Snakemake

Category

Python, development

Description

Snakemake is an MIT-licensed workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files.

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
		3.13.3

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
3.13.3	module load new gcc/4.8.2 python/3.6.0	openblas/0.2.13_seq sqlite/3.15.0

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Interactive session

You can start an interactive snakemake session on the login nodes by loading the corresponding modules and starting the Python interpreter.

[sfux@eu-login-05 ~]$ module load new gcc/4.8.2 python/3.6.0
Autoloading openblas/0.2.13_seq and sqlite/3.15.0
[sfux@eu-login-05 ~]$ python
Python 3.6.0 (default, Feb 10 2017, 09:00:08)
[GCC 4.8.2] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import snakemake
>>> snakemake.__version__
'3.13.3'
>>> 

Please note that you should use interactive sessions only for very short test that do not use a lot of CPU capacity. You have to submit all other computations as a batch job.

License information

MIT License

Links

https://bitbucket.org/snakemake/snakemake/wiki/Home

https://snakemake.readthedocs.io/en/stable/
https://pypi.python.org/pypi/snakemake