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Port details on branch 2026Q3
stacks Software pipeline for building loci from short-read sequences
2.68 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 2.68Version 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: 2025-01-22 11:27:04
Commit Hash: 989b386
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.
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 (26 items)
Collapse this list.
  1. /usr/local/share/licenses/stacks-2.68/catalog.mk
  2. /usr/local/share/licenses/stacks-2.68/LICENSE
  3. /usr/local/share/licenses/stacks-2.68/GPLv2
  4. bin/clone_filter
  5. bin/cstacks
  6. bin/denovo_map.pl
  7. bin/gstacks
  8. bin/kmer_filter
  9. bin/phasedstacks
  10. bin/populations
  11. bin/process_radtags
  12. bin/process_shortreads
  13. bin/ref_map.pl
  14. bin/sstacks
  15. bin/stacks-count-reads-per-sample-per-locus
  16. bin/stacks-dist-extract
  17. bin/stacks-gdb
  18. bin/stacks-hist2d-loci-samples-coverage
  19. bin/stacks-integrate-alignments
  20. bin/stacks-private-alleles
  21. bin/stacks-samtools-tview
  22. bin/tsv2bam
  23. bin/ustacks
  24. @owner
  25. @group
  26. @mode
Collapse this list.
USE_RC_SUBR (Service Scripts)
  • no SUBR information found for this port
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:
TIMESTAMP = 1733920483 SHA256 (stacks-2.68.tar.gz) = 9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650 SIZE (stacks-2.68.tar.gz) = 15552836
Packages (timestamps in pop-ups are UTC):
stacks
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.682.682.4_22.682.68n/an/an/a
FreeBSD:13:quarterly2.682.682.4_22.682.68n/an/an/a
FreeBSD:14:latest2.682.682.4_22.682.682.4_2-2.4_2
FreeBSD:14:quarterly2.682.68-2.682.682.4_22.4_22.4_2
FreeBSD:15:latest2.682.68n/a2.68n/an/a2.4_22.4_2
FreeBSD:15:quarterly2.682.68n/a-n/an/a--
FreeBSD:16:latest2.682.68n/a-n/an/a--
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.4.1 : devel/gmake
  2. python3.11 : lang/python311
Test dependencies:
  1. python3.11 : lang/python311
Runtime dependencies:
  1. python3.11 : lang/python311
This port is required by:
for Run
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. https://catchenlab.life.illinois.edu/stacks/source/
Collapse this list.

There are no commits on branch 2026Q3 for this port
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