simonll / cpg-ppred-test

A simple test to uncover signals of CpG hypermutability using posterior predictive simulations
Simon Laurin-Lemay, Nicolas Rodrigue,\

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0. Get Started

git clone https://github.com/Simonll/CpG-ppred-test.git
cd CpG-ppred-test

1. Install Docker

https://docs.docker.com/engine/install/

2. Install Snakemake

https://snakemake.readthedocs.io/en/stable/getting_started/installation.html

3. Build all Docker containers needed

To run the workflow, you need to build the following Docker containers:

Primary Docker layer

docker build --build-arg USER_NAME=$(whoami) --build-arg USER_ID=$(id -u ${USER}) --build-arg GROUP_ID=$(id -g ${USER}) -t ubuntu20.04/basic:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/basic --pull

Specific layer for IQTREE

docker build -t ubuntu20.04/iqtree:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/iqtree

Specific layer for Phylogenetic Simulator

docker build --build-arg CACHEBUST=$(date +%s) -t ubuntu20.04/lfp:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/LikelihoodFreePhylogenetics

Specific layer for Phylobayes MPI

docker build -t ubuntu20.04/pbmpi:latest https://github.com/Simonll/docker.git#develop:/dockerfiles/phylobayes-mpi

4. Replicate experiments

You need to process all Snakemake files in a semi-automatic way. Begin by activating parts of the workflow selectively (comment out certain sections to obtain the necessary results). Using notebook scripts will help you generate the statistics and figures.