Port details |
- gemma Genome-wide Efficient Mixed Model Association
- 0.98.5_1 biology =2 0.98.5Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-05-17 14:45:38
- Last Update: 2025-01-28 16:42:55
- Commit Hash: e54e2c6
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://xiangzhou.github.io/software/
- https://github.com/genetics-statistics/GEMMA/
- Description:
- 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.
- ¦ ¦ ¦ ¦
- 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/gemma/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/gemma
- pkg install gemma
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: gemma
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1732864105
SHA256 (genetics-statistics-GEMMA-v0.98.5_GH0.tar.gz) = 3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677
SIZE (genetics-statistics-GEMMA-v0.98.5_GH0.tar.gz) = 51259250
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:
-
- eigen3.pc : math/eigen3
- gmake>=4.4.1 : devel/gmake
- Library dependencies:
-
- libgsl.so : math/gsl
- libopenblas.so : math/openblas
- There are no ports dependent upon this port
Configuration Options:
- ===> The following configuration options are available for gemma-0.98.5_1:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
- Options name:
- biology_gemma
- USES:
- blaslapack:openblas compiler:c++11-lang eigen:3 gmake localbase:ldflags
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
0.98.5_1 28 Jan 2025 16:42:55 |
Thierry Thomas (thierry) |
*/*: 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 |
0.98.5 06 Dec 2024 14:36:36 |
Jason W. Bacon (jwb) |
biology/gemma: Update to 0.98.5
Several bug fixes and enhancements since 0.98.3
Changes: https://github.com/genetics-statistics/GEMMA/releases
PR: 283036
Reported by: alster@vinterdalen.se |
0.98.3_5 21 Jun 2024 17:49:24 |
Thierry Thomas (thierry) |
*/*: bump PORTREVISION after the upgrade to OpenBLAS |
0.98.3_4 12 Dec 2023 19:03:50 |
Thierry Thomas (thierry) |
*/*: bump PORTREVISION after the upgrade of OpenBLAS
PR: 273219 |
0.98.3_3 23 Apr 2023 09:09:58 |
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
07 Sep 2022 21:58:51 |
Stefan Eßer (se) |
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) |
0.98.3_2 07 Sep 2022 21:10:59 |
Stefan Eßer (se) |
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 ) |
0.98.3_2 12 Jan 2022 19:41:22 |
Tobias C. Berner (tcberner) |
math/gsl: bump portrevision of consumers after update to 2.7.1
PR: 260201 |
0.98.3_1 16 Jun 2021 19:31:27 |
Tobias C. Berner (tcberner) |
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 ) |
0.98.3 07 Apr 2021 08:09:01 |
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.98.3 06 Apr 2021 14:31:07 |
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.98.3 02 Jan 2021 22:05:58 |
jwb |
biology/gemma: Upgrade to 0.98.3
Minor bug fixes and enhancements
Reported by: portscout |
0.98.1_6 12 Dec 2020 17:04:37 |
thierry |
- 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 |
0.98.1_5 06 May 2020 16:39:12 |
yuri |
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas
because after the recent math/openblas update the library name changed in
openblas |
0.98.1_4 30 Jan 2020 14:17:44 |
swills |
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 |
0.98.1_3 21 Jan 2020 22:03:19 |
swills |
math/openblas: Update to 0.3.7
While here, improve formatting and fix build of dependant ports.
PR: 231371
Submitted by: yuri (initial version), pkubaj (ppc fixes)
Approved by: Eijiro Shibusawa <phd_kimberlite@yahoo.co.jp> (maintainer) |
0.98.1_3 14 Jan 2020 22:35:36 |
jwb |
biology/gemma: Unbreak build
Conflict between cblas.h and gsl_cblas.h |
0.98.1_2 25 Oct 2019 23:41:34 |
tcberner |
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 |
0.98.1_1 26 Jul 2019 20:46:57 |
gerald |
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 |
0.98.1 18 May 2019 22:41:16 |
jwb |
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC
Reported by: danfe, Gerald Pfeifer |
0.98.1 17 May 2019 14:45:20 |
jwb |
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. |