biology/jellyfish 2.3.1 FreeBSD

Fast, memory-efficient counting of k-mers in DNA

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-08
Commit: 2414383046
License: BSD3CLAUSE, GPLv3+
Categories: biology
Package size: 262.6 KiB, 1132.2 KiB installed

Description

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.

In the other systems

The newest version among them is 2.3.1, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

FreeBSD

biology/jellyfish

2.3.1 newest

none known

[email protected]

2026-10-08

DragonFly

biology/jellyfish

2.3.0_4

none known

[email protected]

HardenedBSD

biology/jellyfish

2.3.1 newest

no data

[email protected]

GhostBSD

biology/jellyfish

2.3.1 newest

no data

[email protected]

Install

Binary package:

pkg install Jellyfish

From the ports tree:

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

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

RUN_DEPENDS=	Jellyfish>0:biology/jellyfish
LIB_DEPENDS=	libjellyfish-2.0.so:biology/jellyfish

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	2.3.1	2.3.1	2.3.0_3	-	2.3.1
FreeBSD:14:quarterly	2.3.1	2.3.1	n/a	-	2.3.1
FreeBSD:15:latest	2.3.1	2.3.1	n/a	-	2.3.0_4
FreeBSD:15:quarterly	2.3.1	2.3.1	n/a	n/a	n/a
FreeBSD:16:latest	2.3.1	2.3.1	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependencies

As this port's Makefile names them.

Library 1

libhts.so : biology/htslib

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

Build dependencies 21

Run dependencies 13

Required by 1

biology/biostar-tools

Configuration

Options name: biology_Jellyfish

Option

Default

Description

NLS

off

Native Language Support

USES: compiler:c++11-lib libtool
Service scripts: none

Message after installing

===>   NOTICE:

The Jellyfish port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

Manual pages 1

jellyfish(1)

pkg-plist 57

bin/jellyfish
include/jellyfish-%%VER%%/jellyfish/allocators_mmap.hpp
include/jellyfish-%%VER%%/jellyfish/atomic_bits_array.hpp
include/jellyfish-%%VER%%/jellyfish/atomic_field.hpp
include/jellyfish-%%VER%%/jellyfish/atomic_gcc.hpp
include/jellyfish-%%VER%%/jellyfish/backtrace.hpp
include/jellyfish-%%VER%%/jellyfish/binary_dumper.hpp
include/jellyfish-%%VER%%/jellyfish/bloom_common.hpp
include/jellyfish-%%VER%%/jellyfish/bloom_counter2.hpp
include/jellyfish-%%VER%%/jellyfish/bloom_filter.hpp
include/jellyfish-%%VER%%/jellyfish/circular_buffer.hpp
include/jellyfish-%%VER%%/jellyfish/compare_and_swap.hpp
include/jellyfish-%%VER%%/jellyfish/cooperative_pool.hpp
include/jellyfish-%%VER%%/jellyfish/cooperative_pool2.hpp
include/jellyfish-%%VER%%/jellyfish/cpp_array.hpp
include/jellyfish-%%VER%%/jellyfish/divisor.hpp
include/jellyfish-%%VER%%/jellyfish/dumper.hpp
include/jellyfish-%%VER%%/jellyfish/err.hpp
include/jellyfish-%%VER%%/jellyfish/file_header.hpp
include/jellyfish-%%VER%%/jellyfish/generator_manager.hpp
include/jellyfish-%%VER%%/jellyfish/generic_file_header.hpp
include/jellyfish-%%VER%%/jellyfish/hash_counter.hpp
include/jellyfish-%%VER%%/jellyfish/int128.hpp
include/jellyfish-%%VER%%/jellyfish/jellyfish.hpp
include/jellyfish-%%VER%%/jellyfish/json.h
include/jellyfish-%%VER%%/jellyfish/large_hash_array.hpp
include/jellyfish-%%VER%%/jellyfish/large_hash_iterator.hpp
include/jellyfish-%%VER%%/jellyfish/locks_pthread.hpp
include/jellyfish-%%VER%%/jellyfish/mapped_file.hpp
include/jellyfish-%%VER%%/jellyfish/mer_dna.hpp
include/jellyfish-%%VER%%/jellyfish/mer_dna_bloom_counter.hpp
include/jellyfish-%%VER%%/jellyfish/mer_heap.hpp
include/jellyfish-%%VER%%/jellyfish/mer_iterator.hpp
include/jellyfish-%%VER%%/jellyfish/mer_overlap_sequence_parser.hpp
include/jellyfish-%%VER%%/jellyfish/mer_qual_iterator.hpp
include/jellyfish-%%VER%%/jellyfish/misc.hpp
include/jellyfish-%%VER%%/jellyfish/offsets_key_value.hpp
include/jellyfish-%%VER%%/jellyfish/parser_common.hpp
include/jellyfish-%%VER%%/jellyfish/rectangular_binary_matrix.hpp
include/jellyfish-%%VER%%/jellyfish/sam_format.hpp
include/jellyfish-%%VER%%/jellyfish/simple_circular_buffer.hpp
include/jellyfish-%%VER%%/jellyfish/sorted_dumper.hpp
include/jellyfish-%%VER%%/jellyfish/stdio_filebuf.hpp
include/jellyfish-%%VER%%/jellyfish/storage.hpp
include/jellyfish-%%VER%%/jellyfish/stream_iterator.hpp
include/jellyfish-%%VER%%/jellyfish/stream_manager.hpp
include/jellyfish-%%VER%%/jellyfish/text_dumper.hpp
include/jellyfish-%%VER%%/jellyfish/thread_exec.hpp
include/jellyfish-%%VER%%/jellyfish/time.hpp
include/jellyfish-%%VER%%/jellyfish/token_ring.hpp
include/jellyfish-%%VER%%/jellyfish/whole_sequence_parser.hpp
lib/libjellyfish-2.0.a
lib/libjellyfish-2.0.so
lib/libjellyfish-2.0.so.2
lib/libjellyfish-2.0.so.2.0.0
libdata/pkgconfig/jellyfish-2.0.pc
share/man/man1/jellyfish.1.gz

distinfo 1

File

Size

SHA256

Jellyfish-2.3.1.tar.gz

1.15125e+06

ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd

Master sites 1

https://github.com/gmarcais/Jellyfish/releases/download/v2.3.1/

Commit history 2

Date Commit Credits Log message

2026-10-08

2414383046

Jason W. Bacon

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.

2026-09-04

c001466376

Jason W. Bacon

biology/jellyfish: Update to 2.3.1

A few source code improvements Changes: https://github.com/gmarcais/Jellyfish/releases Reported by: Repology