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Port details
stacks Software pipeline for building loci from short-read sequences
2.4_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 2.4_2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-03-31 13:16:34
Last Update: 2021-04-07 08:09:01
Commit Hash: cf118cc
Also Listed In: perl5 python
License: GPLv2
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (24 items)
Collapse this list.
  1. /usr/local/share/licenses/stacks-2.4_2/catalog.mk
  2. /usr/local/share/licenses/stacks-2.4_2/LICENSE
  3. /usr/local/share/licenses/stacks-2.4_2/GPLv2
  4. bin/clone_filter
  5. bin/count_fixed_catalog_snps.py
  6. bin/cstacks
  7. bin/denovo_map.pl
  8. bin/gstacks
  9. bin/integrate_alignments.py
  10. bin/kmer_filter
  11. bin/phasedstacks
  12. bin/populations
  13. bin/process_radtags
  14. bin/process_shortreads
  15. bin/ref_map.pl
  16. bin/sstacks
  17. bin/stacks-dist-extract
  18. bin/stacks-gdb
  19. bin/stacks-integrate-alignments
  20. bin/tsv2bam
  21. bin/ustacks
  22. @owner
  23. @group
  24. @mode
Collapse this list.
Dependency lines:
  • stacks>0:biology/stacks
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
PKGNAME: stacks
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
stacks
ABIlatestquarterly
FreeBSD:11:aarch641.48_22.4_1
FreeBSD:11:amd642.4_22.4_2
FreeBSD:11:armv6-2.4_1
FreeBSD:11:i3862.4_22.4_2
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch641.48_22.4_2
FreeBSD:12:amd642.4_22.4_2
FreeBSD:12:armv61.48_22.4_1
FreeBSD:12:armv71.48_22.4_1
FreeBSD:12:i3862.4_22.4_2
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-2.4_2
FreeBSD:13:aarch642.4_22.4_2
FreeBSD:13:amd642.4_22.4_2
FreeBSD:13:armv62.4_22.4_2
FreeBSD:13:armv72.4_22.4_2
FreeBSD:13:i3862.4_22.4_2
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc642.4_12.4_2
FreeBSD:14:aarch642.4_2-
FreeBSD:14:amd642.4_2-
FreeBSD:14:armv62.4_2-
FreeBSD:14:armv72.4_2-
FreeBSD:14:i3862.4_2-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc642.4_2-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. python3.8 : lang/python38
Runtime dependencies:
  1. python3.8 : lang/python38
This port is required by:
for Run
  1. biology/ddocent

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://catchenlab.life.illinois.edu/stacks/source/
Collapse this list.

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.4_2
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.4_2
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
11 Jan 2021 17:27:30
Original commit files touched by this commit Revision:561234  2.4_2
jwb search for other commits by this committer
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
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  2.4_1
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
10 May 2019 21:15:42
Original commit files touched by this commit Revision:501200  2.4
jwb search for other commits by this committer
biology/stacks: Remove obsolete pkg-message regarding web interface

PHP code no longer included in dist as of v2.4
10 May 2019 21:04:43
Original commit files touched by this commit Revision:501199  2.4
jwb search for other commits by this committer
biology/stacks: Upgrade to 2.4

Improve check to avoid outdated GCC on 2nd tier platforms

Reported by:    portscout
12 Jan 2019 15:53:01
Original commit files touched by this commit Revision:490062  2.3
jwb search for other commits by this committer
biology/stacks: Upgrade to 2.3

Approved by:    jrm (mentor, implicit)
12 Dec 2018 01:35:36
Original commit files touched by this commit Revision:487272  1.48_3
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
28 Oct 2018 08:58:00
Original commit files touched by this commit Revision:483245  1.48_2
linimon search for other commits by this committer
Fix build with tier-2 arches.

PR:		231448
Submitted by:	Piotr Kubaj
Approved by:	maintainer
01 Sep 2018 14:14:12
Original commit files touched by this commit Revision:478697  1.48_2
jwb search for other commits by this committer
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
29 Jul 2018 22:18:46
Original commit files touched by this commit Revision:475857  1.48_1
gerald search for other commits by this committer
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
18 Jun 2018 19:03:04
Original commit files touched by this commit Revision:472706  1.48
linimon search for other commits by this committer
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)
31 Mar 2018 13:16:05
Original commit files touched by this commit Revision:466048  1.48
jwb search for other commits by this committer
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

Number of commits found: 13