# salmon mit Homebrew, apt, Nix installieren

Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für salmon in AI-Agent-Workflows.

## Installation

```sh
sudo av install brew:salmon
```

Weitere Installationsbefehle:

### macOS

- Homebrew (100%):

```sh
brew install salmon
```

  Evidenz: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install salmon
```

  Evidenz: Debian stable package indexes: salmon from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

- Nix (92%):

```sh
nix profile install nixpkgs#salmon
```

  Evidenz: nixpkgs package indexes: pkgs/by-name/sa/salmon/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1

## Paketfakten

- **Paketschlüssel:** brew:salmon
- **Paketmanager:** Homebrew
- **Paketmanager-Seite:** <https://formulae.brew.sh/formula/salmon>
- **Version:** 2.4.1
- **Quellzusammenfassung:** Transcript-level quantification from RNA-seq reads
- **Homepage:** <https://github.com/COMBINE-lab/salmon>
- **Repository:** <https://github.com/COMBINE-lab/salmon>
- **Lizenz:** BSD-3-Clause
- **Quellarchiv:** <https://github.com/COMBINE-lab/salmon/archive/refs/tags/v2.4.1.tar.gz>
- **Zuletzt aktualisiert:** 2026-07-30T01:26:57Z
- **Generiert:** 2026-08-04T22:13:35+00:00

## Executables

- salmon (cli)
- salmon (Alias)

## Build-Abhängigkeiten

- rust

## Installationsverhalten

- Post-install-Hook: nicht definiert
- Bottle: verfügbar auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## Version und Aktualität

- Seite generiert: 2026-08-04
- Manager-Version: 2.4.1
- Manager aktualisiert: 2026-07-30
- lokale Daten: OK
- Upstream-Repository: https://github.com/COMBINE-lab/salmon
- neueste erkannte Version: v2.4.1 (aktuell)
## Projektgeschichte und Nutzung

salmon is a COMBINE-lab command-line tool for fast, accurate transcript-level quantification from RNA-seq reads. Its current official documentation describes the core workflow as building a reusable transcriptome index with `salmon index`, quantifying reads with `salmon quant`, and consuming the resulting `quant.sf` abundance table in downstream RNA-seq tooling.

### Projektgeschichte

The project is tied to the 2017 Nature Methods paper by Patro, Duggal, Love, Irizarry, and Kingsford, which the official docs and README ask users to cite. The original C++ salmon line became a common bulk RNA-seq quantifier, with selective alignment becoming the default mapping strategy from the 1.0.0 line according to the legacy official documentation.

In 2026 the project released salmon 2.0, a from-scratch Rust rewrite. Official release notes say the rewrite kept the familiar `salmon index` to `salmon quant` to `quant.sf` workflow and downstream output formats while moving to a single portable binary and adding an alignment-free `--sketch` mode.

### Adoptionsgeschichte

salmon is packaged across multiple package-manager ecosystems in the supplied package facts, including Homebrew, Debian, Ubuntu, and Nix. The official installation docs also document install-script binaries, Cargo, conda/Bioconda, Docker Hub, and GHCR images, reflecting its use in reproducible computational-biology pipelines.

The official docs describe `quant.sf` as directly readable by tximport, tximeta, fishpond, and swish, which is why salmon appears frequently in RNA-seq analysis workflows as a quantification stage rather than as a standalone end-user application.

### Wie es verwendet wird

Typical use is to build an index from transcript FASTA input, quantify single-end or paired-end FASTQ reads against that index, and read transcript-level abundance estimates from `quant.sf`. The CLI also supports transcriptome BAM input, RAD input, bias correction flags, bootstraps or Gibbs samples for uncertainty, gene-level output via a transcript-to-gene map, and `quantmerge` for combining columns across samples.

### Warum Paket-Nerds sich dafür interessieren

salmon matters to package maintainers because it sits at the intersection of scientific CLI distribution and performance-sensitive native code. The 2.x Rust rewrite reduced the historic C++ dependency burden while preserving command names and output files, which makes package upgrades easier but still requires users to rebuild old C++ indices.

### Zeitleiste

- 2017: Salmon Nature Methods paper published and cited by the official project docs.
- 1.0.0 line: Selective alignment becomes the default mapping strategy according to the official legacy docs.
- 2026-06-13: salmon 2.0.0 released as the first Rust rewrite, retaining the index/quant/quant.sf workflow.
- 2026-06-23: legacy C++ v1.12.1 release notes recommend 2.x for bulk RNA-seq and reserve 1.x for users needing the original C++ implementation.
- 2026-07-02: GitHub lists v2.3.1 as the latest release.

### Related projects

- Official docs name tximport, tximeta, fishpond, and swish as downstream tools that consume salmon output. They also point users of the removed historical `salmon alevin` single-cell workflow to the alevin-fry ecosystem.

### Quellen

- Official CLI reference: https://combine-lab.github.io/salmon/reference/cli/
- Official GitHub README/releases: https://github.com/COMBINE-lab/salmon
- Official docs introduction: https://combine-lab.github.io/salmon/getting-started/introduction/
- Official docs: https://combine-lab.github.io/salmon/
- Supplied input fields: source_facts.package-manager, source_facts.description, source_facts.repo


## Sicherheitshinweise

Für salmon wurde kein passendes lokales Secret-Handling-Manifest gefunden. Paketmetadaten bleiben hier veröffentlicht, damit künftige Abdeckung eine stabile Paket-URL hat.


## Details aus der Quelldatenbank

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** salmon
- **Version Scheme:** 0
- **Revision:** 0
- **Head Version:** HEAD
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** head, stable

## Andere Paketmanager-Einträge

- Debian apt - salmon - 1.10.2+ds1-1+b5: normalized package name match | Debian stable package indexes: salmon from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | wicked-fast transcript quantification from RNA-seq data | https://github.com/COMBINE-lab/salmon
- Nix - salmon: normalized package name match | nixpkgs package indexes: pkgs/by-name/sa/salmon/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - salmon - 1.10.2+ds1-1build2: normalized package name match | Ubuntu 24.04 LTS package indexes: salmon from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | wicked-fast transcript quantification from RNA-seq data | https://github.com/COMBINE-lab/salmon


## Verwandte Links

- [Source-control packages](https://pkg.so/de/source-control-tools/) - Belongs to a source-control command family.
- [Terminal utility packages](https://pkg.so/de/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Language runtime packages](https://pkg.so/de/language-runtime-packages/) - Matched language runtime, compiler, or interpreter metadata.
- [Networking and protocol packages](https://pkg.so/de/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [rust](https://pkg.so/de/brew/rust/) - Build dependency declared by Homebrew.
- [rna-star](https://pkg.so/de/brew/rna-star/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, rna-seq, science.
- [kallisto](https://pkg.so/de/brew/kallisto/) - Shares pkgdb curated category or tags: bioinformatics, cli, quantification, rna-seq, science.
- [oarfish](https://pkg.so/de/brew/oarfish/) - Shares pkgdb curated category or tags: bioinformatics, cli, rna-seq, rust, science.
- [chopper](https://pkg.so/de/brew/chopper/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, rust, science.
- [samtools](https://pkg.so/de/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [blast](https://pkg.so/de/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [bedtools](https://pkg.so/de/brew/bedtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [minimap2](https://pkg.so/de/brew/minimap2/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [stringtie](https://pkg.so/de/brew/stringtie/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, quantification, rna.

## Combined YAML source

View the package source record on GitHub. [combined/salmon.yml](https://github.com/mxcl/pkgdb/blob/main/combined/salmon.yml)


## Quellen

- pkg.so package database
- package-page enrichment
- curated package history
- package version freshness
- pkgdb category and tag curation
- package relationship graph
- external package-manager database matches
- cross-ecosystem install command graph