Docker¶

This section describes how to share a gsmodutils project inside a docker container.

The objective is to have code for testing models, data for their validation and the framework for running models written in a “write once run anywhere” fashion.

Ideally, even if a platform for running a model is considerably out of date it should produce the same results on new software.

Unfortunately this isn’t always the case. Packaging a constraints based model, with associated software within the same working environment ensures that the results should be reproducable, providing other users can install docker containers.

To install docker on your system please consult the documentation at https://docs.docker.com

Creating a docker container¶

To create a new docker container (with the latest gsmodutils setup scripts, use the docker utility.

$ gsmodutils docker --overwrite

This will overwrite an existing Dockerfile and requirements.txt. If you have additional software requirements (such as python packages) you will want to modify these. If you have large data files in your project that do not need to be shared, consider editing your Dockerfile to ignore these to reduce the size of any resulting images.

Now to create a docker container use the build command

$ docker build -t="example_project" <path_to_gsmodutils_project>

This will install the required python components for gsmodutils.

Running a docker container¶

gsmodutils just provides the basic dockerfile. In future iterations this may be changes. To use code inside a docker image, run the command

$ docker run -it <command>

For example, to load an ipython shell run:

$ docker run -it example_project ipython

You might wish to get the project info:

$ docker run -it example_project gsmodutils info
--------------------------------------------------------
Project description - Example ecoli core model
Author(s): - A user
Author email - A.user@example.com
Designs directory - designs
Tests directory - tests

Models:
 * iJO1366.json
   iJO1366

Designs:
 * cbb_cycle
   calvin cycle
   Reactions necissary for the calvin cycle in ecoli
 * mevalonate_cbb
   mevalonate production
   Reactions for the production of mevalonate
   Parent: cbb_cycle
Conditions:
 * fructose_growth
----------------------------------------------------------

Another example might be to run the gsmodutils test inside this portable environement:

$ docker run -it example_project gsmodutils test
------------------------- gsmodutils test results -------------------------
Running tests: ....
Default project file tests (models, designs, conditions):
Counted 4 test assertions with 0 failures
Project file completed all tests without error
    --model_iJO1366.json

    --conditions_iJO1366.json:model_fructose_growth

    --design_cbb_cycle

    --design_mevalonate_cbb

Ran 4 test assertions with a total of 0 errors (100.0% success)

Docker¶

Creating a docker container¶

Running a docker container¶

Sharing and loading gsmodutils docker images¶