DescriptionSnakemake 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|
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|
Interactive sessionYou can start an interactive snakemake session on the login nodes by loading the corresponding modules and starting the Python interpreter.
[sfux@euler05 ~]$ module load new gcc/4.8.2 python/3.6.0 Autoloading openblas/0.2.13_seq and sqlite/3.15.0 [sfux@euler05 ~]$ 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.