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Snakemake library for various applications, with a focus on bioinformatics and next-generation sequencing.

The Snakemake rules contain general recipies for commonly used applications and bioinformatics programs. The use cases reflect the needs I've had and do by no means have a comprehensive coverage. Nevertheless, many commands are so commonly used that the recipes may be of general interest.

Comparison with biomake

snakemakelib is basically a port of the rules in biomake to Snakemake. The design principles are similar in that my aim is to compile a library of rules that can be reused and configured via a simple configuration interface.

Disclaimer

Use the rules at your own risk, and make sure you understand them before running any commands. I take no responsibility if you'd happen to run a snakemake clean in an inappropriate location, removing precious data in the process. You have been warned!

Installation

Requirements

• Snakemake version >= 3.2 that supports the global config variable.
• Python version >= 3.3. This may require setting up a virtual environment for python3+.

Obviously you also need working installations of the programs whose rules you wish to make use of.

Installation instructions

Clone the repository https://github.com/percyfal/snakemakelib to an appropriate location:

git clone https://github.com/percyfal/snakemakelib /path/to/snakemakelib

Then either

• add the path to your Snakefile, or
• run python setup.py install (python setup.py develop for development installation)

Running the tests

Issue

cd /path/to/snakemakelib/tests
nosetests -v -s

to run a suite of smaller tests. To run a working pipeline, issue

nosetests --attr=slow

Quickstart

Probably the best way to get started is to run a real example. See the repaper repository for workflows that should work out of the box.