# 使用 Homebrew, apt, Nix, pacman 安装 augustus 查看 augustus 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。 ## 安装 ```sh sudo av install brew:augustus ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install augustus ``` 证据: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install augustus ``` 证据: 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 ``` 证据: 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 ``` 证据: Arch Linux sync databases: augustus from https://geo.mirror.pkgbuild.com/extra/os/x86_64/extra.db.tar.gz ## 软件包事实 - **软件包键:** brew:augustus - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 3.5.0 - **来源摘要:** Predict genes in eukaryotic genomic sequences - **主页:** - **仓库:** - **上游文档:** - **许可证:** Artistic-1.0 - **源码归档:** - **最后更新:** 2026-06-25T13:37:37+02:00 - **已生成:** 2026-08-04T22:13:35+00:00 ## 可执行文件 - aln2wig (cli) - augustus (cli) - bam2hints (cli) - bam2wig (cli) - compileSpliceCands (cli) - etraining (cli) - fastBlockSearch (cli) - filterBam (cli) - homGeneMapping (cli) - joingenes (cli) - pp_simScore (cli) - prepareAlign (cli) - aln2wig (别名) - augustus (别名) - bam2hints (别名) - bam2wig (别名) - compileSpliceCands (别名) - etraining (别名) - fastBlockSearch (别名) - filterBam (别名) - homGeneMapping (别名) - joingenes (别名) - pp_simScore (别名) - prepareAlign (别名) ## 依赖 - bamtools - boost - htslib ## 安装行为 - post-install 钩子: 未定义 - Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## 版本和新鲜度 - 页面生成时间: 2026-08-04 - 管理器版本: 3.5.0 - 管理器更新时间: 2026-06-25 - 本地数据: OK - 上游仓库: https://github.com/Gaius-Augustus/Augustus - 检测到的最新版本: v3.5.0 (当前) ## 项目历史与用法 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. ### 项目历史 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. ### 采用历史 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. ### 使用方式 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. ### 为什么软件包爱好者会关心 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. ### 时间线 - 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. ### 来源 - - - - - - ## 安全说明 narrow executable package without higher-risk signals. - **Geiger 风险:** 绿色 / 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 ## 源数据库详情 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** augustus - **Version Scheme:** 0 - **Revision:** 12 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## 其他软件包管理器记录 - 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 ## 相关链接 - [Terminal utility packages](https://pkg.so/zh-hans/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://pkg.so/zh-hans/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://pkg.so/zh-hans/scientific-computing-tools/) - Matched scientific computing metadata. - [Homebrew utility packages](https://pkg.so/zh-hans/brew-utility-packages/) - Matched Homebrew package provider. - [htslib](https://pkg.so/zh-hans/brew/htslib/) - Runtime dependency declared by Homebrew. - [bamtools](https://pkg.so/zh-hans/brew/bamtools/) - Runtime dependency declared by Homebrew. - [tabixpp](https://pkg.so/zh-hans/brew/tabixpp/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [bismark](https://pkg.so/zh-hans/brew/bismark/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [mosdepth](https://pkg.so/zh-hans/brew/mosdepth/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [chopper](https://pkg.so/zh-hans/brew/chopper/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [minigraph](https://pkg.so/zh-hans/brew/minigraph/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [samtools](https://pkg.so/zh-hans/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [blast](https://pkg.so/zh-hans/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [bedtools](https://pkg.so/zh-hans/brew/bedtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [prodigal](https://pkg.so/zh-hans/brew/prodigal/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, gene, gene-prediction, genomics. ## Combined YAML source View the package source record on GitHub. [combined/augustus.yml](https://github.com/mxcl/pkgdb/blob/main/combined/augustus.yml) ## 来源 - pkg.so package database - Geiger risk classifier - package-page enrichment - curated configuration and credential file locations - curated package history - package version freshness - pkgdb category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph