[Biopython-dev] Reproducible Biopython VM images

Christian Brueffer christian at brueffer.de
Tue Mar 17 12:54:29 UTC 2015

Hi Peter,

as far as I understand efforts like BioBoxes, they are geared towards 
shipping released versions of tools.  Vagrant-based VMs are primarily 
meant for developer use, as they enable quick throw-away VM use.

That's also the reason having support for his in the main repository 
would be most beneficial; it allows one to check out the repository, run 
one command and have a fresh VM with a complete set of tests and the 
dependencies to run them.  This sets the bar for contributions very low.

Having something things in a separate repository would also work, 
probably best with instructions like this:

cd biopython
wget url-to-Vagrantfile
wget url-to-bootstrap-file
vagrant up

Tiago, I'd be very interested to hear about your work in this area :-)


On 2015-03-17 13:01, Peter Cock wrote:
> 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?
> Peter
> 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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>> Biopython-dev at mailman.open-bio.org
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