GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
and related models to genome-wide association studies (GWAS) and other
large-scale data sets.
Key features:
1. Fast assocation tests implemented using the univariate linear mixed model
(LMM). In GWAS, this can correct for population structure and sample
non-exchangeability. It also provides estimates of the proportion of
variance in phenotypes explained by available genotypes (PVE), often called
"chip heritability" or "SNP heritability".
2. Fast association tests for multiple phenotypes implemented using a
multivariate linear mixed model (mvLMM). In GWAS, this can correct for
population structure and sample (non)exchangeability - jointly in multiple
complex phenotypes.
3. Bayesian sparse linear mixed model (BSLMM) for estimating PVE, phenotype
prediction, and multi-marker modeling in GWAS.
4. Estimation of variance components ("chip/SNP heritability") partitioned by
different SNP functional categories from raw (individual-level) data or
summary data. For raw data, HE regression or the REML AI algorithm can be
used to estimate variance components when individual-level data are
available. For summary data, GEMMA uses the MQS algorithm to estimate
variance components.
===> The following configuration options are available for gemma-0.98.5_3:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream.
*/*: bump PORTREVISION after OpenBLAS upgrade
Remark: this souldn’t be necessary, because the version of the library is the
same, but due to many changes between these releases, it is safer this way.
PR: 284314
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above )
math/gsl: update to 2.7
From [1]
* What is new in gsl-2.7:
* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
* fixed bug #60335 (spmatrix test failure, J. Lamb)
* fixed bug #36577
* clarified documentation on interpolation accelerators (V. Krishnan)
* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M.
Sitte)
* fixed doc bug #59758
* fixed bug #58202 (rstat median for n=5)
* added support for native C complex number types in gsl_complex
when using a C11 compiler
* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6
(Only the first 15 lines of the commit message are shown above )
- Upgrade math/eigen3 to 3.3.8;
- Add some dependencies which might be detected by Find_Package but not
registered;
- Bump PORTREVISION of consumers.
PR: 250833
Submitted by: /me
Approved by: tcberner@ (KDE / maintainer) + exp-run
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas
because after the recent math/openblas update the library name changed in
openblas
Fix math/openblas and bump dependent ports
* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]
This is correcting issues from r523749 [1][2][4] and r515970 [3]
PR: 231371
Reported by: build cluster [1]
Reported by: Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by: many [5]
Reviewed by: mat, bapt
Approved by: implicit, since this is a build fix
math/gsl: update to 2.6
- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
- this also breaks the two consumers of this port
- biology/gemma: has a conflict with cblas, and is makred broken.
PR: 241363
Exp-run by: antoine
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330
biology/gemma: Genome-wide Efficient Mixed Model Association
GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
and related models to genome-wide association studies (GWAS) and other
large-scale data sets.
