrc@commonwl.org

Yes

N/A

CWL/ELIXIR-NL

DE

2020-02-08T09:00

2020-02-09T19:00

6

Ben Soares

b.soares@dundee.ac.uk

Yes

Yes

University of Dundee/Jalview Team

GB

2020-02-07T18:00

2020-02-10T10:00

7

Ole Streicher

olebole

No

N/A

Debian

DE

2020-02-08T09:00

2020-02-09T??:00

8

Jun Aruga

happy _at_ oh4u _dot_ net

Yes

?

Fedora

CZ

2020-02-06T19:00

2020-02-10T15:00

9

Matúš Kalaš

matus.kalas@uib.no

Yes

Yes

EDAM, ELIXIR

NO

2020-02-07T18:00

2020-02-11T07:00

10

Alex Mestiashvili

mestia

Yes

N/A

Biotec, TU-Dresden

DE

2020-02-08 T09:00

2020-02-09T17:30

11

Tanya Malygina

Yes

Yes

botkin.ai

RU

2020-02-08T??:00

2020-02-10T??:00

12

Evan Nemerson

firsname@lasntname.com

Yes

N/A

None

US

Remote (-0800 timezone, available for a couple hours each morning Berlin time)

13

Liubov Chuprikova

chuprikovalv@gmail.com

Yes

N/A

Autonomous University of Madrid

CH

Remote (from Saturday everning)

Agenda

(tentative/final agenda here before/after the sprint)

Steffen:

Matúš:

Reports

(pointers to communication about the sprint)

Personal Reports

Andreas Tille

  1. Introduction into Debian Med Sprints

  2. Working with Ben Soares on updating Jalview (including mentoring how to package)
  3. Upload python-wordcloud (needed for Debian Med flyer)
  4. Working on bugs
    1. python-deeptools (950911)

    2. paleomix (unable to fix, pinged upstream 933750, 937232)

    3. pywnb (950936)

    4. python-biom-format (forwarded upstream 950929)

    5. python-skbio (forwarded upstream 950930)

    6. psychopy (several bugs will be fixed once python-questplus will be accepted in unstable)
    7. python-neuroshare (937945 - some remaining Python3 porting issues)

  5. Setup new server for blends.debian.net

Sascha Steinbiss

  1. Added autopkgtests to Vmatch and ?GenomeThreader

  2. Investigated IVA FTBFS and disabled tests that need lots of RAM (KMC), will wait for rebuilds
  3. Upstreamed reproducibility patches for
    1. Vmatch: https://github.com/genometools/vstree/pull/7, https://github.com/genometools/vstree/pull/6

    2. ?GenomeThreader: https://github.com/genometools/genomethreader/pull/15

  4. Made Vmatch (theoretically) build on all archs (including Hurd) by setting PATH_MAX
  5. Investigated non-reproducibility of ?GenomeTools and fixed it by using static graphics instead of regenerating them at build

  6. Investigated non-reproducibility of lambda-align and fixed it by reverting to "Release" build mode
  7. Addressed upstream issue in LTRdigest: https://github.com/genometools/genometools/pull/937

  8. (a bit offtopic:) Work towards Suricata builds in Debian without vendored Rust crates
    1. Learned how to package Rust crates using debcargo
    2. Package 6 dependencies as crates not in unstable yet
    3. Made sure these are used in the build
  9. Inquired about the state of Debian Med's Twitter account

Liubov Chuprikova

  1. Worked on qiime bugs:
    1. 950931

    2. 950842

  2. Made SINA build. Needs further investigation, as the build-time tests fail.

Alex Mestiashvili

  1. Uploaded new package bustools, 950922

  2. Uploaded new upstream releases for:
    1. snakemake
    2. plip
  3. Closed bugs:
    1. cufflinks py2 removal, 942930, 936351

    2. snakemake FTBR, 943956

  4. Worked on 950945, prepared systemd service file

  5. Requested removal of giira and tophat, once done, 873866, 938677 can be closed

  6. Updated ugene, replace tophat to hisat2

Olivier Sallou

Jun Aruga

Ben Soares

Acknowledgements

the sprint has been possible thanks to:


CategorySprint