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 like this:
# With channel setup as described in the `bioconda docs`_
conda config --add channels pytorch
conda install pytorch deepnog
Dependencies and model files¶
All package dependencies of deepnog are automatically installed
by pip. We also require model files (= networks parameters/weights),
which are too large for GitHub/PyPI. These 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.