diff --git a/README.md b/README.md index 3d883f9..66e5908 100644 --- a/README.md +++ b/README.md @@ -18,41 +18,82 @@ This release updates Neptune to Python3, removes DRMAA support, fixes a crash wh # Installation # -## Python 3 +## Bioconda Installation + +If you have [Bioconda](https://bioconda.github.io/) 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](https://github.com/phac-nml/neptune/tree/main/tests/data/example): + +``` +neptune -i tests/data/example/inclusion/ -e tests/data/example/exclusion/ -o output/ +``` + + +## Manual Installation + +### Python Ensure your version of Python is compatible (python>=3.10): -`python --version` +``` +python --version +``` You may wish to use [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html) to create an environment specifically for this purpose: -`conda create --name neptune 'python>=3.10'` -`conda activate neptune` - -## pip +``` +conda create --name neptune 'python>=3.10' +conda activate neptune +``` Ensure you can run pip: -`pip --version` or `python -m pip --version` +``` +pip --version +``` + +or + +``` +python -m pip --version +``` If pip is unavailable, please refer to [these instructions](https://packaging.python.org/en/latest/tutorials/installing-packages/) on how to install pip. -## BLAST +### BLAST Neptune requires BLAST to be manually installed and made available as a command-line program: -`sudo apt-get install ncbi-blast+` +``` +sudo apt-get install ncbi-blast+ +``` You can verify BLAST was installed by ensuring the follow commands are available: -`makeblastdb -h` -`blastn -h` +``` +makeblastdb -h +blastn -h +``` -## Neptune and Dependencies +### 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 .` +``` +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. @@ -65,24 +106,31 @@ The following packages and their dependencies will be installed: You can verify the installation was successful with the following: -`neptune --version` +``` +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` +``` +neptune -i tests/data/example/inclusion/ -e tests/data/example/exclusion/ -o output +``` # Running Neptune # Neptune's command line arguments can be found by running: - neptune --help +``` +neptune --help +``` A simple example of running Neptune: - neptune --inclusion /path/to/inclusion/ --exclusion /path/to/exclusion/ - --output /path/to/output/ +``` +neptune --inclusion /path/to/inclusion/ --exclusion /path/to/exclusion/ --output /path/to/output/ +``` -Please refer to the [documentation](https://phac-nml.github.io/neptune/parameters/) for more details. +Please refer to the [documentation](https://phac-nml.github.io/neptune/) for more details. # Contact #