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.
IRC: #debian-med on irc.debian.org (OFTC)
?Sprints/2018/DebianMed2018Notes
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
- Hotel Barcelona House Calle Escudellers 19 08002 Barcelona Tel: +34 933437167 Fax: +34 933011839
[Tony Travis has reserved a triple room here if anyone wants to share?]
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 |
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> |
No |
Yes |
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 |
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 |
Fabian Klötzl |
.de |
No |
|
Max-Planck |
DE |
TBD |
TBD |
9 |
Fabien Pichon |
.com |
Yes |
|
|
FR |
08 or 09 |
TBD |
10 |
Olivier Sallou |
<osallou> |
Yes |
Shared with AT |
Debian |
FR |
2018-02-07 |
2018-02-12 |
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:
- Generate a CTD description for each binary using the hidden --write-ctd option combined
Convert that CTD to CWL with https://github.com/WorkflowConversion/CTDConverter
- 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
- Update on Bio-Linux 8.0.8 point release
- Progress towards Bio-Linux 9
Acknowledgements
the sprint has been possible thanks to:
donations to the Debian project [confirmation pending]