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snakemake-storage-plugin-fs

library1.1.3pypypiunverified

A Snakemake storage plugin for reading and writing from a locally mounted filesystem using rsync. Version 1.1.3 is the latest stable release, with active development and monthly releases focused on bug fixes and compatibility with Snakemake's storage plugin API.

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pip install snakemake-storage-plugin-fs

github ↗package ↗docs ↗

INSTALL

IMPORT

SIG · SNAKEMAKE-STORAGE-

snakemake-storage-plugin-fs

datapythonv1.1.3

Install

2.5s avg

Import

—

Disk

18MB

Pass rate

6/ 10

Env Coverage6 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.1.3 · 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

glibc

py 3.10

✕ build_error

py 3.11

✓ —

✓ 2.8s

py 3.12

✓ —

✓ 2.4s

py 3.13

✓ —

✓ 2.4s

py 3.9

✕ build_error

18MB installed

● package 18MB

Code

Verified usage

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

StorageProviderFS

✓ from snakemake_storage_plugin_fs import StorageProviderFS

✗ from snakemake_storage_plugin_fs import StorageProviderFS

Basic usage of the plugin to interact with a local filesystem storage. The plugin is typically used implicitly by Snakemake when a workflow references storage queries with 'fs://' prefix.

from snakemake_storage_plugin_fs import StorageProviderFS # Example: initialize with remote path and optional prefix provider = StorageProviderFS( remote_path="/path/to/remote", prefix="/local/prefix" ) # Example operations (normally triggered by Snakemake) print(provider.list()) print(provider.stat("some_file.txt"))

Debug

Known issues

gotchaThe plugin relies on rsync being installed on the system. Without it, file transfers will fail silently or with cryptic errors.

fix

Install rsync (e.g., apt-get install rsync on Debian/Ubuntu, or brew install rsync on macOS).

affects: all

deprecatedAs of v1.0.3, the query validation API was deprecated. Old code that used `validate_query` directly will fail. Users should rely on Snakemake's standard query handling.

fix

Upgrade to v1.0.3 or later and remove any manual calls to deprecated validation methods.

affects: <=1.0.2

gotchaThe plugin does not support remote hosts via SSH or any network protocol; it only works with locally mounted filesystems. Users may mistakenly try to use it with remote paths via SSH, which will fail because rsync is called without SSH flags by default.

fix

Ensure the 'remote' path is actually a locally mounted directory (e.g., NFS, FUSE, or local disk). For remote SSH, use a different plugin (e.g., snakemake-storage-plugin-s3, snakemake-storage-plugin-gs).

affects: all

gotchaSymlinks are copied without preserving their targets by default in older versions. This can lead to broken symlinks in the cache.

fix

Upgrade to v1.1.3 or later, which explicitly passes `--links --no-perms --no-owner` to rsync to ensure symlinks are copied correctly.

affects: <1.1.3

Upgrade

Version history

1.1.3latest on PyPI · released Oct 31, 2025

Audit

Dependencies

snakemakerequiredPlugin is loaded as a Snakemake storage plugin; requires Snakemake >=7.0.0

rsyncoptionalUnderlying tool for file transfer; not a Python dependency but must be installed on the system

Agent activity

32 hits · last 30 days

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OpenAI (training)

Resources

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

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

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