- Move biology/p5-bioperl to biology/p5-BioPerl
- Sort *_DEPENDS
- Bump PORTREVISION for dependent ports

- Remove unnecessary USES=shebangfix
- Convert to new options target helper

- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket

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

With hat:	portmgr
Sponsored by:	Absolight

Make it so that the default Perl is always called perl5.

- Move Perl's man1 files along with its man3 files.
- Move where Perl installs its modules man1 pages.
- Convert the ports installing man1 pages.
- Make different Perl versions installable at the same time.
  Though you should note that only the default version can be used to
  install Perl modules, and the non default Perl versions cannot use the
  modules installed via ports if they contain .so as they are installed
  in a version specific directory.

Reviewed by:	bapt (the Mk bits)
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3542

- Fix shebangs
- Add NO_ARCH
- Add missing EXAMPLES option

Approved by:	portmgr blanket
MFH:		2015Q2

Reassign biology/ perl modules to perl@.

While here:

Regenerate p5-AcePerl's patches using makepatch.
Make p5-Bio-ASN1-EntrezGene depend on p5-bioperl, instead of the
other way around. Bump PORTREVISION on those two ports.

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.

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: fix pkg-descr sidenote link

- Update to 1.6.924 [1]
- Reset maintainer to perl@

PR:		192088 [1]
Submitted by:	Kurt Jaeger<pi@FreeBSD.org> [1]

- Update to 1.6.923
- Add STAGE support

PR:		190342
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com>

Mark as broken unstaged perl ports

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 new perl framework
- Trim Makefile header

Approved by:	wen@ (maintainer)

- Avoid of using SITE_PERL
- Remove depend on DB_File.pm since it part of perl distribution

PR:		ports/178877
Submitted by:	az
Approved by:	matainer (timeout)

- Take maintainership

- Reassign to the heap at maintainer's request

- 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

- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)

- Get Rid MD5 support

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

- update to jpeg-8

- Remove unneeded dependencies which is in perl-5.8.9 dist
  (part 19; last!).

Approved by:    portmgr (itetcu)

- Update to 1.6.1

Approved by:    maintainer (via Email)

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

- lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checks

PR:             ports/135398
Tested by:      2 -exp runs by pav
Approved by:    portmgr (pav)

Remove variable PERL_VER from the ports tree at all - because
it is obsolete since Perl 5.6.0.

- Update to 1.6.0

PR:             ports/131989
Submitted by:   maintainer

Fix plist with perl 5.8.9.

Approved by:    portmgr (pav, implicit)

- 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}.

SHA256ify

Approved by:    krion@

Add conflicst:
CONFLICTS=     p5-bioperl-1.[13579]*

Submitted by:   Mauricio Herrera Cuadra <arareko@yahoo.com>,Fernan Aguero
<fernan@iib.unsam.edu.ar>

- add missing MAN1 and MAN3
- apply DATADIR, EXAMPLESDIR, and DOCSDIR in PLIST
- update the usage of NOPORTDOCS

PR:             71322
Submitted by:   leeym
Approved by:    Fernan Aguero <fernan@iib.unsam.edu.ar>

After devel/p5-File-Temp has gained an IGNORE for PERL_LEVEL > 500800, all
these ports were broken because they always depended on it. I've rearranged all
the dependencies to fit the new scheme.

Add size data, approved by maintainers.

Unmark as broken for 4.x; instead, mark as ignore for perl < 5.6.

BROKEN on 4.x: Configure fails

Major update from 0.7.2 to 1.4 by new maintainer.  This is almost a complete
rework of the port.

See the page http://news.open-bio.org/archives/cat_bioperl.html for the
changes between 1.2 and 1.4.  The older changes are in the CVS tree.

From the new maintainer:

        Note that this new port just handles the installation of bioperl and
        not of additional extra stuff (bioperl-gui, bioperl-corba-server,
        bioperl-corba-client). This is unlike the behaviour of the current
        port.

        The extra stuff, though still functional, had very little adoption
        among users, and does not appear to be currently supported/maintained.

PR:             ports/47303 (and subsequent)
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (new maintainer)

utilize SITE_PERL

PR:             58166
Submitted by:   Cheng-Lung Sung <clsung@dragon2.net>

Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

- Update to version 0.7.2, somewhat overdue.  :-)    

- Properly list run-time dependencies in RUN_DEPENDS in Makefile.   - Deploy
%%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout     pkg-plist. 
(Ouch, that was embarrassing.)   - Bump PORTREVISION due to the above.   -
Update my email address and the project's URL in pkg-descr.    

- Update to version 0.7.1   - Add a build-time message to inform the user of
available options.    

Embarrassingly long overdue update to 0.7.0, including optional support for  
GUI (Tk) and CORBA extensions.    

Update to version 0.6.2    

Convert category biology to new layout.  

Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics