Debian 12 (Bookworm) native package

stacks

pipeline for building loci from short-read DNA sequences

Packages / Debian 12 (Bookworm) / science / stacks

Package: stacks (2.62+dfsg-1)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [creskolab.uoregon.edu]

pipeline for building loci from short-read DNA sequences

Other Packages Related to stacks:

dep: [libc6] (>= 2.34)
GNU C Library: Shared libraries
dep: [libgcc-s1] (>= 3.0)
GCC support library
dep: [libgomp1] (>= 6)
GCC OpenMP (GOMP) support library
dep: [libhts3] (>= 1.10)
C library for high-throughput sequencing data formats
dep: [libstdc++6] (>= 11)
GNU Standard C++ Library v3
dep: [zlib1g] (>= 1:1.2.6)
compression library - runtime
dep: [samtools]
processing sequence alignments in SAM, BAM and CRAM formats
dep: [libdbi-perl]
Perl Database Interface (DBI)

rec: [libspreadsheet-writeexcel-perl]
module to create Excel spreadsheets
rec: [python3]
interactive high-level object-oriented language (default python3 version)
rec: [littler]
GNU R scripting and command-line front-end -- transition package

Download stacks

Architecture	Package Size	Installed Size	Files
arm64	956 KiB	5.1 MiB	[list of files]

Package file paths (48)

Paths come from the repository package-file index for the observed builds. They describe archive/package associations, not every file that will exist on a running system after maintainer scripts, alternatives, generated state, diversions, or installation choices.

/usr/bin/stacks
/usr/lib/debian-med/bin/clone_filter
/usr/lib/debian-med/bin/cstacks
/usr/lib/debian-med/bin/denovo_map
/usr/lib/debian-med/bin/denovo_map.pl
/usr/lib/debian-med/bin/gstacks
/usr/lib/debian-med/bin/kmer_filter
/usr/lib/debian-med/bin/phasedstacks
/usr/lib/debian-med/bin/populations
/usr/lib/debian-med/bin/process_radtags
/usr/lib/debian-med/bin/process_shortreads
/usr/lib/debian-med/bin/ref_map
/usr/lib/debian-med/bin/ref_map.pl
/usr/lib/debian-med/bin/sstacks
/usr/lib/debian-med/bin/stacks-count-reads-per-sample-per-locus
/usr/lib/debian-med/bin/stacks-dist-extract
/usr/lib/debian-med/bin/stacks-gdb
/usr/lib/debian-med/bin/stacks-hist2d-loci-samples-coverage
/usr/lib/debian-med/bin/stacks-integrate-alignments
/usr/lib/debian-med/bin/stacks-samtools-tview
/usr/lib/debian-med/bin/tsv2bam
/usr/lib/debian-med/bin/ustacks
/usr/lib/stacks/bin/clone_filter
/usr/lib/stacks/bin/cstacks
/usr/lib/stacks/bin/denovo_map
/usr/lib/stacks/bin/denovo_map.pl
/usr/lib/stacks/bin/gstacks
/usr/lib/stacks/bin/kmer_filter
/usr/lib/stacks/bin/phasedstacks
/usr/lib/stacks/bin/populations
/usr/lib/stacks/bin/process_radtags
/usr/lib/stacks/bin/process_shortreads
/usr/lib/stacks/bin/ref_map
/usr/lib/stacks/bin/ref_map.pl
/usr/lib/stacks/bin/sstacks
/usr/lib/stacks/bin/stacks-count-reads-per-sample-per-locus
/usr/lib/stacks/bin/stacks-dist-extract
/usr/lib/stacks/bin/stacks-gdb
/usr/lib/stacks/bin/stacks-hist2d-loci-samples-coverage
/usr/lib/stacks/bin/stacks-integrate-alignments
/usr/lib/stacks/bin/stacks-samtools-tview
/usr/lib/stacks/bin/tsv2bam
/usr/lib/stacks/bin/ustacks
/usr/share/doc/stacks/changelog.Debian.gz
/usr/share/doc/stacks/changelog.gz
/usr/share/doc/stacks/copyright
/usr/share/doc/stacks/NEWS.Debian.gz
/usr/share/doc/stacks/README.Debian

Field source: Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00

Use this package

OpenFactory can boot this operating system in a browser VM, or start a build that includes the native package name from this record.

Try Debian 12 (Bookworm) in the browser Build an image that includes stacks

Versions, suites, and repositories

Each row is recorded package-index metadata for one version, architecture, suite, and repository. Names, URLs, and sizes are source-reported; a link is a potentially mutable retrieval location, not an OpenFactory redistribution claim or proof that OpenFactory retained the artifact bytes.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
2.62+dfsg-1	bookworm / main	arm64	Debian 12 · main · arm64	956 KiB	5.1 MiB	pool/main/s/stacks/stacks_2.62+dfsg-1_arm64.deb

Field source: Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00

Checksums and observation dates

For an APT source, signature verification authenticates the repository metadata chain and the Packages index containing this source-reported artifact digest. It does not certify package safety.

2.62+dfsg-1 / arm64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: d543dd36d6905d6dc9ab9e7a9dc1ddd33fc765e53cbe152613467d7268372e22

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' 'd543dd36d6905d6dc9ab9e7a9dc1ddd33fc765e53cbe152613467d7268372e22' 'stacks_2.62+dfsg-1_arm64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00

Catalog record completeness

The completeness score measures metadata coverage, not software quality, security, compatibility, or suitability.

Summary and description: 25/25
Artifact path and source digest: 25/25
Dependency metadata: 15/15
Package-file index: 15/15
Homepage: 5/5
License text: 0/5
Source package or maintainer: 10/10

Recorded total: 95/100

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5, Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Sources and provenance

Field-source links above resolve here. Each source entry names the metadata publisher, trust tier, exact snapshot revision, signature result, and observation time; catalog-derived mappings are labeled separately.

Debian 12 (Bookworm) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-amd64/Packages.xz
Expected SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Observed SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Result: match verified
Debian 12 (Bookworm) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-arm64/Packages.xz
Expected SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Observed SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Result: match verified