This repo was used to demo git during the BDSI session on reproducible research. This repo will exist as a reference for the remainder of the summer.

• Project organization
• Documentation
• Version Control
• Capturing the computational environemnt
• Automation

echo "# Title" >> README.md
git init
git add README.md
git commit -a # and fill in commit message

# Then next two steps will link your local repo with a remote on Github and only need to be ran once.
git remote add origin https://github.com/<your_account>/<repo_name>.git
git push --set-upstream origin master

See link below for instructions on how to install Snakemake. The pipeline performs the following steps:

1. Subsets a few chromosomes of public 1000 Genomes data.
2. Generates allele frequency stats from the subsets for each chromosome.
3. Merges the per-chromosome stats into a single file.
4. Generates a plot from the merged file.

# Runs a maximum of 2 jobs in parallel
snakemake --use-conda -j 2 

Conda:

• https://conda.io/docs/user-guide/install/index.html

Snakemake:

• https://snakemake.readthedocs.io/en/stable/getting_started/installation.html

Jupyter notebooks:

• http://jupyter.org/install

Containers:

• https://www.sylabs.io/guides/3.2/user-guide/
• https://docs.docker.com/docker-for-mac/install/
• https://docs.docker.com/docker-for-windows/install/

RStudio:

• https://www.rstudio.com/products/rstudio/download/#download