Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months

Deprecate ports broken for more than 6 months

Mark a few ports BROKEN, unfetchable

Convert to UCL & cleanup pkg-message (categories a-c)

- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with
  Mk/Uses/linux.mk.
- Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with
  USES+=linux:\1 in all ports.
- Replace USE_LINUX_APPS with USE_LINUX in all ports.
- Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some
  ports.
- When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY
  are defined.
- Remove BRANDELF_DIRS and BRANDELF_FILES handling.  In the very rare cases
  that it is still necessary ports can run ${BRANDELF} from post-patch.
- Remove AUTOMATIC_PLIST handling.  Only one port used it.
- Fix Linux MASTER_SITES.
- Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with
  default versions framework.

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

biology/consed: undeprecate, it presumably builds fine but it is restricted.

Add a note to ports/LEGAL

Deprecate ports broken for more than 6 months

${ENV} does not exist, it is called ${SETENV}.

Mark as broken unfetchable ports

update ports:
	biology/phrab
	biology/phred
	biology/consed

Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.

PR:		191336
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)

Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)

Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)

Replace maintainer's email address with one that seems to work

With hat:	portmgr

Remove trailing whitespaces from category biology

According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)

Convert biology to MDOCS and MEXAMPLES

Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)

- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)

- Get Rid MD5 support

Welcome to the new linux ports infrastructure which allows using
both current (fc4) and future linux (f8) distributions at one
ports tree.

The patch contains full changes to ports/Mk files and all ports involved.
But only infrastructure is changed. The resulting packages are the same as
before. Hence no need to bump PORTREVISIONs.

The idea was taken from bsd.gnome.mk and others.

More than 130 ports are switched to follow a new linux infrastructure
introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new
bsd.linux-apps.mk.

Thanks for all who was involved and helped me with this work.
And help from Alexander Leidinger was incredible.

Other changes are coming. Stay tuned!

PR:             ports/132510
Submitted by:   bsam (me)
Exp-run by:     portmgr (pav)

Teach the building cluster that these ports are not to be build

New port: biology/consed viewing and editing workbench for sequence
assembly

        Consed is a tool for viewing, editing, and finishing sequence
assemblies.

        The port is constituted of 4 parts:
        biology/phred: base caller with quality evaluation
        biology/phrap: sequence assembler for shotgun sequencing
        biology/consed: workbench
        biology/phd2fasta: small utility

        All these can be used separately; however, most function
        of consed depends on the others.

        Although these programs are licensed freely for academic
        and nonprofit purposes, users have to contact the authors
        to get the softwares.
        Phred (including phd2fasta) and phrap are emailed,
        and consed can be downloaded to a restricted IP address.
        For commercial users, the licensing fee is ca. $10,000 at
        the time of writing.

PR:             ports/118548
Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>