Advanced PharmCAT Setup

This document teaches you how to set up PharmCAT.

Install Dependencies

Before installing PharmCAT, you will need to install the following dependencies:

1. Java 17 or newer. We currently recommend Java 17.
2. Python 3.10.14 or newer.
3. The following bioinformatic tools:
   • bcftools >= v1.18
   • htslib >= v1.18 (for bgzip) You will need to have the binaries from these packages available in your PATH.

Mac users: bcftools and htslib are available via homebrew.

Environment variables

If you wish, you can customize which versions of PharmCAT's dependencies to use via environment variables:

• JAVA_HOME - the directory where the version of Java you want to use is installed
• BCFTOOLS_PATH - the full path to the bcftools program
• BGZIP_PATH - the full path to the bgzip program

Install PharmCAT

If you are on a Mac or Unix system, you can run:

curl -fsSL https://get.pharmcat.org | bash

This will check to make sure you have the required dependencies listed above and install the PharmCAT in the current directory.

Alternatively, you can download the PharmCAT Pipeline tar file (pharmcat-pipeline-xxx.tar.gz) from our release page and un-tar it.

Whichever way you choose, you will need to manually install the Python dependencies that the Preprocessor requires. These dependencies are listed in a file called requirements.txt. You can either use your preferred Python virtual environment to install these dependencies or run:

pip3 install -r requirements.txt

Done!

And that's it. You should now have all the tools you need to run PharmCAT.

Next steps:

• Learn about PharmCAT's VCF requirements
• Learn how to use the PharmCAT Pipeline
• Learn how to use the PharmCAT VCF Preprocessor
• Learn how to use the core PharmCAT tool