biology/p5-BioPerl 1.007008

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Remove variable PERL_VER from the ports tree at all - because it is obsolete since Perl 5.6.0.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

As announced on May 6, remove the broken p5-bioperl-devel port.

BROKEN: Broken pkg-plist

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.  :-)

- Add NO_LATEST_LINK, which should've been there in the first place.  :-(

- Move the (very) long list of manpages from the port Makefile to a separate   file.

Inspired by:	nectar's treatment of security/heimdal

Add p5-bioperl-devel 0.9.0, a collection of Perl modules for bioinformatics (developer's release).

- 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

PR:		21954
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER

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

PR:		ports/20252
Submitted by:	Johann Visagie <johann@egenetics.com>