Installation Instructions:
Prerequisites for COMETS installation are to have Java 64-bit and Gurobi installed.
Java can be downloaded and installed from: https://www.oracle.com/technetwork/java/javase/downloads/index.html. The minimum version of required 64-bit Java is 1.8.
Gurobi can be downloaded and installed from: http://www.gurobi.com/downloads/gurobi-optimizer-eula/. The installation of Gurobi requires obtaining a license. Free academic license can be obtained from: https://www.gurobi.com/downloads/end-user-license-agreement-academic/.
COMETS Installation:
The installation page contains the following COMETS installers:
Windows (comets_windows-x64_2_10_0.exe)
Mac OS (comets_macos_2_10_0.dmg)
Linux (comets_unix_2_10_0.sh)
The installer is invoked either by a double-click on their icon (Windows, MacOS), or running them from a command line (Windows, Linux).
Troubleshooting: If the installer does not run from command line in Linux, execute the following:chmod a+x comets_unix_2_10_0.sh
In Mac OS, if the system does not allow the application to be installed, holding the command button and clicking on the installer, or going to the apple menu → System Preferences → Security & Privacy → General → Open Anyway, will solve this problem. If another window with security warning opens up, clicking on Open Anyway will allow the installation.
The installer guides the user through a standard GUI installation, procedure that includes accepting the license agreement, choosing the directory where COMETS will be installed (the default directory is recommended), and the option to create a desktop shortcut. The installation takes a few minutes on a typical laptop PC.
COMETS Uninstallation:
To uninstall COMETS, run the Uninstaller which can be found in the directory where COMETS was installed.
COMETS Python toolbox installation:
The prerequisite for this toolbox is to have Python installed (https://www.python.org/). We recommend installing python (version >= 3.6) using the Anaconda distribution which can be installed from https://www.anaconda.com/products/individual. Anaconda will conveniently install the jupyter notebook.
Troubleshooting: On a Linux or MacOS system, if the Anaconda installer does not run, execute the command line: chmod a+x Anaconda3-X.sh where X stands for a specific version name and number.
The COMETS Python toolbox (cometspy) is available from the package manager PyPI cometspy using the pip command. In Linux systems, the pip command is usually installed through available repositories (e.g. sudo apt-get install python3-pipin Debian-based distributions). If Python has been installed through Anaconda, pip will have been installed during this installation. Once pip is installed, cometspy can be installed by running in a terminal command line:
pip3 install cometspy
Troubleshooting: If pip3 does not start, close the terminal and open another one. In Windows this is best done by going to the start menu, and running "Anaconda Powershell Prompt". The above command can be run from the Anaconda Powershell.
COMETS Matlab toolbox installation:
The prerequisites for this toolbox are having MATLAB, git and Cobra installed. Matlab can be installed from https://www.mathworks.com. git should be installed from https://git-scm.com/ before continuing.
Cobra is installed by running the command line:
git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox
The COMETS Matlab toolbox is installed by running in command line:
git clone https://github.com/segrelab/comets-toolbox.git comets-toolbox
Alternatively, these two toolboxes can be installed using GitHub Desktop: https://desktop.github.com/.
The paths to Cobra and COMETS Matlab toolboxes must be added to Matlab by running in Matlab:
addpath(genpath("comets-toolbox"),"-end");
savepath();
and
addpath(genpath("cobratoolbox"),"-end");
savepath();
where "comets-toolbox" and "cobratoolbox" are the full paths where the toolboxes were installed.