notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC		 Ukraine
The recently imposed "must be logged in" restriction is a response to increased bot traffic on the site. This affects search, commits, and vuxml pages.
Search engines are not blocked. Try using "site:www.freshports.org" and your search terms.
After the ports freeze to fix some stuff, the freeze is over. I have some work to do before FreshPorts can start processing commits again before it can start processing again. I've created an issue for that.
Port details
bifrost Parallel construction, indexing and querying of de Bruijn graphs
1.3.9 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.3.5_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-07-07 13:39:14
Last Update: 2026-08-11 21:42:57
Commit Hash: 3fe1059
License: BSD2CLAUSE
WWW:
https://github.com/pmelsted/bifrost
Description:
Bifrost is a tool and API for parallel construction, indexing and querying of colored and compacted de Bruijn graphs from FASTA/FASTQ DNA/RNA sequence files.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (59 items)
Collapse this list.
  1. /usr/local/share/licenses/bifrost-1.3.9/catalog.mk
  2. /usr/local/share/licenses/bifrost-1.3.9/LICENSE
  3. /usr/local/share/licenses/bifrost-1.3.9/BSD2CLAUSE
  4. bin/Bifrost
  5. include/bifrost/BitContainer.hpp
  6. include/bifrost/BlockedBloomFilter.hpp
  7. include/bifrost/ColorSet.hpp
  8. include/bifrost/ColoredCDBG.hpp
  9. include/bifrost/ColoredCDBG.tcc
  10. include/bifrost/Common.hpp
  11. include/bifrost/CompactedDBG.hpp
  12. include/bifrost/CompactedDBG.tcc
  13. include/bifrost/CompressedCoverage.hpp
  14. include/bifrost/CompressedSequence.hpp
  15. include/bifrost/DataAccessor.hpp
  16. include/bifrost/DataAccessor.tcc
  17. include/bifrost/DataManager.hpp
  18. include/bifrost/DataStorage.hpp
  19. include/bifrost/DataStorage.tcc
  20. include/bifrost/FASTX_Parser.hpp
  21. include/bifrost/File_Parser.hpp
  22. include/bifrost/GFA_Parser.hpp
  23. include/bifrost/IO.tcc
  24. include/bifrost/Kmer.hpp
  25. include/bifrost/KmerCovIndex.hpp
  26. include/bifrost/KmerCovIndex.tcc
  27. include/bifrost/KmerHashTable.hpp
  28. include/bifrost/KmerIterator.hpp
  29. include/bifrost/KmerStream.hpp
  30. include/bifrost/Lock.hpp
  31. include/bifrost/MinimizerIndex.hpp
  32. include/bifrost/NeighborIterator.hpp
  33. include/bifrost/NeighborIterator.tcc
  34. include/bifrost/RepHash.hpp
  35. include/bifrost/Search.tcc
  36. include/bifrost/StreamCounter.hpp
  37. include/bifrost/TinyBitmap.hpp
  38. include/bifrost/TinyVector.hpp
  39. include/bifrost/Unitig.hpp
  40. include/bifrost/UnitigIterator.hpp
  41. include/bifrost/UnitigIterator.tcc
  42. include/bifrost/UnitigMap.hpp
  43. include/bifrost/UnitigMap.tcc
  44. include/bifrost/fastmod.h
  45. include/bifrost/getRSS.h
  46. include/bifrost/kseq.h
  47. include/bifrost/libpopcnt.h
  48. include/bifrost/minHashIterator.hpp
  49. include/bifrost/roaring.h
  50. include/bifrost/roaring.hh
  51. include/bifrost/rw_spin_lock.h
  52. include/bifrost/strict_fstream.hpp
  53. include/bifrost/wyhash.h
  54. include/bifrost/zstr.hpp
  55. lib/libbifrost.a
  56. lib/libbifrost.so
  57. @owner
  58. @group
  59. @mode
Collapse this list.
USE_RC_SUBR (Service Scripts)
  • no SUBR information found for this port
Dependency lines:
  • bifrost>0:biology/bifrost
To install the port:
cd /usr/ports/biology/bifrost/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bifrost
  • pkg install bifrost
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bifrost
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 powerpc64 powerpc64le riscv64
distinfo:
TIMESTAMP = 1786468419 SHA256 (pmelsted-bifrost-1.3.9_GH0.tar.gz) = 6e376e8a4918d174e73ee1b42ea1ba8331a11ce35df4fd55d9f11bb9889a4fc0 SIZE (pmelsted-bifrost-1.3.9_GH0.tar.gz) = 357626
Packages (timestamps in pop-ups are UTC):
bifrost
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.3.5_11.3.5_1---n/an/an/a
FreeBSD:13:quarterly1.3.5_11.3.5_1---n/an/an/a
FreeBSD:14:latest1.3.91.3.9------
FreeBSD:14:quarterly1.3.5_11.3.5_1----1.3.11.3.1
FreeBSD:15:latest1.3.91.3.9n/a-n/an/a1.3.11.3.1
FreeBSD:15:quarterly1.3.5_11.3.5_1n/a-n/an/a--
FreeBSD:16:latest1.3.5_11.3.9n/a-n/an/a--
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake-core
  2. ninja : devel/ninja
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
biology_bifrost
USES:
cmake
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/pmelsted/bifrost/tar.gz/1.3.9?dummy=/
Collapse this list.

Number of commits found: 9

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.3.9
11 Aug 2026 21:42:57
commit hash: 3fe10594080ad893c5bba81f970c9afbe04d1202commit hash: 3fe10594080ad893c5bba81f970c9afbe04d1202commit hash: 3fe10594080ad893c5bba81f970c9afbe04d1202commit hash: 3fe10594080ad893c5bba81f970c9afbe04d1202 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Update to 1.3.9

A few bug fixes since 1.3.5
Upstreamed one patch for recent clang
Changes: https://github.com/pmelsted/bifrost/releases

Reported by:    portscout
1.3.5_1
27 May 2025 14:08:27
commit hash: bba37490f1326822c46451866430c78075a48028commit hash: bba37490f1326822c46451866430c78075a48028commit hash: bba37490f1326822c46451866430c78075a48028commit hash: bba37490f1326822c46451866430c78075a48028 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Remove USE_GCC, fix build with clang19

Fix apparent typo in seldom-used code (hayzam@alchemilla.io)

Reported by:    gerald
Tested by:      jwb
1.3.5
15 May 2025 11:37:10
commit hash: 40478d7acd2afd5a09d9fec5edc9821e548f18e2commit hash: 40478d7acd2afd5a09d9fec5edc9821e548f18e2commit hash: 40478d7acd2afd5a09d9fec5edc9821e548f18e2commit hash: 40478d7acd2afd5a09d9fec5edc9821e548f18e2 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Unbreak build on 15-CURRENT

Unable to identify the cause, use GCC as a workaround for now
No change on other FreeBSD versions
1.3.5
18 Mar 2024 14:29:43
commit hash: 719334cd8529dd50b5d4bf9ca9cc48f1090cb88dcommit hash: 719334cd8529dd50b5d4bf9ca9cc48f1090cb88dcommit hash: 719334cd8529dd50b5d4bf9ca9cc48f1090cb88dcommit hash: 719334cd8529dd50b5d4bf9ca9cc48f1090cb88d files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Update to 1.3.5

A few new features and bug fixes
Some important changes in CLI behavior
Changes: https://github.com/pmelsted/bifrost/releases

Reported by:    portscout
1.3.1
21 Nov 2023 12:58:39
commit hash: d1bf49e314068c044c048bf4ecd450d9220b33bdcommit hash: d1bf49e314068c044c048bf4ecd450d9220b33bdcommit hash: d1bf49e314068c044c048bf4ecd450d9220b33bdcommit hash: d1bf49e314068c044c048bf4ecd450d9220b33bd files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Update to 1.3.1

Minor bugfix release
Changes: https://github.com/pmelsted/bifrost/releases

Reported by:    portscout
1.3.0
11 Oct 2023 12:31:57
commit hash: 2650106a619a359d18835139e863a3ff45bb3b2ecommit hash: 2650106a619a359d18835139e863a3ff45bb3b2ecommit hash: 2650106a619a359d18835139e863a3ff45bb3b2ecommit hash: 2650106a619a359d18835139e863a3ff45bb3b2e files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Update to 1.3.0

Performance and memory efficiency improvements
A few new features

Note: New index format incompatible with previous versions

Changes: https://github.com/pmelsted/bifrost/releases

Reported by:    portscout
1.2.1_1
12 Aug 2023 14:38:47
commit hash: f38473fec0a852349f186e1d28358fc2ce5636decommit hash: f38473fec0a852349f186e1d28358fc2ce5636decommit hash: f38473fec0a852349f186e1d28358fc2ce5636decommit hash: f38473fec0a852349f186e1d28358fc2ce5636de files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Control -march via CPUTYPE make variable

Also disable hard-coded -O3 in cmake to respect user env

PR:             272651
Reported by:    yuri
Reviewed by:    nimaje+fbz@bureaucracy.de, dizzy
1.2.1
16 Jul 2023 13:40:30
commit hash: 7d4be2d6fd1e3db4109d266d25a4411fedc05235commit hash: 7d4be2d6fd1e3db4109d266d25a4411fedc05235commit hash: 7d4be2d6fd1e3db4109d266d25a4411fedc05235commit hash: 7d4be2d6fd1e3db4109d266d25a4411fedc05235 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Portability fixes

Tag as only for 64-bit platforms
Fix build on aarch64 (patch out -march=native)

Reported by:    pkg-fallout
1.2.1
07 Jul 2023 13:38:22
commit hash: 964411795080849c96f95a7ce315e1b230b9b93acommit hash: 964411795080849c96f95a7ce315e1b230b9b93acommit hash: 964411795080849c96f95a7ce315e1b230b9b93acommit hash: 964411795080849c96f95a7ce315e1b230b9b93a files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bifrost: Parallel tool for de Bruijn graphs

Bifrost is a tool and API for parallel construction, indexing and
querying of colored and compacted de Bruijn graphs from FASTA/FASTQ
DNA/RNA sequence files.

Number of commits found: 9
Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
Security Policy
Privacy
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
elixirAug 28
elixir-develAug 28
gitlabAug 28
phpbb3Aug 28
nsdAug 27
php-composerAug 27
conduitAug 26
openssl*Aug 26
openssl*Aug 26
openssl34*Aug 26
openssl34*Aug 26
openssl35*Aug 26
openssl35*Aug 26
openssl36*Aug 26
openssl36*Aug 26

28 vulnerabilities affecting 435 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last processed:
2026-08-28 21:08:42 UTC


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)

Calculated hourly:
Port count 35102
Broken 78
Deprecated 335
Ignore 192
Forbidden 0
Restricted 1
No CDROM 1
Vulnerable 42
Expired 18
Set to expire 260
Interactive 0
new 24 hours 1
new 48 hours7
new 7 days40
new fortnight94
new month193
Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD 		Valid HTML, CSS, and RSS. Copyright © 2000-2026 Dan Langille. All rights reserved.