https://github.com/dd-decaf/modeling-base

Base Docker image(s) for metabolic modeling with proprietary solvers.
https://github.com/dd-decaf/modeling-base

Last synced: 6 days ago
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Base Docker image(s) for metabolic modeling with proprietary solvers.

• Host: GitHub
• URL: https://github.com/dd-decaf/modeling-base
• Owner: DD-DeCaF
• License: apache-2.0
• Created: 2018-09-27T17:36:30.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2020-05-26T16:18:19.000Z (over 4 years ago)
• Last Synced: 2024-11-09T14:25:54.570Z (2 months ago)
• Language: Dockerfile
• Size: 40 KB
• Stars: 0
• Watchers: 7
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# modeling-base

[![master Build Status](https://travis-ci.org/DD-DeCaF/modeling-base.svg?branch=master)](https://travis-ci.org/DD-DeCaF/modeling-base)

A base Docker image for our modeling needs. Contains the relevant Python 

packages, e.g., cobra and cameo, as well as chosen solvers, i.e., at the 

moment GLPK and CPLEX.

Note that the sympy cache is disabled by default (by setting the env var

`SYMPY_USE_CACHE=no`) as its usage by optlang causes memory leaks.

## Environment

The following environment variables **must** be defined in the **Travis settings**.

| Variable | Description |

|----------|-------------|

| `REPO_URL` | URL of the private repository storing proprietary solvers. |

| `GITHUB_TOKEN` | A GitHub access token (which should have `repo` permissions only) in order to download proprietary solvers. |

| `GCLOUD_EMAIL` | The Google Cloud e-mail for the Travis service account. |

| `GCLOUD_KEY` | The Google Cloud key. |

## Development

Type `make` to see frequently used workflow commands. Also take a look at the

 `.travis.yml` configuration to get an idea of the general workflow.

### Testing

* To test all dependencies for vulnerabilities run `make safety`.

## Future

Ideas for future improvements:

* Make the installation of various solvers optional.

* Have one base image with the solvers and optlang.

* Layer different images on top of the base image, for example, cobra only, 

  cobra & cameo, add further visualization packages.