Installing AMRFinder

Installation Summary

AMRFinder requires HMMER, BLAST+, Linux, and perl. We provide Linux binaries, and the source code is available if you want to compile it yourself, though we haven't extensively tested compiling AMRFinder on other systems and aren't supporting non-Linux systems at this time.

Prerequisites

We recommend using Bioconda to install the prerequisites and provide instructions for how to do that below. The executables for BLAST, HMMER, and Perl will need to be in your path. See the Troubleshooting section below to test them. Note, it's not a prerequisite, but these instructions use Borne shell style syntax (e.g., that from bash). If you're using another shell syntax you might have to modify them slightly.

Bioconda

While not strictly a prerequisite Bioconda is how we recommend installing the prerequisites. If you don''t have bioconda already installed you should run the following

~$ 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
~$ 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

Install the prerequisites

With bioconda the three prerequisites can be installed in one command

~$ conda install -y blast hmmer libcurl

Installing AMRFinder

~$ mkdir amrfinder && cd amrfinder
~/amrfinder$ curl -sL https://ftp.ncbi.nlm.nih.gov/pathogen/Technical/AMRFinder_technical/amrfinder_binaries_v3.0.tar.gz | tar xvz
~/amrfinder$ ./amrfinder -u
~/amrfinder$ ./amrfinder -p test_prot.fa