This is a snakemake workflow to reproduce figures from Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios.
- Marc J Williams (@marcjwilliams1)
- Clone this repo
git clone https://github.com/marcjwilliams1/dnds-clonesize - Install snakemake if you don't have it installed
- Make a dry-run to ensure that the pipeline will compile
snakemake -n - Run the pipeline with
snakemakeadding additional options if you want to run on a cluster (recommended).
Two scripts are provided that will run the pipeline on either a SGE or LSF cluster. If you are using a different job submission system you can use these as a starting point.
2 containerized images are provided with all the software dependencies. The first includes all relevent R packages and is available here. The second includes the julia dependencies and is available here. The snakemake pipeline will automatically pull these container or you can download them as follows:
singularity pull shub://marcjwilliams1/dnds-clonesize-R-container
singularity pull docker://marcjwilliams1/julia_r_dnds:v1.1
To run the pipeline you will need singularity installed on your cluster.
Also included are jupyter notebooks in the notebooks/ folder for each of the main steps. These are perhaps easier to parse than the pipeline if you're interested in looking at how a particular analysis was done although are by now a bit out of date.