snakemake

snakemake is a software module available on Comet.

snakemake overview

To access snakemake on Comet, run module load snakemake. This will load the default version of snakemake.

An overview of the module information is shown below (module -r spider ^snakemake$): 

snakemake:
     Versions:
        snakemake/8.27.0-foss-2024a
        snakemake/8.27.0 (E)

Names marked by a trailing (E) are extensions provided by another module.

  For detailed information about a specific "snakemake" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider snakemake/8.27.0

If there are multiple versions of snakemake listed, then you can load a specific version as follows: 

$ module load snakemake/version_string

You can find the most up to date information whilst logged on to Comet by running module -r spider ^snakemake$.

snakemake Help

The module snakemake has the following embedded help text (module help snakemake): 

Description
===========
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.

More information
================
 - Homepage: https://snakemake.readthedocs.io

Included extensions
===================
argparse-dataclass-2.0.0, conda-inject-1.3.2, ConfigArgParse-1.7, connection-
pool-0.0.3, datrie-0.8.2, dpath-2.2.0, fastjsonschema-2.19.1,
humanfriendly-10.0, immutables-0.21, jupyter-core-5.7.2, nbformat-5.10.4,
plac-1.4.3, reretry-0.11.8, smart-open-7.1.0, snakemake-8.27.0, snakemake-
executor-plugin-cluster-generic-1.0.9, snakemake-executor-plugin-cluster-
sync-0.1.4, snakemake-executor-plugin-flux-0.1.1, snakemake-executor-plugin-
slurm-0.12.0, snakemake-executor-plugin-slurm-jobstep-0.2.1, snakemake-
interface-common-1.17.4, snakemake-interface-executor-plugins-9.3.3,
snakemake-interface-report-plugins-1.1.0, snakemake-interface-storage-
plugins-3.3.0, stopit-1.1.2, throttler-1.2.2, toposort-1.10, yte-1.5.5

snakemake Dependencies

The default version of the module snakemake has the following dependencies:

  • foss/2024a
  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0
  • SciPy-bundle/2024.05-gfbf-2024a
  • GitPython/3.1.43-GCCcore-13.3.0
  • IPython/8.28.0-GCCcore-13.3.0
  • PyYAML/6.0.2-GCCcore-13.3.0
  • wrapt/1.16.0-gfbf-2024a
  • PuLP/2.8.0-foss-2024a

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