https://github.com/komax/snakemake-tutorial

A minimal tutorial to snakemake
https://github.com/komax/snakemake-tutorial

Last synced: 5 days ago
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A minimal tutorial to snakemake

• Host: GitHub
• URL: https://github.com/komax/snakemake-tutorial
• Owner: komax
• License: mit
• Created: 2020-02-13T14:33:20.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-03-03T13:50:44.000Z (almost 5 years ago)
• Last Synced: 2024-11-08T09:51:13.009Z (about 2 months ago)
• Language: Jupyter Notebook
• Size: 16.6 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# snakemake-tutorial

A minimal tutorial to snakemake

## Requirements

- a [conda installation](https://docs.conda.io/en/latest/) (either Miniconda or Anaconda)

## Install

### 1. Clone the repository

```bash

$ git clone https://github.com/komax/snakemake-tutorial.git

```

### 2. Anaconda environment

1. Create a new environment, e.g., ```snakemake-tutorial``` and install all dependencies.

```bash

$ conda env create --name snakemake-tutorial --file environment.yaml

```

2. Activate the conda environment. Either use the anaconda navigator or use this command in your terminal:

```bash

$ conda activate snakemake-tutorial

```

or

```bash

$ source activate snakemake-tutorial

```

## Basic usage

1. Launch jupyter notebook

```bash

$ jupyter notebook

```

2. Open ```run-snakemake.ipynb```

3. Step through the tutorial