12:32 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

    92927bb

15:19 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

    aafea13

07:17 Michael Osipov (michaelo) 

*/*: Bump PORTREVISION for Ghostscript 10 change

Reported by:	sunpoet
Approved by:	jrm (mentor), sunpoet
Differential Revision:	https://reviews.freebsd.org/D42412

    fcf68ae5e

14:09 Jason W. Bacon (jwb) 

biology/vsearch: Update to 2.24.0

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

Reported by:    portscout

    f71a4e8

19:10 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

    168ecf0

16:24 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

    001947d

16:17 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

    de24c3e

21:10 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.

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)

    b7f0544

22:32 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

    f67392e

00:04 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

    231919f

12:58 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.

    61b6613

12:33 Jason W. Bacon (jwb) 

biology/vsearch: Update to 2.17.1

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

Also enabled powerpc64le

    d571f1f

14:02 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

    a5f08a7

08:09 Mathieu Arnold (mat) 

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

    cf118cc

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

18:43 jwb 

biology/vsearch: Update to 2.16.0

Add "orient" subcommand
A few other fixes and enhancements

Reported by:    portscout

 

15:31 jwb 

biology/vsearch: Update to 2.15.2

Code clean up and modernization

Reported by:    portscout

 

17:51 pkubaj 

biology/vsearch: enable on powerpc64le

 

14:31 jwb 

biology/vsearch: Update to 2.15.0

Numerous minor enhancements

 

22:34 jwb 

biology/vsearch: Upgrade to 2.14.2

Numerous small bug fixes and enhancements

Reported by:    portscout

 

13:42 jwb 

biology/vsearch: Update to 2.13.4

FreeBSD patches incorporated into new upstream release

Reported by:    portscout

 

22:12 jwb 

biology/vsearch: Remove powerpc64 support

Requires little endian mode and FreeBSD currently does not support it

 

21:28 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).