| Port details |
- gkl Accelerated kernel library for genomics
- 0.8.11.9 biology
 =2      0.8.11.9Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2024-08-04 20:12:05
- Last Update: 2024-12-31 08:57:55
- Commit Hash: 0835676
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- 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 = 1722788727
SHA256 (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 743d1eb48c2629454a6dcb98d9adca3aaedfe9c658e6f89e890b03b6e029df61
SIZE (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 5310668
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 : devel/gmake
- cmake : devel/cmake-core
- java : java/openjdk8
- Runtime dependencies:
-
- java : java/openjdk8
- Library dependencies:
-
- libisal.so : devel/isa-l
- This port is required by:
- for Run
-
- 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:
|
Number of commits found: 2
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.8.11.9
31 Dec 2024 08:57:55
 |
Muhammad Moinur Rahman (bofh) |
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
|
Yuri Victorovich (yuri) |
biology/gkl: New port: Accelerated kernel library for genomics |
Number of commits found: 2
|
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