Containerized workflow for calling medaka F2 haplotypes

NOTE: Caution re: this issue: snakemake/snakemake#304

Steps

1. Change directory to your preferred working directory on the cluster, e.g.:

cd path/to/working/directory

2. Clone this repository:

git clone https://github.com/brettellebi/somites.git

3. Install miniconda3:

   • Download appropriate by installer by copying the link from here: https://docs.conda.io/en/latest/miniconda.html, then wget it, e.g.: wget {link}
   • Then follow instructions here: https://conda.io/projects/conda/en/latest/user-guide/install/index.html

4. Create global Snakemake environment:

conda create -f snakemake_6.7.0

5. Edit somites/config/config.yaml and somites/init.sh to adapt to Heidelberg cluster.

6. Run configured bash script somites/init.sh to run snakemake.