[Biopython-dev] Docker containers

[Björn Grüning]

Hi Tiago,

I will give it a try to submit a PR!

Is there any interest in having a biopython dockerhub account?
@peter do you like me to register one?

Idea is to have something like:

biopython/biopython_python2.7:1.65
biopython/biopython_python2.7:dev
biopython/biopython_python3.4:1.65
biopython/notebooks:dev

(I don't like the _python2.7)

Or maybe this ...

biopython/biopython:py27_1.65
biopython/biopython:py27_dev
biopython/biopython:py34_1.65
biopython/notebooks:py34_dev


Thanks again for working on this!
Bjoern

Am 06.04.2015 um 20:07 schrieb 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
>>> _______________________________________________
>>> Biopython-dev mailing list
>>> Biopython-dev at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>>>
>