htslib C library for high-throughput sequencing data formats

1.9 biology =0 1.9Version of this port present on the latest quarterly branch.

Maintainer: cartwright@asu.edu

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:

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: https://www.htslib.org/

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:

TIMESTAMP = 1532906408 SHA256 (samtools-htslib-1.9_GH0.tar.gz) = d2e3cde77b8f874b37453c63390cd992901266336e9f70e871ef42402510467f SIZE (samtools-htslib-1.9_GH0.tar.gz) = 1285580

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)

8. biology/unanimity
9. biology/vcflib
10. Collapse this list.

Configuration Options

===> The following configuration options are available for htslib-1.9: CURL=on: Use libcurl for network file access (HTTPS and S3 support). ===> Use 'make config' to modify these settings

USES:

autoreconf gmake localbase pathfix perl5 shebangfix ssl

Master Sites:

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

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

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)

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

Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093

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)

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

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.

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)

Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight

biology/htslib: update 1.1 -> 1.2.1

PR:		198291
Submitted by:	Reed Cartwright <cartwright@asu.edu>

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>

12 vulnerabilities affecting 34 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2019-10-11 18:37:07