WGS_Pipeline

Pipeline for analysis of DNA-seq on Compute Canada HPC servers.

Authors : Nicolas de Montigny, Golrokh Kiani Professor : Abdoulaye Banire Diallo Organisation : Labobioinfo UQAM

Installation

Dependencies

The pipeline depends on usage of python3 in a virtual environment. To install the virtual environment you will need Miniconda3 installed if on HPC.

1. Run the following on the command line: wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh.
2. Once the download has finished, run: bash Miniconda3-latest-Linux-x86_64.sh and follow the on-screen instructions. Press enter when asked where to install miniconda3 (or specify location).
3. Add the folder /home/$USERNAME/miniconda3/bin to your ~/.bash_profile to easily access your conda
4. Use the environment file to download and install all necessary packages for this workshop into a conda environment:

conda create -n WGS_pipeline -f smk_542_env.yaml.

First setup of snakemake for dev

conda install -c conda-forge mamba
conda create -n WGS_pipeline
mamba install -n WGS_Pipeline bioconda::snakemake

Using venv if needed instead of miniconda

To load the module on HPC.

module load nixpkgs/16.09 python/3.8.2

Download and Then to create the virtual environment using python3 and activate it

python3 -m venv WGS_analysis
source ~/WGS_analysis/bin/activate

Install python3 ressources with pip

pip3 install -r requirements.txt

Usage

• Examples
• References (if needed)

References

Git tutorial on Snakemake https://github.com/bmcconeghy/bioinformatics_pipeline_with_snakemake_2019-06-27