Report of outputs from Debian Med Sprint Weekend 2014

Group Reports

(in no particular order)

Jalview for Debian/Bio-Linux

Tim Booth and Jim Procter worked on this

Setting up the Qlustar HPC cluster demo

Luca Clivio, Tony Travis

Work on Edam/Debtags/Tools registry

Investigate possible mechanisms of data interchange

Steffen Möller, Matúš Kalaš, Kristoffer Rapacki, Olivier Sallou, Piotr Chmura, Emil Rydza (probably splitting into subgroups)

Packaging demonstration

Brad Chapman, Daniel Barker, Andreas Tille, Detlef Wolf, Iain Learmonth

Packaging the PubMed search (C + Java) from BioinfoC

Detlef Wolf, with help from Olivier Sallou, Andreas Tille, Jorge Soares, Iain Learmonth, Steffen Moeller, Tim Booth

Personal Reports

Andreas Tille

Iain Learmonth

Steffen Möller

Jorge Soares

Tim Booth

Niall Beard

Olivier Sallou

Peter Cock

Brad Chapman

A critical missing component of ?CloudBioLinux full and flavor-based custom installs is defining the full environment of packages and versions available on the system. We worked at the 2011 [BOSC] Codefest hackathon to add minimal support for creating this full manifest of packages and versions, but the script required integration into production workflows and numerous cleanups. During the first day of the DebianMed Sprint I focused on converting this manifest creation into a ?production ready importable module. It now handles creation of YAML files with packages and versions for all install methods supported by ?CloudBioLinux (Debian packages; Python, R and Ruby library installs; Homebrew packages; and custom ?CloudBioLinux scripts). The Debian version is 10x faster than previously thanks to tips on querying apt repos from Tim Booth.

These updates to manifest creation make it possible to integrate it into existing tools that use ?CloudBioLinux for installation. The community developed open source bcbio-nextgen next-generation sequencing pipeline uses this, and we adjusted the build scripts to generate manifests on installation and then use these manifests to provide a list of the biological packages that run as part of the pipeline. This replaces brittle code existing in bcbio-nextgen and ties automated installation to the new manifest feature, ensuring that manifest creation will be regularly updated going forward for all ?CloudBioLinux installs.

Additional, I worked to learn Debian package building thanks to help from Andreas Tille. This resulted in creation of my first Debian package for FreeBayes, a highly accurate variant caller from Erik Garrison in the Marth Lab. I pushed a nearly completed version to DebianMed, which Andreas helped to finalize and make available. The hope for future versions of ?CloudBioLinux is to move back to Debian/Ubuntu based support inside Docker containers, which will help this package replace a custom build function in ?CloudBioLinux with a proper package.

Report of tool registry working group (Reporting by Matúš)


The following was achieved:


Constraints and challenges:

Ideas for implementation:

Other sources:

Integration of EDAM annotations into Debian Med

Tool description model draft 4.0


Keysigning all round.