Python / Conda

Versions Installed

Kay: 2.7.5 (System Install) / 2.7.15 (Conda) / 3.7.0 (Conda)

Description

On Kay, we provide the Python interpreters and packages using two methods:

1. System Install (Python 2 Only)

It provides the default Python interpreter on Kay, which only supports Python 2.

2. Conda (Python 2 and 3)

Conda is our preferred method to provide Python 2 and 3 interpreters, and some commonly used packages to users. You can use these by loading the Conda module and then activating the desired Conda environment.

License

Available under Python Software Foundation (PSF) License.

Useful Commands

To load the environment module:

module load conda/2

To list the available Conda environments:

conda info --envs

The base environment provides Python 2 interpreter, while the python3 Conda environment provides Python 3 interpreter. Both the Conda environments provide the following packages:

matplotlib
numpy
opencv
pandas
scikit-learn
scipy

To activate the base (default) Conda environment:

source activate

To activate any other Conda environment from the list of available environments:

# Activates python3 Conda environment
source activate python3

To list the software installed in the Conda environment:

# Lists all software installed in the python3 Conda environment
conda list --name python3

To deactivate the Conda environment:

source deactivate

Installing Python Packages

To install any Python package or to use a different version of Python, you can create a new Conda environment. Your Conda environments are saved in your $HOME directory.

To create a new Conda environment:

# Creates a new Conda environment called myenv with Python (version 3.4) and Biopython (default version)
conda create --name myenv python=3.4 biopython

Since only one Conda environment can be activated at a time, mention all the python packages you want to use together when you create the environment.

To delete your Conda environment:

conda env remove --name myenv

Jupyter Notebooks

To use Jupyter Notebooks on Kay, refer to our documentation here

Additional Notes

For more information see here.