BSD Portsbiology/gkl 0.9.1_3 FreeBSD
Accelerated kernel library for genomics
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
0b23c55e5d- License
- MIT
- Categories
- biology, devel
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.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/gkl | 0.9.1_3 |
| HardenedBSD | biology/gkl | 0.9.1_3 |
| GhostBSD | biology/gkl | 0.9.1_3 |
Install
Binary package:
pkg install gklFrom the ports tree:
cd /usr/ports/biology/gkl/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= gkl>0:biology/gkl
LIB_DEPENDS= libgkl_compression.so:biology/gklPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | - | 0.9.1_3 | - | - | - |
| FreeBSD:14:quarterly | - | 0.9.1_3 | n/a | - | - |
| FreeBSD:15:latest | - | 0.9.1_3 | n/a | - | - |
| FreeBSD:15:quarterly | - | 0.9.1_3 | n/a | n/a | n/a |
| FreeBSD:16:latest | - | 0.9.1_3 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 1
gmake: devel/gmake
Library 1
libisal.so: devel/isa-l
The full lists below include those, and their dependencies in turn.
Build dependencies 50
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- audio/alsa-lib
- devel/cmake-core
- devel/gettext-runtime
- devel/gmake
- devel/isa-l
- devel/jsoncpp
- devel/libunistring
- devel/libuv
- dns/libidn2
- graphics/giflib
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/png
- graphics/tiff
- java/javavmwrapper
- java/openjdk11
- ports-mgmt/pkg
- print/freetype2
- print/indexinfo
- security/rhash
- textproc/expat2
- x11-fonts/dejavu
- x11-fonts/encodings
- x11-fonts/font-bh-ttf
- x11-fonts/font-misc-ethiopic
- x11-fonts/font-misc-meltho
- x11-fonts/fontconfig
- x11-fonts/libfontenc
- x11-fonts/mkfontscale
- x11-fonts/xorg-fonts-truetype
- x11-toolkits/libXt
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXfixes
- x11/libXi
- x11/libXrandr
- x11/libXrender
- x11/libXtst
- x11/libxcb
- x11/xorgproto
Run dependencies 42
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- audio/alsa-lib
- devel/gettext-runtime
- devel/isa-l
- graphics/giflib
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/png
- graphics/tiff
- java/javavmwrapper
- java/openjdk11
- print/freetype2
- print/indexinfo
- textproc/expat2
- x11-fonts/dejavu
- x11-fonts/encodings
- x11-fonts/font-bh-ttf
- x11-fonts/font-misc-ethiopic
- x11-fonts/font-misc-meltho
- x11-fonts/fontconfig
- x11-fonts/libfontenc
- x11-fonts/mkfontscale
- x11-fonts/xorg-fonts-truetype
- x11-toolkits/libXt
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXfixes
- x11/libXi
- x11/libXrandr
- x11/libXrender
- x11/libXtst
- x11/libxcb
- x11/xorgproto
Required by 1
Configuration
No options to configure.
- USES
- cmake:noninja java localbase:ldflags
- Service scripts
- none
Files
pkg-plist 6
- lib/libgkl_compression.so
- lib/libgkl_pairhmm.so
- lib/libgkl_pairhmm_omp.so
- lib/libgkl_pdhmm.so
- lib/libgkl_smithwaterman.so
- lib/libgkl_utils.so
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| Intel-HLS-GKL-0.9.1_GH0.tar.gz | 5.363673e+06 | 8e32bc3c63013ca6468c65fbbb6af80a433652b640be868d0cb82cb70a919799 |