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federatedcloud / COBRAContainers

Containers and scripts for COBRA modeling
BSD 3-Clause "New" or "Revised" License
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nix science

readme

DOI

Requirements

Running the environment

Docker

In short:

  1. source build.sh or source pull.sh.
  2. ./run.sh
  3. Proceed to the Nix instructions below

Nix

Each time

  1. nix-shell default.nix
  2. matlab -glnxa64

IMPORTANT Caveat: If it is necessary to specify the -glnxa64 option, the matlab shell script should instead be modified to hardcode ARCH as glnxa64. Aside from convenience, certain APIs like the MATLAB Engine API will not always work otherwise.

Alternatively, append -nodesktop -nodisplay to the `matlab** command when running in the terminal.

Important: You must execute the nix-shell default.nix command from the same directory specified above, as that directory contains another script that must be run.

If you are wanting a single script to do all this for you, do e.g.:

#!/usr/bin/env bash
cd /home/bebarker/workspace/COBRAContainers && \
  nix-shell default.nix --run "matlab -glnxa64"

You can omit using the script if you have other ways to change the working directory, in e.g. desktop icon-based launchers.

One-time-only for gurobi

In the nix-shell enviroment:

  1. mkdir -p ~/Documents/MATLAB
  2. cp $GUROBI_HOME/examples/matlab/mip1.m ~/Documents/MATLAB/
  3. echo $GUROBI_HOME

In matlab (started from the nix-shell environment)

  1. cd to that directory (obtained from echo $GUROBI_HOME) in MATLAB, then cd matlab
  2. gurobi_setup
  3. Type savepath as instructed
  4. cd ~/Documents/MATLAB/
  5. mip1

You should see a solution printed out.