{"id":22381,"library":"snakemake-executor-plugin-cluster-generic","title":"snakemake-executor-plugin-cluster-generic","description":"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.","status":"active","version":"1.0.9","language":"python","source_language":"en","source_url":"https://github.com/snakemake/snakemake-executor-plugin-cluster-generic","tags":["snakemake","executor-plugin","cluster","hpc","job-scheduler","workflow"],"install":[{"cmd":"pip install snakemake-executor-plugin-cluster-generic","lang":"bash","label":"Install via pip"}],"dependencies":[{"reason":"Required for executor plugin interface.","package":"snakemake-interface-executor-plugins","optional":false}],"imports":[{"note":"Old import path from Snakemake v7.x; plugin is now a separate package.","wrong":"from snakemake.executors.cluster_generic import ClusterGenericExecutor","symbol":"ClusterGenericExecutor","correct":"from snakemake_executor_plugin_cluster_generic import ClusterGenericExecutor"}],"quickstart":{"code":"import os\nfrom snakemake_executor_plugin_cluster_generic import ClusterGenericExecutor\n\n# Typically configured via Snakemake profile, but you can instantiate directly:\nexecutor = ClusterGenericExecutor()\n# Then pass to Snakemake workflow (requires proper context)\nprint('Executor ready')","lang":"python","description":"Instantiate the plugin executor. Usually configured via Snakemake profiles; this shows direct usage."},"warnings":[{"fix":"Upgrade to Python 3.11 or later.","message":"Requires Python >=3.11; not compatible with older Python versions.","severity":"breaking","affected_versions":"all versions (>=1.0.0)"},{"fix":"Use Snakemake >=8.0 or install 'snakemake' together with the plugin.","message":"The 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.","severity":"breaking","affected_versions":"all versions (>=1.0.0)"},{"fix":"Update your Snakemake profile to use the new keys (e.g., 'submit_cmd' instead of 'cluster').","message":"The old configuration keys 'cluster', 'cluster-status', 'cluster-cancel' etc. are deprecated. Use 'submit_cmd', 'status_cmd', 'cancel_cmd', etc. in the profile dict.","severity":"deprecated","affected_versions":"since v1.0.0"},{"fix":"Define 'submit_cmd' in your profile or environment (e.g., --cluster-submit-cmd).","message":"Missing 'submit_cmd' configuration will cause a runtime error: 'submit_cmd must be set'.","severity":"gotcha","affected_versions":"all versions (>=1.0.0)"}],"env_vars":null,"last_verified":"2026-04-27T00:00:00.000Z","next_check":"2026-07-26T00:00:00.000Z","problems":[{"fix":"Use 'from snakemake_executor_plugin_cluster_generic import ClusterGenericExecutor' instead.","cause":"Import from the old Snakemake built-in path after switching to the plugin.","error":"ModuleNotFoundError: No module named 'snakemake.executors.cluster_generic'"},{"fix":"Add 'submit_cmd' to your profile (e.g., 'submit_cmd: \"sbatch --parsable {script}\"') or pass '--cluster-submit-cmd'.","cause":"The plugin requires the 'submit_cmd' configuration to be provided via profile or command-line.","error":"snakemake_executor_plugin_cluster_generic.settings.ExecutorSettingsError: submit_cmd must be set"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}