Pandora Simulations

Setup initial gene alignment data

The first thing that needs to be done before running the pipeline is to get and organise the gene alignment data. This is done with a provided script.

Run the following from the project root directory

bash scripts/setup_panx_data.sh

Install requirements

Snakemake

For a basic installation, run:

pip3 install --user snakemake

Other installation options can be found in the snakemake docs.

Conda

A basic installation (Linux) that also prevents conda from being your default python installation can be done with:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda3.sh
conda_prefix=/usr/local/miniconda
sudo bash miniconda3.sh -b -p "$conda_prefix"
# add conda to the end of your path
echo ". ${conda_prefix}/etc/profile.d/conda.sh" >> ~/.bashrc
source "$HOME"/.bashrc
conda activate base
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

For more installation options, see the conda docs.

Singularity

Snakemake requires Singularity version less than 3.0. For installation of Singularity see the docs.

Run pipeline

From the project root directory, run

snakemake --use-conda --use-singularity