Automic VaultAutomic Vault

brew

Install snakemake with Homebrew, apt, dnf, Nix

Pythonic workflow system. Version 9.23.1 via Homebrew; verified 2026-06-19.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install snakemake

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install snakemake

Debian stable package indexes · snakemake · source: deb.debian.org

Fedora dnfverified · 92%
sudo dnf install snakemake

Fedora Rawhide package metadata · snakemake · source: dl.fedoraproject.org

Nixverified · 92%
nix profile install nixpkgs#snakemake

nixpkgs package indexes · pkgs/by-name/sn/snakemake/package.nix · source: api.github.com

overview

Package summary

Pythonic workflow system

Commands and aliases

  • snakemake

history

Project history and usage

Snakemake is a Python-based workflow management system for reproducible and scalable data analyses, especially common in bioinformatics and scientific computing.

Project history

The official citation page identifies the initial Snakemake publication as a 2012 Bioinformatics article, followed by a 2021 rolling paper for ongoing feature updates. The official GitHub README describes Snakemake workflows as human-readable, Python-based definitions that scale from local machines to server, cluster, grid, and cloud environments.

Adoption history

The official README reports that Snakemake was receiving more than seven new citations per week in 2021 and had almost 400k downloads at that time. The supplied metadata shows distribution through Homebrew, Debian, Ubuntu, Fedora/DNF, and Nix.

How it is used

Users describe workflows in Snakefiles, define rules, inputs, outputs, and software environments, and run snakemake to build requested targets. The official deployment docs recommend a repository layout with workflow code under workflow/ and configuration under config/, including config/config.yaml examples.

Why package nerds care

Snakemake is significant for package maintainers because it bridges language-level workflow definitions, reproducible software deployment, Conda/container integration, and distribution through multiple OS package managers.

Timeline

  • 2012: Initial Snakemake paper published in Bioinformatics.
  • 2019: Current official GitHub repository created.
  • 2021: Sustainable data analysis with Snakemake rolling paper published.
  • 2024: Snakemake 8 release line decomposes functionality into plugins.
  • 2026: Stable documentation tracks Snakemake 9.x.

Related projects

  • Snakemake workflow catalog
  • Snakemake wrappers
  • Snakemake executor plugins
  • Conda
  • Apptainer

security posture

No protected-tool coverage found yet

No matching local secret-handling manifest was found for snakemake. Nucleus package metadata is still published here so future coverage has a stable package URL.

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Installs with 6 runtime dependencies.
  • Build metadata lists 1 build dependencies.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

local files

Configuration and credential file locations

These source-backed paths show where this package keeps local settings or durable credentials. Automic Vault can use them as review targets for secret scanning, migration, and command approval.

Configuration files

Config paths the tool may read or write during local use.

Unix
config/config.yaml

executables

Installed executables

CommandKindExposureNote
snakemakecliglobal executable

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-07-08
manager version9.23.1
manager updated2026-06-19
local dataok
upstreamnot checked
latest detectednot detected

https://snakemake.readthedocs.io/

install metadata

Package metadata

Package keybrew:snakemake
Version9.23.1
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/snakemake
Homepagehttps://snakemake.readthedocs.io/
Repositoryhttps://github.com/snakemake/snakemake
Upstream docshttps://snakemake.readthedocs.io/en/stable
LicenseMIT
Source archivehttps://files.pythonhosted.org/packages/9e/c2/45aa858e55edbb7dbc243ed60859f4f3d92d63ecdd67a80632aa3659fe6b/snakemake-9.23.1.tar.gz
Last updated2026-06-19T11:07:37Z
Pulseupdated
Dependenciescbc, certifi, libyaml, pydantic, python@3.14, rpds-py
Build dependenciesrust
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namesnakemake
Version Scheme0
Revision0
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • stable

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

Debian apt95%

snakemake 7.32.4-7

pythonic workflow management system

https://snakemake.readthedocs.io/

sudo apt install snakemake
  • Section: science
  • Architecture: all
  • 28 dependencies
  • 17 optional deps
  • normalized package name match
  • Matched by: Snakemake
Debian stable package indexes · deb.debian.org · Debian stable package indexes: snakemake from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

snakemake-doc 7.32.4-7

documentation for pythonic workflow management system

https://snakemake.readthedocs.io/

sudo apt install snakemake-doc
  • Section: doc
  • Architecture: all
  • Source Package: snakemake
  • 4 dependencies
  • 1 optional deps
  • normalized package name match
  • Matched by: Snakemake
Debian stable package indexes · deb.debian.org · Debian stable package indexes: snakemake-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

snakemake

nix profile install nixpkgs#snakemake
  • normalized package name match
  • Matched by: Snakemake
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/sn/snakemake/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
Ubuntu apt95%

snakemake 7.32.4-2

pythonic workflow management system

https://snakemake.readthedocs.io/

sudo apt install snakemake
  • Section: universe/science
  • Architecture: all
  • 29 dependencies
  • 17 optional deps
  • normalized package name match
  • Matched by: Snakemake
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: snakemake from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

snakemake-doc 7.32.4-2

documentation for pythonic workflow management system

https://snakemake.readthedocs.io/

sudo apt install snakemake-doc
  • Section: universe/doc
  • Architecture: all
  • Source Package: snakemake
  • 4 dependencies
  • 1 optional deps
  • normalized package name match
  • Matched by: Snakemake
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: snakemake-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
dnf95%

snakemake 9.21.1-3.fc45~bootstrap

Workflow management system to create reproducible and scalable data analyses

https://snakemake.readthedocs.io/en/stable/index.html

sudo dnf install snakemake
  • License: Apache-2.0 AND BSD-2-Clause AND BSD-3-Clause AND ISC AND MIT AND MIT-0
  • Category: Unspecified
  • Architecture: noarch
  • Source Package: snakemake
  • 5 dependencies
  • 5 provides
  • normalized package name match
  • Matched by: Snakemake
Fedora Rawhide package metadata · dl.fedoraproject.org · Fedora Rawhide package metadata: snakemake from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst
dnf95%

snakemake+reports 9.21.1-3.fc45~bootstrap

Metapackage for snakemake: reports extras

https://snakemake.readthedocs.io/en/stable/index.html

sudo dnf install snakemake+reports
  • License: Apache-2.0 AND BSD-2-Clause AND BSD-3-Clause AND ISC AND MIT AND MIT-0
  • Category: Unspecified
  • Architecture: noarch
  • Source Package: snakemake
  • 3 dependencies
  • 3 provides
  • normalized package name match
  • Matched by: Snakemake
Fedora Rawhide package metadata · dl.fedoraproject.org · Fedora Rawhide package metadata: snakemake+reports from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • cbcRuntime dependency declared by Homebrew.
  • python@3.14Runtime dependency declared by Homebrew.
  • rustBuild dependency declared by Homebrew.

Same workflow

  • gnuastroShares av.db curated category or tags: cli, data-analysis, science.
  • healpixShares av.db curated category or tags: cli, data-analysis, science.
  • nextflowShares av.db curated category or tags: cli, reproducibility, science, workflow.
  • qsoasShares av.db curated category or tags: cli, data-analysis, science.
  • rootShares av.db curated category or tags: cli, data-analysis, science.
  • xlispstatShares av.db curated category or tags: cli, data-analysis, science.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Used sources

  • Geiger risk classifier
  • Nucleus package database
  • av.db category and tag curation
  • cross-ecosystem install command graph
  • curated configuration and credential file locations
  • curated package history
  • external package-manager database matches
  • package relationship graph
  • package version freshness
  • package-page enrichment