[Biopython-dev] Reproducible Biopython VM images

Christian Brueffer christian at brueffer.de
Tue Mar 24 09:46:48 UTC 2015

Hi Tiago,

nice work!  Looks like my Vagrant stuff in redundant indeed and I can 
abandon it.

Any chance we can make this a bit more visible?  A paragraph in the 
README would be a good start; I can whip something up if we agree this 
is a good idea.



On 2015-03-17 16:01, Tiago Antao wrote:
> Hi,
> I have been working quite a bit with docker. I have quite a few
> containers available:
> https://github.com/tiagoantao/my-containers/tree/master/biopython
> Here you can find:
> buildbot containers:
> Biopython2-Test
> Biopython3-Test
> Currently operational on buildbot
> Probably more interesting:
> tutorials:
> Biopython2-Tutorial
> Biopython3-Tutorial
> A work in progress with part of the tutorial converted to ipython
> notebooks. They should work fine (but the tutorials are incomplete)
> There is also
> Biopython2
> Biopython3
> Which give you a installed Biopython on a docker container (which you
> can login into and start using from the command line)
> If you want to discuss this, I would be very happy.
> I ended up going for docker and not vagrant...
> Tiago
> On Tue, 17 Mar 2015 13:54:29 +0100
> Christian Brueffer <christian at brueffer.de> wrote:
>> 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 :-)
>> Chris
>> 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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