Registry / workflow / snakemake-executor-plugin-cluster-generic

snakemake-executor-plugin-cluster-generic

library1.0.9pypypi✓ verified 80d ago

A Snakemake executor plugin for generic cluster submission via command-line tools like qsub, sbatch, bsub. It allows users to define cluster submission commands via Snakemake profiles or configuration. Current version: 1.0.9. Releases are driven by upstream Snakemake interface changes; no fixed cadence.

workflow devops

pip install snakemake-executor-plugin-cluster-generic

github ↗package ↗homepage ↗docs ↗

INSTALL

IMPORT

SIG · SNAKEMAKE-EXECUTOR

snakemake-executor-plugin-cluster-generic

workflowpythonv1.0.9

Install

2.1s avg

Import

—

Disk

17MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.0.3 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 0.000s · 19.1MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 2.1s · import 0.000s · 20MB

17MB installed

● package 17MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

Executor

✓ from snakemake_executor_plugin_cluster_generic import Executor

✗ from snakemake_executor_plugin_cluster_generic import ClusterGenericExecutor

Instantiate the plugin executor. Usually configured via Snakemake profiles; this shows direct usage.

import os from snakemake_executor_plugin_cluster_generic import ClusterGenericExecutor # Typically configured via Snakemake profile, but you can instantiate directly: executor = ClusterGenericExecutor() # Then pass to Snakemake workflow (requires proper context) print('Executor ready')

Debug

Known issues

breakingRequires Python >=3.11; not compatible with older Python versions.

fix

Upgrade to Python 3.11 or later.

affects: all versions (>=1.0.0)

breakingThe plugin is incompatible with Snakemake v7.x's built-in cluster support. Must use Snakemake >=7.8 (with adapter module) or >=8.x native plugin support.

fix

Use Snakemake >=8.0 or install 'snakemake' together with the plugin.

affects: all versions (>=1.0.0)

deprecatedThe old configuration keys 'cluster', 'cluster-status', 'cluster-cancel' etc. are deprecated. Use 'submit_cmd', 'status_cmd', 'cancel_cmd', etc. in the profile dict.

fix

Update your Snakemake profile to use the new keys (e.g., 'submit_cmd' instead of 'cluster').

affects: since v1.0.0

gotchaMissing 'submit_cmd' configuration will cause a runtime error: 'submit_cmd must be set'.

fix

Define 'submit_cmd' in your profile or environment (e.g., --cluster-submit-cmd).

affects: all versions (>=1.0.0)

Upgrade

Version history

1.0.9latest on PyPI · released Mar 11, 2024

Audit

Dependencies

snakemake-interface-executor-pluginsrequiredRequired for executor plugin interface.

Agent activity

29 hits · last 30 days

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OpenAI (training)

Resources

githubhttps://github.com/snakemake/snakemake-executor-plugin-cluster-generic ↗

packagehttps://pypi.org/project/snakemake-executor-plugin-cluster-generic/ ↗

homepagehttps://snakemake.github.io ↗

docshttps://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/cluster-generic.html ↗