notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
All times are UTC
Ukraine
non port: biology/vsearch/Makefile

Number of commits found: 23

Sunday, 26 Nov 2023
12:32 Jason W. Bacon (jwb) search for other commits by this committer
biology/vsearch: Update to 2.26.1

A few minor enhancements
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout
commit hash: 92927bbeb6744e47576ba8cd42e3234fea0cf57b commit hash: 92927bbeb6744e47576ba8cd42e3234fea0cf57b commit hash: 92927bbeb6744e47576ba8cd42e3234fea0cf57b commit hash: 92927bbeb6744e47576ba8cd42e3234fea0cf57b 92927bb
Sunday, 12 Nov 2023
15:19 Jason W. Bacon (jwb) search for other commits by this committer
biology/vsearch: Update to 2.25.0

chimeras_denovo: Allow user to specify mismatch tolerance

Changes: https://github.com/torognes/vsearch/releases
commit hash: aafea13ec8abd708f405590b8c85e813d40dd2c6 commit hash: aafea13ec8abd708f405590b8c85e813d40dd2c6 commit hash: aafea13ec8abd708f405590b8c85e813d40dd2c6 commit hash: aafea13ec8abd708f405590b8c85e813d40dd2c6 aafea13
Friday, 3 Nov 2023
07:17 Michael Osipov (michaelo) search for other commits by this committer
*/*: Bump PORTREVISION for Ghostscript 10 change

Reported by:	sunpoet
Approved by:	jrm (mentor), sunpoet
Differential Revision:	https://reviews.freebsd.org/D42412
commit hash: fcf68ae5ecb03e0f4479c9ba7c255d4e2b8adcea commit hash: fcf68ae5ecb03e0f4479c9ba7c255d4e2b8adcea commit hash: fcf68ae5ecb03e0f4479c9ba7c255d4e2b8adcea commit hash: fcf68ae5ecb03e0f4479c9ba7c255d4e2b8adcea fcf68ae5e
Friday, 27 Oct 2023
14:09 Jason W. Bacon (jwb) search for other commits by this committer
biology/vsearch: Update to 2.24.0

Upstream code cleanup
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout
commit hash: f71a4e840eae662ce8ea569a86564c063cb793fa commit hash: f71a4e840eae662ce8ea569a86564c063cb793fa commit hash: f71a4e840eae662ce8ea569a86564c063cb793fa commit hash: f71a4e840eae662ce8ea569a86564c063cb793fa f71a4e8
Saturday, 8 Jul 2023
19:10 Jason W. Bacon (jwb) search for other commits by this committer
biology/vsearch: Update to 2.23.0

Numerous minor fixes and enhancements
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout
commit hash: 168ecf03820a6e7c32f64f89948345c030555a7c commit hash: 168ecf03820a6e7c32f64f89948345c030555a7c commit hash: 168ecf03820a6e7c32f64f89948345c030555a7c commit hash: 168ecf03820a6e7c32f64f89948345c030555a7c 168ecf0
Wednesday, 21 Sep 2022
16:24 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
commit hash: 001947d3e51c6373db11bb480c6ff5a66dad311d commit hash: 001947d3e51c6373db11bb480c6ff5a66dad311d commit hash: 001947d3e51c6373db11bb480c6ff5a66dad311d commit hash: 001947d3e51c6373db11bb480c6ff5a66dad311d 001947d
Friday, 16 Sep 2022
16:17 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
commit hash: de24c3efe81a4e1c90f0e5c0f00eebc6bbb6ceae commit hash: de24c3efe81a4e1c90f0e5c0f00eebc6bbb6ceae commit hash: de24c3efe81a4e1c90f0e5c0f00eebc6bbb6ceae commit hash: de24c3efe81a4e1c90f0e5c0f00eebc6bbb6ceae de24c3e
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Sunday, 23 Jan 2022
22:32 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
commit hash: f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0 commit hash: f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0 commit hash: f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0 commit hash: f67392e69b9c97f2c6ad5d5c86bbc3b3457872c0 f67392e
Saturday, 8 Jan 2022
00:04 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
commit hash: 231919fc1935355a5f7dc5466844c04cb51c6444 commit hash: 231919fc1935355a5f7dc5466844c04cb51c6444 commit hash: 231919fc1935355a5f7dc5466844c04cb51c6444 commit hash: 231919fc1935355a5f7dc5466844c04cb51c6444 231919f
Monday, 25 Oct 2021
12:58 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.
commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8 commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8 commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8 commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8 61b6613
Saturday, 19 Jun 2021
12:33 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
commit hash: d571f1f33222ae3c639baa517f53783fdf759e69 commit hash: d571f1f33222ae3c639baa517f53783fdf759e69 commit hash: d571f1f33222ae3c639baa517f53783fdf759e69 commit hash: d571f1f33222ae3c639baa517f53783fdf759e69 d571f1f
Saturday, 10 Apr 2021
14:02 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
commit hash: a5f08a7c0165ceb7dcaf23944cda43b7264044d0 commit hash: a5f08a7c0165ceb7dcaf23944cda43b7264044d0 commit hash: a5f08a7c0165ceb7dcaf23944cda43b7264044d0 commit hash: a5f08a7c0165ceb7dcaf23944cda43b7264044d0 a5f08a7
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Wednesday, 24 Mar 2021
18:43 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
Original commitRevision:569151 
Saturday, 30 Jan 2021
15:31 jwb search for other commits by this committer
biology/vsearch: Update to 2.15.2

Code clean up and modernization

Reported by:    portscout
Original commitRevision:563418 
Saturday, 16 Jan 2021
17:51 pkubaj search for other commits by this committer
biology/vsearch: enable on powerpc64le
Original commitRevision:561748 
Saturday, 20 Jun 2020
14:31 jwb search for other commits by this committer
biology/vsearch: Update to 2.15.0

Numerous minor enhancements
Original commitRevision:539742 
Wednesday, 19 Feb 2020
22:34 jwb search for other commits by this committer
biology/vsearch: Upgrade to 2.14.2

Numerous small bug fixes and enhancements

Reported by:    portscout
Original commitRevision:526534 
Saturday, 11 May 2019
13:42 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
Original commitRevision:501259 
Thursday, 9 May 2019
22:12 jwb search for other commits by this committer
biology/vsearch: Remove powerpc64 support

Requires little endian mode and FreeBSD currently does not support it
Original commitRevision:501148 
21:28 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).
Original commitRevision:501147 

Number of commits found: 23