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Port details
gemma Genome-wide Efficient Mixed Model Association
0.98.1_5 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. 0.98.1_4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-17 14:45:38
Last Update: 2020-05-06 17:39:12
SVN Revision: 534190
License: GPLv3
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (23 items)
  1. /usr/local/share/licenses/gemma-0.98.1_5/catalog.mk
  2. /usr/local/share/licenses/gemma-0.98.1_5/LICENSE
  3. /usr/local/share/licenses/gemma-0.98.1_5/GPLv3
  4. bin/gemma
  5. share/examples/gemma/BXD_covariates.txt
  6. share/examples/gemma/BXD_covariates2.txt
  7. share/examples/gemma/BXD_geno.txt.gz
  8. share/examples/gemma/BXD_pheno.txt
  9. share/examples/gemma/BXD_snps.txt
  10. share/examples/gemma/HLC.bed
  11. share/examples/gemma/HLC.bim
  12. share/examples/gemma/HLC.fam
  13. share/examples/gemma/HLC.simu.pheno.txt
  14. share/examples/gemma/HLC_covariates.txt
  15. share/examples/gemma/demo.txt
  16. share/examples/gemma/mouse_hs1940.anno.txt
  17. share/examples/gemma/mouse_hs1940.bed
  18. share/examples/gemma/mouse_hs1940.bim
  19. share/examples/gemma/mouse_hs1940.fam
  20. share/examples/gemma/mouse_hs1940.geno.txt.gz
  21. share/examples/gemma/mouse_hs1940.pheno.txt
  22. share/examples/gemma/mouse_hs1940_snps.txt
  23. share/examples/gemma/mouse_hs1940_snps_anno.txt
Collapse this list.
Dependency lines:
  • gemma>0:biology/gemma
To install the port: cd /usr/ports/biology/gemma/ && make install clean
To add the package: pkg install gemma
PKGNAME: gemma
Flavors: there is no flavor information for this port.
distinfo:
Packages:
gemma
ABIlatestquarterly
FreeBSD:11:aarch64-0.98.1_4
FreeBSD:11:amd640.98.1_50.98.1_5
FreeBSD:11:armv6--
FreeBSD:11:i3860.98.1_50.98.1_5
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-0.98.1_4
FreeBSD:12:amd640.98.1_50.98.1_5
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.98.1_50.98.1_5
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-0.98.1_5
FreeBSD:13:aarch640.98.1_5-
FreeBSD:13:amd640.98.1_5-
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3860.98.1_5-
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc640.98.1_5-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. eigen3.pc : math/eigen3
  2. gmake : devel/gmake
Library dependencies:
  1. libgsl.so : math/gsl
  2. libopenblas.so : math/openblas
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/genetics-statistics/GEMMA/tar.gz/0.98.1?dummy=/

Number of commits found: 8

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
06 May 2020 16:39:12
Original commit files touched by this commit  0.98.1_5
Revision:534190
yuri search for other commits by this committer
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas
because after the recent math/openblas update the library name changed in
openblas
30 Jan 2020 14:17:44
Original commit files touched by this commit  0.98.1_4
Revision:524642
swills search for other commits by this committer
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
21 Jan 2020 22:03:19
Original commit files touched by this commit  0.98.1_3
Revision:523749
swills search for other commits by this committer
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)
14 Jan 2020 22:35:36
Original commit files touched by this commit  0.98.1_3
Revision:523074
jwb search for other commits by this committer
biology/gemma: Unbreak build

Conflict between cblas.h and gsl_cblas.h
25 Oct 2019 23:41:34
Original commit files touched by this commit  0.98.1_2
Revision:515671
tcberner search for other commits by this committer
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
26 Jul 2019 20:46:57
Original commit files touched by this commit  0.98.1_1
Revision:507372
gerald search for other commits by this committer
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
18 May 2019 22:41:16
Original commit files touched by this commit  0.98.1
Revision:501990
jwb search for other commits by this committer
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC

Reported by:    danfe, Gerald Pfeifer
17 May 2019 14:45:20
Original commit files touched by this commit  0.98.1
Revision:501873
jwb search for other commits by this committer
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.

Number of commits found: 8

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