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Port details
gkl Accelerated kernel library for genomics
0.9.1_3 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 View this port on Repology. pkg-fallout 0.9.1_3Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2024-08-04 20:12:05
Last Update: 2026-04-08 07:11:51
Commit Hash: 4bc030c
Also Listed In: devel
License: MIT
WWW:
https://github.com/Intel-HLS/GKL
Description:
GKL is a set of optimized versions of compute kernels used in genomics applications like GATK and HTSJDK. Kernels included: * PairHMM AVX and AVX-512 optimized versions of PairHMM used in GATK HaplotypeCaller and MuTect2. OpenMP support for multicore processors. * Smith-Waterman AVX2 and AVX-512 optimized versions of Smith-Waterman used in GATK HaplotypeCaller and MuTect2. * DEFLATE Compression/Decompression: Performance optimized Level 1 and 2 compression and decompression from Intel's ISA-L library. Performance optimized Level 3 through 9 compression from Intel's Open Source Technology Center zlib library. * Partially Determined HMM (PDHMM) AVX2 and AVX-512 optimized versions of PDHMM used in GATK. Serial Implementation for CPU's with no AVX.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (13 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/gkl-0.9.1_3/catalog.mk
  3. /usr/local/share/licenses/gkl-0.9.1_3/LICENSE
  4. /usr/local/share/licenses/gkl-0.9.1_3/MIT
  5. lib/libgkl_compression.so
  6. lib/libgkl_pairhmm.so
  7. lib/libgkl_pairhmm_omp.so
  8. lib/libgkl_pdhmm.so
  9. lib/libgkl_smithwaterman.so
  10. lib/libgkl_utils.so
  11. @owner
  12. @group
  13. @mode
Collapse this list.
USE_RC_SUBR (Service Scripts)
  • no SUBR information found for this port
Dependency lines:
  • gkl>0:biology/gkl
To install the port:
cd /usr/ports/biology/gkl/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/gkl
  • pkg install gkl
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: gkl
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1755972512 SHA256 (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 8e32bc3c63013ca6468c65fbbb6af80a433652b640be868d0cb82cb70a919799 SIZE (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 5363673
Packages (timestamps in pop-ups are UTC):
gkl
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-0.9.1_3---n/an/an/a
FreeBSD:13:quarterly-0.9.1_1---n/an/an/a
FreeBSD:14:latest-0.9.1_3------
FreeBSD:14:quarterly-0.9.1_3------
FreeBSD:15:latest-0.9.1_3n/a-n/an/a--
FreeBSD:15:quarterly-0.9.1_3n/a-n/an/a--
FreeBSD:16:latest-0.9.1_3n/a-n/an/a--
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. cmake : devel/cmake-core
  3. java : java/openjdk11
Runtime dependencies:
  1. java : java/openjdk11
Library dependencies:
  1. libisal.so : devel/isa-l
This port is required by:
for Run
  1. biology/gatk
Configuration Options:
No options to configure
Options name:
biology_gkl
USES:
cmake:noninja java localbase:ldflags
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/Intel-HLS/GKL/tar.gz/0.9.1?dummy=/
Collapse this list.

Number of commits found: 8

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.9.1_3
08 Apr 2026 07:11:51
commit hash: 4bc030c70187e3afd1e7360df1a151704f95375ecommit hash: 4bc030c70187e3afd1e7360df1a151704f95375ecommit hash: 4bc030c70187e3afd1e7360df1a151704f95375ecommit hash: 4bc030c70187e3afd1e7360df1a151704f95375e files touched by this commit		 Ronald Klop (ronald) search for other commits by this committer 
*/*: bump portrevision for openjdk dependency change

Other USES=java ports use JAVA_DEFAULT or are pinned to a specific version.

PR:	293756
0.9.1_2
02 Apr 2026 21:06:57
commit hash: 86813e9ccf597695e26c8104e678f913689f1e93commit hash: 86813e9ccf597695e26c8104e678f913689f1e93commit hash: 86813e9ccf597695e26c8104e678f913689f1e93commit hash: 86813e9ccf597695e26c8104e678f913689f1e93 files touched by this commit		 Ronald Klop (ronald) search for other commits by this committer 
*/*: bump portrevision after java_default=25 update

Included all ports that have USES=java.

PR:	293559
0.9.1_1
01 Mar 2026 21:58:50
commit hash: 693b58e8e4103ea5218c7a335f1e1052356b7120commit hash: 693b58e8e4103ea5218c7a335f1e1052356b7120commit hash: 693b58e8e4103ea5218c7a335f1e1052356b7120commit hash: 693b58e8e4103ea5218c7a335f1e1052356b7120 files touched by this commit		 Ronald Klop (ronald) search for other commits by this committer 
biology/gkl: mark broken on aarch64

multiple errors in the log like:
/usr/lib/clang/19/include/ia32intrin.h:312:10: error: use of undeclared
identifier '__builtin_ia32_readeflags_u32'

PR:	293534
Reported-by:	https://portsfallout.com/fallout?port=biology%2Fgkl%24
Approved-by:	yuri@ (maintainer)
0.9.1_1
26 Feb 2026 08:10:21
commit hash: 2baaf16375792e66c71bc985f99e147f90be47fccommit hash: 2baaf16375792e66c71bc985f99e147f90be47fccommit hash: 2baaf16375792e66c71bc985f99e147f90be47fccommit hash: 2baaf16375792e66c71bc985f99e147f90be47fc files touched by this commit		 Ronald Klop (ronald) search for other commits by this committer 
*/*: bump portrevision after java_default=21 update

PR:	272855
0.9.1
21 Jan 2026 10:29:46
commit hash: ed25d4e234ff7deee31c2501b6f910188dd501e8commit hash: ed25d4e234ff7deee31c2501b6f910188dd501e8commit hash: ed25d4e234ff7deee31c2501b6f910188dd501e8commit hash: ed25d4e234ff7deee31c2501b6f910188dd501e8 files touched by this commit		 Ronald Klop (ronald) search for other commits by this committer 
biology/gkl: pin to jdk 8 and 11

Error on jdk17+:
Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 AWT JVM)
...
CMake Error: The following variables are used in this project, but they are set
to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake
files:
JAVA_AWT_INCLUDE_PATH (ADVANCED)

PR:	292244
Approved-by:	maintainer timeout
0.9.1
23 Aug 2025 18:26:47
commit hash: 25848df4724ce501e9d6966f5b5547a8d459c9b2commit hash: 25848df4724ce501e9d6966f5b5547a8d459c9b2commit hash: 25848df4724ce501e9d6966f5b5547a8d459c9b2commit hash: 25848df4724ce501e9d6966f5b5547a8d459c9b2 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/gkl: update 0.8.11-9 → 0.9.1
0.8.11.9
31 Dec 2024 08:57:55
commit hash: 0835676e361bca74b28b09fe0425ed5ee958f26bcommit hash: 0835676e361bca74b28b09fe0425ed5ee958f26bcommit hash: 0835676e361bca74b28b09fe0425ed5ee958f26bcommit hash: 0835676e361bca74b28b09fe0425ed5ee958f26b files touched by this commit		 Muhammad Moinur Rahman (bofh) search for other commits by this committer 
Mk/**java.mk: Convert bsd.java.mk to USES

The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
  USES=java:build,run if NO_BUILD is undefined. Else it defaults to
  USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
  USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
  extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
  build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
  build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>

Approved by: mat (portmgr), glewis
Differential Revision:  https://reviews.freebsd.org/D48201
0.8.11.9
04 Aug 2024 20:09:41
commit hash: 73bbe7b7f0814a152a169c859ed208cee8a13152commit hash: 73bbe7b7f0814a152a169c859ed208cee8a13152commit hash: 73bbe7b7f0814a152a169c859ed208cee8a13152commit hash: 73bbe7b7f0814a152a169c859ed208cee8a13152 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/gkl: New port: Accelerated kernel library for genomics

Number of commits found: 8
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