====== 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$''):

<code lang=text>
  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
</code>

If there are multiple versions of **snakemake** listed, then you can load a //specific// version as follows:
<code lang=bash>
$ module load snakemake/version_string
</code>

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''):

<code lang=text>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

</code>

----

===== 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

----

[[:advanced:software|Back to software]]