biology/rubygem-bio-shell 1.0.1

Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby

Switch from Mk/bsd.ruby.mk to Mk/Uses/ruby.mk

Notable changes are.

- Mk/bsd.ruby.mk is moved to Mk/Uses/ruby.mk.
- USE_RUBY=yes is replaced with USES=ruby.
- USE_RUBY_EXTCONF is replaced with USES=ruby:extconf.
- USE_RUBY_RDOC is replaced with USES=ruby:rdoc.
- USE_RUBY_SETUP is replaces with USES=ruby:setup.
- RUBY_NO_BUILD_DEPENDS and RUBY_NO_RUN_DEPENDS are replaced with
  USES=ruby:{build,none,run}.
- RUBY_REQUIRE isn't used anywhere, so removed.
- USES=gem now implies USES=ruby.

This is mainly the work of yasu@ at https://reviews.freebsd.org/D27863

I have just made some cosmetic changes and ran exp-run to test that the
tree is not in a BROKEN state.

Approved by:	portmgr
Differential Revision:	https://reviews.freebsd.org/D37925

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)

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)

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

Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
cannot conflict with itself (due to logic in bsd.port.mk that
supresses the pattern match result in that case).

A few ports that set the conflicts variables depending on complex
conditions (e.g. port options), have been left unmodified, despite
probably containing outdated package names.

These changes should only affect the installation of locally built
ports, not the package building with poudriere. They should give an
early indication of the install conflict in cases where currently
the pkg command aborts an installation when it detects that an
existing file would be overwritten,

Approved by:	portmgr (implicit)

biology/rubygem-bio-shell: Update to 1.0.1

Changes:	https://github.com/bioruby/bioruby-shell/commits/master

Remove # $FreeBSD$ from Makefiles.

Add rubygem-bio-shell 1.0.0

bio-shell, providing BioRuby Shell, is a command-line interface for BioRuby, an
open source bioinformatics library for Ruby.

This code has historically been part of the BioRuby gem, but has been split into
its own gem as part of an effort to modularize BioRuby. bio-shell and many more
plugins are available at biogems.info.

WWW: https://github.com/bioruby/bioruby-shell