# augustus を Homebrew, apt, Nix, pacman でインストール
augustus のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。
## インストール
```sh
sudo av install brew:augustus
```
追加のインストールコマンド:
### macOS
- Homebrew (100%):
```sh
brew install augustus
```
証拠: local Homebrew formula metadata
### Linux
- Debian apt (92%):
```sh
sudo apt install augustus
```
証拠: Debian stable package indexes: augustus from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
- Nix (92%):
```sh
nix profile install nixpkgs#augustus
```
証拠: nixpkgs package indexes: pkgs/by-name/au/augustus/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- pacman (92%):
```sh
sudo pacman -S augustus
```
証拠: Arch Linux sync databases: augustus from https://geo.mirror.pkgbuild.com/extra/os/x86_64/extra.db.tar.gz
## パッケージ情報
- **パッケージキー:** brew:augustus
- **パッケージマネージャ:** Homebrew
- **バージョン:** 3.5.0
- **ソース概要:** Predict genes in eukaryotic genomic sequences
- **ホームページ:**
- **リポジトリ:**
- **最終更新:** 2026-06-25T13:37:37+02:00
- **生成日時:** 2026-08-03T19:37:03+00:00
## 実行可能ファイル
- aln2wig (エイリアス)
- augustus (エイリアス)
- bam2hints (エイリアス)
- bam2wig (エイリアス)
- compileSpliceCands (エイリアス)
- etraining (エイリアス)
- fastBlockSearch (エイリアス)
- filterBam (エイリアス)
- homGeneMapping (エイリアス)
- joingenes (エイリアス)
- pp_simScore (エイリアス)
- prepareAlign (エイリアス)
## インストール挙動
- Bottle: 利用不可
## バージョンと鮮度
- ページ生成日: 2026-08-03
- マネージャ版: 3.5.0
## プロジェクトの歴史と使われ方
AUGUSTUS is a gene prediction system for eukaryotic genomic sequences. In package-manager terms it is a bioinformatics CLI suite with a large config/species data payload, training parameters, auxiliary tools, and workflows that bridge local command-line runs, web services, and genome annotation pipelines.
### プロジェクトの歴史
The University of Greifswald project site identifies AUGUSTUS as a program for predicting genes in eukaryotic genomic sequences and carries 2003 metadata. The official reference list traces the research lineage from Mario Stanke's 2003 hidden-Markov-model work through the 2004 AUGUSTUS web-server paper and later papers on hints, alternative transcripts, cDNA alignments, and comparative gene prediction.
The current GitHub README says AUGUSTUS can find genes and gene structures in one or more genomes, can run ab initio, and can incorporate hints from EST, protein alignments, MS/MS, and syntenic genomic alignments. The ABOUT document notes that since version 3.0 it can predict genes simultaneously in several aligned genomes.
The project site records several adoption-era milestones: an automatic annotation pipeline was distributed by 2009, RNA-Seq integration was documented in 2012, and source-code issue handling moved to GitHub. Releases on GitHub include 3.3.2 in 2018, 3.3.3 in 2019, 3.4.0 in 2020, and 3.5.0 in 2022.
### 採用の歴史
AUGUSTUS adoption is driven by genome annotation workflows rather than casual CLI use. The official site offers web interfaces, a larger WebAUGUSTUS service, local downloads, training, species parameter sets, and links to accuracy results. The supplied package-manager facts show Homebrew, Debian, Nix, Arch, and Ubuntu packages, reflecting its role as a reproducible command-line dependency in bioinformatics environments.
### 使われ方
The official running guide describes the basic command as augustus [parameters] --species=SPECIES queryfilename, with uncompressed FASTA input and GTF-like output. Users choose species parameter sets, redirect output to GFF/GTF files, pass hints files and extrinsic configuration, retrain species parameters, and run auxiliary programs such as etraining and bam2hints.
### パッケージ好きにとっての重要性
AUGUSTUS is package-interesting because the executable alone is not enough: the config directory, species parameters, extrinsic.cfg, scripts, examples, and auxiliary programs must line up with AUGUSTUS_CONFIG_PATH or the executable-relative ../config fallback. It is a classic scientific package where data files, environment variables, and compiled tools are one deployable unit.
### タイムライン
- 2003: Foundational HMM gene-prediction thesis and related Bioinformatics paper appeared.
- 2004: AUGUSTUS web-server paper was published.
- 2006: Papers covered alternative transcripts and extrinsic hints.
- 2008: cDNA and syntenic alignment improvements were published.
- 2009: The project site announced an automatic annotation pipeline for download.
- 2012: RNA-Seq integration for the download version was documented.
- 2016: Multi-genome gene finding was published.
- 2018: GitHub release 3.3.2 was published.
- 2022: GitHub release 3.5.0 was published.
### Related projects
- AUGUSTUS is commonly discussed with WebAUGUSTUS, BRAKER, comparative gene prediction workflows, RNA-Seq hint generation, genome browsers such as Gbrowse, and the broader University of Greifswald bioinformatics toolchain.
### ソース
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## セキュリティノート
narrow executable package without higher-risk signals.
- **Geiger リスク:** グリーン / 低
- narrow executable package without higher-risk signals
## 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
- Unix: $AUGUSTUS_CONFIG_PATH, ../config relative to the augustus executable, $AUGUSTUS_CONFIG_PATH/extrinsic/extrinsic.cfg
## 他のパッケージマネージャ記録
- Debian apt - augustus - 3.5.0+dfsg-5: normalized package name match | Debian stable package indexes: augustus from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | gene prediction in eukaryotic genomes | https://bioinf.uni-greifswald.de/augustus/
- Debian apt - augustus-data - 3.5.0+dfsg-5: normalized package name match | Debian stable package indexes: augustus-data from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | data files for AUGUSTUS | https://bioinf.uni-greifswald.de/augustus/
- Debian apt - augustus-doc - 3.5.0+dfsg-5: normalized package name match | Debian stable package indexes: augustus-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | documentation files for AUGUSTUS | https://bioinf.uni-greifswald.de/augustus/
- Nix - augustus: normalized package name match | nixpkgs package indexes: pkgs/by-name/au/augustus/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - augustus - 3.5.0+dfsg-4build5: normalized package name match | Ubuntu 24.04 LTS package indexes: augustus from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | gene prediction in eukaryotic genomes | https://bioinf.uni-greifswald.de/augustus/
- Ubuntu apt - augustus-data - 3.5.0+dfsg-4build5: normalized package name match | Ubuntu 24.04 LTS package indexes: augustus-data from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | data files for AUGUSTUS | https://bioinf.uni-greifswald.de/augustus/
- Ubuntu apt - augustus-doc - 3.5.0+dfsg-4build5: normalized package name match | Ubuntu 24.04 LTS package indexes: augustus-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | documentation files for AUGUSTUS | https://bioinf.uni-greifswald.de/augustus/
- pacman - augustus - 4.0.0-2: normalized package name match | Arch Linux sync databases: augustus from https://geo.mirror.pkgbuild.com/extra/os/x86_64/extra.db.tar.gz | An enhanced re-implementation of Caesar III | https://github.com/Keriew/augustus
## Combined YAML source
View the package source record on GitHub. [combined/augustus.yml](https://github.com/mxcl/pkgdb/blob/main/combined/augustus.yml)
## ソース
- pkg.so package database
- Geiger risk classifier
- curated configuration and credential file locations
- curated package history
- pkgdb category and tag curation
- external package-manager database matches
- cross-ecosystem install command graph