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• Debian Med ...020, Berlin

Debian Med Sprint 2020

Location, Date

• when: Feb 8/9, 2020

• where: DCSO GmbH , EUREF-Campus 22, 10829 Berlin, Germany

• Venue will be open at ~9AM, please ring the bell outside building number 22 ("DCSO" 2nd floor, main reception). If no one opens, please call organiser (+49 (0)151 54150155)

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:

• Within walking distance: https://www.google.com/maps/place/Hotel+Sch%C3%B6neberg/@52.4838617,13.3538017,17.5z/data=!4m8!3m7!1s0x0:0x7cbdc6094eb22597!5m2!4m1!1i2!8m2!3d52.4849925!4d13.3545083

• Few S-Bahn stations away: https://www.google.com/maps/place/Hotel+Novotel+Suites+Berlin+City+Potsdamer+Platz/@52.5048022,13.3817308,16.54z/data=!4m8!3m7!1s0x0:0x1c4720a47f155c71!5m2!4m1!1i2!8m2!3d52.50457!4d13.38312 and others in the area

• On campus: https://euref.de/en/euref-campus_en/campus-life/#overnight (only few spaces available, might go quickly)

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:

• computers
• adaptors for EU power plugs, if necessary
• power bars
• Mohnschnecken

Participants

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

Agenda

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

Steffen:

• Revisiting workflows (pigx, bcbio)
• Report on experiences with med.functional.domains semi-autobuilds
• Exchange on how Andreas' "routine-upgrade" and the nagging workflows changed my view on d/patches
• Revisiting refs to conda and bio.tools
• Collecting thoughts on our tasks pages
• Packaging load - should we prioritize? Automate? Learn from conda?
• Open Science/Med Hardware and apps in Debian

Matúš:

• Adding refs between Bioconda, Debian Med, and bio.tools; adding EDAM annotation

Reports

(pointers to communication about the sprint)

• announcement: (e.g. link to lists.d.o archives)
  • Steffen+Matus: Prepared package for bash kernel for Jupyter notebooks - only to then learn about the "!" prefix
  • Export of Debian annotation and references to bio.tools (pull request pending) - with refs to conda, omictools, biii, scicrunch
  • Inspection of udd via psql - removed last RRID references
  • Steffen+Matus+Michael: Identified need for a package-landing page for non-developers
    • should give instructions how to install
    • should not confuse too much
    • should have many distribution-independent problem-solving spirits
    • ties to CWL would be nice
    • should affect Debian as a whole, Debian Med starts out with something somewhen
• report: (e.g. link to lists.d.o archives)
• other:
• other:
• ...

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

• Patch biomaj3 package to workaround python-influxdb panda ftbs issue
• Bug squashing:
  • pbsuite (uploaded)
  • obitools (py3 port, compiles and unit tests ok, pushed to git but expects to still be buggy)
  • kinetictools (#936797): tried py3 port, but depends on pbcommand which now has a different API.
  • Investigations on opensurgsim ftbs bug(#925797): uploaded

Jun Aruga

• Worked to build application on multiple CPU architectures.

  • picard-tools: https://github.com/broadinstitute/picard/issues/1467

  • GKL: https://github.com/Intel-HLS/GKL

Ben Soares

• Learnt about packaging requirements and process, in particular issues pertinent to Jalview:
  • Gradle build / handling dynamic plugin dependencies. Create patch to create a minimal build.gradle (investigage mh_make, other gradle built packages).
  • Java lib dependencies, some already packaged for debian, others not. Intend to create packages for these too if possible.

Acknowledgements

the sprint has been possible thanks to:

• The venue is provided by DCSO GmbH.

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