# Installer oarfish avec Homebrew Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de oarfish pour les workflows d'agents IA. ## installation ```sh sudo av install brew:oarfish ``` Commandes d'installation supplémentaires: ### macOS - Homebrew (100%): ```sh brew install oarfish ``` Preuve: local Homebrew formula metadata ## Faits du paquet - **Clé du paquet:** brew:oarfish - **Gestionnaire de paquets:** Homebrew - **Page du gestionnaire de paquets:** - **Version:** 0.10.0 - **Résumé source:** Long read RNA-seq quantification - **Page d'accueil:** - **Dépôt:** - **Docs amont:** - **Licence:** BSD-3-Clause - **Archive source:** - **Dernière mise à jour:** 2026-06-21T00:20:16Z - **Généré:** 2026-07-08T18:08:21+00:00 ## exécutables - oarfish (cli) - oarfish (alias) ## Dépendances de compilation - rust ## 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: 0.10.0 - gestionnaire mis à jour: 2026-06-21 - données locales: OK - dépôt amont: https://github.com/COMBINE-lab/oarfish - dernière version détectée: v0.10.0 (à jour) ## Historique du projet et usages oarfish is a Rust tool from COMBINE-lab for transcript-level quantification from long-read RNA-seq data, including Oxford Nanopore cDNA/direct RNA and PacBio reads. It allocates multi-mapping reads probabilistically with an expectation-maximization model and adds coverage information to improve isoform-level estimates. ### Historique du projet The GitHub repository was created on June 27, 2022. The project emerged from the COMBINE-lab lineage of RNA-seq quantification tools, applying probabilistic transcript-assignment ideas to long-read sequencing rather than short-read workflows. ### Historique d'adoption The method was described in the 2024 preprint and later Bioinformatics paper "Enhanced probabilistic modeling leads to improved accuracy in long-read transcriptome quantification." Distribution through GitHub releases, Cargo, Bioconda, and Homebrew made it available to both Rust users and bioinformatics workflow environments. ### Modes d'utilisation oarfish accepts transcriptome BAM alignments, raw reads that it maps internally, genome reads that are spliced-aligned and projected to transcripts, or existing genome BAMs projected against a transcript annotation. The common workflow is to supply long-read RNA-seq data plus transcript sequences or annotation, then produce transcript abundance estimates with optional bootstrap uncertainty and coverage modeling. ### Pourquoi les passionnés de paquets s'y intéressent For package watchers, oarfish is a good example of scientific software moving through several distribution channels at once: a Rust codebase and Cargo package, prebuilt GitHub release binaries, Bioconda recipes for workflow managers, and a Homebrew formula for local command-line installs. ### Chronologie - 2022-06-27: COMBINE-lab/oarfish repository was created. - 2024-02-28: The oarfish preprint was posted to bioRxiv. - 2026-06-07: GitHub release v0.10.0 was published. ### Related projects - The documentation compares or connects oarfish with NanoCount-style filters, minimap2 and other aligners for BAM input, rammap for in-process long-read mapping, and bramble for genome-to-transcript projection. ### Sources - - - - - - - - ## Notes de sécurité narrow executable package without higher-risk signals. - **Risque Geiger:** vert / faible - narrow executable package without higher-risk signals ## Détails de la base source - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** oarfish - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Liens liés - [Source-control packages](https://www.automicvault.com/fr/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/fr/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Language runtime packages](https://www.automicvault.com/fr/pkg/language-runtime-packages/) - Matched language runtime, compiler, or interpreter metadata. - [Networking and protocol packages](https://www.automicvault.com/fr/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [rust](https://www.automicvault.com/fr/pkg/brew/rust/) - Build dependency declared by Homebrew. - [flye](https://www.automicvault.com/fr/pkg/brew/flye/) - Shares av.db curated category or tags: bioinformatics, cli, long-read-sequencing, science. - [kallisto](https://www.automicvault.com/fr/pkg/brew/kallisto/) - Shares av.db curated category or tags: bioinformatics, cli, rna-seq, science. - [rna-star](https://www.automicvault.com/fr/pkg/brew/rna-star/) - Shares av.db curated category or tags: bioinformatics, cli, rna-seq, science. - [stringtie](https://www.automicvault.com/fr/pkg/brew/stringtie/) - Shares av.db curated category or tags: bioinformatics, cli, rna-seq, 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. ## Combined YAML source View the package source record on GitHub. [combined/oarfish.yml](https://github.com/automic-vault/db/blob/main/combined/oarfish.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 - cross-ecosystem install command graph