Installation

This installation guide assumes the use of the BASH Unix shell and a 64-bit Linux system.

Direct

The following instructions describe how to install Neptune directly. These instructions may require administrative privilages. Directly installing Neptune from the source files involves the following:

  1. Installing Python>=3.10
  2. Installing pip
  3. Installing BLAST (aptitude: sudo apt-get install ncbi-blast+)
  4. Installing Neptune (pip install .)

More detailed instructions are provided below.

Python 3

Ensure your version of Python is compatible (python>=3.10):

python --version

You may wish to use Conda to create an environment specifically for this purpose:

conda create --name neptune 'python>=3.10'
conda activate neptune

pip

Ensure you can run pip:

pip --version or python -m pip --version

If pip is unavailable, please refer to these instructions on how to install pip.

BLAST

Neptune requires BLAST to be manually installed and made available as a command-line program:

sudo apt-get install ncbi-blast+

You can verify BLAST was installed by ensuring the follow commands are available:

makeblastdb -h
blastn -h

Neptune and Dependencies

After downloading Neptune's source files, you can install Neptune and all of its pip dependencies with the following:

pip install /path/to/neptune_directory/ or pip install .

CAUTION: If you attempt pip install neptune (not interpreted as a file path), then you'll download a different package that's also named "neptune" that's available directly from pip.

The following packages and their dependencies will be installed:

  • numpy
  • scipy
  • biopython
  • neptune

You can verify the installation was successful with the following:

neptune --version

And you can test the installation with simple test inputs with the following:

neptune -i tests/data/example/inclusion/ -e tests/data/example/exclusion/ -o output

Bioconda

Currently, there is no Bioconda package for Neptune v2.0.0. If you wish to install Neptune v1.2.5 with Bioconda, please use the following command to create an environment with Neptune installed:

conda create -n neptune bioconda::neptune -c conda-forge -c default

Please note that specifying bioconda::neptune is necessary, because otherwise Conda is likely to resolve the name to different software that's also named neptune.

You may also wish to review an older version of these installation instructions for installing Neptune v1.2.5.