Installation instructions

AmpliGone is only available on Linux (or Linux-based) operating systems. MacOS may also work but is not tested. AmpliGone will not work on Windows.

AmpliGone can be installed easily with Conda or pip.

Installation with conda

AmpliGone releases are published in Bioconda, and can be installed with the following command:

conda install -c bioconda ampligone

Tip

You can also use mamba as a replacement for installing conda packages, use the following command if you have mamba installed on your system

mamba install -c bioconda ampligone

Installation through conda/mamba is the recommended method for installing AmpliGone

Installation with pip

AmpliGone releases are also published on PyPI, and can be installed using pip using the following command:

pip install AmpliGone

Download and installation from source

Make a new Conda environment before continuing

If you have Conda installed on your system, please create and activate a new environment before continuing.

Use the following command to create and activate a new Conda environment named "AmpliGone" based on the environment-recipe we provide in the github-repository

conda env create -f env.yml; conda activate AmpliGone

The "AmpliGone" conda-environment should now be active

First start by cloning the repository and make sure you're on the latest released version of AmpliGone, then install the downloaded package with pip:

# clone the repository from github and switch to the latest released version
git clone https://github.com/RIVM-bioinformatics/AmpliGone.git; cd AmpliGone; git checkout tags/$(git tag --sort=committerdate | tail -1) >> /dev/null
# Install the downloaded package with pip
pip install .

AmpliGone should now be installed!
You can verify if installation was successful by typing ampligone --version on the command-line, this should show the installed AmpliGone version.

Pipeline/workflow integration

You can easily integrate AmpliGone in your SnakeMake or Nextflow bioinformatics workflow if you use Conda environments in your workflow.

To do this, add ampligone and the correct channels to your conda-environment recipe as below:

name: example-env
channels:
    - bioconda
    - conda-forge
    - anaconda
    - defaults
dependencies:
    - ampligone

Conda will now install AmpliGone and its dependencies in the specified snakemake conda-environment.