Snakemake executor plugin: drmaa

Warning

No documentation found in repository https://github.com/snakemake/snakemake-executor-plugin-drmaa. 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 instractions presented in this catalog.

Installation

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

pip install snakemake-executor-plugin-drmaa

Usage

In order to use the plugin, run Snakemake (>=8.0) with the corresponding value for the executor flag:

snakemake --executor drmaa ...

with ... being any additional arguments you want to use.

The executor plugin has the following settings:

Settings

CLI argument	Description	Default	Choices	Required	Type
--drmaa-args VALUE	Args that shall be passed to each DRMAA job submission. Can be used to specify options of the underlying cluster system, thereby using the job properties name, rulename, input, output, params, wildcards, log, threads and dependencies, e.g.: ‘-pe threaded {threads}’. Note that ARGS must be given in quotes.	None		✗
--drmaa-log-dir VALUE	Directory in which stdout and stderr files of DRMAA jobs will be written. The value may be given as a relative path, in which case Snakemake will use the current invocation directory as the origin. If given, this will override any given ‘-o’ and/or ‘-e’ native specification. If not given, all DRMAA stdout and stderr files are written to the current working directory.	None		✗