BSD Ports

biology/htslib 1.24_1 FreeBSD

C library for high-throughput sequencing data formats

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
BSD3CLAUSE, MIT
Categories
biology, devel
Package size
1013.8 KiB, 6318.1 KiB installed

Description

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools.

In the other systems

SystemPortVersion
FreeBSDbiology/htslib1.24_1
NetBSDbiology/htslib1.21nb9
DragonFlybiology/htslib1.21

Install

Binary package:

pkg install htslib

From the ports tree:

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

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

RUN_DEPENDS=	htslib>0:biology/htslib
LIB_DEPENDS=	libhts.so:biology/htslib

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:latest1.24_11.24_11.16-1.24_1
FreeBSD:14:quarterly1.241.24n/a-1.24
FreeBSD:15:latest1.24_11.24_1n/a-1.22
FreeBSD:15:quarterly1.241.24n/an/an/a
FreeBSD:16:latest1.241.24_1n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Library 1

Test 1

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

Build dependencies 18
Run dependencies 11

Configuration

Options name: biology_htslib

OptionDefaultDescription
CURLonUse libcurl for network file access (HTTPS and S3 support).
PLUGINSonBuild and/or install plugins
USES
autoreconf cpe gmake localbase:ldflags perl5 shebangfix tar:bzip2
Service scripts
none

Message after installing

===>   NOTICE:

The htslib 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 9
  • annot-tsv(1)
  • bgzip(1)
  • faidx(5)
  • htsfile(1)
  • htslib-s3-plugin(7)
  • ref-cache(1)
  • sam(5)
  • tabix(1)
  • vcf(5)
pkg-plist 48
  • bin/annot-tsv
  • bin/bgzip
  • bin/htsfile
  • bin/ref-cache
  • bin/tabix
  • include/htslib/bgzf.h
  • include/htslib/cram.h
  • include/htslib/faidx.h
  • include/htslib/hfile.h
  • include/htslib/hts.h
  • include/htslib/hts_alloc.h
  • include/htslib/hts_defs.h
  • include/htslib/hts_endian.h
  • include/htslib/hts_expr.h
  • include/htslib/hts_log.h
  • include/htslib/hts_os.h
  • include/htslib/kbitset.h
  • include/htslib/kfunc.h
  • include/htslib/khash.h
  • include/htslib/khash_str2int.h
  • include/htslib/klist.h
  • include/htslib/knetfile.h
  • include/htslib/kroundup.h
  • include/htslib/kseq.h
  • include/htslib/ksort.h
  • include/htslib/kstring.h
  • include/htslib/regidx.h
  • include/htslib/sam.h
  • include/htslib/synced_bcf_reader.h
  • include/htslib/tbx.h
  • include/htslib/thread_pool.h
  • include/htslib/vcf.h
  • include/htslib/vcf_sweep.h
  • include/htslib/vcfutils.h
  • lib/libhts.a
  • lib/libhts.so
  • lib/libhts.so.
  • lib/libhts.so.3
  • libdata/pkgconfig/htslib.pc
  • share/man/man1/annot-tsv.1.gz
  • share/man/man1/bgzip.1.gz
  • share/man/man1/htsfile.1.gz
  • share/man/man1/ref-cache.1.gz
  • share/man/man1/tabix.1.gz
  • share/man/man5/faidx.5.gz
  • share/man/man5/sam.5.gz
  • share/man/man5/vcf.5.gz
  • share/man/man7/htslib-s3-plugin.7.gz
distinfo 1
FileSizeSHA256
htslib-1.24.tar.bz25.004265e+0628a8de191381c7a97a35675ceac76fa1ea95e7b678d6a2e9d600a7874e4077de
Master sites 1
  • https://github.com/samtools/htslib/releases/download/1.24/

Commit history 3

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.
20a3f9548d Jason W. Bacon biology/htslib: Remove obsolete patches
Patches for aarch64 were erroneously restored due to a transient build failure on my M1, which was misinterpreted.
b44b3ccb00 Jason W. Bacon biology/htslib: Update to 1.24
Numerous fixes and enhancements Changes: https://github.com/samtools/htslib/releases Reported by: portscout