kelly-sovacool / bioinf545-group3-project

bioinf545-group3-project

Group members:

• Nicole Bowers
• Brittany Hicks
• Christina Kang-Yun
• Katelyn Polemi
• Kelly Sovacool

Setup

Most dependencies are listed in the conda environment file. If you don't already have conda, I recommend installing the Miniconda Python 3 distribution.

You can create the conda environment with:

conda env create -f environment.yml

Then activate it with:

conda activate bf545

Additionally, you will need to install a TeX distribution to compile the documents to PDF.

As you install new dependencies, add them to the environment file too. You can update your active environment (e.g. after a collaborator adds a new dependency) with:

conda env update -f environment.yml

Usage

Run the snakemake workflow with:

snakemake --use-conda

Visualize the workflow with:

snakemake --rulegraph | dot -T png > figures/rulegraph.png

See the rendered PDF and HTML files here.