notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Port details
stacks Software pipeline for building loci from short-read sequences
2.4_1 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 2.4Version 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: 2019-07-26 21:46:57
SVN Revision: 507372
Also Listed In: perl5 python
License: GPLv2
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (21 items)
  1. /usr/local/share/licenses/stacks-2.4_1/catalog.mk
  2. /usr/local/share/licenses/stacks-2.4_1/LICENSE
  3. /usr/local/share/licenses/stacks-2.4_1/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
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: pkg install stacks
PKGNAME: stacks
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. python3.6 : lang/python36
  3. gcc9 : lang/gcc9
  4. as : devel/binutils
Runtime dependencies:
  1. python3.6 : lang/python36
  2. gcc9 : lang/gcc9
This port is required by:
for Run
  1. biology/ddocent

Configuration Options

USES:

Master Sites:
  1. http://catchenlab.life.illinois.edu/stacks/source/

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 Jul 2019 20:46:57
Original commit files touched by this commit  2.4_1
Revision:507372
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  2.4
Revision:501200
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  2.4
Revision:501199
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  2.3
Revision:490062
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  1.48_3
Revision:487272
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  1.48_2
Revision:483245
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  1.48_2
Revision:478697
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  1.48_1
Revision:475857
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  1.48
Revision:472706
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  1.48
Revision:466048
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: 10

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
python37Oct 19
py-pillowOct 15
mod_perl2Oct 09
xpdfOct 06
xpdf3Oct 06
xpdf4Oct 06
unboundOct 03
cactiOct 02
gitlab-ceOct 02
gitlab-ceOct 02
ruby24Oct 02
ruby25Oct 02
mongodb34Sep 30
mongodb34Sep 30
mongodb36Sep 30

4 vulnerabilities affecting 12 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last updated:
2019-10-19 10:52:46


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 37705
Broken 75
Deprecated 102
Ignore 340
Forbidden 3
Restricted 156
No CDROM 73
Vulnerable 26
Expired 15
Set to expire 73
Interactive 0
new 24 hours 3
new 48 hours6
new 7 days12
new fortnight40
new month141

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2019 Dan Langille. All rights reserved.