Debian Med 2018 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.

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

Steffen Möller

Sascha Steinbiss

Matúš Kalaš

Reports

Personal Reports

Tony Travis

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

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 b. updated bedtools

Acknowledgements

the sprint has been possible thanks to:


CategorySprint