opencobra/memote-docker

Name: memote-docker

Owner: openCOBRA

Description: Easily use the memote command line interface from a docker container.

Created: 2017-10-24 08:29:10.0

Updated: 2017-10-24 15:04:16.0

Pushed: 2017-11-10 11:30:09.0

Homepage: https://github.com/opencobra/memote

Size: 55

Language: Shell

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README

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'.

er 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.

er 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 owner from root to your own user.

er 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:

odel.xml > docker run opencobra/memote memote run
Contact

For comments and questions get in touch via

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

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.