| Port details on branch 2026Q2 |
- htslib C library for high-throughput sequencing data formats
- 1.23.1 biology
 =0      1.23.1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2026-04-21 20:18:18
- Last Update: 2026-04-21 20:16:07
- Commit Hash: d690c7c
- Also Listed In: devel
- License: BSD3CLAUSE MIT
- WWW:
- https://www.htslib.org/
- 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.
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- Manual pages:
-
- pkg-plist: as obtained via:
make generate-plist - USE_RC_SUBR (Service Scripts)
- no SUBR information found for this port
- Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/htslib/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/htslib
- pkg install htslib
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: htslib
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1774783712
SHA256 (htslib-1.23.1.tar.bz2) = f8a3f36effeec38f043c53ab1f2d9ed45064f14205c5ef8e3c815763b90803c4
SIZE (htslib-1.23.1.tar.bz2) = 4987046
No package information for this port in our database- Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link:
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.4.1 : devel/gmake
- autoconf>=2.73 : devel/autoconf
- automake>=1.18.1 : devel/automake
- Test dependencies:
-
- bash : shells/bash
- perl5>=5.42.r<5.43 : lang/perl5.42
- Library dependencies:
-
- libdeflate.so : archivers/libdeflate
- libcurl.so : ftp/curl
- This port is required by:
- for Libraries
-
- biology/ugene
Configuration Options:- ===> The following configuration options are available for htslib-1.23.1:
CURL=on: Use libcurl for network file access (HTTPS and S3 support).
PLUGINS=on: Build and/or install plugins
===> Use 'make config' to modify these settings
- Options name:
- biology_htslib
- USES:
- autoreconf cpe gmake localbase:ldflags perl5 shebangfix tar:bzip2 ssl
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 1
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
1.23.1
21 Apr 2026 20:16:07
 |
Robert Clausecker (fuz) |
biology/htslib: fix build on armv7 (again)
The patches provided by me in 2023 to fix the build on armv7 were
upstreamed shortly after. In a subsequent update to the port, it
appears that the maintainer had then reversed these patches (?!),
effectively undoing my now upstreamed bug fix.
Remove the bogus patches to fix the build.
Fixes: aafe5d31c5f3afdaad0f6345bee06e7a3e2c5ced
See also: https://github.com/samtools/htscodecs/issues/81
Approved by: portmgr (build fix blanket)
MFH: 2026Q2
(cherry picked from commit 89c7d793da2638cfdc15252825a5548c3eb2f147) |
Number of commits found: 1
|
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