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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 will be made available for installation through Conda and pip. However, this is currently not yet working.
We will update these docs when installation through Conda and/or pip is available.

Prerequisites

AmpliGone requires Python 3.7 or later to be installed on your system (or in an environment).

Other dependencies will be installed during the installation, you don't have to install them manually. These extra dependencies are as follows:

  • pysam>=0.16
  • pandas>=1.2.3
  • numpy>=1.20
  • mappy>=2.17
  • biopython>=1.78
  • parmap>=1.5.2
  • tqdm>=4.59.0

We strongly advise you to use a conda environment (or similar) to make sure there won't be any conflicts in package dependencies.

Download and install from source

First start by cloning the repository and make sure you're on the latest released version of AmpliGone: 

git clone https://github.com/RIVM-bioinformatics/AmpliGone.git; cd AmpliGone; git checkout tags/$(git tag --sort=committerdate | tail -1) >> /dev/null

You're now in the newly created "AmpliGone" directory.

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

You can now install AmpliGone via the following command: 

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 bioinformatics workflow if you use Conda environments in your workflow.

To do this, simply add the following structure to your conda-environment recipe, replace {VERSION} with the AmpliGone version you wish to use:

dependencies:
    - pip
    - pip:
        - git+https://github.com/RIVM-bioinformatics/AmpliGone.git@{VERSION}

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

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