snakemake-storage-plugin-s3
A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)
Decision gist · record as of 2026-08-14
Yes, if you run Snakemake workflows that need S3 or S3-compatible storage integration. The plugin is actively maintained, has low install friction, carries a permissive MIT license, and has no known vulnerabilities. It is a straightforward way to enable cloud storage support in Snakemake without custom scripting.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires Python 3.11 or later.
- AWS credentials or MinIO endpoint configuration must be available in the environment (via AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, or similar).
- Low friction install with a pure-Python wheel.
License · maintenance · safety
MIT (permissive) — MIT license permits commercial and private use with minimal restrictions—suitable for most projects without licensing concerns.
last release 2025-09-11 (337 days) · last repo commit 2026-04-27 · 5 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 439,308 downloads/mo, #6,657 on PyPI
Alternatives
Verify before relying
pip install snakemake-storage-plugin-s3
# In a Snakefile, reference S3 paths directly:
# rule example:
# output: "s3://my-bucket/output.txt"
# shell: "echo hello > {output}"- Whether the plugin auto-discovers S3 credentials from IAM roles, environment variables, or config files, or requires explicit setup.
- Performance characteristics and any limits on object size or concurrent operations.
- Whether MinIO and other S3-compatible endpoints are tested and fully supported or require additional configuration.
What it is and what it does
This package is a Snakemake storage plugin that extends Snakemake's workflow engine to treat S3-compatible object storage as a native file backend. Instead of managing local files or manually uploading to cloud storage, you can declare workflow outputs directly as S3 paths (e.g., s3://bucket/file.txt), and Snakemake will handle reading and writing through the S3 API. It works with AWS S3, MinIO, and other S3-compatible services.
The plugin integrates with Snakemake's plugin interface and relies on boto3 and botocore to communicate with S3 endpoints. Once installed, it becomes available to any Snakemake workflow on the same system. It is actively maintained and supports Python 3.11 through 3.13, with no known security vulnerabilities.
Use it for
- Run Snakemake workflows that read input data from S3 buckets and write results back to S3 without intermediate local storage.
- Use MinIO or other S3-compatible storage as a workflow backend for on-premises or air-gapped environments.
- Integrate Snakemake pipelines with AWS data lakes where intermediate and final outputs live in S3.
- Simplify CI/CD pipelines by treating cloud object storage as a transparent file system within workflow definitions.
Worth the install?
AI-flagged interpretation of the facts on this page. Verify before relying on it.
Yes, if you run Snakemake workflows that need S3 or S3-compatible storage integration.
The plugin is actively maintained, has low install friction, carries a permissive MIT license, and has no known vulnerabilities. It is a straightforward way to enable cloud storage support in Snakemake without custom scripting.
Install
snakemake-storage-plugin-s3 on PyPI
Before you install
Low friction install with a pure-Python wheel. Actively maintained as of April 2026, with recent updates. Depends on boto3 and botocore for AWS SDK functionality, which are standard and well-maintained.
Requires Python 3.11 or later. AWS credentials or MinIO endpoint configuration must be available in the environment (via AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, or similar).
License in practice
MIT license permits commercial and private use with minimal restrictions—suitable for most projects without licensing concerns.
Quickstart
pip install snakemake-storage-plugin-s3
# In a Snakefile, reference S3 paths directly:
# rule example:
# output: "s3://my-bucket/output.txt"
# shell: "echo hello > {output}"Verify before relying
- Whether the plugin auto-discovers S3 credentials from IAM roles, environment variables, or config files, or requires explicit setup.
- Performance characteristics and any limits on object size or concurrent operations.
- Whether MinIO and other S3-compatible endpoints are tested and fully supported or require additional configuration.
Package facts
| License | MIT permissive |
| Python support | Supports the current Python release <4.0,>=3.11 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 4 packagessnakemake-interface-commonsnakemake-interface-storage-pluginsboto3botocore |
| Maintenance | Actively maintained 337 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 439,308 / month, #6,657 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | License :: OSI Approved :: MIT LicenseProgramming Language :: Python :: 3Programming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.13 |
Evidence: snakemake_storage_plugin_s3-0.3.6-py3-none-any.whl
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See also snakemake-storage-plugin-gcs · snakemake · minio · snakemake-interface-storage-plugins · snakemake-interface-report-plugins · snakemake-interface-executor-plugins · snakemake-interface-common · miniopy-async · snakemake-interface-logger-plugins · django-storages