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|| 5|| Michael R. Crusoe || mrc commonwl.org || No || || CWL/Debian || LT || TBD || TBD || || 5|| Michael R. Crusoe || mrc commonwl.org || No || || CWL/Debian || LT || 2018-02-07 || TBD ||

Debian Med 2018 Sprint

Location, Date

  • January 26-28 shifted to February 10 (Saturday) - 12 (Monday), 2018 to synchronize with an ELIXIR event.

  • Pre-meetings + tutorials for locals already happen on Friday (9th).
  • Location: Barcelona, Biomedical Research Park, Marie Curie room

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

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

TBD

Food at the venue

TBD

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

Debian

DE

2018-02-08

2018-02-13

3

Andreas Tille

<tille>

Yes

Debian

DE

2018-02-08

2018-02-15

4

Sascha Steinbiss

<satta>

No

Debian

DE

2018-02-09

2018-02-12

5

Michael R. Crusoe

mrc commonwl.org

No

CWL/Debian

LT

2018-02-07

TBD

6

Matúš Kalaš

matus.kalas uib.no

Yes

Not yet

Uni Bergen & EDAM

NO

2018-02-07

2018-02-12 or 2018-02-13

7

Tony Travis

tony.travis

Yes

No

minke.informatics.co.uk

UK

TBD

TBD

8

Fabian Klötzl

.de

No

Max-Planck

DE

TBD

TBD

9

Fabien Pichon

.com

Yes

FR

08 or 09

TBD

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.

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?

Reports

Personal Reports

Tony Travis

  1. Update on Bio-Linux 8.0.8 point release
  2. Progress towards Bio-Linux 9

Acknowledgements

the sprint has been possible thanks to:

  • donations to the Debian project [confirmation pending]


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