Installation¶

REEFFIT can be downloaded for non-commercial use at the RMDB. Commercial users, please contact us.

• Download the zip or tar file of the repository and unpack; or

git clone https://github.com/ribokit/REEFFIT.git

• To install REEFFIT, simply:

cd path/to/REEFFIT/
python setup.py install

For system-wide installation, you must have permissions and use with sudo.

REEFFIT requires the following Python packages as dependencies, all of which can be installed through pip:

cvxopt >= 1.1.6
joblib >= 0.5.4
matplotlib >= 1.1.1
numpy >= 1.6.1
scipy >= 0.9.0
pymc >= 2.2

rdatkit >= 1.0.4

• Note that you should have RDATKit installed and properly set up as well (see ribokit/RDATKit).
• In your profile (e.g. .bashrc), include an environment variable REEFFIT_HOME that points to the REEFFIT home directory, e.g.:

export REEFFIT_HOME=/path/to/REEFFIT

• Be sure to add the REEFFIT_HOME/bin directory to your path. Similarly in ~/.bashrc or ~/.bash_profile, include:

export PATH=$PATH:$REEFFIT_HOME/bin

• Check that REEFFIT is correctly installed. Execute the REEFFIT command by running reeffit -h in your shell.