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snakemake-storage-plugin-gcs

library1.1.4pypypiunverified

A Snakemake storage plugin providing read/write access to Google Cloud Storage (GCS). Version 1.1.4, compatible with Snakemake ≥7.x plugin interface. Release cadence is irregular, tied to Snakemake plugin API updates.

gcp data workflow

pip install snakemake-storage-plugin-gcs

github ↗package ↗docs ↗

INSTALL

IMPORT

SIG · SNAKEMAKE-STORAGE-

snakemake-storage-plugin-gcs

gcppythonv1.1.4

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

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

StorageProviderGCS

✓ from snakemake_storage_plugin_gcs import StorageProviderGCS

✗ from snakemake_storage_plugin_gcs import StorageProviderGCS

Basic usage: install plugin, set up GCS authentication, and use gs:// URIs in Snakemake rules. The plugin auto-detects gs:// prefixes.

import os # Set authentication (uses Application Default Credentials) os.environ['GOOGLE_APPLICATION_CREDENTIALS'] = '/path/to/service-account-key.json' # Or use implicit default credentials # In your Snakefile, reference files with gs:// prefix # Example rule: rule download: input: "gs://my-bucket/data.txt" output: "data.txt" shell: "cp {input} {output}"

Debug

Known issues

gotchaGCS authentication uses Application Default Credentials (ADC) by default. OAuth2 tokens from ADC may expire during long runs, causing failures.

fix

Use a service account key and set GOOGLE_APPLICATION_CREDENTIALS environment variable, or use workload identity federation for long-running workflows.

affects: all

breakingPlugin version 1.x requires Snakemake >=7.0.0 plugin API. Not compatible with older Snakemake versions that used the legacy storage API (pre-7.0).

fix

Upgrade Snakemake to 7.x or later, or use an older storage plugin if locked to Snakemake 6.x (not available).

affects: 1.0.0 and above

gotchaThe plugin does not support GCS object versioning or generation numbers. If you need to retrieve a specific version, you must handle it separately.

fix

Use gsutil or google-cloud-storage API directly for versioned access.

affects: all

Upgrade

Version history

1.1.4latest on PyPI · released Mar 24, 2025

Audit

Dependencies

snakemakerequiredCore workflow manager that this plugin extends

Agent activity

39 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/snakemake/snakemake-storage-plugin-gcs ↗

packagehttps://pypi.org/project/snakemake-storage-plugin-gcs/ ↗

docshttps://snakemake.github.io/snakemake-plugin-catalog/plugins/storage/gcs.html ↗