Installation¶

Python installation¶

Installation with pip¶

The Python version of MAGIC can be installed using:

pip install --user magic-impute

Installation from source¶

The Python version of MAGIC can be installed from GitHub by running the following from a terminal:

git clone --recursive git://github.com/KrishnaswamyLab/MAGIC.git
cd MAGIC/python
python setup.py install --user

MATLAB installation¶

The MATLAB version of MAGIC can be accessed using:

git clone git://github.com/KrishnaswamyLab/MAGIC.git
cd MAGIC/Matlab

Add the MAGIC/Matlab directory to your MATLAB path and run any of our run or test scripts to get a feel for MAGIC.

R installation¶

In order to use MAGIC in R, you must also install the Python package.

If python or pip are not installed, you will need to install them. We recommend Miniconda3 to install Python and pip together, or otherwise you can install pip from https://pip.pypa.io/en/stable/installing/.

Installation from CRAN¶

In R, run this command to install MAGIC and all dependencies:

install.packages("Rmagic")

In a terminal, run the following command to install the Python repository:

pip install --user magic-impute

Installation from source¶

The latest source version of MAGIC can be accessed by running the following in a terminal:

git clone https://github.com/KrishnaswamyLab/MAGIC.git
cd MAGIC/Rmagic
R CMD INSTALL .
cd ../python
python setup.py install --user

If the Rmagic folder is empty, you have may forgotten to use the –recursive option for git clone. You can rectify this by running the following in a terminal:

cd MAGIC
git submodule init
git submodule update
cd Rmagic
R CMD INSTALL
cd ../python
python setup.py install --user