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Virtual environment (Docker) for EvoMS

This Docker image has the virtual environment for Evolutionary Metabolic Synthesizer (EvoMS), an evolutionary tool capable of finding novel metabolic pathways linking several compounds through feasible reactions.

To get the virtual environment up and running, you just need to run the following command. The parameters allows the MATLAB session inside to get access to your X11 session. Replace /usr/local/MATLAB/R2013a/ with the path where MATLAB is installed in your computer (where the bin/ directory resides). Keep in mind that the code has been tested with MATLAB R2013a.

$ sudo docker run -ti -e DISPLAY=$DISPLAY -e uid=$UID -v /tmp/.X11-unix:/tmp/.X11-unix:ro -v /usr/local/MATLAB/R2013a/:/MATLAB sinclab/webdemo-evoms

Once inside the container, you will see a shell prompt like this:

developer@CONTAINER_ID:/workdir/EvoMS-0.2.3-Toolbox$

where CONTAINER_ID is a unique identifier of this container (you can get this ID by running sudo docker ps). You can use this identifier to control your container and, in those cases, the first four characters are usually enough.

In this shell prompt, simply run:

$ ./run.sh

By opening a new terminal in your computer (not from inside the container itself), you can copy any files generated by EvoMS from the container to your computer using a command like this:

$ sudo docker cp CONTAINER_ID:/workdir/EvoMS-0.2.3-Toolbox/out .
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