Examples

A Snakefile for running the whole pipeline can be found here.

Users need to install conda first. See conda installation for instruction. We recommend users use mamba to create the virtual environment, because mamba is much faster than conda.

Users can dry-run the whole pipeline as follows:

git clone https://github.com/xin-huang/sstar
cd ./sstar/examples/snakepipe
conda install mamba -n base -c conda-forge
mamba env create -f conda-env.yml
conda activate sstar
export R_LIBS=$CONDA_PREFIX/lib/R/library
snakemake -n -p

Users can use snakemake -c 1 for running the whole pipeline locally or submit jobs to SLURM with mkdir logs_slurm && snakemake --profile . -j 1. Users can modify config.yaml for submitting jobs to other scheduling system, such as SGE.