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Two new features

Two new features were added on 2020-05-30:
  1. Repology links - each port now has a link to repology.org. See issue 148 for details.
  2. Ports I maintain report - port maintainers can now subscribe to a daily report of commits to the ports they maintain. See Watch ports I maintain at Report Subscriptions. Details at issue 138
Port details
bolt-lmm Mixed model association testing and variance component analysis
2.3.4_4 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. 2.3.4_4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-26 03:37:05
Last Update: 2020-05-06 17:11:15
SVN Revision: 534185
License: GPLv3
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (9 items)
  1. /usr/local/share/licenses/bolt-lmm-2.3.4_4/catalog.mk
  2. /usr/local/share/licenses/bolt-lmm-2.3.4_4/LICENSE
  3. /usr/local/share/licenses/bolt-lmm-2.3.4_4/GPLv3
  4. bin/bolt
  5. share/bolt-lmm/tables/LDSCORE.1000G_EUR.tab.gz
  6. share/bolt-lmm/tables/genetic_map_hg17_withX.txt.gz
  7. share/bolt-lmm/tables/genetic_map_hg18_withX.txt.gz
  8. share/bolt-lmm/tables/genetic_map_hg19_withX.txt.gz
  9. share/bolt-lmm/tables/genetic_map_hg38_withX.txt.gz
Collapse this list.
Dependency lines:
  • bolt-lmm>0:biology/bolt-lmm
To install the port: cd /usr/ports/biology/bolt-lmm/ && make install clean
To add the package: pkg install bolt-lmm
PKGNAME: bolt-lmm
Flavors: there is no flavor information for this port.
distinfo:
Packages: (move your mouse over the cells for more information)
bolt-lmm
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642.3.4_42.3.4_4
FreeBSD:11:armv6--
FreeBSD:11:i3862.3.4_42.3.4_4
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd642.3.4_42.3.4_4
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3862.3.4_42.3.4_4
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-2.3.4_4
FreeBSD:13:aarch64--
FreeBSD:13:amd642.3.4_4-
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3862.3.4_4-
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc642.3.4_4-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. gcc9 : lang/gcc9
  3. as : devel/binutils
Runtime dependencies:
  1. gcc9 : lang/gcc9
Library dependencies:
  1. libnlopt.so : math/nlopt
  2. libopenblas.so : math/openblas
  3. libboost_program_options.so : devel/boost-libs
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/

Number of commits found: 8

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
06 May 2020 16:11:15
Original commit files touched by this commit  2.3.4_4
Revision:534185
yuri search for other commits by this committer
Bump 46 ports depending on math/openblas because the 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  2.3.4_3
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
11 Dec 2019 17:53:49
Original commit files touched by this commit  2.3.4_2
Revision:519824
jbeich search for other commits by this committer
devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
19 Aug 2019 15:35:28
Original commit files touched by this commit  2.3.4_1
Revision:509290
jbeich search for other commits by this committer
devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
13 Aug 2019 15:30:22
Original commit files touched by this commit  2.3.4
Revision:508832
jwb search for other commits by this committer
biology/bolt-lmm: Upgrade to 2.3.4

Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream
04 Aug 2019 23:48:22
Original commit files touched by this commit  2.3.2_2
Revision:508135
jwb search for other commits by this committer
PR:             239613
Submitted by:   pkubaj
26 Jul 2019 20:46:57
Original commit files touched by this commit  2.3.2_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
26 May 2019 03:36:49
Original commit files touched by this commit  2.3.2
Revision:502673
jwb search for other commits by this committer
biology/bolt-lmm: Mixed model association testing and variance component
analysis

The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).

Number of commits found: 8

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