Installation¶

Installation from PyPI¶

The current release of deepnog can be installed from PyPI:

pip install deepnog

For typical use cases, and quick start, this is sufficient. Note that this guide assumes Linux, and may work under macOS. We currently don’t provide detailed instructions for Windows.

Alternative: Installation from bioconda¶

Alternatively, deepnog can be installed from bioconda with channel setup as described in the bioconda docs like this:

conda install deepnog

Note: Previously, bioconda required installing PyTorch from Facebook’s pytorch channel manually. Since PyTorch is now available on conda-forge, this is not necessary anymore.

Dependencies and model files¶

All package dependencies of deepnog are automatically installed by pip or conda. We also require model files (= networks parameters/weights), which are too large for GitHub/PyPI/bioconda. Models are hosted on separate servers, and downloaded automatically by deepnog, when required. By default, models are cached in $HOME/deepnog_data/.

You can change this path by setting the DEEPNOG_DATA environment variable. Choose among the following options to do so:

# Set data path temporarily
DEEPNOG_DATA="/custom/path/models" deepnog infer sequences.fa

# Set data path for the current shell
export DEEPNOG_DATA="/custom/path/models"

# Set data path permanently
printf "\n# Set path to DeepNOG models\nexport DEEPNOG_DATA=\"/custom/path/models\"\n" >> ~/.bashrc

Installation from source¶

You can always grab the latest version of deepnog directly from GitHub:

cd install_dir
git clone git@github.com:univieCUBE/deepnog.git
cd deepnog
pip install -e .

This is the recommended approach, if you want to contribute to the development of deepnog.

Supported platforms¶

deepnog currently supports all major operating systems:

Linux
MacOS X
Windows