I wanted to share some code with the galaxy community and I am looking for opinions on the
We want to create a standardized galaxy tool development environment to address specific
problems we faced in the past while minimizing training and hand-holding efforts
associated with galaxy development.
Getting start with Galaxy tool development is complicated as it requires an understanding
of the whole system (not just Galaxy and the tool shed).
Devs accidentally use the latest galaxy release to develop their tools instead of the
in-house production server release.
Dev's environment is tainted with system-wide installed software ->
tool-dependencies can't be verified because the system installed binaries are on the
Dev's environment is substantially different from production server environment ->
tool dependencies work in dev but not in prod.
Several other issues that I can't quite remember
Solution and outcomes:
Use provisioning software such as vagrant to standardize the dev environment.
· Reduce time and training required on getting galaxy/toolshed installed and
· Provides ability to easily blow away the dev environment and re-instantiate it
· Provides a clean dev environment every time that isn't tainted with
system-wide installations of software
· Provides a more similar environment to the production server (assuming it runs
the same OS)
I hope that this is useful for other galaxy tool devs. I am open to collaboration to
improve this initiative and I am looking for insight on some problems we are facing.
The repo is on github: https://github.com/AAFC-MBB/vagrant-galaxy
Forked from the
Bioinformatics Application Developer, Science and Technology Branch
Agriculture and Agri-Food Canada / Government of Canada
Iyad.Kandalaft(a)Agr.gc.ca / Tel: 613-759-1228 / TTY: 613-773-2600
Développeur de logiciels bioinformatique, Direction Général de Science et Technology
Agriculture et Agroalimentaire Canada / Gouvernement du Canada
Iyad.Kandalaft(a)Agr.gc.ca / Tél. : 613-759-1228 / ATS: 613-773-2600