FreeBSD Ports

biology/bifrost 1.3.9

Parallel construction, indexing and querying of de Bruijn graphs

Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
BSD2CLAUSE
Categories
biology
Package size
838.0 KiB, 5935.6 KiB installed

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.

Install

As a binary package — by origin, or by package name:

pkg install biology/bifrost
pkg install bifrost

From the ports tree:

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

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

RUN_DEPENDS=	bifrost>0:biology/bifrost
LIB_DEPENDS=	libbifrost.so:biology/bifrost

Packages

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

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest1.3.91.3.9---
FreeBSD:14:quarterly1.3.91.3.9n/a--
FreeBSD:15:latest1.3.91.3.9n/a--
FreeBSD:15:quarterly1.3.91.3.9n/an/an/a
FreeBSD:16:latest1.3.91.3.9n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

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

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

All build dependencies 15

No port depends on this one.

Configuration

No options to configure.

USES
cmake
Service scripts
none

Files

pkg-plist 53
  • bin/Bifrost
  • include/bifrost/BitContainer.hpp
  • include/bifrost/BlockedBloomFilter.hpp
  • include/bifrost/ColorSet.hpp
  • include/bifrost/ColoredCDBG.hpp
  • include/bifrost/ColoredCDBG.tcc
  • include/bifrost/Common.hpp
  • include/bifrost/CompactedDBG.hpp
  • include/bifrost/CompactedDBG.tcc
  • include/bifrost/CompressedCoverage.hpp
  • include/bifrost/CompressedSequence.hpp
  • include/bifrost/DataAccessor.hpp
  • include/bifrost/DataAccessor.tcc
  • include/bifrost/DataManager.hpp
  • include/bifrost/DataStorage.hpp
  • include/bifrost/DataStorage.tcc
  • include/bifrost/FASTX_Parser.hpp
  • include/bifrost/File_Parser.hpp
  • include/bifrost/GFA_Parser.hpp
  • include/bifrost/IO.tcc
  • include/bifrost/Kmer.hpp
  • include/bifrost/KmerCovIndex.hpp
  • include/bifrost/KmerCovIndex.tcc
  • include/bifrost/KmerHashTable.hpp
  • include/bifrost/KmerIterator.hpp
  • include/bifrost/KmerStream.hpp
  • include/bifrost/Lock.hpp
  • include/bifrost/MinimizerIndex.hpp
  • include/bifrost/NeighborIterator.hpp
  • include/bifrost/NeighborIterator.tcc
  • include/bifrost/RepHash.hpp
  • include/bifrost/Search.tcc
  • include/bifrost/StreamCounter.hpp
  • include/bifrost/TinyBitmap.hpp
  • include/bifrost/TinyVector.hpp
  • include/bifrost/Unitig.hpp
  • include/bifrost/UnitigIterator.hpp
  • include/bifrost/UnitigIterator.tcc
  • include/bifrost/UnitigMap.hpp
  • include/bifrost/UnitigMap.tcc
  • include/bifrost/fastmod.h
  • include/bifrost/getRSS.h
  • include/bifrost/kseq.h
  • include/bifrost/libpopcnt.h
  • include/bifrost/minHashIterator.hpp
  • include/bifrost/roaring.h
  • include/bifrost/roaring.hh
  • include/bifrost/rw_spin_lock.h
  • include/bifrost/strict_fstream.hpp
  • include/bifrost/wyhash.h
  • include/bifrost/zstr.hpp
  • lib/libbifrost.a
  • lib/libbifrost.so
distinfo 1
FileSizeSHA256
pmelsted-bifrost-1.3.9_GH0.tar.gz3576266e376e8a4918d174e73ee1b42ea1ba8331a11ce35df4fd55d9f11bb9889a4fc0

Commit history 2

DateCommitCreditsLog message
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.
3fe1059408 Jason W. Bacon 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