Compile from source

• Install with bioconda
• Install with binary

Manual installation summary

If you want to compile AMRFinderPlus yourself you'll need gcc and GNU make to compile the software as well as the other prerequisites BLAST+, HMMER, and libcurl. We have only tested compiling AMRFinderPlus with GNU tools on Linux. Your mileage may vary.

AMRFinderPlus was developed with g++ (GCC) 4.9.3 and libcurl 7.29.0

To install binaries see Installing AMRFinder.

Downloading

You can clone the repository using

git clone https://github.com/ncbi/amr.git
git checkout master

Or download the source from the AMRFinderPlus github site.

Compiling

make 

To adjust the default database directory use something like the following (we are working on a more flexible way to define directories, but this solves the problem in the short term):

make clean
make DEFAULT_DB_DIR=/usr/local/share/amrfinder/data

You may also have to adjust flags in the Makefile for libcurl and for different versions of GCC.

Installation

make install

will copy the AMRFinderPlus executables to /usr/local/share/amrfinder. To change the installation location add a INSTALL_DIR option to make e.g.:

make install INSTALL_DIR=$HOME/amrfinder

See Test your installation.