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Compile from source
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.
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.
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 $CONDA_PREFIX. Please ignore this warning, it will go away in the next release.
You may also have to adjust flags in the Makefile for libcurl and for different versions of GCC.
make install
will copy the AMRFinderPlus executables to /usr/local/share/amrfinder
. To change the installation location add a INSTALL_DIR option to make e.g.:
make install INSTALL_DIR=$HOME/amrfinder
- New in AMRFinderPlus
- Documentation for AMRFinder v1 (Depricated)
- Overview
- Install with bioconda (recommended)
- Docker Image
- Install with binary
- Compile from source
- Test your installation
- Usage (syntax/options)
- --organism option
- Examples
- Input file formats
- Output format
- Common errors
- Known issues
- Tips and tricks
- Database updates
- Software upgrades
- Genotypes vs. Phenotypes
- Scope: plus vs. core
- AMRFinderPlus "Method" column
- Element type and Subtype
- Class and Subclass