[Biopython-dev] Docker containers

[Tiago Antao]

Hi Björn,

The current docker files were my first attempt at producing docker
containers. They work (hopefully) but they are far from being
best-practices. Furthermore I developed them quite some time ago
(before docker 1.0).

So, if you want to take this  and re-write according
to better practices, I would be very happy to replace the current stuff
with anything better you produce.

I particularly like the idea of having the databases at the very end.

Tiago

On Mon, 06 Apr 2015 17:18:38 +0200
Björn Grüning <bjoern at gruenings.eu> wrote:

> 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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> >