Snakemake executor plugin: slurm

Error

Not a valid plugin:  WARN Using local manifest /tmp/tmpy6hopsfh/pixi.toml rather than /home/runner/work/snakemake-plugin-catalog/snakemake-plugin-catalog/pixi.toml from environment variable `PIXI_PROJECT_MANIFEST`
✨ Pixi task (extract-info): python -c "from snakemake_interface_executor_plugins.registry import ExecutorPluginRegistry; plugin = ExecutorPluginRegistry().get_plugin('slurm'); import json; fmt_type = lambda thetype: thetype.__name__ if thetype is not None else None; fmt_setting_item = lambda key, value: (key, fmt_type(value)) if key == 'type' else (key, value); fmt_setting = lambda setting: dict(map(lambda item: fmt_setting_item(*item), setting.items())); print(json.dumps(list(map(fmt_setting, plugin.get_settings_info()))))"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    from snakemake_interface_executor_plugins.registry import ExecutorPluginRegistry; plugin = ExecutorPluginRegistry().get_plugin('slurm'); import json; fmt_type = lambda thetype: thetype.__name__ if thetype is not None else None; fmt_setting_item = lambda key, value: (key, fmt_type(value)) if key == 'type' else (key, value); fmt_setting = lambda setting: dict(map(lambda item: fmt_setting_item(*item), setting.items())); print(json.dumps(list(map(fmt_setting, plugin.get_settings_info()))))
                                                                                               ~~~~~~~~~~~~~~~~~~~~~~^^
  File "/tmp/tmpy6hopsfh/.pixi/envs/default/lib/python3.14/site-packages/snakemake_interface_common/plugin_registry/__init__.py", line 40, in __init__
    self.collect_plugins()
    ~~~~~~~~~~~~~~~~~~~~^^
  File "/tmp/tmpy6hopsfh/.pixi/envs/default/lib/python3.14/site-packages/snakemake_interface_executor_plugins/registry/__init__.py", line 63, in collect_plugins
    super().collect_plugins()
    ~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/tmp/tmpy6hopsfh/.pixi/envs/default/lib/python3.14/site-packages/snakemake_interface_common/plugin_registry/__init__.py", line 97, in collect_plugins
    module = importlib.import_module(moduleinfo.name)
  File "/tmp/tmpy6hopsfh/.pixi/envs/default/lib/python3.14/importlib/__init__.py", line 88, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1398, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1371, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1342, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 938, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 759, in exec_module
  File "<frozen importlib._bootstrap>", line 491, in _call_with_frames_removed
  File "/tmp/tmpy6hopsfh/.pixi/envs/default/lib/python3.14/site-packages/snakemake_executor_plugin_slurm/__init__.py", line 115, in <module>
    class ExecutorSettings(ExecutorSettingsBase):
    ...<158 lines>...
            validate_executor_settings(self)
  File "/tmp/tmpy6hopsfh/.pixi/envs/default/lib/python3.14/site-packages/snakemake_executor_plugin_slurm/__init__.py", line 235, in ExecutorSettings
    "help": _get_status_command_help(),
            ~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/tmp/tmpy6hopsfh/.pixi/envs/default/lib/python3.14/site-packages/snakemake_executor_plugin_slurm/__init__.py", line 76, in _get_status_command_help
    default_cmd = _get_status_command_default()
  File "/tmp/tmpy6hopsfh/.pixi/envs/default/lib/python3.14/site-packages/snakemake_executor_plugin_slurm/__init__.py", line 63, in _get_status_command_default
    raise WorkflowError(
    ...<3 lines>...
    )
snakemake_interface_common.exceptions.WorkflowError: Neither 'sacct' nor 'squeue' commands are available on this system. At least one of these commands is required for job status queries.


Please file a corresponding issue in the plugin's `repository <https://github.com/snakemake/snakemake-executor-plugin-slurm>`__ (if there is none yet).

SLURM is a widely used batch system for performance compute clusters. This executor plugin allows to use it in a seamless and straightforward way.