[Biopython-dev] Docker containers

[Björn Grüning]

Hi Tiago,

thanks for working on this! Looks very nice and works as expected.

I have a few suggestions and want to ask if you agree before I start to
implement.

1. optimise apt-apt usage
  Docker has a max numbers of layers and it would be nice to have less
  commands (PUN) and less layers.
  This will also greatly reduce the size of the image.

2. Do we want to have these images in dockerhub?
  In this case I would like to introduce tagged images with biopython
  versions, installed from pypi and a dev image with the latest changes
  from github.

2. Replace the template system with docker layers
  I would like to have some python2/python3 base image and put
  on top the Biopython dependencies. Based on the Biopython Image
  we can create the IPython extra Image w/wo documentation.

4. mysql and postgresql are really heavy dependencies I would like to
move these at the end of the docker hierarchy and offer images
(especially the IPython notebooks) with less dependencies (and file
size) as possible. This will simplify it for others to reuse your docker
container in other projects.

Sorry for being so late to this game. Let me know what you think and I
will try to implement this.

Ciao,
Bjoern

> Dear all,
> 
> Before I port my containers to the project there are a few things that
> you should be made aware of:
> 
> 1. There are 4 containers x 2 versions (Python 2 and 3): empty (shell),
> notebook, notebook with tutorial and buildbot. The buildbot one is
> currently under maintenance, but I would expect all the others to work.
> 
> 2. I am maintaining all these containers with a simple template system
> on my repository (https://github.com/tiagoantao/my-containers). It is
> clumsy, but does the work. I will probably port the script also to the
> new main repo.
> 
> 3. The containers themselves were my first attempt at doing docker
> containers, so they are a bit naive. But they do work. A future plan
> would be to use anaconda (well, miniconda) as a basis. Also force the
> versions of all packages.
> 
> 4. You can find instructions here:
> http://fe.popgen.net/2015/03/docker-containers-for-biopython/ .
> 
> Comments and criticism appreciated.
> 
> When everyone is happy, I will put everything under the biopython repo.
> 
> Tiago
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