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Port details
htslib C library for high-throughput sequencing data formats
1.9 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 1.9Version of this port present on the latest quarterly branch.
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 2014-12-14 22:35:26
Last Update: 2018-08-02 20:27:13
SVN Revision: 476245
Also Listed In: devel
License: BSD3CLAUSE MIT
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (46 items)
  1. /usr/local/share/licenses/htslib-1.9/catalog.mk
  2. /usr/local/share/licenses/htslib-1.9/LICENSE
  3. /usr/local/share/licenses/htslib-1.9/BSD3CLAUSE
  4. /usr/local/share/licenses/htslib-1.9/MIT
  5. bin/bgzip
  6. bin/htsfile
  7. bin/tabix
  8. include/htslib/bgzf.h
  9. include/htslib/cram.h
  10. include/htslib/faidx.h
  11. include/htslib/hfile.h
  12. include/htslib/hts.h
  13. include/htslib/hts_defs.h
  14. include/htslib/hts_endian.h
  15. include/htslib/hts_log.h
  16. include/htslib/hts_os.h
  17. include/htslib/kbitset.h
  18. include/htslib/kfunc.h
  19. include/htslib/khash.h
  20. include/htslib/khash_str2int.h
  21. include/htslib/klist.h
  22. include/htslib/knetfile.h
  23. include/htslib/kseq.h
  24. include/htslib/ksort.h
  25. include/htslib/kstring.h
  26. include/htslib/regidx.h
  27. include/htslib/sam.h
  28. include/htslib/synced_bcf_reader.h
  29. include/htslib/tbx.h
  30. include/htslib/thread_pool.h
  31. include/htslib/vcf.h
  32. include/htslib/vcf_sweep.h
  33. include/htslib/vcfutils.h
  34. lib/libhts.a
  35. lib/libhts.so
  36. lib/libhts.so.1.9
  37. lib/libhts.so.2
  38. libdata/pkgconfig/htslib.pc
  39. man/man1/bgzip.1.gz
  40. man/man1/htsfile.1.gz
  41. man/man1/tabix.1.gz
  42. man/man5/faidx.5.gz
  43. man/man5/sam.5.gz
  44. man/man5/vcf.5.gz
  45. @postexec /usr/sbin/service ldconfig restart > /dev/null
  46. @postunexec /usr/sbin/service ldconfig restart > /dev/null
Collapse this list.
Dependency lines:
  • htslib>0:biology/htslib
  • libhts.so:biology/htslib
To install the port: cd /usr/ports/biology/htslib/ && make install clean
To add the package: pkg install htslib
PKGNAME: htslib
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. autoconf>=2.69 : devel/autoconf
  2. automake>=1.16.1 : devel/automake
  3. gmake : devel/gmake
Library dependencies:
  1. libcurl.so : ftp/curl
This port is required by:
for Build
  1. biology/bcftools
  2. biology/samtools
for Libraries
  1. biology/bcftools
  2. biology/cufflinks
  3. biology/jellyfish
  4. biology/kallisto
  5. biology/pbbam
  6. biology/samtools
  7. biology/tabixpp
Expand this list (9 items / 2 hidden)
  1. biology/unanimity
  2. biology/vcflib
  3. Collapse this list.

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/samtools/htslib/tar.gz/1.9?dummy=/

Number of commits found: 11

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
02 Aug 2018 19:27:13
Original commit files touched by this commit  1.9
Revision:476245
fernape search for other commits by this committer
biology/htslib: update to 1.9

PR:	230170
Submitted by:	ndowens.fbsd@yandex.com
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16568
16 Jul 2018 18:11:44
Original commit files touched by this commit  1.8
Revision:474752
yuri search for other commits by this committer
biology/htslib: Update 1.6 -> 1.8

Port changes:
* Use DISTVERSION
* Add USES=localbase instead of CPPFLAGS/LDFLAGS
* Move USES=ssl to CURL_USES=ssl
* Update WWW

PR:		228908
Approved by:	maintainer's timeout (cartwright@asu.edu; 35 days)
25 Oct 2017 10:19:50
Original commit files touched by this commit  1.6
Revision:452840
pizzamig search for other commits by this committer
biology/htslib biology/bcftools biology/samtools: Update to 1.6

PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768
21 Oct 2016 15:21:13
Original commit files touched by this commit  1.3.1
Revision:424427
mat search for other commits by this committer
Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093
26 May 2016 20:28:55
Original commit files touched by this commit  1.3.1
Revision:415914
pi search for other commits by this committer
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)
01 Apr 2016 13:29:17
Original commit files touched by this commit  1.3
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
29 Dec 2015 15:05:44
Original commit files touched by this commit  1.3
Revision:404749
marino search for other commits by this committer
biology/htslib: Replace FreeBSD-specific fix with a generic one

This port will not build if ENOTRECOVERABLE is not defined, period.
It's not necessary to check OPSYS and version, just apply the fallback
definition if it's not defined.  This unbreaks DragonFly after last
commit.
25 Dec 2015 01:31:09
Original commit files touched by this commit  1.3
Revision:404398
junovitch search for other commits by this committer
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)
06 May 2015 15:16:54
Original commit files touched by this commit  1.2.1
Revision:385521
mat search for other commits by this committer
Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight
06 Mar 2015 12:45:23
Original commit files touched by this commit  1.2.1
Revision:380596
robak search for other commits by this committer
biology/htslib: update 1.1 -> 1.2.1

PR:		198291
Submitted by:	Reed Cartwright <cartwright@asu.edu>
14 Dec 2014 22:35:08
Original commit files touched by this commit  1.1
Revision:374729
pawel search for other commits by this committer
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.

WWW: http://www.htslib.org/

PR:		195591
Submitted by:	Reed A. Cartwright <cartwright@asu.edu>

Number of commits found: 11

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