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Debian Med 2018 Sprint

Location, Date

  • February 10 (Saturday) - 12 (Monday), 2018
  • Pre-meetings + tutorials for locals already happen on Friday (9th).
  • Location: Barcelona, Biomedical Research Park, Marie Curie room (Friday - Sunday), Ramon Y Cajal Sala (Monday)

This is an informal co-working and co-learning event, participants are welcome to attend on the days that work for their schedule.

Participants of the sprint

Getting there

Barcelona is well connected. You will know how to get there. Should there be someone who is kind of new to this "travel alone to foreign countries where you do not know anybody and do not speak the language" thingy, traveling with too much luggage to carry or be there some other need for assistance then we can certainly arrange these individuals to be collected from the airport.

Hotel proposal

A couple of emails back and forth, the hotel to go for is

Otherwise, the hotel is full now. To join, check one of the typical hotel booking places and select something in the center. The meeting is directly at the sea side (as it should be).

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

Cedric Notredame

Yes

N/A

local

-

-

2

Steffen Möller

<moeller>

Yes

Yes

Debian

DE

2018-02-08

2018-02-13

3

Andreas Tille

<tille>

Yes

Shared with OS

Debian

DE

2018-02-08

2018-02-15

4

Sascha Steinbiss

<satta>

Yes

Yes

Debian

DE

2018-02-09

2018-02-12

5

Michael R. Crusoe

mrc commonwl.org

Yes

Yes

CWL/Debian

LT

2018-02-07T20:20

2018-02-13T10:15

6

Matúš Kalaš

matus.kalas uib.no

Yes

Yes

Uni Bergen & EDAM

NO

2018-02-07T20:05

2018-02-13T17:20

7

Tony Travis

tony.travis

Yes

Yes

minke-informatics.co.uk

UK

2018-02-09

2018-02-12

8

Fabien Pichon

.com

Yes

?

-

FR

08 or 09

TBD

9

Olivier Sallou

<osallou>

Yes

Shared with AT

Debian

FR

2018-02-07

2018-02-12

10

Cédric Lood

cedric.lood kuleuven.be

Yes

Yes

KU Leuven

BE

2018-02-09

2018-02-13

11

Hervé Ménager

herve.menager pasteur.fr

Yes

Yes

Insitut Pasteur, Paris

FR

2018-02-07

2018-02-10T14:30

Please use ISO 3166 two-letter country codes and YYYY-MM-DDTHH:MM format.

Agenda

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, Arvados, and Rabix Bunny.

Bring CWL workflows to Debian in their own right with automated testing.

Discuss Salsa migration from Alioth and the future of SVN.

Personal agendas

Tony Travis

  • Bio-Linux as an alternative platform for Debian-Med

Steffen Möller

  • RFD: What should our next task pages look alike, how does this compare with what the RRID providers and the CWL are doing?
  • RFD: How should Debian present itself at scientific conferences
  • RFD: What do we expect from our task pages?
  • RFD: What do Biomedical Workflows mean to us?
    • How do we support them?
    • How do we test them?
    • How do we display them?

Sascha Steinbiss

  • Coming up with some degree of automation for migrating repos to Salsa
  • (Revisiting Nextflow packaging, maybe with Paolo? -- less likely than expected)

Matúš Kalaš

  • Improvements to EDAM using the users' and potential users' feedback
  • Sketch out the support of EDAM-communities (e.g. EDAM-bioimaging)
  • Debian vs Debian Med vs Bio-Linux, and dev|b community vs scientists community: outreach, visibility, training, impact
    • PR: Wikipedia, Bio-Linux and Debian Med websites, mutual endorsements (with explanations and links) on websites and splashscreens where applicable

    • The next Debian Med paper:
      • EDAM and links to Bio- and OMICtools etc.
      • CWL and scientific workflows
      • Bio-Linux and trainingshowed
      • Bioconda, ?BioContainers and HPC and training

      • Popularity statistics
      • Salsa, git, and accessiblity for contributors
      • Community building and grassroot effort
      • Tools comparisons? (aka "benchmarking")
      • ...
  • Attempt to propose an ELIXIR Debian "Community"? Worth the effort?
  • Any need to improve interface with the bioimage informatics community? (NEUBIAS is a great community network supported by EU COST)

  • Personal task: Add|update some EDAM annotations to EDAM 1.20 and EDAM-bioimaging alpha03 (or maybe even release alpha04 first)
  • How to license descriptions of software? (permisive vs copyleft, attribution, how to attribute?)
  • Persisting topic: (Any new ideas?) How to sync software descriptions between Debian (Med), Bio.Tools, NEUBIAS biii.eu, SEQwiki, etc.

Reports

Personal Reports

Tony Travis

  1. Update on Bio-Linux 8.0.9 point release
    1. Demonstrated a Bio-Linux 8.0.9 VM running on CyVerse Atmosphere a Biologist-friendly front-end to OpenStack

    2. Created a Bio-Linux 8.1.0 Bio-Linux USB stick with a custom kernel patched to support the Microsoft Surface keyboard, but it didn't
  2. Progress towards Bio-Linux 9
    1. Steffen Moeller taught me how to port missing/out-of-date packages from Debian Sid into the Ubuntu Debian-Med PPA
    2. Gave Andreas Tille a list of packages installed by default in Bio-Linux for comparison with Debian-Med/bio*
    3. Advice from Andreas Tille to try Debian-live for Bio-Linux 9
    4. Reported support for continued development of Bio-Linux from NERC/EOS director Peter Kille at Cardif University

Andreas Tille

  1. Migration to Salsa of some Debian-Med relevant packages of ?DebiChem team

  2. Introduce Fabien Pichon into script to obtain package metadata

  3. Uploads
    1. sponsored libbpp* and bppsuite
    2. updated bedtools
    3. updated python-cutadapt (+ depencency python-xopen)
    4. updated diamond-aligner
    5. updated examl
    6. sponsored galaxy-lib to new
    7. updated hilive
    8. updated libsbml (fixing 890089)

    9. fix bio-travis (890096)

    10. fix kalign (890256)

  4. Start script to read machine readable data from salsa

  5. Mentoring Cédric Lood at the example of packages bandage and porechop (both need more work)
  6. Fixed and uploaded rejected packages:
    1. python-bd2k
    2. nanook
    3. obitools
    4. r-cran-rmarkdown
  7. Assemble list of missings in Debian compared to Bio-Linux

  8. Moved team policy to Git

Sascha Steinbiss

  1. Misc bug fixing and improvements
    1. Fixed autopkgtest in golang-github-thecreeper-go-notify, migrate to Salsa and housekeeping
    2. Fixed watchfiles in iva and ariba to not report pre-release tags
    3. Updated rna-star to new upstream version
    4. gnome-keysign: Helped upstream reproduce FTBFS due to test failures on a shared machine
  2. Salsa migration
    1. Wrote script to automate Salsa migration and disable pushes to Alioth: https://salsa.debian.org/satta/salsa-migration-tools

    2. Mass-migrated team repositories to Salsa
    3. Sent MR to anonscm->salsa redirector service

    4. Enabled integrations (email on push, IRC notifications, tagpending hook)
    5. Sent emails to mailing lists
    6. Fixed URLs with dots: https://salsa.debian.org/salsa/AliothRewriter/merge_requests/145/diffs

    7. Wrote new setup-repository script: https://salsa.debian.org/satta/salsa-migration-tools/blob/master/setup-repository.rb

    8. Migrated my own repos to Salsa (orchid, mussort) -> these could go to the new collab-maint replacement at some point

  3. Keysigning with two new contributors=

Olivier Sallou

  1. Tried to fix shared lib in gatb
    1. Failed to fix the issue after investigation and test
  2. Upgrade biomaj3-* to latest upstream
    1. status: uploaded new releases and pushed to salsa
  3. Upgrade biojava4-live to latest upstream
    1. status: uploaded
  4. Upgrade ncbi-blast+ to latest upstream
    1. status: uploaded
  5. Polishing of scripts to inject DebianMed packages to ?BioContainers (Docker container repo for bioinformatics)

    1. Script are ready and tested, expect to upload recipes to biocontainers
      • this month.

Michael R. Crusoe

Started DebianMedAutoBackports planning

Acknowledgements

the sprint has been possible thanks to:

  • donations to the Debian project [confirmation pending]


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