Software Packages

This page provides a comprehensive overview of the installation processes for various software packages required for Nextflow workflow. Running Tractor GWAS requires one to perform phasing, local ancestry inference, running an extract ancestry-specific tract step, and finally running Tractor GWAS. Each section covers specific tools, detailing their installation, configuration, and verification to guarantee that all dependencies are met and the tools function as expected.

  1. Phasing using SHAPEIT5
  2. Local Ancestry Inference
  3. Tractor (via Tractor GitHub)

1. Phasing using SHAPEIT5

This workflow utilizes SHAPEIT 5 for phasing and requires it to be installed on the system where the workflow will run. While there are multiple installation methods available—such as building from source, downloading static binaries, or using Docker images—we recommend using the Static Binaries and adding them to your system’s PATH for simplicity.

SHAPEIT 5 dependencies

  • Ensure SHAPEIT 5 dependencies (AVX2, GCC > 4.4, bcftools) and required libraries (HTSLib, Boost, etc.) are installed on your system. More details are available in the documentation.

Installation Steps

  1. Download SHAPEIT 5 Static Binaries
    The latest version (as of August 15, 2024) is v5.1.1. Follow these steps to install:

    cd /path/to/software_downloads/
git clone https://github.com/odelaneau/shapeit5.git
cd shapeit5/static_bins/
wget https://github.com/odelaneau/shapeit5/releases/download/v5.1.1/phase_common_static
wget https://github.com/odelaneau/shapeit5/releases/download/v5.1.1/ligate_static

  2. Add to PATH
    Add the downloaded binaries to your PATH by running:

    echo 'export PATH="/path/to/software_downloads/shapeit5/static_bins:$PATH"' >> ~/.bashrc
source ~/.bashrc

  3. Verify Installation
    Ensure the tools are correctly installed by running:

    cd
which phase_common_static
which ligate_static

    Expected output:

    /path/to/software_downloads/shapeit5/static_bins/phase_common_static
/path/to/software_downloads/shapeit5/static_bins/ligate_static

  4. Test the Tools
    Confirm that the tools work by running:

    phase_common_static -h
ligate_static -h

Alternative Installation Option

2. Local Ancestry Inference

We support a range of Local Ancestry Inference (LAI) tools, including many of the most widely used ones. Selecting the right tool for calculating local ancestry estimates tailored to your dataset is essential. Accurate local ancestry estimates are vital for Tractor GWAS, as they enable the identification of ancestry-specific hits. Therefore, it’s important to carefully choose both the LAI tool and the reference dataset.

Currently, we support the following LAI tools: RFMix2, G-Nomix, and FLARE. Be aware that each tool has different input requirements, often in different formats. We recommend users familiarize themselves with each tool thoroughly before attempting to run workflows.

Below are the basic installation instructions for these tools. Please note that these instructions are meant to help you get started, but you should always refer to the original documentation of each tool to ensure all dependencies are properly installed.

1. RFMix2

  1. Visit the RFMix2 GitHub page for the additional information and ensure all dependencies are installed (e.g., bcftools, etc.).
  2. Refer to the RFMix2 Manual for detailed usage instructions.

To install RFMix2:

cd /path/to/software_downloads/
git clone https://github.com/slowkoni/rfmix.git

# Follow the instructions as described on GitHub (https://github.com/slowkoni/rfmix)
autoreconf --force --install # Creates the configure script and its dependencies
./configure                  # Generates the Makefile
make

To add RFMix2 to your PATH:

echo 'export PATH="/path/to/software_downloads/rfmix:$PATH"' >> ~/.bashrc
source ~/.bashrc

Test the installation:

cd
which rfmix

Expected output:

/path/to/software_downloads/rfmix/rfmix

To verify that RFMix2 is working correctly, run:

rfmix --help

2. G-Nomix

  1. Visit the G-Nomix GitHub page for installation instructions and dependency requirements.
  2. Ensure the environment with all necessary dependencies is active when running G-Nomix jobs. If using a specific Conda environment, be sure to specify it in the Nextflow config file (see the Documentation section).
  3. Note that G-Nomix requires significant CPU and memory resources due to its model pre-training phase.
  4. Make sure to add G-Nomix executable to your PATH.

3. FLARE

  1. FLARE is a recently published tool, and is known for its speed and memory efficiency.
  2. Installation instructions and requirements can be found here.
  3. Ensure the appropriate environment with all necessary dependencies (e.g. Java) is active when running FLARE jobs.
  4. Add the FLARE executable to your PATH.

3. Tractor (via Tractor GitHub)

To set up Tractor, follow these instructions:

  1. Clone the Tractor GitHub Repository

    Navigate to your desired directory and clone the Tractor repository:

    cd /path/to/software_downloads/
git clone https://github.com/Atkinson-Lab/Tractor.git

  2. Create and Activate the Conda Environment

    Change to the Tractor directory, then create and activate the Conda environment:

    cd Tractor/
conda env create -f conda_py3_tractor.yml
conda activate py3_tractor

  3. Add Tractor Scripts to PATH

    To ensure you can run Tractor scripts from any directory, add them to your PATH. Use the following commands:

    echo 'export PATH="/path/to/software_downloads/Tractor/scripts:$PATH"' >> ~/.bashrc
source ~/.bashrc

    Replace /path/to/software_downloads with the actual path where you cloned the repository.

  4. Verify the Installation

    You can check if the scripts are accessible by running:

    cd
which extract_tracts.py
which run_tractor.R

    To confirm that the installation works and see the help instructions, use:

    extract_tracts.py --help
extract_tracts_flare.py --help
run_tractor.R --help

    If everything is set up correctly, these commands will display the help information for each script.

Summary

Once all the necessary pre-requisites and softwares are installed and tested successfully, you are ready to run the Nextflow workflow pipeline. Check out the Documentation page for instructions on how to get started.