./biology/plink, Whole-genome association analysis toolset

[ CVSweb ] [ Homepage ] [ RSS ] [ Required by ] [ Add to tracker ]

Branch: CURRENT, Version: 1.07nb1, Package name: plink-1.07nb1, Maintainer: bacon

PLINK is a free, open-source whole genome association analysis
toolset, designed to perform a range of basic, large-scale
analyses in a computationally efficient manner.

The focus of PLINK is purely on analysis of genotype/phenotype
data, so there is no support for steps prior to this (e.g. study
design and planning, generating genotype or CNV calls from raw
data). Through integration with gPLINK and Haploview, there is
some support for the subsequent visualization, annotation and
storage of results.


Required to run:
[lang/g95] [math/lapack] [math/blas] [devel/libf2c]

Required to build:
[pkgtools/cwrappers]

Master sites:

Filesize: 2204.392 KB

Version history: (Expand)

CVS history: (Expand)


   2023-12-24 17:26:42 by Jason Bacon | Files touched by this commit (1) 
Log message:
biology/plink: Unbreak build on Darwin

Remove -lcrypt from link:
macOS does not have libcrypt, but has crypt() in libc
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Remove SHA1 hashes for distfiles
   2020-10-12 23:52:05 by Jason Bacon | Files touched by this commit (87) 
Log message:
math/blas, math/lapack: Install interchangeable BLAS system

Install the new interchangeable BLAS system created by Thomas Orgis,
currently supporting Netlib BLAS/LAPACK, OpenBLAS, cblas, lapacke, and
Apple's Accelerate.framework.  This system allows the user to select any
BLAS implementation without modifying packages or using package options, by
setting PKGSRC_BLAS_TYPES in mk.conf. See mk/blas.buildlink3.mk for details.

This commit should not alter behavior of existing packages as the system
defaults to Netlib BLAS/LAPACK, which until now has been the only supported
implementation.

Details:

Add new mk/blas.buildlink3.mk for inclusion in dependent packages
Install compatible Netlib math/blas and math/lapack packages
Update math/blas and math/lapack MAINTAINER approved by adam@
OpenBLAS, cblas, and lapacke will follow in separate commits
Update direct dependents to use mk/blas.buildlink3.mk
Perform recursive revbump
   2019-01-13 23:06:42 by Jason Bacon | Files touched by this commit (6) 
Log message:
Multiple packages: Replace obsolete maintainer email

jwbacon@tds.net ==> bacon@NetBSD.org
   2018-01-01 02:18:03 by Roland Illig | Files touched by this commit (1) 
Log message:
Cleanup: replace curly braces with parentheses.
   2017-09-03 10:37:04 by Thomas Klausner | Files touched by this commit (182) 
Log message:
Comment out dead MASTER_SITES/HOMEPAGEs.
   2016-02-25 12:21:12 by Jonathan Perkin | Files touched by this commit (1) 
Log message:
Use OPSYSVARS.