| Port details on branch 2020Q3 |
- htslib C library for high-throughput sequencing data formats
- 1.23.1 biology
 =1      1.23.1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2014-12-14 22:35:26
- Last Update: 2026-04-21 20:14:30
- Commit Hash: 89c7d79
- People watching this port, also watch:: cytoscape, openjdk8, tmux, xen-kernel, python311
- 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
Packages (timestamps in pop-ups are UTC):
- 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 Build
-
- biology/bcf-score
- biology/bcftools
- biology/bio-mocha
- biology/samtools
- for Libraries
-
- biology/augustus
- biology/bcf-score
- biology/bcftools
- biology/bio-mocha
- biology/cufflinks
- biology/freebayes
- biology/jellyfish
-
Deleted ports which required this port:
- * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
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:
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