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
- Packaging of main workbench
- Set up new build environment for Jim
- Build of all Ubuntu packages on Debian
- Updated to latest Jalview bugfix release (2.8.0b1) and wrapper package for BL finished
- Added SVG icon and default configuration
- Committed all work to pkg-java SVN
- Further customisation of package and launch without network enabled
- Jaba/JabaWS for Debian
- Herve requested Jalview applet, so looking at server-side components related to deploying JV on Qlustar
- Jim - tacking hard problems with Debian/Jaba and has Jaba working but not clustering.
- Planned to progress towards a package in the near future.
Setting up the Qlustar HPC cluster demo
Luca Clivio, Tony Travis
- Objective: Credible demo of Bio-Linux GUI running on front-end of Qlustar cluster
- #0 Resolve DHCP problems preventing access to Cluster FE (Frontend) VM
- #1 Install Ubuntu Desktop on common NFS shared cluster chroot
- #2 Install x2go server and Gnome fall-back session
- #3 Tested from x2go client running under Bio-Linux on laptop
- #4 Install “ARB” X11 GUI phylogenetics suite (part of Bio-Linux)
Looking at ?MrBayes MPI on Sunday. There were some issues getting this to work.
Personal Reports
Andreas Tille
- Package uploads
- Sponsored gnuhealth
- New version of gnumed-server + gnumed-client
- New version of flexbar, checking tests, contacted upstream about failing tests
- Some changes at staden packaging
- Worked with Detlef Wolf on upstream build system of bioinfo-c
- seqtk (created in a life packaging session)
- dnaclust (created in a life packaging session)
- snp-sites sponsored for Jorge Soares
- python3-fitbitscraper sponsored for Iain R. Learmonth
Presentation: Introduction into Mentoring of the Month
- Live packaging session at Saturday afternoon packaging randomly picked (simple) packages suggested by the audience
- Discussing issues about creating an ontology based in data in UDD (debtags+descriptions) with EDAM people
Working on the FAQ section of the Blends documentation (relation to ?DebTags)
- Working together with Luiz Ibanez on VistA packaging
- Running around to help people gaining their first packaging experience after the life packaging session yesterday
Enabling kgb for Git repositories
- Other stuff than Debian Med
- uscan enhancements
- Sponsering libcitygml for Debian GIS
- Activate 4096bit GPG key
- Fixing Debian Games tasks
Iain Learmonth
- Learnt Debian packaging through participating in Andreas' live packaging of dnaclust and seqtk.
- Sorted out a man page for dnaclust
- Packaged python3-fitbitscraper
- Spoke with Luca and agreed to package HEAVyBASE once there is documentation available for the package
Gave a demo of a Python application visualising personal health data from ?FitBit (Screenshot).
- Took some pictures, link at bottom of main page.
Tim Booth
- Gave a short talk on Bio-Linux and recent updates
- Discussed EOS cloud plans with Tony (private clouds running BL for data analysis)
- Worked on Jalview with Jim (see above) - uploaded new pkgs to Bio-Linux
- Demonstrated packaging to Jim
- Showed Galaxy packaging to Peter and got feedback
- Discussed roadmap to making Bio-Linux love the Galaxy toolshed with Brad and Peter C
- Planned with Kristoffer how to use the Tools Registry in BL and how to contribute
- Connected to the Qlustar cluster and tried some basic ops