Workflow manager hello world tests

This repo consists of code and dataused to complete the Snakemake General Use tutorial

Directory structure

.
├── README.md
├── config
├── resources
├── results
├── snakemake-environment.yml
└── workflow
    ├── Snakefile
    ├── envs
    ├── notebooks
    ├── report
    ├── rules
    └── scripts

Snakemake tutorial

Environment setup

Install pixi. The shell may require restarting after pixi and miniconda installation.

curl -fsSL https://pixi.sh/install.sh | bash

Ensure that miniconda is installed

curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -o Miniforge3-Linux-x86_64.sh

bash Miniforge3-Linux-x86_64.sh

If minifconda has not been previously installed, answer "yes" to Do you wish the installer to prepend the install location to PATH ...? [yes|no].

Enter the snakemake tutorial directory

cd snakemake-tutorial

Download example data

curl -L https://api.github.com/repos/snakemake/snakemake-tutorial-data/tarball -o snakemake-tutorial-data.tar.gz

Extract example data

tar --wildcards -xf snakemake-tutorial-data.tar.gz --strip 1 "*/data" "*/environment.yaml"

Initialize conda environment with pixi

pixi init --import environment.yaml

Activation of conda environment

pixi shell

Test that environment is activated my invoking the snakemake help message:

snakemake --help

Create DAG of all jobs

snakemake --dag | dot -Tsvg > alljobs_dag.svg

Run all jobs in Snakefile

snakemake -p --cores 1