Debian Med 2017 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

Splaiul Independenței 91-95
București 050095
România

Pictures of the walk from the hotel and other pictures from the event

Google Map, Directions

If arriving via airplane you may have a bus transfer from the plane to the airport terminal, so be prepared for temperatures approaching -13 °C.

Local travel: Taxis won't have working seat belts, Uber will

(M. Crusoe: Normally I recommend anything but Uber, but in Romania it is the only taxi option with seat belts)

Bus information: http://www.ratb.ro/eng/index.php (Google Maps has the schedules as well)

Route planner: http://www.ratb.ro/eng/calcul_ruta_en.php

Metro: run by a different company and it doesn't connect with the airport, so it is unlikely to be useful for most people

Recommended souvenir & gift store: Romartizana Cal. Victoriei, 16-20

Hotel proposal

Olivier: I have a reservation at this place: 

Hotel Trianon
Cobalcescu Grigore 9, Sector 1, 010191 Bucarest, Roumanie

http://www.hoteltrianon.ro/

There is free wifi, a restaurant and rooms with twin beds if you want to share a room. It is not far from Splaiul Independenței. Hotel is referenced on booking.com etc..

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

Michael R. Crusoe

michael.crusoe@gmail.com

Yes

N/A

Common Workflow Language

Bucharest, Romania

-

-

2

Steffen Möller

<moeller>

Yes

Hotel Trianon

Debian

 D

12.1.17 10:50

17.1.17

3

Olivier Sallou

<osallou>

Yes

Yes

Debian

 FR

12.1.17, 13h55 (OTP)

16.1.17, 14h40 (OTP)

4

Sascha Steinbiss

<satta>

Yes

Yes

Debian

D

Fri, 13.1.2017, 10:25

Sun, 15.1.2017, 20:10

5

Andreas Tille

<tille>

Yes

Hotel Trianon

Debian

D

Thu, 12.1.2017, 13:30 (arrival OTP)

Mon, 16.1.2017, 14:15 (departure OTP)

6

Anton Khodak

anton.khodak@ukr.net

Yes

Yes

Common Workflow Language

Kyiv, Ukraine

Wed, 11.1.2017, 16:20

Sun, 15.1.2017, 17:00

7

Matúš Kalaš

matus.kalas@uib.no

Yes

N/A

Bio.Tools & EDAM

Bergen, Norway

Sun, 15.1.2017, 00:30 (OTP)

Tue, 17.1.2017, 13:50 (OTP)

N

Your name

Your email address

Confirmed?

Booked accommodations?

Your affiliation

Your homebase

Arrival day & time

Departure day & time

Agenda

Free to take CWL+Debian items:

  1. Teach Lintian that cwl-runner is an acceptable interpreter https://bugs.debian.org/851126

  2. Copy CWL descriptions to existing packages, to be installed in /usr/share/commonwl/ as per http://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem

Personal agendas

M. Crusoe:

  1. Getting existing CWL descriptions for tools inside packages, upstreaming them, and writing new descriptions.

  2. Proof-of-concept for returning a Debian package name for a software identifier such as RRID (example: https://identifiers.org/rrid/RRID:SCR_001156 ) or bio.tools (example: https://bio.tools/tool/SignalP/version/4.1 )

It would also be great to see progress on packaging the various implementations https://github.com/common-workflow-language/common-workflow-language#implementations

S. Möller:

  1. Decide about how to present Debian Med on scientific conferences. Would very much like to implement a routine workflow dynamically on a cloud.
  2. Proceed on bio.tools integration with Matus and Jon

A. Tille:

  1. Packaging
    • cytoscape
    • freebayes
    • gatk
    • kronatools
    • malt
    • sra-sdk update
    • snpeff

    • sift/blimps -> free

    • dcm4che 3

  2. Ask sprint participants to join me in nagging upstream to free their code

    • blat
    • paml
    • r-cran-edger (locfit)
    • segemehl
    • trf
    • varscan
  3. Mentoring about packaging
  4. Fixing bugs
  5. Updating existing packages

O. Sallou

M. Kalas

  1. Representing Debian Med packages in Bio.Tools
    • EDAM annotations in Debian (Med)
    • Export package descriptions in biotoolsSchema. Extended? Living on github?
    • Import to Bio.Tools
    • Directions for further improvements
  2. Listing all relevant "bio" data/file formats in EDAM
    • Plus, how to proceed further with registering IANA media types?
  3. How to provide a custom sequence annotation DB with minimum effort, using Debian building blocks?
    • This may ideally serve also as a platform for building data formats interoperability and data optimisation on top of it
  4. How to convince computational biologists to use Debian?

Reports

Personal Reports

A. Tille

  1. Packaging
    • sra-toolkit update: done
    • freebayes: uploaded to new
  2. Bugs fixed
  3. Updated
    • r-cran-shiny to 1.0.0
    • snakemake to 3.9.1
    • bamtools to 2.4.1
    • sniffles to 1.0.2
    • r-bioc-annotationdbi to 1.36.1
    • r-cran-spdep to 0.6-9
    • r-cran-maptools to 0.8-41
    • r-cran-maldiquant to 1.16.1-1
    • r-cran-googlevis to 0.6.2-1
    • qtltools to 1.1
    • yaggo to 1.5.9
  4. Fix autopkgtests
    • njplot
    • pirs
    • art-nextgen-simulation-tools
    • artfastqgenerator
    • htslib
    • bioperl
    • pbbarcode
    • r-bioc-annotationdbi
    • r-bioc-limma
    • Test for r-bioc-geneplotter removed since not packaged databases would be needed
    • python-biopython
    • r-bioc-metagenomeseq
    • r-bioc-s4vectors
    • r-bioc-rsamtools
    • r-bioc-summarizedexperiment
    • r-cran-adephylo
    • r-cran-bbmle
    • r-cran-googlevis
  5. Mentoring
    • Anton by packaging gxargparse and galaxyxml
  6. Sponsoing
    • python-pybedtools (Michael Crusoe)
    • python-gffutils (Michael Crusoe)
  7. New packages
    • r-cran-triebeard
    • r-cran-httpcode
    • r-cran-urltools
    • r-cran-crul

S. Steinbiss

Acknowledgements

the sprint has been possible thanks to:

CategorySprint