snakemake-course

Short setup for the Carpentries Snakemake novice bioinformatics course.

Quick start

1. Create the course environment:

bash create-snakemake-env.sh

2. Activate it:

conda activate snakemake_carpentry

3. Check Snakemake:

snakemake --version

Course data

The dataset is already included in this repository at:

• snakemake_data/yeast/reads
• snakemake_data/yeast/transcriptome

Course revision notes

Install setq instead of FastX since the latter is no longer maintained

conda install -c bioconda seqtk

Use these paths as inputs while following the lesson: https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/index.html