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
cd amr
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

NOTE: Right now when using a DEFAULT_DB_DIR AMRFinderPlus will print a WARNING message about $CONDA_PREFIX. Please ignore this warning, it will go away in the next release.

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.