| Port details |
- freebayes Bayesian haplotype-based polymorphism discovery and genotyping
- 1.3.9 biology
 =2      1.3.6_2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-20 00:07:39
- Last Update: 2025-02-18 20:45:11
- Commit Hash: bac90e8
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: MIT
- WWW:
- https://github.com/ekg/freebayes
- Description:
- FreeBayes is a Bayesian genetic variant detector designed to find small
polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels
(insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex
events (composite insertion and substitution events) smaller than the length of
a short-read sequencing alignment.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- freebayes>0:biology/freebayes
- To install the port:
- cd /usr/ports/biology/freebayes/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/freebayes
- pkg install freebayes
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: freebayes
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1739833701
SHA256 (ekg-freebayes-v1.3.9_GH0.tar.gz) = 41ed3074c7648375286168a6708e02dac6788eaca4ca6039ff5a7ed91f257b53
SIZE (ekg-freebayes-v1.3.9_GH0.tar.gz) = 2896143
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:
-
- fastahack>=1.0.0 : biology/fastahack
- multichoose>=1.0.3.2 : math/multichoose
- simde>=0.8.2 : devel/simde
- vcflib>=1.0.12 : biology/vcflib
- intervaltree>=0.1.2 : devel/intervaltree
- smithwaterman>=g20160702 : biology/smithwaterman
- wfa2-lib>=2.3.5 : biology/wfa2-lib
- tabixpp>=1.1.2 : biology/tabixpp
- meson : devel/meson
- ninja : devel/ninja
- pkgconf>=1.3.0_1 : devel/pkgconf
- perl5>=5.36<5.37 : lang/perl5.36
- Library dependencies:
-
- libhts.so : biology/htslib
- This port is required by:
- for Run
-
- biology/biostar-tools
- biology/ddocent
Configuration Options:- No options to configure
- Options name:
- biology_freebayes
- USES:
- compiler:c++14-lang localbase meson perl5 pkgconfig
- 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 |
|---|
1.3.9
18 Feb 2025 20:45:11
 |
Jason W. Bacon (jwb) |
biology/freebayes: Update to 1.3.9
Upstream moved away from git submodules to external deps
Several fixes since 1.3.6
Changes: https://github.com/freebayes/freebayes/releases
Reported by: portscout |
1.3.6_2
22 Jan 2023 16:42:34
|
Jason W. Bacon (jwb) |
biology/freebayes: Drop redundant tabixpp dep
tabixpp is included as a git submodule |
1.3.6_1
06 Jan 2023 01:22:33
|
Jason W. Bacon (jwb) |
biology/freebayes: Bump PORTREVISION for biology/htslib update |
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) |
1.3.6
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  ) |
1.3.6
06 Feb 2022 20:23:45
|
Jason W. Bacon (jwb) |
biology/freebayes: Update to 1.3.6
Minor dependency updates, but mostly build system improvements
Changes: https://github.com/freebayes/freebayes/tags
Reported by: portscout |
1.3.5
17 Dec 2021 13:26:57
|
Piotr Kubaj (pkubaj) |
biology/freebayes: enable on riscv64 |
1.3.5
05 Nov 2021 01:14:22
|
Piotr Kubaj (pkubaj) |
biology/freebayes: builds fine on armv7 |
1.3.5
03 Nov 2021 20:49:05
|
Jason W. Bacon (jwb) |
biology/freebayes: Update to 1.3.5
Fixes build on powerpc64 and aarch64, possibly others.
Changes: https://github.com/freebayes/freebayes/tags
PR: 259627
Reported by: pkubaj |
1.2.0_3
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
1.2.0_3
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
1.2.0_3
02 Jan 2021 01:46:09
 |
linimon |
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
them BROKEN.
While here, pet portlint (Makevar order).
Approved by: portmgr (tier-2 blanket) |
1.2.0_3
21 Sep 2020 18:14:57
|
se |
Fix build with -fno-common |
1.2.0_2
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 |
1.2.0_1
12 Dec 2018 01:35:36
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
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, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590 |
1.2.0
18 Sep 2018 09:28:35
|
linimon |
Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-based
archs such as powerpc64.
Tested for no effect on amd64.
While here, pet portlint.
Approved by: portgmr (tier-2 blanket) |
1.2.0
21 Jun 2018 23:52:37
|
linimon |
Mark as broken on aarch64, and, where appropriate, armvX.
While here, pet portlint.
Approved by: portmgr (tier-2 blanket) |
1.2.0
20 Apr 2018 00:07:28
|
jwb |
biology/freebayes: Bayesian haplotype-based polymorphism discovery and
genotyping
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15116 |
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