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Port details
freebayes Bayesian haplotype-based polymorphism discovery and genotyping
1.3.6_2 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. pkg-fallout 1.3.6_2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-20 00:07:39
Last Update: 2023-01-22 16:42:34
Commit Hash: b0cafd4
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/bamleftalign
  2. bin/freebayes
  3. /usr/local/share/licenses/freebayes-1.3.6_2/catalog.mk
  4. /usr/local/share/licenses/freebayes-1.3.6_2/LICENSE
  5. /usr/local/share/licenses/freebayes-1.3.6_2/MIT
Collapse this list.
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 = 1644155282 SHA256 (ekg-freebayes-v1.3.6_GH0.tar.gz) = d668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044 SIZE (ekg-freebayes-v1.3.6_GH0.tar.gz) = 2898209

Expand this list (26 items)

Collapse this list.

SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1 SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488 SHA256 (ekg-vcflib-d4073c3_GH0.tar.gz) = 27ed96714eeaa871b8036bcb308db5256b8266cadd2689fbd1dbf3771611b879 SIZE (ekg-vcflib-d4073c3_GH0.tar.gz) = 19215364 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070 SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053 SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686 SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815 SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223 SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295 SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297 SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558 SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160 SHA256 (ekg-tabixpp-b255df1_GH0.tar.gz) = 96d9aa41f55f74498e267b582e93e986605913fbd830dca6bf4cac5d9f927bb9 SIZE (ekg-tabixpp-b255df1_GH0.tar.gz) = 3739 SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63 SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996 SHA256 (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 19b5c27402d955909fcbf601ed02bcd7d9f2aa841e2158ecd93b9ff8f7ec1d98 SIZE (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 6609 SHA256 (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5e658965f7c8730d7f29642ebb40b0e0beb701f992e391a1273af3b132ff66b8 SIZE (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5826

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Packages (timestamps in pop-ups are UTC):
freebayes
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.3.6_21.3.6_2-1.3.6_21.3.6_2---
FreeBSD:13:quarterly1.3.6_21.3.6_21.3.6_21.3.6_21.3.6_21.3.6_21.3.6_21.3.6_2
FreeBSD:14:latest1.3.6_21.3.6_21.3.6_11.3.6_21.3.6_21.3.6_2-1.3.6_2
FreeBSD:14:quarterly1.3.6_21.3.6_2-1.3.6_21.3.6_21.3.6_21.3.6_21.3.6_2
FreeBSD:15:latest1.3.6_21.3.6_2n/a1.3.6_2n/a1.3.6_21.3.6_21.3.6_2
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. meson>=0.57.1_1 : devel/meson
  2. ninja : devel/ninja
  3. pkgconf>=1.3.0_1 : devel/pkgconf
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
Library dependencies:
  1. libhts.so : biology/htslib
This port is required by:
for Run
  1. biology/biostar-tools
  2. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ekg/freebayes/tar.gz/v1.3.6?dummy=/
Collapse this list.

Number of commits found: 17

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.3.6_2
22 Jan 2023 16:42:34
commit hash: b0cafd4b1d5be5c256717eae0062ca28a50d5f79commit hash: b0cafd4b1d5be5c256717eae0062ca28a50d5f79commit hash: b0cafd4b1d5be5c256717eae0062ca28a50d5f79commit hash: b0cafd4b1d5be5c256717eae0062ca28a50d5f79 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/freebayes: Drop redundant tabixpp dep

tabixpp is included as a git submodule
1.3.6_1
06 Jan 2023 01:22:33
commit hash: fea5f773c7b493dda2861fffa734fcf8e0612145commit hash: fea5f773c7b493dda2861fffa734fcf8e0612145commit hash: fea5f773c7b493dda2861fffa734fcf8e0612145commit hash: fea5f773c7b493dda2861fffa734fcf8e0612145 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/freebayes: Bump PORTREVISION for biology/htslib update
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
1.3.6
06 Feb 2022 20:23:45
commit hash: 09167ae22b6631ec9a9d52fb66c3b177976d4c2ccommit hash: 09167ae22b6631ec9a9d52fb66c3b177976d4c2ccommit hash: 09167ae22b6631ec9a9d52fb66c3b177976d4c2ccommit hash: 09167ae22b6631ec9a9d52fb66c3b177976d4c2c files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: b473e2091d12c0a210f4ad91580bb2b5ed779700commit hash: b473e2091d12c0a210f4ad91580bb2b5ed779700commit hash: b473e2091d12c0a210f4ad91580bb2b5ed779700commit hash: b473e2091d12c0a210f4ad91580bb2b5ed779700 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/freebayes: enable on riscv64
1.3.5
05 Nov 2021 01:14:22
commit hash: 0e5026aa1ecfd8af00d8e881b3f3d0b013afb8e6commit hash: 0e5026aa1ecfd8af00d8e881b3f3d0b013afb8e6commit hash: 0e5026aa1ecfd8af00d8e881b3f3d0b013afb8e6commit hash: 0e5026aa1ecfd8af00d8e881b3f3d0b013afb8e6 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/freebayes: builds fine on armv7
1.3.5
03 Nov 2021 20:49:05
commit hash: dc64b13129b889531be2dae60218484f9444cf92commit hash: dc64b13129b889531be2dae60218484f9444cf92commit hash: dc64b13129b889531be2dae60218484f9444cf92commit hash: dc64b13129b889531be2dae60218484f9444cf92 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
1.2.0_3
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.2.0_3
02 Jan 2021 01:46:09
Revision:559904Original commit files touched by this commit
linimon search for other commits by this committer
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
Revision:549476Original commit files touched by this commit
se search for other commits by this committer
Fix build with -fno-common
1.2.0_2
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
1.2.0_1
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
gerald search for other commits by this committer
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
Revision:480003Original commit files touched by this commit
linimon search for other commits by this committer
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
Revision:473009Original commit files touched by this commit
linimon search for other commits by this committer
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
Revision:467806Original commit files touched by this commit
jwb search for other commits by this committer
biology/freebayes: Bayesian haplotype-based polymorphism discovery and
genotyping

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15116

Number of commits found: 17