# Installer bedtools avec Homebrew, apt, MacPorts, Nix Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de bedtools pour les workflows d'agents IA. ## installation ```sh sudo av install brew:bedtools ``` Commandes d'installation supplémentaires: ### macOS - Homebrew (100%): ```sh brew install bedtools ``` Preuve: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install bedtools ``` Preuve: MacPorts ports tree: science/bedtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install bedtools ``` Preuve: Debian stable package indexes: bedtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#bedtools ``` Preuve: nixpkgs package indexes: pkgs/by-name/be/bedtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Faits du paquet - **Clé du paquet:** brew:bedtools - **Gestionnaire de paquets:** Homebrew - **Page du gestionnaire de paquets:** - **Version:** 2.31.1 - **Résumé source:** Tools for genome arithmetic (set theory on the genome) - **Page d'accueil:** - **Dépôt:** - **Docs amont:** - **Licence:** MIT - **Archive source:** - **Généré:** 2026-07-08T07:18:31+00:00 ## exécutables - annotateBed (cli) - bamToBed (cli) - bamToFastq (cli) - bed12ToBed6 (cli) - bedToBam (cli) - bedToIgv (cli) - bedpeToBam (cli) - bedtools (cli) - closestBed (cli) - clusterBed (cli) - complementBed (cli) - coverageBed (cli) - expandCols (cli) - fastaFromBed (cli) - flankBed (cli) - genomeCoverageBed (cli) - getOverlap (cli) - groupBy (cli) - intersectBed (cli) - linksBed (cli) - mapBed (cli) - maskFastaFromBed (cli) - mergeBed (cli) - multiBamCov (cli) - multiIntersectBed (cli) - nucBed (cli) - pairToBed (cli) - pairToPair (cli) - randomBed (cli) - shiftBed (cli) - shuffleBed (cli) - slopBed (cli) - sortBed (cli) - subtractBed (cli) - tagBam (cli) - unionBedGraphs (cli) - windowBed (cli) - windowMaker (cli) - annotateBed (alias) - bamToBed (alias) - bamToFastq (alias) - bed12ToBed6 (alias) - bedToBam (alias) - bedToIgv (alias) - bedpeToBam (alias) - bedtools (alias) - closestBed (alias) - clusterBed (alias) - complementBed (alias) - coverageBed (alias) - expandCols (alias) - fastaFromBed (alias) - flankBed (alias) - genomeCoverageBed (alias) - getOverlap (alias) - groupBy (alias) - intersectBed (alias) - linksBed (alias) - mapBed (alias) - maskFastaFromBed (alias) - mergeBed (alias) - multiBamCov (alias) - multiIntersectBed (alias) - nucBed (alias) - pairToBed (alias) - pairToPair (alias) - randomBed (alias) - shiftBed (alias) - shuffleBed (alias) - slopBed (alias) - sortBed (alias) - subtractBed (alias) - tagBam (alias) - unionBedGraphs (alias) - windowBed (alias) - windowMaker (alias) ## Dépendances - xz ## Bibliothèques fournies par macOS - bzip2 ## Comportement d'installation - hook post-installation: non défini - Bouteille: disponible sur arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Version et fraîcheur - page générée: 2026-07-08 - version du gestionnaire: 2.31.1 - données locales: OK - dépôt amont: https://github.com/arq5x/bedtools2 - dernière version détectée: v2.31.1 (à jour) - info: No package-manager update timestamp was available. ## Historique du projet et usages bedtools is one of the standard command-line toolkits for genome arithmetic: set-theory style operations over BED, BAM, GFF/GTF, VCF, and related genomic interval data. ### Historique du projet Aaron Quinlan first created bedtools in spring 2009 to answer genomics questions that were too slow or awkward with existing web tools and locally installed UCSC/Kent utilities. The official overview says the initial public version appeared in spring 2009 and originally supported only 6-column BED files. The project was described in the 2010 Bioinformatics paper 'BEDTools: a flexible suite of utilities for comparing genomic features.' The toolkit later expanded beyond BED to support BAM alignments, GFF, blocked BED, and VCF, while keeping the command-line pipeline model. The modern bedtools2 GitHub repository was created in December 2013. The README describes bedtools as the 'swiss army knife for genome arithmetic' and says it is maintained by the Quinlan Laboratory at the University of Virginia. ### Historique d'adoption The supplied metadata shows bedtools packaged across Homebrew, Debian, Ubuntu, MacPorts, Nix, and other distribution indexes, reflecting broad adoption as a default genomics CLI dependency. bedtools adoption is also visible in downstream tooling: the README asks users to cite pybedtools separately, and the docs emphasize combining bedtools operations with Unix pipes for more sophisticated analyses. ### Modes d'utilisation Common bedtools workflows include intersecting intervals, merging nearby features, computing coverage, extracting FASTA sequence, shuffling or randomizing intervals, generating genome coverage, mapping summaries over overlaps, and converting between BAM, BED, FASTQ, and other formats. The toolkit is designed for shell composition. The official overview highlights stdin support so users can stream multiple commands together and control exactly how overlap results are reported. ### Pourquoi les passionnés de paquets s'y intéressent bedtools is package-nerd significant because it is a canonical scientific Unix package: a suite of many small executables, stable command names, text formats, manpage-like docs, and enormous downstream workflow dependence. It also demonstrates the tension package managers handle for research software: upstream users expect old command aliases such as intersectBed and newer unified bedtools subcommands, while distributions need reproducible builds for C++ genomics tooling that is commonly used in pipelines and papers. In the bioinformatics package graph, bedtools is not just an application; it is infrastructure. Other tools, workflow examples, papers, and wrappers often assume it exists on PATH. ### Chronologie - 2009: Initial public version released in spring 2009. - 2010: BEDTools paper published in Bioinformatics. - 2013: bedtools2 GitHub repository created. - 2021: v2.30.0 release published. - 2023: v2.31.1 release published. ### Related projects - BEDOPS is a close peer focused on sorted-data performance, Starch compression, and scalable interval operations. - pybedtools wraps bedtools functionality for Python users and has its own Bioinformatics citation. - UCSC Genome Browser, Galaxy, and Kent source utilities are named in the official overview as predecessor tools that shaped bedtools' motivation. ### Sources - - - - - source_facts.package-manager ## Notes de sécurité infrastructure mutation or orchestration signal. - **Risque Geiger:** orange / moyen - infrastructure mutation or orchestration signal ## Détails de la base source - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** bedtools - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Autres enregistrements de gestionnaires de paquets - Debian apt - bedtools - 2.31.1+dfsg-2: normalized package name match | Debian stable package indexes: bedtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | suite of utilities for comparing genomic features | https://github.com/arq5x/bedtools2 - Debian apt - bedtools-test - 2.31.1+dfsg-2: normalized package name match | Debian stable package indexes: bedtools-test from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | test data for the bedtools package | https://github.com/arq5x/bedtools2 - Nix - bedtools: normalized package name match | nixpkgs package indexes: pkgs/by-name/be/bedtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - bedtools - 2.31.1+dfsg-2: normalized package name match | Ubuntu 24.04 LTS package indexes: bedtools from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | suite of utilities for comparing genomic features | https://github.com/arq5x/bedtools2 - Ubuntu apt - bedtools-test - 2.31.1+dfsg-2: normalized package name match | Ubuntu 24.04 LTS package indexes: bedtools-test from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | test data for the bedtools package | https://github.com/arq5x/bedtools2 - MacPorts - bedtools: normalized package name match | MacPorts ports tree: science/bedtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## Liens liés - [Source-control packages](https://www.automicvault.com/fr/pkg/source-control-tools/) - Belongs to a source-control command family. - [Secret-risk packages](https://www.automicvault.com/fr/pkg/secret-risk-packages/) - Has protected-tool coverage, approval-gate, or non-low Geiger security signals. - [Terminal utility packages](https://www.automicvault.com/fr/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/fr/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [xz](https://www.automicvault.com/fr/pkg/brew/xz/) - Runtime dependency declared by Homebrew. - [autocycler](https://www.automicvault.com/fr/pkg/brew/autocycler/) - Shares av.db curated category or tags: bioinformatics, cli, genome, science. - [abpoa](https://www.automicvault.com/fr/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abricate](https://www.automicvault.com/fr/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abyss](https://www.automicvault.com/fr/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [adapterremoval](https://www.automicvault.com/fr/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [alevin-fry](https://www.automicvault.com/fr/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [any2fasta](https://www.automicvault.com/fr/pkg/brew/any2fasta/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [augustus](https://www.automicvault.com/fr/pkg/brew/augustus/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [fastk](https://www.automicvault.com/fr/pkg/brew/fastk/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, science, xz. - [tabixpp](https://www.automicvault.com/fr/pkg/brew/tabixpp/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, science, xz. - [vcflib](https://www.automicvault.com/fr/pkg/brew/vcflib/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, science, xz. ## Combined YAML source View the package source record on GitHub. [combined/bedtools.yml](https://github.com/automic-vault/db/blob/main/combined/bedtools.yml) ## Sources - 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