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:
- Subsets a few chromosomes of public 1000 Genomes data.
- Generates allele frequency stats from the subsets for each chromosome.
- Merges the per-chromosome stats into a single file.
- Generates a plot from the merged file.
# Runs a maximum of 2 jobs in parallel
snakemake --use-conda -j 2
Conda:
Snakemake:
Jupyter notebooks:
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: