Moved from app-sci/bioperl to sci-biology/bioperl.

17 files changed, 665 insertions, 0 deletions

diff --git a/sci-biology/bioperl/ChangeLog b/sci-biology/bioperl/ChangeLog
new file mode 100644
index 000000000000..64b660abeff2
--- /dev/null
+++ b/sci-biology/bioperl/ChangeLog
@@ -0,0 +1,77 @@
+# ChangeLog for app-sci/bioperl
+# Copyright 2002-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/ChangeLog,v 1.1 2004/12/23 22:05:32 ribosome Exp $
+
+*bioperl-1.2 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/biodbgff-enable-1.2.2.patch, +files/biodbgff-enable-1.2.3.patch,
+  +files/bioperl-1.2-manpage.diff, +files/domanpages-1.2.2.patch,
+  +bioperl-1.0.2.ebuild, +bioperl-1.2.2.ebuild, +bioperl-1.2.3.ebuild,
+  +bioperl-1.2.ebuild, +bioperl-1.4.ebuild:
+  Moved from app-sci/bioperl to sci-biology/bioperl.
+
+  30 Oct 2004; Olivier Fisette <ribosome@gentoo.org> bioperl-1.4.ebuild,
+  bioperl-1.0.2.ebuild:
+  Q.A.: Fixed RDEPEND=$DEPEND, fixed LICENSE.
+
+  03 Aug 2004; David Holm <dholm@gentoo.org> bioperl-1.4.ebuild:
+  Added to ~ppc.
+
+  03 Jul 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.4.ebuild:
+  Stable on alpha.
+
+  02 Jun 2004; Aron Griffis <agriffis@gentoo.org> bioperl-1.2.2.ebuild,
+  bioperl-1.2.3.ebuild:
+  Fix use invocation
+
+  05 May 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild:
+  bumped 1.4 to stable
+
+  05 May 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.2.ebuild:
+  Stable on alpha.
+
+  20 Apr 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.4.ebuild:
+  Added ~alpha to keywords.
+
+  14 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild:
+  removed src_test; fixes bug #38169, or at least works around it
+
+*bioperl-1.4 (08 Jan 2004)
+
+  08 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild:
+  version bump
+
+  24 Nov 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.3.ebuild:
+  bump to stable.
+
+*bioperl-1.2.3 (24 Oct 2003)
+
+  24 Oct 2003; <sediener@gentoo.org> bioperl-1.2.3.ebuild:
+  new release added.
+
+*bioperl-1.2.2 (28 Aug 2003)
+
+  28 Aug 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.2.ebuild:
+  Bumped to stable x86
+
+*bioperl-1.2.2 (02 Aug 2003)
+
+  02 Aug 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.2.ebuild,
+  files/biodbgff-enable-1.2.2.patch, files/domanpages-1.2.2.patch:
+  New Version thanks to Gontran Zepeda <gontran@gontran.net> in bug# 24467 :
+  Also fixes bug# 25079
+
+*bioperl-1.2 (24 Apr 2003)
+
+  24 Apr 2003; Jon Portnoy <avenj@gentoo.org> bioperl-1.2.ebuild :
+  Version bump, ebuild submitted by Gontran Zepeda <gontran@gontran.net>
+  in bug #13826
+
+*bioperl-1.0.2 (21 Dec 2002)
+
+  21 Dec 2002; Michael Cummings <mcummings@gentoo.org>
+  bioperl-1.0.2.ebuild:
+
+  Initial import.  Ebuild submitted by Gontran Zepeda <gontran@gontran.net>
+  Bug 11498
diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest
new file mode 100644
index 000000000000..31fbc55140a2
--- /dev/null
+++ b/sci-biology/bioperl/Manifest
@@ -0,0 +1,16 @@
+MD5 7e363b2d0a741eca3070d31384dc79f4 bioperl-1.0.2.ebuild 1485
+MD5 78e0ffe0dc39547ccd257274720c5dae bioperl-1.2.3.ebuild 2063
+MD5 489552b0291b2c365cba1d314f8d9554 bioperl-1.2.ebuild 1514
+MD5 f2b9c1b81698a61d2783d18afd33b317 bioperl-1.2.2.ebuild 2178
+MD5 e90784817c0d42b6301d11661bfff929 bioperl-1.4.ebuild 1152
+MD5 043fd61f9f8bcb61afca590109dbf371 ChangeLog 2175
+MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
+MD5 8f6c3beb108aaa2b78b0b4f8d218187a files/biodbgff-enable-1.2.2.patch 3355
+MD5 1828ff2ba6225e17a98d27bfbad5c7c9 files/bioperl-1.2-manpage.diff 712
+MD5 8f6c3beb108aaa2b78b0b4f8d218187a files/biodbgff-enable-1.2.3.patch 3355
+MD5 14b9e16331895fe40e231065f7dda942 files/digest-bioperl-1.2 64
+MD5 d5d0bc711fb345c9b91086c5d47e1442 files/digest-bioperl-1.4 65
+MD5 08539f1d1fed6d673140cdc221ae13e6 files/domanpages-1.2.2.patch 412
+MD5 dfdb9921cbef92f60e9746a9531d8de7 files/digest-bioperl-1.0.2 66
+MD5 d8df3477f72bba80de83cfdb5416ecbf files/digest-bioperl-1.2.2 66
+MD5 a67f149bd10684a4b584bcd23282d5bf files/digest-bioperl-1.2.3 67
diff --git a/sci-biology/bioperl/bioperl-1.0.2.ebuild b/sci-biology/bioperl/bioperl-1.0.2.ebuild
new file mode 100644
index 000000000000..c80d5b66983d
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.0.2.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.0.2.ebuild,v 1.1 2004/12/23 22:05:32 ribosome Exp $
+
+inherit perl-module
+CATEGORY="app-sci"
+
+DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI="http://bioperl.org/DIST/${P}.tar.gz"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="x86 ~ppc ~sparc ~alpha"
+IUSE="mysql gd"
+
+DEPEND="dev-perl/File-Temp
+	dev-perl/HTML-Parser
+	dev-perl/IO-String
+	dev-perl/IO-stringy
+	dev-perl/SOAP-Lite
+	dev-perl/Storable
+	dev-perl/XML-DOM
+	dev-perl/XML-Parser
+	dev-perl/XML-Writer
+	dev-perl/XML-Twig
+	dev-perl/libxml-perl
+	dev-perl/libwww-perl
+	dev-perl/Text-Shellwords
+	gd? ( >=dev-perl/GD-1.32-r1 )
+	mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
+
+src_compile() {
+	# there's a test to run for BioGFFDB if using mysql
+	# note: these echo's are for the default values for testing. Not that we're
+	# testing.
+	use mysql && (
+		echo y
+		echo test
+		echo localhost
+		echo undef
+		echo undef
+		) | perl-module_src_compile || perl-module_src_compile || die "compile failed"
+
+	# Sadly, it's not advisable to run make test for this installation, as the
+	# tests are used by the bioperl developers as a sort of todo list. :)  IOW,
+	# it's OK if some fail.
+	#perl-module_src_test || die "test failed"
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl/bioperl-1.2.2.ebuild b/sci-biology/bioperl/bioperl-1.2.2.ebuild
new file mode 100644
index 000000000000..653a27669cc8
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.2.2.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.2.2.ebuild,v 1.1 2004/12/23 22:05:32 ribosome Exp $
+
+inherit perl-module eutils
+CATEGORY="app-sci"
+
+DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
+HOMEPAGE="http://www.bioperl.org/"
+#SRC_URI="http://www.cpan.org/modules/by-module/Bio/${P}.tar.gz"
+SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.gz"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="x86"
+IUSE="mysql gd"
+
+DEPEND="${DEPEND}
+	dev-perl/File-Temp
+	dev-perl/HTML-Parser
+	dev-perl/IO-String
+	dev-perl/IO-stringy
+	dev-perl/SOAP-Lite
+	dev-perl/Storable
+	dev-perl/XML-DOM
+	dev-perl/XML-Parser
+	dev-perl/XML-Writer
+	dev-perl/XML-Twig
+	dev-perl/libxml-perl
+	dev-perl/libwww-perl
+	dev-perl/Graph
+	dev-perl/Text-Shellwords
+	gd? ( >=dev-perl/GD-1.32-r1 )
+	mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+	# remove interactiveness
+	use mysql && epatch ${FILESDIR}/biodbgff-enable-${PV}.patch
+	# want man pages in addition to perldoc documentation??
+	#epatch ${FILESDIR}/domanpages-${PV}.patch
+}
+
+src_compile() {
+	# there's a test to run for BioGFFDB if using mysql
+	perl-module_src_compile || die "compile failed"
+	# make test
+##	perl-module_src_test || die "src test failed"
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+	# get the bptutorial installed and executeable
+	dodir /usr/bin
+	dosym /usr/lib/perl5/site_perl/5.8.0/bptutorial.pl /usr/bin/bptutorial.pl
+	fperms +x /usr/lib/perl5/site_perl/5.8.0/bptutorial.pl
+
+	# bioperl scripts and examples
+	einfo 'Adding bioperl examples and scripts to /usr/share/...'
+	dodir /usr/share/${PF}/scripts
+	#insinto /usr/share/${PF}/scripts
+	cd ${S}/scripts/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
+	dodir /usr/share/${PF}/examples
+	cd ${S}/examples/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/examples; tar xf -)
+	cd ${S}
+
+	# some pods in maindir
+	eval `perl '-V:installsitelib'`
+	MY_SITE_LIB=${installsitelib}
+	insinto ${MY_SITE_LIB}
+	doins biodatabases.pod  biodesign.pod  bioperl.pod  bioscripts.pod
+}
diff --git a/sci-biology/bioperl/bioperl-1.2.3.ebuild b/sci-biology/bioperl/bioperl-1.2.3.ebuild
new file mode 100644
index 000000000000..e4445131c086
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.2.3.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.2.3.ebuild,v 1.1 2004/12/23 22:05:32 ribosome Exp $
+
+inherit perl-module eutils
+
+CATEGORY="app-sci"
+
+DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
+HOMEPAGE="http://www.bioperl.org/"
+#SRC_URI="http://www.cpan.org/modules/by-module/Bio/${P}.tar.gz"
+SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.bz2"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="x86"
+IUSE="mysql gd"
+
+DEPEND="${DEPEND}
+	dev-perl/File-Temp
+	dev-perl/HTML-Parser
+	dev-perl/IO-String
+	dev-perl/IO-stringy
+	dev-perl/SOAP-Lite
+	dev-perl/Storable
+	dev-perl/XML-DOM
+	dev-perl/XML-Parser
+	dev-perl/XML-Writer
+	dev-perl/XML-Twig
+	dev-perl/libxml-perl
+	dev-perl/libwww-perl
+	dev-perl/Graph
+	dev-perl/Text-Shellwords
+	gd? ( >=dev-perl/GD-1.32-r1 )
+	mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+	# remove interactiveness
+	use mysql && epatch ${FILESDIR}/biodbgff-enable-${PV}.patch
+	# want man pages in addition to perldoc documentation??
+	#epatch ${FILESDIR}/domanpages-${PV}.patch
+}
+
+src_compile() {
+	# there's a test to run for BioGFFDB if using mysql
+	perl-module_src_compile || die "compile failed"
+	# make test
+##	perl-module_src_test || die "src test failed"
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+
+	# bioperl scripts and examples
+	einfo 'Adding bioperl examples and scripts to /usr/share/...'
+	dodir /usr/share/${PF}/scripts
+	cd ${S}/scripts/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
+	dodir /usr/share/${PF}/examples
+	cd ${S}/examples/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/examples; tar xf -)
+	dodir /usr/share/doc/${P}
+	cd ${S}
+	tar cf - ./ | ( cd ${D}/usr/share/doc/${P}; tar xf -)
+
+	# some pods in maindir
+	eval `perl '-V:installvendorlib'`
+	MY_SITE_LIB=${installvendorlib}/Bio
+	insinto ${MY_SITE_LIB}
+	doins biodatabases.pod  biodesign.pod  bioperl.pod  bioscripts.pod
+
+	dobin bptutorial.pl
+
+}
diff --git a/sci-biology/bioperl/bioperl-1.2.ebuild b/sci-biology/bioperl/bioperl-1.2.ebuild
new file mode 100644
index 000000000000..cee63dc5d16f
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.2.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.2.ebuild,v 1.1 2004/12/23 22:05:32 ribosome Exp $
+
+inherit perl-module debug
+
+DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI="http://bioperl.org/ftp/DIST/${P}.tar.gz"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="x86 ~ppc ~sparc alpha"
+IUSE="mysql gd"
+
+DEPEND="dev-perl/File-Temp
+	dev-perl/Graph
+	dev-perl/HTML-Parser
+	dev-perl/IO-String
+	dev-perl/IO-stringy
+	dev-perl/Parse-RecDescent
+	dev-perl/SOAP-Lite
+	dev-perl/Storable
+	dev-perl/XML-DOM
+	dev-perl/XML-Parser
+	dev-perl/XML-Writer
+	dev-perl/XML-Twig
+	dev-perl/libxml-perl
+	dev-perl/libwww-perl
+	dev-perl/Text-Shellwords
+	gd? ( >=dev-perl/GD-1.32-r1 )
+	mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
+
+# uncomment this if you'd like to access bioperl docs via man in addition to
+# perldoc.
+#src_unpack() {
+#	unpack ${A}
+#	cd ${S}
+#	echo
+#	einfo " Patching to build manified pods..."
+#	echo
+#	patch < ${FILESDIR}/${P}-manpage.diff
+#}
+
+src_compile() {
+	# note: these echo's give the default values for testing.
+	use mysql && (
+		echo y
+		echo test
+		echo localhost
+		echo undef
+		echo undef
+		) | perl-module_src_compile || perl-module_src_compile || die "compile failed"
+
+	# This dies at RootIO.t:
+	# perl-module_src_test || die "test failed"
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl/bioperl-1.4.ebuild b/sci-biology/bioperl/bioperl-1.4.ebuild
new file mode 100644
index 000000000000..a5213436567d
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.4.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.4.ebuild,v 1.1 2004/12/23 22:05:32 ribosome Exp $
+
+inherit perl-module eutils
+
+CATEGORY="app-sci"
+
+DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.bz2"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="x86 alpha ~ppc"
+IUSE="mysql gd"
+
+DEPEND="
+	dev-perl/File-Temp
+	dev-perl/HTML-Parser
+	dev-perl/IO-String
+	dev-perl/IO-stringy
+	dev-perl/SOAP-Lite
+	dev-perl/Storable
+	dev-perl/XML-DOM
+	dev-perl/XML-Parser
+	dev-perl/XML-Writer
+	dev-perl/XML-Twig
+	dev-perl/libxml-perl
+	dev-perl/libwww-perl
+	dev-perl/Graph
+	dev-perl/Text-Shellwords
+	gd? (
+			>=dev-perl/GD-1.32-r1
+			dev-perl/SVG
+			dev-perl/GD-SVG
+		)
+	mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
+
+src_compile() {
+	yes "" | perl Makefile.PL ${myconf} \
+	         PREFIX=${D}/usr INSTALLDIRS=vendor
+	#perl-module_src_test || die "Test Failed"
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl/files/biodbgff-enable-1.2.2.patch b/sci-biology/bioperl/files/biodbgff-enable-1.2.2.patch
new file mode 100644
index 000000000000..7bd66206a0b4
--- /dev/null
+++ b/sci-biology/bioperl/files/biodbgff-enable-1.2.2.patch
@@ -0,0 +1,98 @@
+--- Makefile.PL.orig	2003-07-14 16:09:49.000000000 +0100
++++ Makefile.PL	2003-07-14 16:15:56.000000000 +0100
+@@ -83,9 +83,6 @@
+ # Prompt user for BioDBGFF stuff
+ #
+ 
+-if(  eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
+-  my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql database) y/n",'n');
+-  if( $proceed =~ /^[yY]/) {
+     my $cfg = {dbd_driver => 'mysql'};
+     GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
+     if (open T,">t/do_biodbgff.tests") {
+@@ -94,13 +91,6 @@
+       }
+       close T;
+     }
+-  } else {
+-    if( -e "t/do_biodbgff.tests" ) {
+-      unlink "t/do_biodbgff.tests";
+-    }
+-  }
+-}
+-
+ 
+ ############################################################################
+ #
+@@ -124,55 +114,27 @@
+   my $d = lc $driver;
+   my $prompt = $options->{'prompt'};
+ 
+-  my $test_db =  exists($options->{"$d-test-db"}) ?
+-    $options->{"$d-test-db"} : ($cfg->{'test_db'} || 'test');
+-  $test_db = prompt
+-    ("Which database should I use for testing the $db drivers?",
+-     $test_db) if $prompt;
+-
+-  my $test_host = exists($options->{"$d-test-host"}) ?
+-    $options->{"$d-test-host"} : ($cfg->{'test_host'} || 'localhost');
+-  $test_host = prompt
+-    ("On which host is database $test_db running (hostname, ip address or host:port)", $test_host) if $prompt;
+-
+-  my($test_user, $test_pass);
+-
+-  $test_user = exists($options->{"$d-test-user"}) ?
+-    $options->{"$d-test-user"} : ($cfg->{'test_user'} || "undef");
+-  $test_user = prompt
+-    ("User name for connecting to database $test_db?", $test_user)
+-      if $prompt;
+-  $test_user = undef if $test_user eq 'undef';
+-
+-  $test_pass = exists($options->{"$d-test-pass"}) ?
+-    $options->{"$d-test-pass"} : ($cfg->{'test_pass'} || "undef");
+-  $test_pass = prompt
+-    ("Password for connecting to database $test_db?", $test_pass)
+-      if $prompt;
+-  $test_pass = undef if $test_pass eq 'undef';
+-
+-  $cfg->{'test_db'}   = $test_db;
+-  $cfg->{'test_host'} = $test_host;
+-  $cfg->{'test_user'} = $test_user;
+-  $cfg->{'test_pass'} = $test_pass;
+-  if ($test_host eq 'undef'  ||  $test_host eq 'localhost') {
+-    $test_host = '';
+-  }
+-  my $test_dsn = "DBI:$driver:database=$test_db";
+-  $cfg->{test_dsn} = $test_dsn;
+-  if ($test_host) {
+-    $cfg->{'test_dsn'} .= ";host=$test_host";
+-  }
++  $options->{"$d-test-db"} = 'test';
++  $options->{"$d-test-host"} = 'localhost';
++  $options->{"$d-test-user"} = n0b0dy;
++  $options->{"$d-test-pass"} = undef;
++
++  $cfg->{'test_db'}   = $options->{"$d-test-db"};
++  $cfg->{'test_host'} = $options->{"$d-test-host"};
++  $cfg->{'test_user'} = $options->{"$d-test-user"};
++  $cfg->{'test_pass'} = $options->{"$d-test-pass"};
+ 
++  my $test_dsn = "DBI:$driver:database=" . $cfg->{test_db};
++  $cfg->{'test_dsn'} = $test_dsn;
+ 
+   if ($options->{'verbose'}) {
+     local $^W=0;  # some uninitialized variable warning coming through
+     print("Driver $driver is using the following settings for tests:\n",
+-	  "    Database $test_db\n",
+-	  "    Host     $test_host\n",
+-	  "    DSN      $test_dsn\n",
+-	  "    User     $test_user\n",
+-	  "    Password $test_pass\n");
++	  "    Database ".$cfg->{test_db}.  "\n",
++	  "    Host     ".$cfg->{test_host}."\n",
++	  "    DSN      ".$cfg->{test_dsn}. "\n",
++	  "    User     ".$cfg->{test_user}."\n",
++	  "    Password ".$cfg->{test_pass}."\n");
+   }
+ }
+ 
diff --git a/sci-biology/bioperl/files/biodbgff-enable-1.2.3.patch b/sci-biology/bioperl/files/biodbgff-enable-1.2.3.patch
new file mode 100644
index 000000000000..7bd66206a0b4
--- /dev/null
+++ b/sci-biology/bioperl/files/biodbgff-enable-1.2.3.patch
@@ -0,0 +1,98 @@
+--- Makefile.PL.orig	2003-07-14 16:09:49.000000000 +0100
++++ Makefile.PL	2003-07-14 16:15:56.000000000 +0100
+@@ -83,9 +83,6 @@
+ # Prompt user for BioDBGFF stuff
+ #
+ 
+-if(  eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
+-  my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql database) y/n",'n');
+-  if( $proceed =~ /^[yY]/) {
+     my $cfg = {dbd_driver => 'mysql'};
+     GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
+     if (open T,">t/do_biodbgff.tests") {
+@@ -94,13 +91,6 @@
+       }
+       close T;
+     }
+-  } else {
+-    if( -e "t/do_biodbgff.tests" ) {
+-      unlink "t/do_biodbgff.tests";
+-    }
+-  }
+-}
+-
+ 
+ ############################################################################
+ #
+@@ -124,55 +114,27 @@
+   my $d = lc $driver;
+   my $prompt = $options->{'prompt'};
+ 
+-  my $test_db =  exists($options->{"$d-test-db"}) ?
+-    $options->{"$d-test-db"} : ($cfg->{'test_db'} || 'test');
+-  $test_db = prompt
+-    ("Which database should I use for testing the $db drivers?",
+-     $test_db) if $prompt;
+-
+-  my $test_host = exists($options->{"$d-test-host"}) ?
+-    $options->{"$d-test-host"} : ($cfg->{'test_host'} || 'localhost');
+-  $test_host = prompt
+-    ("On which host is database $test_db running (hostname, ip address or host:port)", $test_host) if $prompt;
+-
+-  my($test_user, $test_pass);
+-
+-  $test_user = exists($options->{"$d-test-user"}) ?
+-    $options->{"$d-test-user"} : ($cfg->{'test_user'} || "undef");
+-  $test_user = prompt
+-    ("User name for connecting to database $test_db?", $test_user)
+-      if $prompt;
+-  $test_user = undef if $test_user eq 'undef';
+-
+-  $test_pass = exists($options->{"$d-test-pass"}) ?
+-    $options->{"$d-test-pass"} : ($cfg->{'test_pass'} || "undef");
+-  $test_pass = prompt
+-    ("Password for connecting to database $test_db?", $test_pass)
+-      if $prompt;
+-  $test_pass = undef if $test_pass eq 'undef';
+-
+-  $cfg->{'test_db'}   = $test_db;
+-  $cfg->{'test_host'} = $test_host;
+-  $cfg->{'test_user'} = $test_user;
+-  $cfg->{'test_pass'} = $test_pass;
+-  if ($test_host eq 'undef'  ||  $test_host eq 'localhost') {
+-    $test_host = '';
+-  }
+-  my $test_dsn = "DBI:$driver:database=$test_db";
+-  $cfg->{test_dsn} = $test_dsn;
+-  if ($test_host) {
+-    $cfg->{'test_dsn'} .= ";host=$test_host";
+-  }
++  $options->{"$d-test-db"} = 'test';
++  $options->{"$d-test-host"} = 'localhost';
++  $options->{"$d-test-user"} = n0b0dy;
++  $options->{"$d-test-pass"} = undef;
++
++  $cfg->{'test_db'}   = $options->{"$d-test-db"};
++  $cfg->{'test_host'} = $options->{"$d-test-host"};
++  $cfg->{'test_user'} = $options->{"$d-test-user"};
++  $cfg->{'test_pass'} = $options->{"$d-test-pass"};
+ 
++  my $test_dsn = "DBI:$driver:database=" . $cfg->{test_db};
++  $cfg->{'test_dsn'} = $test_dsn;
+ 
+   if ($options->{'verbose'}) {
+     local $^W=0;  # some uninitialized variable warning coming through
+     print("Driver $driver is using the following settings for tests:\n",
+-	  "    Database $test_db\n",
+-	  "    Host     $test_host\n",
+-	  "    DSN      $test_dsn\n",
+-	  "    User     $test_user\n",
+-	  "    Password $test_pass\n");
++	  "    Database ".$cfg->{test_db}.  "\n",
++	  "    Host     ".$cfg->{test_host}."\n",
++	  "    DSN      ".$cfg->{test_dsn}. "\n",
++	  "    User     ".$cfg->{test_user}."\n",
++	  "    Password ".$cfg->{test_pass}."\n");
+   }
+ }
+ 
diff --git a/sci-biology/bioperl/files/bioperl-1.2-manpage.diff b/sci-biology/bioperl/files/bioperl-1.2-manpage.diff
new file mode 100644
index 000000000000..54ba46aa680e
--- /dev/null
+++ b/sci-biology/bioperl/files/bioperl-1.2-manpage.diff
@@ -0,0 +1,28 @@
+--- Makefile.PL.orig	2003-01-09 19:22:26.000000000 -0700
++++ Makefile.PL	2003-01-09 19:23:06.000000000 -0700
+@@ -270,16 +270,16 @@
+ 		   },
+ );
+ 
+-
+-sub MY::manifypods {
+-    my $self = shift;
+-    #print STDERR "In manifypods moment\n";
+-    if( 1 ) {
+-        return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
+-      }
+-      else {
+-        return $self->SUPER::manifypods(@_);
+-      }
+-    }
++# build pods by commenting out
++#sub MY::manifypods {
++#    my $self = shift;
++#    #print STDERR "In manifypods moment\n";
++#    if( 1 ) {
++#        return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
++#      }
++#      else {
++#        return $self->SUPER::manifypods(@_);
++#      }
++#    }
diff --git a/sci-biology/bioperl/files/digest-bioperl-1.0.2 b/sci-biology/bioperl/files/digest-bioperl-1.0.2
new file mode 100644
index 000000000000..226e52d402eb
--- /dev/null
+++ b/sci-biology/bioperl/files/digest-bioperl-1.0.2
@@ -0,0 +1 @@
+MD5 1e4b14269a321aeb1d35d1bdb8c4d75e bioperl-1.0.2.tar.gz 2645781
diff --git a/sci-biology/bioperl/files/digest-bioperl-1.2 b/sci-biology/bioperl/files/digest-bioperl-1.2
new file mode 100644
index 000000000000..183c203289e2
--- /dev/null
+++ b/sci-biology/bioperl/files/digest-bioperl-1.2
@@ -0,0 +1 @@
+MD5 23c0de12d08c394b336331caf33d3e94 bioperl-1.2.tar.gz 3425575
diff --git a/sci-biology/bioperl/files/digest-bioperl-1.2.2 b/sci-biology/bioperl/files/digest-bioperl-1.2.2
new file mode 100644
index 000000000000..f9d1b2b95180
--- /dev/null
+++ b/sci-biology/bioperl/files/digest-bioperl-1.2.2
@@ -0,0 +1 @@
+MD5 c630a5f13a452a65cfa1cbbed1d10378 bioperl-1.2.2.tar.gz 3585206
diff --git a/sci-biology/bioperl/files/digest-bioperl-1.2.3 b/sci-biology/bioperl/files/digest-bioperl-1.2.3
new file mode 100644
index 000000000000..05b4fc161597
--- /dev/null
+++ b/sci-biology/bioperl/files/digest-bioperl-1.2.3
@@ -0,0 +1 @@
+MD5 c64219b6540a722e781a53aea215ebc8 bioperl-1.2.3.tar.bz2 3086024
diff --git a/sci-biology/bioperl/files/digest-bioperl-1.4 b/sci-biology/bioperl/files/digest-bioperl-1.4
new file mode 100644
index 000000000000..43354ceffe03
--- /dev/null
+++ b/sci-biology/bioperl/files/digest-bioperl-1.4
@@ -0,0 +1 @@
+MD5 c49922bb58699cf42765056da8944f6e bioperl-1.4.tar.bz2 4224508
diff --git a/sci-biology/bioperl/files/domanpages-1.2.2.patch b/sci-biology/bioperl/files/domanpages-1.2.2.patch
new file mode 100644
index 000000000000..14cbe35de59a
--- /dev/null
+++ b/sci-biology/bioperl/files/domanpages-1.2.2.patch
@@ -0,0 +1,19 @@
+--- Makefile.PL.orig	2003-07-14 17:31:03.000000000 +0100
++++ Makefile.PL	2003-07-14 17:31:15.000000000 +0100
+@@ -270,16 +270,3 @@
+ 		   },
+ );
+ 
+-
+-sub MY::manifypods {
+-    my $self = shift;
+-    #print STDERR "In manifypods moment\n";
+-    if( 1 ) {
+-        return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
+-      }
+-      else {
+-        return $self->SUPER::manifypods(@_);
+-      }
+-    }
+-
+-
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
new file mode 100644
index 000000000000..8a4bcd47220d
--- /dev/null
+++ b/sci-biology/bioperl/metadata.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer><email>sediener@gentoo.org</email></maintainer>
+</pkgmetadata>