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NOTE: There is a known problem on production with searching pkg-plist - it returns no results. This problem is not present on stage.freshports.org
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 Version 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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: perl5 python
License: GPLv2
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
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
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:

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:armv6pkg-fallout2.4_1
FreeBSD:11:i3862.4_22.4_2
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
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:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-fallout2.4_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:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc642.4_12.4_2
FreeBSD:13:riscv64pkg-fallout2.4_2
FreeBSD:14:aarch642.4_2pkg-fallout
FreeBSD:14:amd642.4_2pkg-fallout
FreeBSD:14:armv62.4_2pkg-fallout
FreeBSD:14:armv72.4_2pkg-fallout
FreeBSD:14:i3862.4_2pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc642.4_2pkg-fallout
FreeBSD:14:riscv642.4_2pkg-fallout
 

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. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
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: 15

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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)
2.4_2
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)
2.4_2
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
2.4_2
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.
2.4_2
11 Jan 2021 17:27:30
Revision:561234Original commit files touched by this commit
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
2.4_1
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
2.4
10 May 2019 21:15:42
Revision:501200Original commit files touched by this commit
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
2.4
10 May 2019 21:04:43
Revision:501199Original commit files touched by this commit
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
2.3
12 Jan 2019 15:53:01
Revision:490062Original commit files touched by this commit
jwb search for other commits by this committer
biology/stacks: Upgrade to 2.3

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

PR:		231448
Submitted by:	Piotr Kubaj
Approved by:	maintainer
1.48_2
01 Sep 2018 14:14:12
Revision:478697Original commit files touched by this commit
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
1.48_1
29 Jul 2018 22:18:46
Revision:475857Original 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
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
Revision:472706Original commit files touched by this commit
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)
1.48
31 Mar 2018 13:16:05
Revision:466048Original commit files touched by this commit
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: 15