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Port details
bifrost Parallel construction, indexing and querying of de Bruijn graphs
1.3.5 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 1.3.5Version 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: 2024-03-18 14:29:43
Commit Hash: 719334c
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-1.3.5/catalog.mk
  2. /usr/local/share/licenses/bifrost-1.3.5/LICENSE
  3. /usr/local/share/licenses/bifrost-1.3.5/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.
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 = 1710590640 SHA256 (pmelsted-bifrost-v1.3.5_GH0.tar.gz) = e1b2491328b0cc1a32e433a8a9780f05547fa4b8d674b58abdda9ac8809f5341 SIZE (pmelsted-bifrost-v1.3.5_GH0.tar.gz) = 356701
Packages (timestamps in pop-ups are UTC):
bifrost
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.3.51.3.5------
FreeBSD:13:quarterly1.3.51.3.5----1.3.11.3.1
FreeBSD:14:latest1.3.51.3.5------
FreeBSD:14:quarterly1.3.51.3.5----1.3.11.3.1
FreeBSD:15:latest1.3.51.3.5n/a-n/a-1.3.11.3.1
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/v1.3.5?dummy=/
Collapse this list.

Number of commits found: 6

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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: 6
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