Removed obsolete versions. Ebuild clean-up.

Package-Manager: portage-2.0.53

18 files changed, 21 insertions, 586 deletions

diff --git a/sci-biology/bioperl-run/ChangeLog b/sci-biology/bioperl-run/ChangeLog
index c55412595bc0..61e5de453b24 100644
--- a/sci-biology/bioperl-run/ChangeLog
+++ b/sci-biology/bioperl-run/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/bioperl-run
-# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/ChangeLog,v 1.6 2005/11/28 12:02:35 mcummings Exp $
+# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/ChangeLog,v 1.7 2006/01/21 17:34:58 ribosome Exp $
+
+  21 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
+  -bioperl-run-1.2.2.ebuild, bioperl-run-1.4.ebuild:
+  Removed obsolete versions. Ebuild clean-up.
 
   28 Nov 2005; <mcumming@gentoo.org> bioperl-run-1.2.2.ebuild,
   bioperl-run-1.4.ebuild:
diff --git a/sci-biology/bioperl-run/bioperl-run-1.2.2.ebuild b/sci-biology/bioperl-run/bioperl-run-1.2.2.ebuild
deleted file mode 100644
index 7b5c44f27ef1..000000000000
--- a/sci-biology/bioperl-run/bioperl-run-1.2.2.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/bioperl-run-1.2.2.ebuild,v 1.6 2005/11/28 12:02:35 mcummings Exp $
-
-inherit perl-app eutils
-
-DESCRIPTION="A collection of tools for bioinformatics, genomics and life science research: subset required to run analyses"
-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=""
-
-RDEPEND="
-	dev-perl/Algorithm-Diff
-	perl-core/File-Temp
-	dev-perl/IO-String
-	dev-perl/XML-Parser"
-
-DEPEND=""
-
-src_unpack() {
-	unpack ${A}
-	cd ${S}
-	# remove interactiveness
-	epatch ${FILESDIR}/bioperl-run-Pise-test-patch.diff
-}
-
-src_compile() {
-	# there's a test to run for BioGFFDB if using mysql
-	perl-module_src_compile || die "compile failed"
-	# make test
-##	perl-module_src_test || die "src test failed"
-}
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-
-	# bioperl scripts and examples
-	einfo 'Adding bioperl examples and scripts to /usr/share/...'
-	dodir /usr/share/${PF}/scripts
-	#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}
-
-}
diff --git a/sci-biology/bioperl-run/bioperl-run-1.4.ebuild b/sci-biology/bioperl-run/bioperl-run-1.4.ebuild
index 147a9c83f42c..1fc72ede89cf 100644
--- a/sci-biology/bioperl-run/bioperl-run-1.4.ebuild
+++ b/sci-biology/bioperl-run/bioperl-run-1.4.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/bioperl-run-1.4.ebuild,v 1.6 2005/11/28 12:02:35 mcummings Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/bioperl-run-1.4.ebuild,v 1.7 2006/01/21 17:34:58 ribosome Exp $
 
 inherit perl-app eutils
 
@@ -36,11 +36,10 @@ src_install() {
 	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 -)
+	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 ${S}
-
+	cd "${S}"/examples/
+	tar cf - ./ | ( cd "${D}"/usr/share/${PF}/examples; tar xf -)
+	cd "${S}"
 }
diff --git a/sci-biology/bioperl-run/files/digest-bioperl-run-1.2.2 b/sci-biology/bioperl-run/files/digest-bioperl-run-1.2.2
deleted file mode 100644
index cf92f27aa20d..000000000000
--- a/sci-biology/bioperl-run/files/digest-bioperl-run-1.2.2
+++ /dev/null
@@ -1 +0,0 @@
-MD5 2ffbaa69e713f102f86c7b7462ccff52 bioperl-run-1.2.2.tar.gz 811989
diff --git a/sci-biology/bioperl/bioperl-1.0.2.ebuild b/sci-biology/bioperl/bioperl-1.0.2.ebuild
deleted file mode 100644
index bdb3ed04c575..000000000000
--- a/sci-biology/bioperl/bioperl-1.0.2.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2005 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 1.7 2005/11/28 12:03:14 mcummings Exp $
-
-inherit perl-app
-
-DESCRIPTION="A 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="perl-core/File-Temp
-	dev-perl/HTML-Parser
-	dev-perl/IO-String
-	dev-perl/IO-stringy
-	dev-perl/SOAP-Lite
-	perl-core/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
deleted file mode 100644
index c12ab5134bb7..000000000000
--- a/sci-biology/bioperl/bioperl-1.2.2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2005 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 1.7 2005/11/28 12:03:14 mcummings Exp $
-
-inherit perl-app eutils
-
-DESCRIPTION="A 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="perl-core/File-Temp
-	dev-perl/HTML-Parser
-	dev-perl/IO-String
-	dev-perl/IO-stringy
-	dev-perl/SOAP-Lite
-	perl-core/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
deleted file mode 100644
index f4eae261077d..000000000000
--- a/sci-biology/bioperl/bioperl-1.2.3.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2005 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 1.7 2005/11/28 12:03:14 mcummings Exp $
-
-inherit perl-app eutils
-
-DESCRIPTION="A 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="perl-core/File-Temp
-	dev-perl/HTML-Parser
-	dev-perl/IO-String
-	dev-perl/IO-stringy
-	dev-perl/SOAP-Lite
-	perl-core/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
deleted file mode 100644
index 2fd265d242ee..000000000000
--- a/sci-biology/bioperl/bioperl-1.2.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2005 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 1.7 2005/11/28 12:03:14 mcummings Exp $
-
-inherit perl-app debug
-
-DESCRIPTION="A 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="perl-core/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
-	perl-core/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
index 3a31d6619edf..9d1c23296790 100644
--- a/sci-biology/bioperl/bioperl-1.4.ebuild
+++ b/sci-biology/bioperl/bioperl-1.4.ebuild
@@ -1,20 +1,19 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 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 1.10 2005/11/28 12:03:14 mcummings Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.4.ebuild,v 1.11 2006/01/21 17:32:30 ribosome Exp $
 
 inherit perl-app eutils
 
-DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
+DESCRIPTION="Collection of tools for bioinformatics, genomics and life science research"
 HOMEPAGE="http://www.bioperl.org/"
-SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.bz2"
+SRC_URI="http://www.${PN}.org/ftp/DIST/${P}.tar.bz2"
 
 LICENSE="Artistic GPL-2"
 SLOT="0"
 KEYWORDS="alpha ~amd64 ~ppc ~sparc x86"
 IUSE="mysql gd"
 
-DEPEND="
-	perl-core/File-Temp
+DEPEND="perl-core/File-Temp
 	dev-perl/HTML-Parser
 	dev-perl/IO-String
 	dev-perl/IO-stringy
@@ -37,7 +36,7 @@ DEPEND="
 
 src_compile() {
 	yes "" | perl Makefile.PL ${myconf} \
-	         PREFIX=${D}/usr INSTALLDIRS=vendor
+	         PREFIX="${D}"/usr INSTALLDIRS=vendor
 }
 
 src_test() {
diff --git a/sci-biology/bioperl/files/biodbgff-enable-1.2.2.patch b/sci-biology/bioperl/files/biodbgff-enable-1.2.2.patch
deleted file mode 100644
index 7bd66206a0b4..000000000000
--- a/sci-biology/bioperl/files/biodbgff-enable-1.2.2.patch
+++ /dev/null
@@ -1,98 +0,0 @@
---- 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
deleted file mode 100644
index 7bd66206a0b4..000000000000
--- a/sci-biology/bioperl/files/biodbgff-enable-1.2.3.patch
+++ /dev/null
@@ -1,98 +0,0 @@
---- 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
deleted file mode 100644
index 54ba46aa680e..000000000000
--- a/sci-biology/bioperl/files/bioperl-1.2-manpage.diff
+++ /dev/null
@@ -1,28 +0,0 @@
---- 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
deleted file mode 100644
index 226e52d402eb..000000000000
--- a/sci-biology/bioperl/files/digest-bioperl-1.0.2
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 183c203289e2..000000000000
--- a/sci-biology/bioperl/files/digest-bioperl-1.2
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index f9d1b2b95180..000000000000
--- a/sci-biology/bioperl/files/digest-bioperl-1.2.2
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 05b4fc161597..000000000000
--- a/sci-biology/bioperl/files/digest-bioperl-1.2.3
+++ /dev/null
@@ -1 +0,0 @@
-MD5 c64219b6540a722e781a53aea215ebc8 bioperl-1.2.3.tar.bz2 3086024
diff --git a/sci-biology/bioperl/files/domanpages-1.2.2.patch b/sci-biology/bioperl/files/domanpages-1.2.2.patch
deleted file mode 100644
index 14cbe35de59a..000000000000
--- a/sci-biology/bioperl/files/domanpages-1.2.2.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- 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/clustalx/Manifest b/sci-biology/clustalx/Manifest
index 7b9315609791..0339ff04af1a 100644
--- a/sci-biology/clustalx/Manifest
+++ b/sci-biology/clustalx/Manifest
@@ -1,6 +1,4 @@
-MD5 6de8fe67a323953225ddf6235114341e ChangeLog 1975
-MD5 0f5a065a208f1b86c23cff8992d0c4b1 clustalx-1.83-r1.ebuild 1352
-MD5 272b5b012593acd07a7a60b8b64e6761 metadata.xml 509
+MD5 ab525fd01e6f22fee5fec0c376f35be2 ChangeLog 2089
 MD5 a72da78ea67f9b3bc3f70a62d7289660 clustalx-1.83-r2.ebuild 1820
-MD5 800c4da737d4fb9af3d8ffb7f6f44892 files/digest-clustalx-1.83-r1 68
 MD5 800c4da737d4fb9af3d8ffb7f6f44892 files/digest-clustalx-1.83-r2 68
+MD5 272b5b012593acd07a7a60b8b64e6761 metadata.xml 509