[Biopython-dev] Reproducible Biopython VM images

[Tiago Antao]

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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