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Installation
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Dependencies
=============

AMRrules requires Python 3.12 or higher, and needs pip to be installed.


Download and install AMRrules
=============================

Currently, AMRrules is only available for installation via source. We recommend you set up a new conda environment. ::

    # create your conda environment
    conda create -n amrrules -c bioconda python=3.12 pip
    conda activate amrrules

    # clone the repository
    git clone https://github.com/AMRverse/AMRrules
    cd AMRrules

    # install AMRrules
    make dev

After installation, you must download the required AMRFinderPlus resource files. Run::
    
    amrrules --download-resources

This will download and cache the necessary files for AMRrules to function. You only need to run this **once** after installation, or when updating resources (eg a new AMRFinderPlus database has been released).


Check the installation
======================

Check which organisms have rule-sets available in the installation::
    
    amrrules --list-organisms

Test on one of the included example dataset::
    
    amrrules --input tests/data/input/test_ecoli_wildtype.tsv --output-prefix test_ecoli_wildtype --organism 's__Escherichia coli'

Compare these resulting output files to those in ``tests/data/example_output``...

``tests/data/example_output/test_ecoli_wildtype_interpreted.tsv``:

.. csv-table::
   :file: ../../tests/data/example_output/test_ecoli_wildtype_interpreted.tsv
   :delim: tab
   :header-rows: 1

``tests/data/example_output/test_ecoli_wildtype_genome_summary.tsv``:

.. csv-table::
   :file: ../../tests/data/example_output/test_ecoli_wildtype_genome_summary.tsv
   :delim: tab
   :header-rows: 1

Usage info and test data
========================

More info on usage options can be found on the :ref:`Usage <usage>` page.

Additional test data and example commands can be found on the :ref:`Tests <test>` page.