Snakemake executor plugin: lsf-jobstep

Warning

This plugin is not maintained and reviewed by the official Snakemake organization.

Warning

No documentation found in repository https://github.com/BEFH/snakemake-executor-plugin-lsf-jobstep. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instructions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-executor-plugin-lsf-jobstep

Usage

In order to use the plugin, run Snakemake (>=8.0) in the folder where your workflow code and config resides (containing either workflow/Snakefile or Snakefile) with the corresponding value for the executor flag:

snakemake --executor lsf-jobstep --default-resources --jobs N ...

with N being the number of jobs you want to run in parallel and ... being any additional arguments you want to use (see below). The machine on which you run Snakemake must have the executor plugin installed, and, depending on the type of the executor plugin, have access to the target service of the executor plugin (e.g. an HPC middleware like slurm with the sbatch command, or internet access to submit jobs to some cloud provider, e.g. azure).

The flag --default-resources ensures that Snakemake auto-calculates the mem and disk resources for each job, based on the input file size. The values assumed there are conservative and should usually suffice. However, you can always override those defaults by specifying the resources in your Snakemake rules or via the --set-resources flag.

Depending on the executor plugin, you might either rely on a shared local filesystem or use a remote filesystem or storage. For the latter, you have to additionally use a suitable storage plugin (see section storage plugins in the sidebar of this catalog) and eventually check for further recommendations in the sections below.

All arguments can also be persisted via a profile, such that they don’t have to be specified on each invocation. Here, this would mean the following entries inside of the profile

executor: lsf-jobstep
default_resources: []

For specifying other default resources than the built-in ones, see the docs.