Upgrading the package dependency of probabilistic2020 to version >=1.0.6 is recommended.
Once downloaded, please add the directory to your
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:
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:
Where, in this case, the R libraries will be installed in the ~/Rlibs directory.
20/20+ also requires the following python packages:
- 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.
Check your PATH variable¶
Make sure that you have add the 20/20+ directory to your PATH variable. We recommend you add this line to your bashrc file.
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