Snakemake Storage Plugin: LFS

A Snakemake storage plugin for downloading files from Git LFS (Large File Storage) servers with optional local caching.

Features

• Git LFS protocol: Fetches objects via the Git LFS Batch API
• Local repo lookup: Checks a local git repository's LFS store before downloading remotely
• Local caching: Downloaded objects can be cached to avoid redundant transfers
• Checksum verification: Verifies SHA-256 integrity (the LFS OID is the SHA-256 digest)
• Authentication: Supports token-based Basic Auth via environment variable
• Concurrent download control: Limits simultaneous downloads
• Progress bars: Shows download progress with tqdm
• Immutable objects: Returns mtime=0 (LFS objects are content-addressed and never change)
• Environment variable support: Configure via environment variables for CI/CD

Installation

pip install snakemake-storage-plugin-lfs

URL Format

LFS objects are referenced using the lfs:// scheme:

lfs://{oid}/{path}

• {oid} — SHA-256 hex digest of the object (64 hex characters)
• {path} — logical file path used as the local filename

Example:

lfs://3b4c5d6e7f8a9b0c1d2e3f4a5b6c7d8e9f0a1b2c3d4e5f6a7b8c9d0e1f2a3b4/data/natura.tiff

Configuration

Register the plugin in your Snakefile:

storage lfs:
    provider="lfs",
    repo_url="https://github.com/org/repo",  # required

Settings

Usage

Use lfs:// URLs directly in your rules:

rule use_lfs_file:
    input:
        storage.lfs(
            "lfs://3b4c5d6e7f8a9b0c1d2e3f4a5b6c7d8e9f0a1b2c3d4e5f6a7b8c9d0e1f2a3b4/data/natura.tiff"
        ),
    output:
        "resources/natura.tiff"
    shell:
        "cp {input} {output}"

The plugin will:

1. Check the local git repository's LFS store (if local_repo is set)
2. Check the local cache (if cache is set)
3. If not found locally, query the LFS Batch API for a download URL
4. Download the object with a progress bar
5. Verify the SHA-256 checksum against the OID
6. Store in the cache (if cache is set)

Authentication

To access private repositories, set token_envvar to the name of an environment variable that holds the token:

storage lfs:
    provider="lfs",
    repo_url="https://github.com/org/private-repo",
    token_envvar="GITHUB_TOKEN",

export GITHUB_TOKEN="ghp_..."
snakemake --cores all

CI/CD Configuration

# GitHub Actions example
- name: Run snakemake workflows
  env:
    SNAKEMAKE_STORAGE_LFS_REPO_URL: "https://github.com/org/repo"
    SNAKEMAKE_STORAGE_LFS_SKIP_REMOTE_CHECKS: "1"
    GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  run: |
    snakemake --cores all

How LFS Objects Are Located

Priority order in managed_retrieve():

1. Local repo (local_repo setting): Looks up the file by its path in the working tree ({local_repo}/{lfs_path}). LFS pointer stubs are skipped (with a warning). If the file is present but its SHA-256 does not match the OID, a WorkflowError is raised — the local repo contains a different version of the file.
2. Cache (cache setting): Checks the configured cache directory.
3. Remote: Queries the LFS Batch API ({repo_url}.git/info/lfs/objects/batch) and downloads from the returned URL.

License

MIT License