A template + script to set up a basic conda env with snakemake and a sensible directory structure.
Projects based on this template require a working install of miniconda and conda-env.
- Download this repo and
cdinto it cp snakestart.bash ~/bin/snakestartcp snakestart $XDG_CONFIG_HOME/
Snakestart takes 1 argument: the name of the project.
e.g. snakestart my_project
It will create a directory with the name of the project and the current date and create a conda environment with the project name. This conda environment includes snakemake, python3 and the bioconda and r channels.
The Snakefile contains some useful rules for updating defined dependencies when pushing to a remote git repo.
Example:
snakestart my_project
cd my_project_2016-08-15
git init && git add -A && git commit -m "first"
git remote add origin...
snakemake push