Getting started

RnaChipIntegrator is Python software which runs with Python version 3.6 or higher.

Installing RnaChipIntegrator from PyPI using virtualenv and pip

The recommended way to get the latest version of RnaChipIntegrator is to create a Python virtual environment, and then install the software using the pip utility.

For example: to create and activate a virtual environment called venv.rci using the virtualenv utility:

virtualenv venv.rci
source venv.rci/bin/activate

RnaChipIntegrator can then be installed using pip, by running:

pip install RnaChipIntegrator

which will make the RnaChipIntegrator program available.

Note

If using RnaChipIntegrator from a virtual environment in this way, make sure to activate the environment each time before using it, for example:

source venv.rci/bin/activate

To deactive the virtual environment afterwards, do deactivate.

Note

For an introduction to pip and virtualenv, see for example:

• http://www.dabapps.com/blog/introduction-to-pip-and-virtualenv-python/

• https://www.biostars.org/p/109179/

To update an existing version of the program to a newer one, use:

pip install -U RnaChipIntegrator

from within the activated virtual environment.

Installing RnaChipIntegrator using Conda

Another approach for installing RnaChipIntegrator to use Conda (most easily obtained via the Miniconda Python distribution).

Once you have Conda installed you can create a new Conda environment with RnaChipIntegrator installed using the following command:

conda create -c bioconda -n rci rnachipintegrator

Alternatively you can install RnaChipIntegrator into an existing Conda environment using:

conda install -c bioconda rnachipintegrator

Warning

It’s recommended that RnaChipIntegrator be installed into a new Conda environment to avoid issues with incompatible packages (which is possible for example when trying to install directly into the Conda’s base distribution).