vimalkvn/pyfba repository overview

⁠A docker image for PyFBA

This repository contains the Dockerfile for building a Docker⁠ image for PyFBA⁠ - A python implementation of flux balance analysis to model microbial metabolism. If you have Docker installed, you can pull this image using:

docker pull vimalkvn/pyfba

⁠Notes

1. The docker image built using this Dockerfile will have the latest version of PyFBA from Github along with all the dependencies pre-installed - GLPK, PyGLPK, libSBML, lxml, Beautiful Soup 4 and the ModelSEED database.

2. To run a script using this container, download the run-pyfba⁠) wrapper script available from the Github repository, save it in a location accesible in PATH and run it like this:

    run-pyfba python your_fba_script.py
   

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   or run the docker container directly:

    docker run --rm \
    -e LOGNAME=$(logname) \
    -e USER=$(logname) \
    -u ${UID}:${UID} \
    -v $(pwd):/wdir \
    -w /wdir \
    vimalkvn/pyfba \
    python your_fba_script.py
   

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3. The ModelSEED database is stored inside the container at /data/ModelSEEDDatabase and the PyFBA media directoy is copied to /data/media. The following environmental variables are also set

    ModelSEEDDatabase="/data/ModelSEEDDatabase"
    PYFBA_MEDIA_DIR="/data/media"
   

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   The -e and -u options are used so that the container has permissions to read input files and the generated output files will be owned by the user running the container and not root. Default user is pyfba.

   Input files are assumed to be present in the directory where the command is run.

   User must have either:

   • sudo access to run this script (script should be run as sudo run-pyfba) or the

   • user must be part of the docker user group.