[Biopython-dev] Reproducible Biopython VM images

Peter Cock p.j.a.cock at googlemail.com
Tue Mar 17 12:01:51 UTC 2015

Hi Christian,

This seems interesting, although perhaps better in a separate repository
to the Biopython source code, which targets the current Biopython release?

Tiago might have looked at something similar when he was setting up
additional buildbot slaves for testing...

See also https://github.com/bioboxes/ - possibly of relevance?


On Tue, Mar 17, 2015 at 11:34 AM, Christian Brueffer
<christian at brueffer.de> wrote:
> Hi everyone,
> for development, testing, and release engineering, it would be nice to have
> a comprehensive VM image that has all dependencies, and tools we have
> wrappers for already installed.  Even better if it's easy to re-create by
> anyone!
> I've started working on this based on Vagrant (https://www.vagrantup.com/).
> My current (minimal) work is in the "vm" branch at
> https://github.com/cbrueffer/biopython ; it consists the two added files
> Vagrantfile and vmbootstrap.sh.
> A VM can be created by first installing Vagrant and a supported VM software
> (e.g., Virtualbox). Then:
> git clone -b vm https://git@github.com/cbrueffer/biopython.git
> cd biopython
> vagrant up  # downloads the base OS image and executes vmbootstrap.sh
> vagrant ssh  # SSH access to the VM
> The vmbootstrap.sh script currently installs an (incomplete) set of
> dependencies, installs the checked out Biopython version and runs the tests
> in offline mode.  Some tests still fail due to the aforementioned
> (currently) unmet dependencies.
> The directory from which "vagrant up" was called (in this case the
> repository root) is available as /vagrant from within the VM.
> Feedback welcome!
> Cheers,
> Chris
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