# 使用 Homebrew, apt, Nix 安装 bedops

查看 bedops 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:bedops
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install bedops
```

  证据: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install bedops
```

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

- Nix (92%):

```sh
nix profile install nixpkgs#bedops
```

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

## 软件包事实

- **软件包键:** brew:bedops
- **软件包管理器:** Homebrew
- **软件包管理器页面:** <https://formulae.brew.sh/formula/bedops>
- **版本:** 2.4.42
- **来源摘要:** Set and statistical operations on genomic data of arbitrary scale
- **主页:** <https://github.com/bedops/bedops>
- **仓库:** <https://github.com/bedops/bedops>
- **上游文档:** <https://bedops.readthedocs.io/en/latest>
- **许可证:** GPL-2.0-or-later
- **源码归档:** <https://github.com/bedops/bedops/archive/refs/tags/v2.4.42.tar.gz>
- **最后更新:** 2026-07-10T11:16:59-04:00
- **已生成:** 2026-07-26T07:20:29+00:00

## 可执行文件

- bam2bed (cli)
- bam2bed_gnuParallel (cli)
- bam2bed_sge (cli)
- bam2bed_slurm (cli)
- bam2starch (cli)
- bam2starch_gnuParallel (cli)
- bam2starch_sge (cli)
- bam2starch_slurm (cli)
- bedextract (cli)
- bedmap (cli)
- bedops (cli)
- closest-features (cli)
- convert2bed (cli)
- gff2bed (cli)
- gff2starch (cli)
- gtf2bed (cli)
- gtf2starch (cli)
- gvf2bed (cli)
- gvf2starch (cli)
- psl2bed (cli)
- psl2starch (cli)
- rmsk2bed (cli)
- rmsk2starch (cli)
- sam2bed (cli)
- sam2starch (cli)
- sort-bed (cli)
- starch (cli)
- starch-diff (cli)
- starchcat (cli)
- starchcluster_gnuParallel (cli)
- starchcluster_sge (cli)
- starchcluster_slurm (cli)
- starchstrip (cli)
- unstarch (cli)
- update-sort-bed-migrate-candidates (cli)
- update-sort-bed-slurm (cli)
- update-sort-bed-starch-slurm (cli)
- vcf2bed (cli)
- vcf2starch (cli)
- wig2bed (cli)
- wig2starch (cli)
- bam2bed (别名)
- bam2bed_gnuParallel (别名)
- bam2bed_sge (别名)
- bam2bed_slurm (别名)
- bam2starch (别名)
- bam2starch_gnuParallel (别名)
- bam2starch_sge (别名)
- bam2starch_slurm (别名)
- bedextract (别名)
- bedmap (别名)
- bedops (别名)
- closest-features (别名)
- convert2bed (别名)
- gff2bed (别名)
- gff2starch (别名)
- gtf2bed (别名)
- gtf2starch (别名)
- gvf2bed (别名)
- gvf2starch (别名)
- psl2bed (别名)
- psl2starch (别名)
- rmsk2bed (别名)
- rmsk2starch (别名)
- sam2bed (别名)
- sam2starch (别名)
- sort-bed (别名)
- starch (别名)
- starch-diff (别名)
- starchcat (别名)
- starchcluster_gnuParallel (别名)
- starchcluster_sge (别名)
- starchcluster_slurm (别名)
- starchstrip (别名)
- unstarch (别名)
- update-sort-bed-migrate-candidates (别名)
- update-sort-bed-slurm (别名)
- update-sort-bed-starch-slurm (别名)
- vcf2bed (别名)
- vcf2starch (别名)
- wig2bed (别名)
- wig2starch (别名)

## 依赖

- jansson

## macOS 提供的库

- bzip2

## 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: 2026-07-26
- 管理器版本: 2.4.42
- 管理器更新时间: 2026-07-10
- 本地数据: OK
- 上游仓库: https://github.com/bedops/bedops
- 检测到的最新版本: v2.4.42 (当前)
## 项目历史与用法

BEDOPS is an open-source command-line toolkit for scalable genomic interval operations, statistical mapping, format conversion, and Starch compression.

### 项目历史

BEDOPS grew out of genomics workflows that needed efficient Boolean and statistical operations over large BED-like datasets. The upstream documentation describes it as a toolkit for arbitrary-scale genomic data, built around sorted BED data, streaming Unix I/O, and chromosome-level partitioning.

The project was published in Bioinformatics in 2012 as 'BEDOPS: high-performance genomic feature operations.' The GitHub repository dates to 2013, while copyright and documentation history identify the project line as active from 2011 onward.

A major part of BEDOPS history is the Starch archive format, which the docs describe as lossless compression with metadata and random access by chromosome. That made the suite more than a set-operations command: it became a file-management layer for large interval collections.

### 采用历史

BEDOPS is packaged for Homebrew, Debian, Ubuntu, and Nix in the supplied metadata. Its official installation documentation also documents Homebrew, Bioconda, Docker, source builds, and prebuilt binaries, reflecting adoption in both workstation and cluster-style bioinformatics environments.

The revision history shows sustained maintenance across the v2.4 series, including large-input sorting fixes, conversion fixes for GTF/GFF/WIG/SAM/BAM-derived formats, GitHub Actions migration, and a v2.4.42 release in April 2025.

### 使用方式

Typical BEDOPS use chains tools such as bedops, bedmap, closest-features, sort-bed, starch, unstarch, and format converters through standard input and output. The docs emphasize streaming pipelines, per-chromosome work splitting, and map-reduce-style parallelization.

BEDOPS is most valuable when researchers need to intersect, merge, subtract, complement, map, summarize, compress, or convert large genomic feature datasets without loading entire whole-genome inputs into memory.

### 为什么软件包爱好者会关心

BEDOPS matters to package nerds because it is a classic Unix-philosophy scientific toolkit: many specialized binaries, streamable text interfaces, stable file conventions, and performance claims that matter directly to package users handling large local datasets.

It is also a useful contrast with bedtools. Both live in the genomic-interval ecosystem, but BEDOPS leans hard into sorted data, low memory overhead, Starch compression, and easy chromosome-level parallelism, making packaging details such as compiler support, binary type, and converter scripts unusually important.

### 时间线

- 2011: BEDOPS project line begins, per upstream copyright and documentation history.
- 2012: BEDOPS paper published in Bioinformatics.
- 2013: GitHub repository created.
- 2021: v2.4.40 migrated CI to GitHub Actions and continued converter/starch maintenance.
- 2022: v2.4.41 released with compiler and conversion fixes.
- 2025: v2.4.42 released.

### Related projects

- bedtools is the closest peer in genome arithmetic and interval manipulation.
- BED, BAM, SAM, GFF, GTF, VCF, WIG, and Starch are central formats in BEDOPS workflows.
- Bioconda, Homebrew, Debian, Ubuntu, and Nix are relevant distribution channels for command-line bioinformatics users.

### 来源

- <https://api.github.com/repos/bedops/bedops>
- <https://bedops.readthedocs.io/en/latest>
- <https://bedops.readthedocs.io/en/latest/content/overview.html>
- <https://bedops.readthedocs.io/en/latest/content/revision-history.html>
- <https://github.com/bedops/bedops#readme>
- source_facts.package-manager


## 安全说明

infrastructure mutation or orchestration signal.

- **Geiger 风险:** orange / 中
- infrastructure mutation or orchestration signal

## 源数据库详情

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

## 其他软件包管理器记录

- Debian apt - bedops - 2.4.41+dfsg-3: normalized package name match | Debian stable package indexes: bedops from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | high-performance genomic feature operations | https://github.com/bedops/bedops
- Debian apt - bedops-doc - 2.4.41+dfsg-3: normalized package name match | Debian stable package indexes: bedops-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | high-performance genomic feature operations (documentation) | https://github.com/bedops/bedops
- Nix - bedops: normalized package name match | nixpkgs package indexes: pkgs/by-name/be/bedops/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - bedops - 2.4.41+dfsg-2build1: normalized package name match | Ubuntu 24.04 LTS package indexes: bedops from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | high-performance genomic feature operations | https://github.com/bedops/bedops
- Ubuntu apt - bedops-doc - 2.4.41+dfsg-2build1: normalized package name match | Ubuntu 24.04 LTS package indexes: bedops-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | high-performance genomic feature operations (documentation) | https://github.com/bedops/bedops


## 相关链接

- [Source-control packages](https://www.automicvault.com/zh-hans/pkg/source-control-tools/) - Belongs to a source-control command family.
- [Secret-risk packages](https://www.automicvault.com/zh-hans/pkg/secret-risk-packages/) - Has protected-tool coverage, approval-gate, or non-low Geiger security signals.
- [Terminal utility packages](https://www.automicvault.com/zh-hans/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://www.automicvault.com/zh-hans/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [bedtk](https://www.automicvault.com/zh-hans/pkg/brew/bedtk/) - Shares av.db curated category or tags: bed, bioinformatics, cli, genomics, science.
- [bedtools](https://www.automicvault.com/zh-hans/pkg/brew/bedtools/) - Shares av.db curated category or tags: bed, bioinformatics, cli, genomics, science.
- [abricate](https://www.automicvault.com/zh-hans/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [any2fasta](https://www.automicvault.com/zh-hans/pkg/brew/any2fasta/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [augustus](https://www.automicvault.com/zh-hans/pkg/brew/augustus/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [bamtools](https://www.automicvault.com/zh-hans/pkg/brew/bamtools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [bbtools](https://www.automicvault.com/zh-hans/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [bioawk](https://www.automicvault.com/zh-hans/pkg/brew/bioawk/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.

## Combined YAML source

View the package source record on GitHub. [combined/bedops.yml](https://github.com/automic-vault/db/blob/main/combined/bedops.yml)


## 来源

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