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Port details
vsearch Versatile open-source tool for metagenomics
2.21.1 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 View this port on Repology. pkg-fallout 2.17.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-09 21:29:03
Last Update: 2022-01-23 22:32:43
Commit Hash: f67392e
License: GPLv3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/vsearch
  2. man/man1/vsearch.1.gz
  3. /usr/local/share/licenses/vsearch-2.21.1/catalog.mk
  4. /usr/local/share/licenses/vsearch-2.21.1/LICENSE
  5. /usr/local/share/licenses/vsearch-2.21.1/GPLv3
Collapse this list.
Dependency lines:
  • vsearch>0:biology/vsearch
To install the port:
cd /usr/ports/biology/vsearch/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/vsearch
  • pkg install vsearch
PKGNAME: vsearch
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 powerpc64le
distinfo:
Packages (timestamps in pop-ups are UTC):
vsearch
ABIlatestquarterly
FreeBSD:11:aarch64-2.15.0
FreeBSD:11:amd642.17.12.17.1
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-2.21.1
FreeBSD:12:amd642.21.12.21.1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch642.21.12.21.1
FreeBSD:13:amd642.21.12.21.1
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch642.21.1-
FreeBSD:14:amd642.21.1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. ghostscript9-agpl-base>=9.16_2 : print/ghostscript9-agpl-base
  2. gmake>=4.3 : devel/gmake
  3. autoconf>=2.69 : devel/autoconf
  4. automake>=1.16.1 : devel/automake
Library dependencies:
  1. libsysinfo.so : devel/libsysinfo
There are no ports dependent upon this port

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. https://codeload.github.com/torognes/vsearch/tar.gz/v2.21.1?dummy=/
Collapse this list.

Number of commits found: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 Jan 2022 22:32:43
 files touched by this commit commit hash:f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0  2.21.1
Jason W. Bacon (jwb) search for other commits by this committer
biology/vsearch: Update to 2.21.1

Adds the sample, qsegout and tsegout options. It also enables the use of
UDB databases with uchime_ref.

Changes:        https://github.com/torognes/vsearch/releases

Reported by:    portscout
08 Jan 2022 00:04:02
 files touched by this commit commit hash:231919fc1935355a5f7dc5466844c04cb51c6444  2.19.0
Jason W. Bacon (jwb) search for other commits by this committer
biology/vsearch: Update to 2.19.0

A few bug fixes, new subcommands and options

Changes:        https://github.com/torognes/vsearch/tags
Reporte by:     portscout
25 Oct 2021 12:58:29
 files touched by this commit commit hash:61b661339366b6ee95ca1de0667979da9240c6b8  2.17.1
Alexey Dokuchaev (danfe) search for other commits by this committer
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)

ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.

While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names.
19 Jun 2021 12:33:58
 files touched by this commit commit hash:d571f1f33222ae3c639baa517f53783fdf759e69  2.17.1
Jason W. Bacon (jwb) search for other commits by this committer
biology/vsearch: Update to 2.17.1

Changes:    https://github.com/torognes/vsearch/releases

Also enabled powerpc64le
10 Apr 2021 14:02:55
 files touched by this commit commit hash:a5f08a7c0165ceb7dcaf23944cda43b7264044d0  2.17.0
Jason W. Bacon (jwb) search for other commits by this committer
biology/vsearch: Update to 2.17.0

Afterthoughts from the recent 2.16.0 release
(Minor bug fixes and enhancements to the new orient subcommand)

Reported by:    portscout
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.16.0
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  2.16.0
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
24 Mar 2021 18:43:42
Original commit files touched by this commit Revision:569151  2.16.0
jwb search for other commits by this committer
biology/vsearch: Update to 2.16.0

Add "orient" subcommand
A few other fixes and enhancements

Reported by:    portscout
30 Jan 2021 15:31:12
Original commit files touched by this commit Revision:563418  2.15.2
jwb search for other commits by this committer
biology/vsearch: Update to 2.15.2

Code clean up and modernization

Reported by:    portscout
16 Jan 2021 17:51:56
Original commit files touched by this commit Revision:561748  2.15.0
pkubaj search for other commits by this committer
biology/vsearch: enable on powerpc64le
20 Jun 2020 14:31:59
Original commit files touched by this commit Revision:539742  2.15.0
jwb search for other commits by this committer
biology/vsearch: Update to 2.15.0

Numerous minor enhancements
19 Feb 2020 22:34:36
Original commit files touched by this commit Revision:526534  2.14.2
jwb search for other commits by this committer
biology/vsearch: Upgrade to 2.14.2

Numerous small bug fixes and enhancements

Reported by:    portscout
11 May 2019 13:42:33
Original commit files touched by this commit Revision:501259  2.13.4
jwb search for other commits by this committer
biology/vsearch: Update to 2.13.4

FreeBSD patches incorporated into new upstream release

Reported by:    portscout
09 May 2019 22:12:27
Original commit files touched by this commit Revision:501148  2.13.3
jwb search for other commits by this committer
biology/vsearch: Remove powerpc64 support

Requires little endian mode and FreeBSD currently does not support it
09 May 2019 21:28:49
Original commit files touched by this commit Revision:501147  2.13.3
jwb search for other commits by this committer
biology/vsearch: Versatile open-source tool for metagenomics

VSEARCH supports de novo and reference based chimera detection, clustering,
full-length and prefix dereplication, rereplication, reverse complementation,
masking, all-vs-all pairwise global alignment, exact and global alignment
searching, shuffling, subsampling and sorting. It also supports FASTQ file
analysis, filtering, conversion and merging of paired-end reads.

The aim of this project is to create an alternative to the USEARCH tool
developed by Robert C. Edgar (2010).

Number of commits found: 15