biology/diamond 2.2.8 FreeBSD

BLAST-compatible local sequence aligner

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-10
Commit: 1385a5b629
License: GPLv3
Categories: biology
Package size: 1386.7 KiB, 5120.4 KiB installed

Description

DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.

In the other systems

System

Port

Version

FreeBSD

biology/diamond

2.2.8

DragonFly

biology/diamond

2.1.9

HardenedBSD

biology/diamond

2.2.5

GhostBSD

biology/diamond

2.2.5

Install

Binary package:

pkg install diamond

From the ports tree:

cd /usr/ports/biology/diamond/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	diamond>0:biology/diamond

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository	aarch64	amd64	armv6	armv7	i386
FreeBSD:14:latest	2.2.5	2.2.8	-	-	-
FreeBSD:14:quarterly	2.2.5	2.2.5	n/a	-	-
FreeBSD:15:latest	2.2.8	2.2.8	n/a	-	-
FreeBSD:15:quarterly	2.2.5	2.2.5	n/a	n/a	n/a
FreeBSD:16:latest	2.2.5	2.2.8	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

Build dependencies 19

Run dependencies 4

No port depends on this one.

Configuration

No options to configure.

USES: cmake localbase sqlite
Service scripts: none

Files

distinfo 1

File

Size

SHA256

bbuchfink-diamond-v2.2.8_GH0.tar.gz

1.6800398e+07

a9cc37bd955fa7ed25447278a0b4f97e7036a9abd64f60e6565a56c28219c54c

Commit history 6

Date Commit Credits Log message

2026-10-10

1385a5b629

Joseph Mingrone

biology/diamond: Update to 2.2.8

Release notes: https://github.com/bbuchfink/diamond/releases/tag/v2.2.8 Sponsored by: The FreeBSD Foundation

2026-10-10

1aa6b21580

Joseph Mingrone

biology/diamond: Update to 2.2.7

Release notes: https://github.com/bbuchfink/diamond/releases/tag/v2.2.7 Sponsored by: The FreeBSD Foundation

2026-10-10

5c5d7f2eba

Joseph Mingrone

biology/diamond: Update to 2.2.6

Release notes: https://github.com/bbuchfink/diamond/releases/tag/v2.2.6 Sponsored by: The FreeBSD Foundation

2026-08-04

9cd93f98a4

Joseph Mingrone

biology/diamond: Update to 2.2.5 and fix deepclust crash

Initialize the seed_only member in the Hsp constructor that takes an ApproxHsp. deepclust builds Hsps through this constructor for its approximate alignments, so seed_only was left uninitialized. When it evaluated to true, the SEED_ONLY flag was set on an otherwise full-length intermediate output record. The multiblock join later parsed that record as seed-only, stopped four bytes short, and aborted with "Unexpected end of file", failing the deepclust-multiblock regression test. On Linux, the uninitialized member consistently evaluated to false, masking the bug. On FreeBSD, it evaluated to true, and triggered the crash. Release notes: https://github.com/bbuchfink/diamond/releases/tag/v2.2.5 Sponsored by: The FreeBSD Foundation

2026-07-28

c12c6fa513

Joseph Mingrone

biology/diamond: Update to 2.2.4

Release notes: https://github.com/bbuchfink/diamond/releases/tag/v2.2.4 Sponsored by: The FreeBSD Foundation

The latest 5 of 6 in the history this site was built from.