| Port details |
- vsearch Versatile open-source tool for metagenomics
- 2.30.0 biology
 =2      2.29.2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2019-05-09 21:29:03
- Last Update: 2025-03-02 12:37:09
- Commit Hash: 84399ce
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://github.com/torognes/vsearch
- Description:
- 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).
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - 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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: vsearch
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: aarch64 amd64 powerpc64le
- distinfo:
- TIMESTAMP = 1740867400
SHA256 (torognes-vsearch-v2.30.0_GH0.tar.gz) = 6d11ce960206ab64cf6d7907e539348d192a5b3f32f82d37c9bfbc4d789b576c
SIZE (torognes-vsearch-v2.30.0_GH0.tar.gz) = 285775
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- ghostscript10>=10.02.0 : print/ghostscript10
- gmake>=4.4.1 : devel/gmake
- autoconf>=2.72 : devel/autoconf
- automake>=1.17 : devel/automake
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for vsearch-2.30.0:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
- Options name:
- biology_vsearch
- USES:
- autoreconf ghostscript:build gmake localbase
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.30.0
02 Mar 2025 12:37:09
 |
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.30.0
Add options --n_mismatch, --fastq_minqual, and --fastq_truncee_rate
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.29.4
16 Feb 2025 14:21:06
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.29.4
Fix regression from 2.23.0 regarding chimera detection
Add pragma to ensure correct code
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.29.2
29 Dec 2024 20:59:05
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.29.2
Fix seg fault when cluster set is empty
Reported by: portscout |
2.29.1
27 Oct 2024 22:51:28
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.29.1
Fix a seg fault in 2.29.0
Reported by: portscout |
2.29.0
21 Oct 2024 20:15:58
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.29.0
Several bug fixes
Support for RISC-V
Improved testing
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.28.1
01 May 2024 13:41:05
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.28.1
A few bug fixes and enhancements
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.27.1
08 Apr 2024 21:43:20
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.27.1
Fix weak_id option and make searches report weak hits in some cases
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.27.0_1
02 Mar 2024 20:35:56
|
Nuno Teixeira (eduardo) |
biology/vsearch: Move man pages to share/man
Approved by: portmgr (blanket) |
2.27.0
23 Jan 2024 13:16:13
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.27.0
Add FASTQ support to usearch_global and search_exact
Code cleanup and manual clarifications
Reported by: portscout |
2.26.1
26 Nov 2023 12:32:55
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.26.1
A few minor enhancements
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.25.0
12 Nov 2023 15:19:08
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.25.0
chimeras_denovo: Allow user to specify mismatch tolerance
Changes: https://github.com/torognes/vsearch/releases |
2.24.0_1
03 Nov 2023 07:17:38
|
Michael Osipov (michaelo) |
*/*: Bump PORTREVISION for Ghostscript 10 change
Reported by: sunpoet
Approved by: jrm (mentor), sunpoet
Differential Revision: https://reviews.freebsd.org/D42412 |
2.24.0
27 Oct 2023 14:09:57
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.24.0
Upstream code cleanup
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.23.0
08 Jul 2023 19:10:45
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.23.0
Numerous minor fixes and enhancements
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.22.1
21 Sep 2022 16:24:14
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.22.1
Add the derep_smallmem command for dereplication with less memory usage
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout |
2.21.2
16 Sep 2022 16:17:55
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.21.2
Fix problems with the --lcaout option
Changes: https://github.com/torognes/vsearch/tags
Reported by: portscout |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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) |
2.21.1
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
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  ) |
2.21.1
23 Jan 2022 22:32:43
|
Jason W. Bacon (jwb) |
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 |
2.19.0
08 Jan 2022 00:04:02
|
Jason W. Bacon (jwb) |
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 |
2.17.1
25 Oct 2021 12:58:29
|
Alexey Dokuchaev (danfe) |
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. |
2.17.1
19 Jun 2021 12:33:58
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.17.1
Changes: https://github.com/torognes/vsearch/releases
Also enabled powerpc64le |
2.17.0
10 Apr 2021 14:02:55
|
Jason W. Bacon (jwb) |
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 |
2.16.0
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.16.0
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.16.0
24 Mar 2021 18:43:42
 |
jwb |
biology/vsearch: Update to 2.16.0
Add "orient" subcommand
A few other fixes and enhancements
Reported by: portscout |
2.15.2
30 Jan 2021 15:31:12
|
jwb |
biology/vsearch: Update to 2.15.2
Code clean up and modernization
Reported by: portscout |
2.15.0
16 Jan 2021 17:51:56
|
pkubaj |
biology/vsearch: enable on powerpc64le |
2.15.0
20 Jun 2020 14:31:59
|
jwb |
biology/vsearch: Update to 2.15.0
Numerous minor enhancements |
2.14.2
19 Feb 2020 22:34:36
|
jwb |
biology/vsearch: Upgrade to 2.14.2
Numerous small bug fixes and enhancements
Reported by: portscout |
2.13.4
11 May 2019 13:42:33
|
jwb |
biology/vsearch: Update to 2.13.4
FreeBSD patches incorporated into new upstream release
Reported by: portscout |
2.13.3
09 May 2019 22:12:27
|
jwb |
biology/vsearch: Remove powerpc64 support
Requires little endian mode and FreeBSD currently does not support it |
2.13.3
09 May 2019 21:28:49
|
jwb |
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). |
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