Installation

Installation#

Requirements#

  • python >= 3.10

  • gurobipy >= 11.0.0

  • numpy >= 1.12

  • pandas >= 0.20

  • scikit-learn >= 0.19

  • scipy >= 1.0

Install Compass#

If Numpy is not installed, you can install it with

python -m pip install numpy

This needs to be installed before the other requirements because a C extension needs the location of numpy headers to compile.

Note

Accessing pip through python -m pip is done to emphasize that on systems with multiple python installations (e.g. python 2.7 and python 3.6) Compass and Cplex must be installed to the same version of python. It is otherwise identical to just using pip. Using sudo can also invoke a different version of python depending on your environment.

Warning

Installing from the compass_v2 branch is temporary and will be fixed as all changes are merged into master.

Then simplest way to install Compass is using pip to install from the github repository. This can be done with the following command in the terminal:

python -m pip install git+https://github.com/yoseflab/Compass.git@compass_v2 --upgrade

This command will also update Compass to the newest version. Alternatively, you can clone the Compass repository and run setup.py.

Now to test if everything is installed, simply run:

compass -h

You should see the help text print out if installation was succesful. For more details on how to use Compass you can visit our tutorial.

Obtain a Gurobi WLS license#

At the heart of the Compass algorithm is linear programming. Compass computes a penalty score for each reaction in each cell by solving a constrained optimization problem using the Gurobi linear solver. In order to use Compass, you need to obtain a Gurobi WLS license, which is free for academic use.

Please refer to this link to obtain a Gurobi WLS license. If you follow the instructions correctly, you should be able to obtain a gurobi.lic file that contains the access ID, secret, and license ID of your WLS license. Please store this file as it is required to set up Compass.

Set up your Gurobi WLS license#

In order to use Compass, you must provide your Gurobi WLS license to the Gurobi API. To do this, you can run the command

compass --set-license <PATH_TO_LICENSE>

where <PATH_TO_LICENSE> is the path to the gurobi.lic file you obtained in the previous step. This stores your license information in a default location within Compass. After you have successfully done so, you can proceed to run Compass without the --set-license parameter as Compass will directly read your license information from the default location. Refer to the next section of the documentation to learn how to run Compass.