# Installation¶

## Package requirements¶

Note

Upgrading the package dependency of probabilistic2020 to version >=1.0.6 is recommended.

Once downloaded, please add the directory to your PATH variable. Because 20/20+ internally uses the random forest package in R, you will both need R and the randomForest library installed. Once R is installed, you can install the random forest package:

> install.packages("randomForest")


If you do not have permission to install randomForest on the system wide R, you can install in your local user directory by creating an ~/.Renviron file as the following:

R_LIBS=~/Rlibs


Where, in this case, the R libraries will be installed in the ~/Rlibs directory.

20/20+ also requires the following python packages:

• numpy
• scipy
• pandas>=0.17
• scikit-learn
• rpy2
• probabilistic2020
• matplotlib (optional)

To install these packages via pip you can use the following command:

$pip install -r requirements.txt  Note, the above command won’t install the optional matplotlib package. Matplotlib is used for creating plots, if you want plotting output than issue the following command to install matplotlib: $ pip install matplotlib


The probabilistic2020 python package is used to generate features used by 20/20+ from the mutations in MAF format.

export PATH=$PATH:/path/to/2020plus  Where “/path/to/2020plus” represents the path where you placed 20/20+. If you have done this correctly, the following command should print the location of the 2020plus.py script. $ which 2020plus.py