I wanted to share some code with the galaxy community and I am looking for
opinions on the following approach.
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 path regardless.
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 started
· Provides ability to easily blow away the dev environment and
· 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 Smithsonian/vagrant-galaxy repo
Bioinformatics Application Developer, Science and Technology Branch
Agriculture and Agri-Food Canada / Government of Canada
iyad.kandal...@agr.gc.ca / Tel: 613-759-1228 / TTY: 613-773-2600
Développeur de logiciels bioinformatique, Direction Général de Science et
Agriculture et Agroalimentaire Canada / Gouvernement du Canada
iyad.kandal...@agr.gc.ca / Tél. : 613-759-1228 / ATS: 613-773-2600
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