Bioconda prerequisite installation

Prerequisites

AMRFinder requires BLAST+ and HMMER to run as well as libcurl.

You may already have all of the prerequisites installed in another way. You will need libcurl. The executables for BLAST and HMMER will need to be in your path. Note, it's not a prerequisite, but these instructions use Borne shell syntax (e.g., bash). If you're using another shell you might have to modify them slightly.

Bioconda

While not strictly a prerequisite Bioconda is how we recommend installing the prerequisites and indeed AMRFinderPlus. 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

With bioconda the three prerequisites can be installed in one command

~$ conda install -y blast hmmer libcurl

Install AMRFinder