Database Updates

This should be as easy as running:

amrfinder --update

Some users have reported errors with the automatic updating. You can automatically update to a directory different from the default by using amrfinder_update. Ex:

amrfinder_update -d <database_directory>

To use that directory when you run amrfinder use the -d option:

amrfinder -d <database_directory>/latest  ...

Note that if you're running under sudo your path might change (e.g., https://github.com/ncbi/amr/issues/74). The following should work:

sudo PATH="$PATH" amrfinder --force_update

Software Upgrades

Instructions for upgrading AMRFinderPlus depend on how it was installed in the first place. A summary and new features for each release can be seen in the list of releases.

Bioconda installations

For Bioconda installations upgrading is simple:

If necessary

source ~/miniconda3/bin/activate

Then

conda update -c conda-forge -c bioconda ncbi-amrfinderplus

Binary installations

Basically just re-install, though you shouldn't have to install any prerequisites since presumably they're already installed so you just need to follow the instructions to download and untar the binary

Source installation

You should update your sources to the latest release version of the software (e.g., git pull) or download the latest sources from the latest release. For example:

git pull
git submodule update
make clean
make

See Compile from source for more details.