Installing kGWASflow

Installation

Installing via Bioconda

‼️This is the preferred method.‼️

In order to use this worklow, you need conda to be installed (to install conda, please follow the instructions here).

# Create a new conda environment with kgwasflow 
# and its dependencies
conda create -c bioconda -n kgwasflow kgwasflow

# Activate kGWASflow conda environment
conda activate kgwasflow

# test kGWASflow
kgwasflow --help

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Installing via GitHub (Alternative Method)

Alternatively, kGWASflow can be installed by cloning the GitHub repository.

# Clone this repository to your local machin
git clone https://github.com/akcorut/kGWASflow.git

# Change into the kGWASflow directory
cd kGWASflow

After cloning the GitHub repo, you can install snakemake and the other dependencies using conda as below:

# This assumes conda is installed
conda env create -f environment.yaml

# Activate kGWASflow conda environment
conda activate kGWASflow

Finally, you can install kGWASflow using the setup script as below:

# Install kgwasflow
python setup.py install

# Test kgwasflow
kgwasflow --help

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If installed correctly, you should see the below prompt on the command line when you execute the command kgwasflow --help.

     _     _______          __      _____  __ _
    | |   / ____\ \        / /\    / ____|/ _| |
    | | _| |  __ \ \  /\  / /  \  | (___ | |_| | _____      __
    | |/ / | |_ | \ \/  \/ / /\ \  \___ \|  _| |/ _ \ \ /\ / /
    |   <| |__| |  \  /\  / ____ \ ____) | | | | (_) \ V  V /
    |_|\_\_____|   \/  \/_/    \_\_____/|_| |_|\___/ \_/\_/

    kGWASflow: A Snakemake Workflow for k-mers Based GWAS

Usage: kgwasflow [OPTIONS] COMMAND [ARGS]...

  kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

  For more options, run: kgwasflow --help kgwasflow init --help kgwasflow run
  --help kgwasflow test --help

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  init  Initialize a new kGWASflow working directory.
  run   Run kGWASflow workflow.
  test  Test kGWASflow workflow.