Installation

Dependencies

PyIM requires Python 3.4 and has been tested on macOS and Linux.

The following external dependencies are also required for full functionality:

• Bowtie2
• Cutadapt
• CIMPL (R package, via rpy2)

These external tools should be available in $PATH. CIMPL, which is an R package, should be loadable in the default R installation.

Using bioconda (recommended)

The recommended way to install PyIM is using bioconda, as this installs PyIM together with its external dependencies into an isolated environment using a single command:

conda create -n pyim pyim

This assumes that condas channels have been configured as recommended by bioconda.

Alternatively, PyIM can be installed in an existing environment using:

conda install pyim

Using pip

IM-Fusion can also be installed from PyPI using pip:

pip install pyim

Note that this does not install any of the required external dependencies, which must therefore be installed manually.