- Move biology/p5-bioperl-run to biology/p5-BioPerl-Run
- Sort *_DEPENDS
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming

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

With hat:	portmgr
Sponsored by:	Absolight

For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME to
include GH_PROJECT/GH_ACCOUNT/GH_TAGNAME. This prevents the distfile
having the same name despite changing one of these values and causing
a bad checksum.

Differential Revision:	https://reviews.freebsd.org/D2103
Reviewed by:	mat
With hat:	bdrewery

Convert to new USE_GITHUB.

While there, cleanup.

Sponsored by:	Absolight

Some OCD cleanups on some of the perl@ ports.

- Remove dependencies in core
- Put testing depends in TEST_DEPENDS
- Remove unnecessary bsd.port.options.mk inclusions
- Remove checks for Perl versions that no longer exist in the ports tree
- Sort plists, some of which were so jumbled that I have to assume
  the plist was randomized before committing

A lot of the plist changes in this commit are moving PERL5_MAN3 after
SITE_PERL. It's repo churn now, but it makes updating the ports later
far easier.

- Simplify Makefile
- Use tab instead of space
- Sort PLIST
- Pass maintainership to perl@

Change the way Perl modules are installed, update the default Perl to 5.18.

Before, we had:

  site_perl :           lib/perl5/site_perl/5.18
  site_perl/perl_arch : lib/perl5/site_perl/5.18/mach
  perl_man3 :           lib/perl5/5.18/man/man3

Now we have:

  site_perl : lib/perl5/site_perl
  site_arch : lib/perl5/site_perl/mach/5.18
  perl_man3 : lib/perl5/site_perl/man/man3

Modules without any .so will be installed at the same place regardless of the

Cleanup plist

biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify

Reset maintainership for ports not staged with no pending PR

With hat:	portmgr

Mark BROKEN: Fails to configure

===>  Configuring for p5-bioperl-run-1.6.1_4
Invalid prerequisite condition '0/processing XML
data/Bio::Tools::Run::EMBOSSacd' for XML::Twig at
/usr/local/lib/perl5/site_perl/5.16/Module/Build/Base.pm line 1702.
*** [do-configure] Error code 25

Reported by:	pkg-fallout
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)

- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@ (bapt@)

- update png to 1.5.10

At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450
ports use BUILD_DEPENDS:= ${RUN_DEPENDS}. This patch fixes ports that are
currently broken. This is a temporary measure until we organically stop using
:= or someone(s) spend a lot of time changing all the ports over.

Explicit duplication > := > = and this just moves ports one step to the left

Approved by:    portmgr

- Get Rid MD5 support

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

- update to jpeg-8

- Relax check on bioperl version; people keep forgetting to update this check
  when updating bioperl port

Reported by:    pointyhat

- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin

- Update to 1.6.1

PR:             132122
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer

- Unbreak after p5-bioperl changed portrevision

- Take advantage of CPAN macro from bsd.sites.mk, change
${MASTER_SITE_PERL_CPAN} to CPAN.

PR:             ports/122674
Submitted by:   Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:    araujo (myself)
Approved by:    portmgr (pav)

Welcome bsd.perl.mk.  Add support for constructs such as USE_PERL5=5.8.0+.
Drop support for antique perl.

Work done by:   gabor
Sponsored by:   Google Summer of Code 2007
Hat:            portmgr

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:             ports/93674
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>