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brew

abyss mit Homebrew, apt, MacPorts installieren

Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für abyss in AI-Agent-Workflows.

InstallationsbefehlSicherheitshinweise

Installation

Weitere Installationsbefehle

macOS

Homebrewverifiziert · 100%
brew install abyss

local Homebrew formula metadata

MacPortsverifiziert · 94%
sudo port install abyss

MacPorts ports tree · www/abyss/Portfile · Quelle: api.github.com

Linux

Debian aptverifiziert · 92%
sudo apt install abyss

Debian stable package indexes · abyss · Quelle: deb.debian.org

Überblick

Paketzusammenfassung

Genome sequence assembler for short reads

Befehle und Aliase

  • ABYSS
  • ABYSS-P
  • AdjList
  • Consensus
  • DAssembler
  • DistanceEst
  • DistanceEst-ssq
  • KAligner
  • MergeContigs
  • MergePaths
  • Overlap
  • ParseAligns
  • PathConsensus
  • PathOverlap
  • PopBubbles
  • SimpleGraph
  • abyss-align
  • abyss-bloom
  • abyss-bloom-dbg
  • abyss-bloom-dist.mk
  • abyss-bowtie
  • abyss-bowtie2
  • abyss-bwa
  • abyss-bwamem
  • abyss-bwasw
  • abyss-db-csv
  • abyss-db-txt
  • abyss-dida
  • abyss-fac
  • abyss-fatoagp
  • abyss-filtergraph
  • abyss-fixmate

Verlauf

Projektgeschichte und Nutzung

ABySS is a de novo genome sequence assembler for short paired-end reads, developed at the BC Cancer Genome Sciences Centre and distributed as command-line tools such as abyss-pe and ABYSS-P.

Projektgeschichte

The official changelog records ABySS 1.0 on 2008-08-07. Its 2009 Genome Research paper described ABySS as a parallel assembler for short-read sequence data, and the project page identifies it as a parallel, paired-end assembler using MPI for larger genomes.

ABySS 2.0, released in 2016 and described in a 2017 Genome Research paper, added a Bloom filter assembly mode to reduce memory use for large genomes. Later releases continued to tune Bloom filter assembly, linked-read scaffolding, RResolver integration, and compiler/platform support.

Adoptionsgeschichte

ABySS became part of bioinformatics packaging culture because it exposed a substantial Unix-style command suite around a reproducible assembly pipeline and was packaged by Homebrew, Debian, Ubuntu, MacPorts, and Bioconda.

The project page notes a 2015 International Bioinformatics Resource Award from the Swiss Institute of Bioinformatics, reflecting broader scientific use beyond the original BC Cancer group.

Wie es verwendet wird

Typical use is batch-oriented: users install ABySS through Conda, Homebrew, or from source, then run abyss-pe with parameters such as k and Bloom filter memory settings for paired-end short-read assembly.

The README documents cluster-oriented MPI mode, Bloom filter mode, scaffolding, linked-read workflows, and related tools such as ARCS, Tigmint, Konnector, Sealer, and abyss-bloom.

Warum Paket-Nerds sich dafür interessieren

ABySS matters to package maintainers because it combines compiled C++ code, MPI/OpenMP, optional scientific dependencies, many installed executables, and large-memory workloads in one formula.

It is a good example of a scientific CLI whose packaging value is not just the top-level binary but a coordinated toolchain used inside reproducible bioinformatics pipelines.

Zeitleiste

  • 2008: ABySS 1.0 released.
  • 2009: Genome Research paper presents ABySS as a parallel assembler for short-read sequence data.
  • 2015: ABySS wins the Swiss Institute of Bioinformatics International Bioinformatics Resource Award.
  • 2016: ABySS 2.0 introduces Bloom filter assembly mode.
  • 2017: ABySS 2.0 paper describes resource-efficient large-genome assembly using a Bloom filter.
  • 2021: ABySS 2.3.0 makes RResolver part of the default pipeline.

Related projects

  • Related projects in the official README include Trans-ABySS, ARCS, Tigmint, Konnector, Sealer, btllib, Open MPI, Boost, and samtools.

Sicherheitslage

Risikostufe: grün

narrow executable package without higher-risk signals.

Risikoklassifikator

grün Risiko · niedrig Konfidenz · appliance

Warum

  • narrow executable package without higher-risk signals

Signale

  • metadata:no-higher-risk-signals

Installationsverhalten

  • In den Formelmetadaten ist kein Homebrew-Post-install-Hook erfasst.
  • Homebrew-Bottle-Metadaten sind für 6 Plattformziele verfügbar.
  • Installiert mit 3 Laufzeitabhängigkeiten.
  • Build-Metadaten listen 2 Build-Abhängigkeiten.

Empfohlene Prüfung

Prüfe vor unbeaufsichtigter Agent-Nutzung, ob das Tool Klartext-Credentials liest, Remote-Zustand schreibt, Artefakte veröffentlicht oder Plugins ausführt.

Executables

Installierte Executables

BefehlArtSichtbarkeitHinweis
ABYSScliglobales Executable
ABYSS-Pcliglobales Executable
AdjListcliglobales Executable
Consensuscliglobales Executable
DAssemblercliglobales Executable
DistanceEstcliglobales Executable
DistanceEst-ssqcliglobales Executable
KAlignercliglobales Executable
MergeContigscliglobales Executable
MergePathscliglobales Executable
Overlapcliglobales Executable
ParseAlignscliglobales Executable
PathConsensuscliglobales Executable
PathOverlapcliglobales Executable
PopBubblescliglobales Executable
SimpleGraphcliglobales Executable
abyss-aligncliglobales Executable
abyss-bloomcliglobales Executable
abyss-bloom-dbgcliglobales Executable
abyss-bloom-dist.mkcliglobales Executable
abyss-bowtiecliglobales Executable
abyss-bowtie2cliglobales Executable
abyss-bwacliglobales Executable
abyss-bwamemcliglobales Executable
abyss-bwaswcliglobales Executable
abyss-db-csvcliglobales Executable
abyss-db-txtcliglobales Executable
abyss-didacliglobales Executable
abyss-faccliglobales Executable
abyss-fatoagpcliglobales Executable
abyss-filtergraphcliglobales Executable
abyss-fixmatecliglobales Executable
abyss-fixmate-ssqcliglobales Executable
abyss-gapfillcliglobales Executable
abyss-gccliglobales Executable
abyss-indexcliglobales Executable
abyss-junctioncliglobales Executable
abyss-kalignercliglobales Executable
abyss-layoutcliglobales Executable
abyss-longseqdistcliglobales Executable
abyss-mapcliglobales Executable
abyss-map-ssqcliglobales Executable
abyss-mergepairscliglobales Executable
abyss-overlapcliglobales Executable
abyss-paired-dbgcliglobales Executable
abyss-paired-dbg-mpicliglobales Executable
abyss-pecliglobales Executable
abyss-rresolver-shortcliglobales Executable
abyss-samtoafgcliglobales Executable
abyss-scaffoldcliglobales Executable
abyss-sealercliglobales Executable
abyss-stack-sizecliglobales Executable
abyss-tabtomdcliglobales Executable
abyss-todotcliglobales Executable
abyss-tofastqcliglobales Executable
konnectorcliglobales Executable
logcountercliglobales Executable

Aktualität

Version und Aktualität

Diese Signale trennen das Alter der Seitengenerierung, Aktivität des Paketmanagers und Upstream-Release-Vergleich. Versionsrückstand wird nur gemeldet, wenn eine Evidenz-URL und vergleichbare Versionen vorhanden sind.

Seite generiert2026-07-08
Manager-Version2.3.10
Manager aktualisiert2026-07-04
lokale DatenOK
Upstreamnot checked
neueste erkannte Versionnicht erkannt

https://github.com/BirolLab/abyss

Installationsmetadaten

Paketmetadaten

Paketschlüsselbrew:abyss
Version2.3.10
PaketmanagerHomebrew
Paketmanager-Seitehttps://formulae.brew.sh/formula/abyss
Homepagehttps://www.bcgsc.ca/resources/software/abyss
Repositoryhttps://github.com/BirolLab/abyss
Upstream-Dokumentationhttps://github.com/bcgsc/abyss#readme
LizenzGPL-3.0-only AND LGPL-2.1-or-later AND MIT AND BSD-3-Clause
Quellarchivhttps://github.com/BirolLab/abyss/releases/download/2.3.10/abyss-2.3.10.tar.gz
Zuletzt aktualisiert2026-07-04T16:53:41+09:00
Pulseupdated
Abhängigkeitenbtllib, libomp, open-mpi
Build-Abhängigkeitenboost, google-sparsehash
Von macOS bereitgestellte Bibliothekensqlite
Bottleverfügbar (auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnicht definiert
Dienstkeiner deklariert

Registry-Fakten

Details aus der Quelldatenbank

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Nameabyss
Version Scheme0
Revision1
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • stable

Source-Datenbank-Treffer

Andere Paketmanager-Einträge

Treffer stammen aus externen Paketmanager-Indizes und bleiben von lokalen Automic-Vault-Paketlinks getrennt.

Debian apt95%

abyss 2.3.10-1+b1

de novo, parallel, sequence assembler for short reads

https://github.com/bcgsc/abyss

sudo apt install abyss
  • Section: science
  • Architecture: amd64
  • Source Package: abyss
  • 11 Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Abyss
Debian stable package indexes · deb.debian.org · Debian stable package indexes: abyss from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Ubuntu apt95%

abyss 2.3.7-2ubuntu3

de novo, parallel, sequence assembler for short reads

https://github.com/bcgsc/abyss

sudo apt install abyss
  • Section: universe/science
  • Architecture: amd64
  • 11 Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Abyss
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: abyss from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
MacPorts95%

abyss

sudo port install abyss
  • normalized package name match
  • Abgeglichen nach: Abyss
MacPorts ports tree · api.github.com · MacPorts ports tree: www/abyss/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

Paketgraph

Links stammen aus dem lokalen Paketbeziehungsgraph, Ergänzungen, Abhängigkeitskanten, Ecosystem-Matches und Paket-Hub-Mitgliedschaft.

Verwandte Tools

  • btllibRuntime dependency declared by Homebrew.
  • open-mpiRuntime dependency declared by Homebrew.

Gleicher Workflow

  • flyeShares av.db curated category or tags: bioinformatics, cli, genome-assembly, science.
  • spadesShares av.db curated category or tags: bioinformatics, cli, genome-assembly, science.
  • polypolishShares av.db curated category or tags: bioinformatics, cli, genome-assembly, science, short-reads.
  • bwaShares av.db curated category or tags: bioinformatics, cli, science, short-reads.
  • abpoaShares av.db curated category or tags: bioinformatics, cli, science.
  • abricateShares av.db curated category or tags: bioinformatics, cli, science.

Quellspur

Aus Repository-Daten generiert

Diese Seite wird von av-web aus dem privaten Paket-SQLite-Artefakt bereitgestellt, das scripts/generate-pkg-sqlite.py erstellt.

Verwendete Quellen

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