memote – the genome-scale metabolic model test suite

Easily run the memote command line tools from a docker container. You can find the main documentation on readthedocs.

Installation

We aim to release containers for every memote release from version 0.4.5 onwards. You can thus use a specific version tag or simply 'latest'.

docker pull opencobra/memote:latest

Usage

The container exposes the memote command line tool. If you run the container without any arguments you will see the base help message.

docker run opencobra/memote

For now, the best way to have memote interact with files is to mount a local directory into the container. The only hurdle is that you may have to afterwards change the permissions of the output file to your own user.

docker run -v ~/local/path/to/models/directory:/opt opencobra/memote memote run /opt/my-model.xml

We may work on allowing you to pipe the model to the docker container. So in future you would be able to do the following:

my-model.xml > docker run opencobra/memote memote run

Contact

For comments and questions get in touch via

• our gitter chatroom

Are you excited about this project? Consider contributing by adding novel tests, reporting or fixing bugs, and generally help us make this a better software for everyone.

Copyright

• Copyright (c) 2017, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark.
• Free software: Apache Software License 2.0