18:44 Nuno Teixeira (eduardo) 

biology/biolibc-tools: Move man pages to share/man

Approved by:	portmgr (blanket)

    17190fc

22:41 Jason W. Bacon (jwb) 

biology/biolibc-tools: Update to 0.1.4.13

Updates for new libxtend API

    91d1591

20:40 Jason W. Bacon (jwb) 

biology/biolibc-tools: Update to 0.1.4.9

Update for biolibc GFF3 API changes

    e9b6ad4

11:57 Jason W. Bacon (jwb) 

biology/biolibc-tools: Update to 0.1.4.6

Improvements to deromanize
Updates for libxtend API changes

    e696f19

00:11 Jason W. Bacon (jwb) 

biology/biolibc-tools: Update to 0.1.4.1

deromanize:

Check for NULL field to prevent crash in some situations
Take optional input file as second argument

    9d72e41

00:47 Jason W. Bacon (jwb) 

biology/biolibc-tools: Update to 0.1.4

Add deromanize subcommand to convert Roman numeral chromosome IDs
fastx-stats: Report standard deviation for read length

Changes:    https://github.com/auerlab/biolibc-tools/releases

    a069656

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

18:51 Matthias Andree (mandree) 

*: bump PORTREVISION of all devel/xxhash users...

...except archivers/py-borgbackup, which requires a more complete fix.

    875d7c7

14:20 Tobias C. Berner (tcberner) 

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

    37526bb

14:26 Jason W. Bacon (jwb) 

biology/biolibc-tools: Update to 0.1.3

Add vcf-downsample subcommand
Improvements to build system
extract-seq: Recurse to output subfeatures
Numerous other minor enhancements and fixes

Changes:        https://github.com/auerlab/biolibc-tools/tags

    f869d6b

21:36 Jason W. Bacon (jwb) 

biology/biolibc-tools: Update to 0.1.2

New fastx-stats and ensembl2gene subcommands
Minor updates for biolibc 0.2.2 API changes
Minor bug fixes and ennancements

    b8604e8

19:45 Jason W. Bacon (jwb) 

biology/biolibc-tools: Update to 0.1.1

Make all programs subcommands of "blt"
Several new commands
Updates for evolving libxtend and biolibc APIs
Add --version flag
Numerous minor fixes and enhancements

Changes: https://github.com/auerlab/biolibc-tools/releases/tag/0.1.1

    3a7f92e

13:09 Jason W. Bacon (jwb) 

biology/biolibc-tools: High-performance tools based on biolibc

Biolibc-tools is a collection of simple fast, memory-efficient,
programs for processing biological data.  These are simple programs
built on biolibc that are not complex enough to warrant a separate
project.

    904aa60