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.

• IRC: #debian-med on irc.debian.org (OFTC)

• Sprints/2017/DebianMed2017Notes

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)

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

   • libgraphics-colornames-perl: libgraphics-colornames-perl: Build-Depends on perl-modules-5.22

   • libgraphics-colorobject-perl: Build-Depends on perl-modules-5.22

   • libbio-perl-run-perl: fails to upgrade from 'jessie'

   • primer3 FTCBFS: uses build architecture c++ compiler via unconventional variable CPP

   • sra-toolkit: /usr/bin/kget is already shipped by the package kget

   • snap: Update autokpgtest for name change

   • mricron FTBFS because fpc check got more strict

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

• 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

  • datatables.js: Build uses static filenames in /tmp, does not catch errors

  • OpenSlide Python 1.1.1 is out

  • 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.

Acknowledgements

the sprint has been possible thanks to:

• the Faculty of Biology, University of Bucharest (Bucharest, Romania)

• the Common Workflow Language project

• donations to the Debian project

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