Install with bioconda

AMRFinderPlus supports installation to Linux and MacOS via bioconda

There are two steps.

1. Install conda if you don't already have it

If you don't already have bioconda installed, otherwise skip ahead.

See the official install miniconda instructions for Linux

OR

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash ./Miniconda3-latest-Linux-x86_64.sh

Follow prompts to accept license, choose install path, and allow the new bin directory to be added to .bashrc

See Install miniconda instructions for MacOS

OR

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash ./Miniconda3-latest-MacOSX-x86_64.sh

Follow prompts to accept license, choose install path, and allow the new bin directory to be added to .bashrc

We recommend you set up bioconda as the default channel, but it is not required:

export PATH=$HOME/miniconda3/bin:$PATH # Change to match installation location, if not default.
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

2. Install AMRFinder with bioconda

Make sure the conda environment you just created is activated

source ~/miniconda3/bin/activate

Install AMRFinder and all of the prerequisites in a new environment.

conda create -y -c conda-forge -c bioconda -n amrfinder --strict-channel-priority ncbi-amrfinderplus

What next?

Note that conda will have to be activated for AMRFinderPlus and its prerequisites to be in your path. To make that happen automatically on login run the following to add activation commands to your login scripts:

~/miniconda3/bin/conda init

Otherwise to activate conda on a case-by-case basis use:

source ~/miniconda3/bin/activate

Testing your installation

See Test your installation for testing instructions

To update your installation

conda update -y -c conda-forge -c bioconda --strict-channel-priority ncbi-amrfinderplus

Email

If you are still having trouble installing AMRFinderPlus or have any questions open an issue or let us know by emailing us at [email protected] and we'll do what we can to help.