| Port details |
- vsearch Versatile open-source tool for metagenomics
- 2.21.1 biology
 =0      2.17.1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2019-05-09 21:29:03
- Last Update: 2022-01-23 22:32:43
- Commit Hash: f67392e
- License: GPLv3
- 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).
WWW: https://github.com/torognes/vsearch
- SVNWeb : git : Homepage
- 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
- PKGNAME: vsearch
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: aarch64 amd64 powerpc64le
- distinfo:
- TIMESTAMP = 1642976868
SHA256 (torognes-vsearch-v2.21.1_GH0.tar.gz) = 0c5f4c981bc8ecbf23ee618d1b45667f81ae9845d64b9d6a310edbd196c84638
SIZE (torognes-vsearch-v2.21.1_GH0.tar.gz) = 257434
- 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:
-
- ghostscript9-agpl-base>=9.16_2 : print/ghostscript9-agpl-base
- gmake>=4.3 : devel/gmake
- autoconf>=2.69 : devel/autoconf
- automake>=1.16.1 : devel/automake
- Library dependencies:
-
- libsysinfo.so : devel/libsysinfo
- There are no ports dependent upon this port
- Configuration Options:
- ===> The following configuration options are available for vsearch-2.21.1:
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: see SVNWeb link above for full details) |
| Date | By | Description |
|---|
23 Jan 2022 22:32:43
  2.21.1
|
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 |
08 Jan 2022 00:04:02
2.19.0
|
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 |
25 Oct 2021 12:58:29
2.17.1
|
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. |
19 Jun 2021 12:33:58
2.17.1
|
Jason W. Bacon (jwb) |
biology/vsearch: Update to 2.17.1
Changes: https://github.com/torognes/vsearch/releases
Also enabled powerpc64le |
10 Apr 2021 14:02:55
2.17.0
|
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 |
07 Apr 2021 08:09:01
2.16.0
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
06 Apr 2021 14:31:07
2.16.0
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
24 Mar 2021 18:43:42
  2.16.0
|
jwb |
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
2.15.2
|
jwb |
biology/vsearch: Update to 2.15.2
Code clean up and modernization
Reported by: portscout |
16 Jan 2021 17:51:56
2.15.0
|
pkubaj |
biology/vsearch: enable on powerpc64le |
20 Jun 2020 14:31:59
2.15.0
|
jwb |
biology/vsearch: Update to 2.15.0
Numerous minor enhancements |
19 Feb 2020 22:34:36
2.14.2
|
jwb |
biology/vsearch: Upgrade to 2.14.2
Numerous small bug fixes and enhancements
Reported by: portscout |
11 May 2019 13:42:33
2.13.4
|
jwb |
biology/vsearch: Update to 2.13.4
FreeBSD patches incorporated into new upstream release
Reported by: portscout |
09 May 2019 22:12:27
2.13.3
|
jwb |
biology/vsearch: Remove powerpc64 support
Requires little endian mode and FreeBSD currently does not support it |
09 May 2019 21:28:49
2.13.3
|
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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