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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
 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
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==== Tony Travis ====

 Bio-Linux as an alternative platform for Debian-Med
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==== Tony Travis ====

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

Debian Med 2018 Sprint

Location, Date

  • January 26-28 shifted to February 10-12, 2018 to synchronize with an ELIXIR event

  • Barcelona

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

Hotel proposal

TBD

Food at the venue

TBD

Food nearby

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

2018-02-09

2018-02-13

3

Andreas Tille

<tille>

Yes

Debian

DE

2018-01-25

2018-01-29

4

Sascha Steinbiss

<satta>

No

Debian

DE

2018-01-26

2018-01-29

5

Michael R. Crusoe

mrc commonwl.org

No

CWL/Debian

LT

TBD

TBD

6

Matúš Kalaš

matus.kalas uib.no

No

Uni Bergen & EDAM

NO

2018-02-07

2018-02-12

7

Tony Travis

tony.travis

Yes

No

minke.informatics.co.uk

UK

TBD

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.

Personal agendas

Tony Travis

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

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]


CategorySprint