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Some details on the 2023-01-16 website outage.
We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
Port details
vsearch Versatile open-source tool for metagenomics
2.22.1 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 Version 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: 2022-09-21 16:24:14
Commit Hash: 001947d
License: GPLv3
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
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-2.22.1/catalog.mk
  4. /usr/local/share/licenses/vsearch-2.22.1/LICENSE
  5. /usr/local/share/licenses/vsearch-2.22.1/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
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:

Packages (timestamps in pop-ups are UTC):
vsearch
ABIlatestquarterly
FreeBSD:11:aarch64pkg-fallout2.15.0
FreeBSD:11:amd642.17.12.17.1
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout2.22.1
FreeBSD:12:amd642.22.12.22.1
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch642.22.12.22.1
FreeBSD:13:amd642.22.12.22.1
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch642.22.1pkg-fallout
FreeBSD:14:amd642.22.1pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

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>=2.71 : devel/autoconf
  4. automake>=1.16.5 : 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/v2.22.1?dummy=/
Collapse this list.

Number of commits found: 19

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.22.1
21 Sep 2022 16:24:14
commit hash:001947d3e51c6373db11bb480c6ff5a66dad311dcommit hash:001947d3e51c6373db11bb480c6ff5a66dad311dcommit hash:001947d3e51c6373db11bb480c6ff5a66dad311dcommit hash:001947d3e51c6373db11bb480c6ff5a66dad311d files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash:de24c3efe81a4e1c90f0e5c0f00eebc6bbb6ceaecommit hash:de24c3efe81a4e1c90f0e5c0f00eebc6bbb6ceaecommit hash:de24c3efe81a4e1c90f0e5c0f00eebc6bbb6ceaecommit hash:de24c3efe81a4e1c90f0e5c0f00eebc6bbb6ceae files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
2.21.1
23 Jan 2022 22:32:43
commit hash:f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0commit hash:f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0commit hash:f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0commit hash:f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0 files touched by this commit
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
2.19.0
08 Jan 2022 00:04:02
commit hash:231919fc1935355a5f7dc5466844c04cb51c6444commit hash:231919fc1935355a5f7dc5466844c04cb51c6444commit hash:231919fc1935355a5f7dc5466844c04cb51c6444commit hash:231919fc1935355a5f7dc5466844c04cb51c6444 files touched by this commit
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
2.17.1
25 Oct 2021 12:58:29
commit hash:61b661339366b6ee95ca1de0667979da9240c6b8commit hash:61b661339366b6ee95ca1de0667979da9240c6b8commit hash:61b661339366b6ee95ca1de0667979da9240c6b8commit hash:61b661339366b6ee95ca1de0667979da9240c6b8 files touched by this commit
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.
2.17.1
19 Jun 2021 12:33:58
commit hash:d571f1f33222ae3c639baa517f53783fdf759e69commit hash:d571f1f33222ae3c639baa517f53783fdf759e69commit hash:d571f1f33222ae3c639baa517f53783fdf759e69commit hash:d571f1f33222ae3c639baa517f53783fdf759e69 files touched by this commit
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
2.17.0
10 Apr 2021 14:02:55
commit hash:a5f08a7c0165ceb7dcaf23944cda43b7264044d0commit hash:a5f08a7c0165ceb7dcaf23944cda43b7264044d0commit hash:a5f08a7c0165ceb7dcaf23944cda43b7264044d0commit hash:a5f08a7c0165ceb7dcaf23944cda43b7264044d0 files touched by this commit
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
2.16.0
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.16.0
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.16.0
24 Mar 2021 18:43:42
Revision:569151Original commit files touched by this commit
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
2.15.2
30 Jan 2021 15:31:12
Revision:563418Original commit files touched by this commit
jwb search for other commits by this committer
biology/vsearch: Update to 2.15.2

Code clean up and modernization

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

Numerous minor enhancements
2.14.2
19 Feb 2020 22:34:36
Revision:526534Original commit files touched by this commit
jwb search for other commits by this committer
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
Revision:501259Original commit files touched by this commit
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
2.13.3
09 May 2019 22:12:27
Revision:501148Original commit files touched by this commit
jwb search for other commits by this committer
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
Revision:501147Original commit files touched by this commit
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: 19