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 * January or February 2017
 * Constanța, Romania
 * January 12-16, 2017

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

 * IRC: [[irc://irc.debian.org/debian-med|#debian-med]] on irc.debian.org (OFTC)
 * [[Sprints/2017/DebianMed2017Notes]]
Line 9: Line 13:

TBD
{{{
Splaiul Independenței 91-95
București 050095
România
}}}

[[https://photos.google.com/share/AF1QipM70_6O2_mD__CQMErqYhejmvTS_Y8ZNGLzWq-7SuQv0mNKmg2kISNFFXHvOhqqlQ?key=RjBUQmxWWnhUTk5IaE9kRVFaMGM3dS1SdXpzTERn|Pictures]] of the walk from the hotel and other pictures from the event

[[https://www.google.com/maps/place/Facultatea+de+Biologie/@44.4354485,26.0841636,14z/data=!4m12!1m6!3m5!1s0x40b1ff473869f53f:0xee62eda4d786c152!2sUniversitatea+din+Bucure%C8%99ti!8m2!3d44.4354447!4d26.1016731!3m4!1s0x0:0x9e6f994a1c8a0014!8m2!3d44.4331478!4d26.0837692?shorturl=1&dg=dbrw&newdg=1|Google Map]], [[https://www.rome2rio.com/s/My-hometown/Splaiul-Independen%C8%9Bei-91-Bucure%C8%99ti-Romania|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 [[https://www.google.ro/maps/place/S.C.M.+ROMARTIZANA/@44.4332038,26.0956113,17z/data=!3m1!4b1!4m5!3m4!1s0x40b1ff40f74698a3:0xacc485076ce11102!8m2!3d44.4332!4d26.0978?hl=ro|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..
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|| 1|| Michael R. Crusoe || michael.crusoe@gmail.com || - || - || Common Workflow Language || Romania || - || - ||
|| 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||
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TBD
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
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=== Collaboration with ELIXIR ===
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
 1. Ask sprint participants to join me in nagging upstream to free [[DebianMed/SoftwareLiberation|their code]]
   * blat
   * paml
   * r-cran-edger (locfit)
   * segemehl
   * trf
   * varscan
 1. Mentoring about packaging
 1. Fixing bugs
 1. Updating existing packages

O. Sallou

 * bedops packaging [uploaded, in NEW]
 * BaitFilter packaging [uploaded, in NEW]
 * Look for biomaj3 packaging [uploaded, in NEW]
 * CWL discussions
 * Galaxy analysis for packaging [created git repo with first steps and list of missing deps ]
 * update ncbi-blast+
 * Fixing bugs

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?

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A. Tille

 1. Packaging
   * sra-toolkit update: done
   * freebayes: uploaded to new
 1. Bugs fixed
   * [[https://bugs.debian.org/839022|libgraphics-colornames-perl: libgraphics-colornames-perl: Build-Depends on perl-modules-5.22]]
   * [[https://bugs.debian.org/839023|libgraphics-colorobject-perl: Build-Depends on perl-modules-5.22]]
   * [[https://bugs.debian.org/850029|libbio-perl-run-perl: fails to upgrade from 'jessie']]
   * [[https://bugs.debian.org/851230|primer3 FTCBFS: uses build architecture c++ compiler via unconventional variable CPP]]
   * [[https://bugs.debian.org/851219|sra-toolkit: /usr/bin/kget is already shipped by the package kget]]
   * [[https://bugs.debian.org/851459|snap: Update autokpgtest for name change]]
   * [[https://bugs.debian.org/813718|mricron FTBFS because fpc check got more strict]]
 1. 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
 1. 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
 1. Mentoring
   * Anton by packaging gxargparse and galaxyxml
 1. Sponsoing
   * python-pybedtools (Michael Crusoe)
   * python-gffutils (Michael Crusoe)
 1. New packages
   * r-cran-triebeard
   * r-cran-httpcode
   * r-cran-urltools
   * r-cran-crul

S. Steinbiss

  * Backports uploaded
    * python-pyelftools
    * yapf
    * forensic-artifacts
  * New upstream versions
    * openslide-python 1.1.1
    * swarm-cluster 2.1.10
    * tifffile 20151006
    * igv 2.3.90
    * bowtie2 2.3.0
    * embassy-phylip 3.69.660
    * cwltool 1.0.20170114120503
    * libzstd 1.1.2
    * python-pbcommand 0.5.3
    * hhsuite 3.0 beta 2
  * Other uploads
    * datatables.js
    * njplot 2.4-7
    * khmer 2.0+dfsg-8
  * Bugs fixed
    * [[https://bugs.debian.org/850879|datatables.js: Build uses static filenames in /tmp, does not catch errors]]
    * [[https://bugs.debian.org/827143|OpenSlide Python 1.1.1 is out]]
    * [[https://bugs.debian.org/846487|src:hhsuite: New version available]]
  * Misc
    * autopkgtests for tifffile
    * autopkgtest rework (Xvfb) for njplot
    * Fix pkg-config and autopkgtests for khmer
    * Add alternatives setup to cwltool.

Line 39: Line 233:
 * [[http://debconf15.debconf.org/sponsors.xhtml|sponsors]] of DebConf15  * the Faculty of Biology, University of Bucharest (Bucharest, Romania)
 * the [[http://www.commonwl.org|Common Workflow Language project]]
Line 41: Line 236:
 * sponsor ...
 * venue ...
 * etc ...

Debian Med 2017 Sprint

Location, Date

  • January 12-16, 2017

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

  • bedops packaging [uploaded, in NEW]
  • ?BaitFilter packaging [uploaded, in NEW]

  • Look for biomaj3 packaging [uploaded, in NEW]
  • CWL discussions
  • Galaxy analysis for packaging [created git repo with first steps and list of missing deps ]
  • update ncbi-blast+
  • Fixing bugs

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