| Port details |
- stacks Software pipeline for building loci from short-read sequences
- 2.68 biology
 =2      2.4_2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2018-03-31 13:16:34
- Last Update: 2025-01-22 11:27:04
- Commit Hash: 989b386
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: perl5 python
- License: GPLv2
- WWW:
- https://catchenlab.life.illinois.edu/stacks/
- Description:
- Stacks is a software pipeline for building loci from short-read sequences, such
as those generated on the Illumina platform. Stacks was developed to work with
restriction enzyme-based data, such as RAD-seq, for the purpose of building
genetic maps and conducting population genomics and phylogeography.
  ¦  ¦  ¦  ¦ 
- 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/stacks/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/stacks
- pkg install stacks
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: stacks
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1733920483
SHA256 (stacks-2.68.tar.gz) = 9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650
SIZE (stacks-2.68.tar.gz) = 15552836
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:
-
- gmake>=4.4.1 : devel/gmake
- python3.11 : lang/python311
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- python3.11 : lang/python311
- This port is required by:
- for Run
-
- biology/ddocent
Configuration Options:- No options to configure
- Options name:
- biology_stacks
- USES:
- gmake python shebangfix compiler:c++11-lang
- 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 |
|---|
2.68
22 Jan 2025 11:27:04
 |
Piotr Kubaj (pkubaj) |
biology/stacks: fix build without libomp
src/process_radtags.cc:1578:6: error: unknown type name 'omp_lock_t'
1578 | omp_lock_t &thread_outbuf_lock =
outbuf_lock[thread_index];
| ^
25 warnings and 10 errors generated. |
2.68
17 Jan 2025 22:38:18
|
Jason W. Bacon (jwb) |
biology/stacks: Update to 2.68
Numerous fixes and improvements since 2.4
Changes: http://catchenlab.life.illinois.edu/stacks/changelog.php
PR: 283257
Reported by: alster@vinterdalen.se |
2.4_2
28 May 2024 21:17:25
|
Jason W. Bacon (jwb) |
biology/stacks: Unbreak build on aarch64
ARM clang is intolerant of implicit demotions in initializers
Reported by: pkg-fallout |
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) |
2.4_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  ) |
2.4_2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.4_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.4_2
11 Jan 2021 17:27:30
 |
jwb |
biology/stacks: Drop dependency on gcc
Replace compiler:openmp with compiler:c++11-lang and localbase
Set USE_GCC for i386 to work around limitations in clang atomic (PR 230888)
PR: port/247753, ports/252379 |
2.4_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 |
2.4
10 May 2019 21:15:42
|
jwb |
biology/stacks: Remove obsolete pkg-message regarding web interface
PHP code no longer included in dist as of v2.4 |
2.4
10 May 2019 21:04:43
|
jwb |
biology/stacks: Upgrade to 2.4
Improve check to avoid outdated GCC on 2nd tier platforms
Reported by: portscout |
2.3
12 Jan 2019 15:53:01
|
jwb |
biology/stacks: Upgrade to 2.3
Approved by: jrm (mentor, implicit) |
1.48_3
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 |
1.48_2
28 Oct 2018 08:58:00
|
linimon |
Fix build with tier-2 arches.
PR: 231448
Submitted by: Piotr Kubaj
Approved by: maintainer |
1.48_2
01 Sep 2018 14:14:12
|
jwb |
biology/stacks: Enable OpenMP (oversight in previous commit)
Upgrade to latest release will follow, after testing
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D16973 |
1.48_1
29 Jul 2018 22:18:46
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.
This includes ports
- featuring USE_GCC=yes or USE_GCC=any,
- featuring USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and those
- with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.
PR: 222542 |
1.48
18 Jun 2018 19:03:04
|
linimon |
Adjust USES to fix builds on gcc-based architectures.
While here, pet portlint.
Tested for no regression on amd64.
Approved by: portmgr (tier-2 blanket) |
1.48
31 Mar 2018 13:16:05
|
jwb |
biology/stacks: Software pipeline for building loci from short-read sequences
Reviewed by: mat
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D14885 |
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