Installation

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

Bioconda Installation

If you have Bioconda installed, you may install Neptune directly into its own environment with the following:

conda create -n neptune neptune-signature
conda activate neptune
neptune -h

You can test the install with the provided test data:

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

Direct Installation

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

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

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

You can test the install with the provided test data:

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