Moving sci-biology category to the stable overlay again

svn path=/broken/; revision=748

28 files changed, 0 insertions, 647 deletions

diff --git a/sci-biology/autoprime/Manifest b/sci-biology/autoprime/Manifest
deleted file mode 100644
index 8550d31..0000000
--- a/sci-biology/autoprime/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-MD5 9d92f632ade80a2f6e5ec60d82fb4cce autoprime-2.0.0.ebuild 761
-MD5 97c7532df6bbfd7ad008aec4887b4de3 autoprime-2.0.1.ebuild 649
-MD5 fbe4fdc3bebd9831e9990477561d72da autoprime-2.0.ebuild 746
-MD5 3460ece729b38b487daade18802c3285 files/digest-autoprime-2.0.0 66
-MD5 09a9c57f415ba24fcfa6fae440f49968 files/digest-autoprime-2.0.1 66
-MD5 7784311d2ac1eb36499051b488cbd1bc files/digest-autoprime-2.0 62
diff --git a/sci-biology/autoprime/autoprime-2.0.0.ebuild b/sci-biology/autoprime/autoprime-2.0.0.ebuild
deleted file mode 100644
index 659d86c..0000000
--- a/sci-biology/autoprime/autoprime-2.0.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /home/fsk/.cvsroot/AutoPrime/ebuilds/sci-biology/autoprime/autoprime-2.0.0.ebuild,v 1.1.1.1 2005/09/03 20:17:54 fsk Exp $
-
-inherit perl-module
-
-MY_P=${P/autoprime/AutoPrime}
-
-CATEGORY="sci-biology"
-
-DESCRIPTION="A command line tool to generate primers for RT-PCR"
-HOMEPAGE="http://www.autoprime.de/"
-SRC_URI="http://www.gunnarwrobel.de/downloads/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-DEPEND=">=sci-biology/bioperl-1.4
-	>=sci-biology/repbase-9.12
-	>=sci-biology/primer3-1.0.0
-	"
-
-src_compile()
-{
-	cd ${WORKDIR}/${MY_P}
-
-	perl-module_src_compile
-}
-
-src_install()
-{
-	cd ${WORKDIR}/${MY_P}
-
-	perl-module_src_install
-}
diff --git a/sci-biology/autoprime/autoprime-2.0.1.ebuild b/sci-biology/autoprime/autoprime-2.0.1.ebuild
deleted file mode 100644
index f6b2708..0000000
--- a/sci-biology/autoprime/autoprime-2.0.1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2004-2005 Gunnar Wrobel
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit perl-module
-
-MY_P=${P/autoprime/AutoPrime}
-
-CATEGORY="sci-biology"
-
-DESCRIPTION="A command line tool to generate primers for RT-PCR"
-HOMEPAGE="http://www.autoprime.de/"
-SRC_URI="http://www.gunnarwrobel.de/downloads/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-DEPEND=">=sci-biology/ensembl-perl-33
-	>=sci-biology/repbase-10.07
-	>=sci-biology/primer3-1.0.0
-	"
-
-src_compile()
-{
-	cd ${WORKDIR}/${MY_P}
-
-	perl-module_src_compile
-}
-
-src_install()
-{
-	cd ${WORKDIR}/${MY_P}
-
-	perl-module_src_install
-}
diff --git a/sci-biology/autoprime/autoprime-2.0.ebuild b/sci-biology/autoprime/autoprime-2.0.ebuild
deleted file mode 100644
index cfac2ec..0000000
--- a/sci-biology/autoprime/autoprime-2.0.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /home/fsk/.cvsroot/AutoPrime/ebuilds/sci-biology/autoprime/autoprime-2.0.ebuild,v 1.1.1.1 2005/09/03 20:17:54 fsk Exp $
-
-inherit perl-module
-
-CATEGORY="sci-biology"
-
-DESCRIPTION="A command line tool to generate primers for RT-PCR"
-HOMEPAGE="http://www.autoprime.de/"
-SRC_URI="http://www.gunnarwrobel.de/downloads/AutoPrime-2.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-DEPEND=">=sci-biology/bioperl-1.4
-	>=sci-biology/repbase-9.12
-	>=sci-biology/primer3-1.0.0
-	"
-
-src_compile()
-{
-	cd ${WORKDIR}/${A/.tar.gz//}
-
-	perl-module_src_compile
-}
-
-src_install()
-{
-	cd ${WORKDIR}/${A/.tar.gz//}
-
-	perl-module_src_install
-}
diff --git a/sci-biology/autoprime/files/digest-autoprime-2.0 b/sci-biology/autoprime/files/digest-autoprime-2.0
deleted file mode 100644
index 3d38458..0000000
--- a/sci-biology/autoprime/files/digest-autoprime-2.0
+++ /dev/null
@@ -1 +0,0 @@
-MD5 6cfd9178f1d769aeebc45ae2b28cb71f AutoPrime-2.tar.gz 24042
diff --git a/sci-biology/autoprime/files/digest-autoprime-2.0.0 b/sci-biology/autoprime/files/digest-autoprime-2.0.0
deleted file mode 100644
index bdee895..0000000
--- a/sci-biology/autoprime/files/digest-autoprime-2.0.0
+++ /dev/null
@@ -1 +0,0 @@
-MD5 ad8c629fa33cbff631a0413191f857dd AutoPrime-2.0.0.tar.gz 27658
diff --git a/sci-biology/autoprime/files/digest-autoprime-2.0.1 b/sci-biology/autoprime/files/digest-autoprime-2.0.1
deleted file mode 100644
index 1a4558b..0000000
--- a/sci-biology/autoprime/files/digest-autoprime-2.0.1
+++ /dev/null
@@ -1 +0,0 @@
-MD5 70b857e0563898db9ad15acf8babd014 AutoPrime-2.0.1.tar.gz 25737
diff --git a/sci-biology/autoprimeweb/Manifest b/sci-biology/autoprimeweb/Manifest
deleted file mode 100644
index db785a4..0000000
--- a/sci-biology/autoprimeweb/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 7cd78cb7228942db282ec1271aaa6319 autoprimeweb-2.0.0.ebuild 747
-MD5 2fbf1c8f321aa131fd60a5a0a5055308 files/digest-autoprimeweb-2.0.0 70
diff --git a/sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild b/sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild
deleted file mode 100644
index e2f427d..0000000
--- a/sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 2004-2005 Gunnar Wrobel
-# $Header: $
-
-inherit webapp
-
-MY_P=${P/autoprimeweb/AutoPrimeWeb}
-
-DESCRIPTION="A web frontend for AutoPrime"
-HOMEPAGE="http://www.autoprime.de/"
-SRC_URI="http://www.gunnarwrobel.de/downloads/${MY_P}.tar.bz2"
-
-LICENSE="GPL-2"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-DEPEND="virtual/httpd-php
-        dev-perl/XML-XSLT
-        sci-biology/autoprime"
-
-S=${WORKDIR}/${PN/autoprimeweb/AutoPrimeWeb}
-
-src_install () {
-
-    webapp_src_preinst
-
-    cp -r . ${D}${MY_HTDOCSDIR}
-    keepdir ${MY_HTDOCSDIR}/xmlfiles
-
-    webapp_serverowned ${MY_HTDOCSDIR}/xmlfiles
-
-    rm -rf ${D}${MY_HTDOCSDIR}/cgi
-
-    mkdir -p ${D}${MY_CGIBINDIR}/autoprimeweb
-    cp -r cgi/* ${D}${MY_CGIBINDIR}/autoprimeweb
-
-    webapp_src_install
-
-}
-
-
-
-
diff --git a/sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0 b/sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0
deleted file mode 100644
index fa17cb1..0000000
--- a/sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0
+++ /dev/null
@@ -1 +0,0 @@
-MD5 580b9c0665889a1ababd05f3f14415be AutoPrimeWeb-2.0.0.tar.bz2 30337
diff --git a/sci-biology/ensembl-perl/Manifest b/sci-biology/ensembl-perl/Manifest
deleted file mode 100644
index cc791f2..0000000
--- a/sci-biology/ensembl-perl/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-MD5 4167bbcf0e0b05c834ac8b680e2e0955 ensembl-perl-31.ebuild 773
-MD5 92dcb9f863ac5144527c046e5b2d3746 ensembl-perl-32.ebuild 780
-MD5 92dcb9f863ac5144527c046e5b2d3746 ensembl-perl-33.ebuild 780
-MD5 b17aafa4efc4e955cbc2374091962976 files/Makefile.PL 311
-MD5 d41d8cd98f00b204e9800998ecf8427e files/digest-ensembl-perl-31 0
-MD5 d41d8cd98f00b204e9800998ecf8427e files/digest-ensembl-perl-32 0
-MD5 d41d8cd98f00b204e9800998ecf8427e files/digest-ensembl-perl-33 0
diff --git a/sci-biology/ensembl-perl/ensembl-perl-31.ebuild b/sci-biology/ensembl-perl/ensembl-perl-31.ebuild
deleted file mode 100644
index d00116e..0000000
--- a/sci-biology/ensembl-perl/ensembl-perl-31.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit cvs perl-module
-
-CATEGORY="sci-biology"
-
-DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database"
-HOMEPAGE="http://www.ensembl.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-ECVS_LOCALNAME="EnsEMBL"
-ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster"
-ECVS_MODULE="ensembl/modules/Bio/EnsEMBL"
-ECVS_BRANCH="branch-ensembl-${PV}"
-ECVS_USER="cvsuser"
-ECVS_PASS="CVSUSER"
-
-
-DEPEND="=sci-biology/bioperl-1.4"
-
-src_unpack()
-{
-	cvs_src_unpack
-
-	cp ${FILESDIR}/Makefile.PL ${WORKDIR}/
-}
-
-src_compile()
-{
-	cd ${WORKDIR}
-
-	perl-module_src_compile
-}
-
-src_install()
-{
-	cd ${WORKDIR}
-
-	perl-module_src_install
-}
diff --git a/sci-biology/ensembl-perl/ensembl-perl-32.ebuild b/sci-biology/ensembl-perl/ensembl-perl-32.ebuild
deleted file mode 100644
index bcd7ff4..0000000
--- a/sci-biology/ensembl-perl/ensembl-perl-32.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit cvs perl-module
-
-CATEGORY="sci-biology"
-
-DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database"
-HOMEPAGE="http://www.ensembl.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-ECVS_LOCALNAME="EnsEMBL"
-ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster"
-ECVS_MODULE="ensembl/modules/Bio/EnsEMBL"
-ECVS_BRANCH="branch-ensembl-${PV}"
-ECVS_USER="cvsuser"
-ECVS_PASS="CVSUSER"
-
-
-DEPEND="=sci-biology/bioperl-1.4"
-
-src_unpack()
-{
-	cvs_src_unpack
-
-	cp ${FILESDIR}/Makefile.PL ${WORKDIR}/
-}
-
-src_compile()
-{
-	cd ${WORKDIR}
-
-	perl-module_src_compile
-}
-
-src_install()
-{
-	cd ${WORKDIR}
-
-	perl-module_src_install
-}
diff --git a/sci-biology/ensembl-perl/ensembl-perl-33.ebuild b/sci-biology/ensembl-perl/ensembl-perl-33.ebuild
deleted file mode 100644
index bcd7ff4..0000000
--- a/sci-biology/ensembl-perl/ensembl-perl-33.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit cvs perl-module
-
-CATEGORY="sci-biology"
-
-DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database"
-HOMEPAGE="http://www.ensembl.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-ECVS_LOCALNAME="EnsEMBL"
-ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster"
-ECVS_MODULE="ensembl/modules/Bio/EnsEMBL"
-ECVS_BRANCH="branch-ensembl-${PV}"
-ECVS_USER="cvsuser"
-ECVS_PASS="CVSUSER"
-
-
-DEPEND="=sci-biology/bioperl-1.4"
-
-src_unpack()
-{
-	cvs_src_unpack
-
-	cp ${FILESDIR}/Makefile.PL ${WORKDIR}/
-}
-
-src_compile()
-{
-	cd ${WORKDIR}
-
-	perl-module_src_compile
-}
-
-src_install()
-{
-	cd ${WORKDIR}
-
-	perl-module_src_install
-}
diff --git a/sci-biology/ensembl-perl/files/Makefile.PL b/sci-biology/ensembl-perl/files/Makefile.PL
deleted file mode 100644
index cafb2aa..0000000
--- a/sci-biology/ensembl-perl/files/Makefile.PL
+++ /dev/null
@@ -1,10 +0,0 @@
-use ExtUtils::MakeMaker 5.0;
-
-WriteMakefile(
-	      NAME        => "Bio::EnsEMBL",
-	      VERSION     => "31",
-	      AUTHOR      => "Sanger Center (ensembl-dev@ebi.ac.uk)",
-	      ABSTRACT    => "BioPerl modules to access ensembl",
-	      INSTALLDIRS => "vendor",
-	      PMLIBDIRS   => [ "EnsEMBL" ]
-	      );
diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-31 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-31
deleted file mode 100644
index e69de29..0000000
--- a/sci-biology/ensembl-perl/files/digest-ensembl-perl-31
+++ /dev/null
diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-32 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-32
deleted file mode 100644
index e69de29..0000000
--- a/sci-biology/ensembl-perl/files/digest-ensembl-perl-32
+++ /dev/null
diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-33 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-33
deleted file mode 100644
index e69de29..0000000
--- a/sci-biology/ensembl-perl/files/digest-ensembl-perl-33
+++ /dev/null
diff --git a/sci-biology/repbase/Manifest b/sci-biology/repbase/Manifest
deleted file mode 100644
index f727e94..0000000
--- a/sci-biology/repbase/Manifest
+++ /dev/null
@@ -1,9 +0,0 @@
-MD5 389a1a303497d5503f334e60466195a3 repbase-10.03.ebuild 1463
-MD5 91b78f561ed7a033faf48d1e4d5c68e3 repbase-10.04.ebuild 1456
-MD5 389a1a303497d5503f334e60466195a3 repbase-9.12.ebuild 1463
-MD5 24860972eb7dd95216a72d60acbd5d84 repbase-10.07.ebuild 1465
-MD5 943163c2456b74490a384738b63d6d94 files/clean 1161
-MD5 6d3280263178010862efcb1b59c4c816 files/digest-repbase-10.03 71
-MD5 3d53f3eb616d7665c620cf1ff30f5f99 files/digest-repbase-10.04 71
-MD5 6d171b2224c472ad2ab93a3033b09c96 files/digest-repbase-9.12 70
-MD5 899787e1cc59fab954e7331592a2d857 files/digest-repbase-10.07 71
diff --git a/sci-biology/repbase/files/clean b/sci-biology/repbase/files/clean
deleted file mode 100755
index 37ee59c..0000000
--- a/sci-biology/repbase/files/clean
+++ /dev/null
@@ -1,59 +0,0 @@
-#!/usr/bin/perl -w 
-
-use strict;
-
-my $name="";
-my $sequence="";
-my $infile  = $ARGV[0];
-my $outfile = $ARGV[1];
-
-open(LIB, $infile);
-
-open(CLIB, ">", $outfile);
-
-while (<LIB>)
-{
-    if (m/^>/)
-    {
-	if (not $name eq "")
-	{
-	    if ($sequence eq "")
-	    {
-		print "---------------------------------------------------------------------------------------\n";
-		print "Empty sequence: " . $name . "\n";
-	    } 
-	    else
-	    {
-		if ($sequence =~ m/^[ACGTNWSYRMHKXDVB]*$/)
-		{
-		    $sequence =~ s/[WSYRMHKXDVB]/N/g;
-		    if (not $sequence =~ m/NNNN/)
-		    {
-			print CLIB $name;
-			print CLIB $sequence . "\n";
-		    }
-		    else
-		    {
-			print "---------------------------------------------------------------------------------------\n";
-			print "Too many N's:  " . $name;
-		    }
-		}
-		else
-		{
-		    print "---------------------------------------------------------------------------------------\n";
-		    print "Invalid entry: " . $name;
-		    $sequence =~ s/[ACGTN]//g;
-		    print "Reduced sequence:\n";
-		    print $sequence . "\n";
-		}
-		$sequence = "";
-	    }
-	}
-	$name = $_;
-    }
-    else
-    {
-	$sequence .= uc($_);
-	$sequence =~ s/\n//g;
-    }
-}
diff --git a/sci-biology/repbase/files/digest-repbase-10.03 b/sci-biology/repbase/files/digest-repbase-10.03
deleted file mode 100644
index c718f4e..0000000
--- a/sci-biology/repbase/files/digest-repbase-10.03
+++ /dev/null
@@ -1 +0,0 @@
-MD5 c530ff51d4f60a8ae2114f3185b0235f RepBase10.03.fasta.tar.gz 3530082
diff --git a/sci-biology/repbase/files/digest-repbase-10.04 b/sci-biology/repbase/files/digest-repbase-10.04
deleted file mode 100644
index ede3594..0000000
--- a/sci-biology/repbase/files/digest-repbase-10.04
+++ /dev/null
@@ -1 +0,0 @@
-MD5 76b1ac539ad79a64ab48904027631cea RepBase10.04.fasta.tar.gz 3562104
diff --git a/sci-biology/repbase/files/digest-repbase-10.07 b/sci-biology/repbase/files/digest-repbase-10.07
deleted file mode 100644
index 1a0810a..0000000
--- a/sci-biology/repbase/files/digest-repbase-10.07
+++ /dev/null
@@ -1 +0,0 @@
-MD5 54669e3eb561fa101903c681a594e2c7 RepBase10.07.fasta.tar.gz 4061677
diff --git a/sci-biology/repbase/files/digest-repbase-9.12 b/sci-biology/repbase/files/digest-repbase-9.12
deleted file mode 100644
index 3188ee7..0000000
--- a/sci-biology/repbase/files/digest-repbase-9.12
+++ /dev/null
@@ -1 +0,0 @@
-MD5 fdf7cf4befd28b6b902da0f4a9263c72 RepBase9.12.fasta.tar.gz 3271264
diff --git a/sci-biology/repbase/repbase-10.03.ebuild b/sci-biology/repbase/repbase-10.03.ebuild
deleted file mode 100644
index 32f0e4f..0000000
--- a/sci-biology/repbase/repbase-10.03.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-CATEGORY="sci-biology"
-
-MY_P="RepBase${PV}.fasta"
-
-DESCRIPTION="A database of repetetive genetic elements in various organisms."
-HOMEPAGE="http://www.girinst.org"
-SRC_URI="${MY_P}.tar.gz"
-
-LICENSE="repbase-agreement"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-RESTRICT="fetch"
-
-REPBASELOC="${HOMEPAGE}/server/RepBase/"
-
-REPLIBRARIES="
-angrep.ref=repeat_lib_A.gambiae
-cbrrep.ref=repeat_lib_C.briggsae
-celrep.ref=repeat_lib_C.elegans
-drorep.ref=repeat_lib_D.melanogaster
-fugrep.ref=repeat_lib_F.rubripes
-humrep.ref=repeat_lib_H.sapiens
-prirep.ref=repeat_lib_P.troglodyte
-rodrep.ref=repeat_lib_M.musculus
-rodrep.ref=repeat_lib_R.norvegicus
-zebrep.ref=repeat_lib_D.rerio
-"
-
-pkg_nofetch() 
-{
-    einfo "Please download ${SRC_URI}"
-    einfo "from ${REPBASELOC} and place it in ${DISTDIR}."
-    einfo "You will need to register as an academic user at"
-    einfo "${HOMEPAGE} in order to be"
-    einfo "allowed to download the file."
-}
-
-src_compile() 
-{
-    cp ${FILESDIR}/clean ${WORKDIR}
-    cd ${WORKDIR}
-    for lib in ${REPLIBRARIES}
-    do
-      einfo Cleaning library file ${lib/=*/} to ${lib/*=/}
-      ./clean ${MY_P}/${lib/=*/} ${lib/*=/} 
-    done
-}
-
-src_install() 
-{
-    cd ${WORKDIR}
-    install -m 755 -d ${D}/usr/share/${P}/
-    for lib in ${REPLIBRARIES}
-    do
-      install -m 644 ${lib/*=/} ${D}/usr/share/${P}/
-    done
-}
diff --git a/sci-biology/repbase/repbase-10.04.ebuild b/sci-biology/repbase/repbase-10.04.ebuild
deleted file mode 100644
index 90cfaa9..0000000
--- a/sci-biology/repbase/repbase-10.04.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-CATEGORY="sci-biology"
-
-MY_P="RepBase${PV}.fasta"
-
-DESCRIPTION="A database of repetetive genetic elements in various organisms."
-HOMEPAGE="http://www.girinst.org"
-SRC_URI="${MY_P}.tar.gz"
-
-LICENSE="repbase-agreement"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-RESTRICT="fetch"
-
-REPBASELOC="${HOMEPAGE}/server/RepBase/"
-
-REPLIBRARIES="
-angrep.ref=repeat_lib_A.gambiae
-cbrrep.ref=repeat_lib_C.briggsae
-celrep.ref=repeat_lib_C.elegans
-drorep.ref=repeat_lib_D.melanogaster
-fugrep.ref=repeat_lib_F.rubripes
-humrep.ref=repeat_lib_H.sapiens
-prirep.ref=repeat_lib_P.troglodyte
-rodrep.ref=repeat_lib_M.musculus
-rodrep.ref=repeat_lib_R.norvegicus
-zebrep.ref=repeat_lib_D.rerio
-"
-
-pkg_nofetch() 
-{
-    einfo "Please download ${SRC_URI}"
-    einfo "from ${REPBASELOC} and place it in ${DISTDIR}."
-    einfo "You will need to register as an academic user at"
-    einfo "${HOMEPAGE} in order to be"
-    einfo "allowed to download the file."
-}
-
-src_compile() 
-{
-    cp ${FILESDIR}/clean ${WORKDIR}
-    cd ${WORKDIR}
-    for lib in ${REPLIBRARIES}
-    do
-      einfo Cleaning library file ${lib/=*/} to ${lib/*=/}
-      ./clean ${MY_P}/${lib/=*/} ${lib/*=/} 
-    done
-}
-
-src_install() 
-{
-    cd ${WORKDIR}
-    install -m 755 -d ${D}/usr/share/${P}/
-    for lib in ${REPLIBRARIES}
-    do
-      install -m 644 ${lib/*=/} ${D}/usr/share/${P}/
-    done
-}
diff --git a/sci-biology/repbase/repbase-10.07.ebuild b/sci-biology/repbase/repbase-10.07.ebuild
deleted file mode 100644
index 50549fd..0000000
--- a/sci-biology/repbase/repbase-10.07.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-CATEGORY="sci-biology"
-
-MY_P="RepBase${PV}.fasta"
-
-DESCRIPTION="A database of repetetive genetic elements in various organisms."
-HOMEPAGE="http://www.girinst.org"
-SRC_URI="${MY_P}.tar.gz"
-
-LICENSE="repbase-agreement"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-RESTRICT="fetch"
-
-REPBASELOC="${HOMEPAGE}/server/RepBase/"
-
-REPLIBRARIES="
-angrep.ref=repeat_lib_A.gambiae
-cbrrep.ref=repeat_lib_C.briggsae
-celrep.ref=repeat_lib_C.elegans
-drorep.ref=repeat_lib_D.melanogaster
-fugrep.ref=repeat_lib_F.rubripes
-humrep.ref=repeat_lib_H.sapiens
-prirep.ref=repeat_lib_P.troglodyte
-rodrep.ref=repeat_lib_M.musculus
-rodrep.ref=repeat_lib_R.norvegicus
-zebrep.ref=repeat_lib_D.rerio
-"
-
-pkg_nofetch() 
-{
-    einfo "Please download ${SRC_URI}"
-    einfo "from ${REPBASELOC} and place it in ${DISTDIR}."
-    einfo "You will need to register as an academic user at"
-    einfo "${HOMEPAGE} in order to be"
-    einfo "allowed to download the file."
-}
-
-src_compile() 
-{
-    cp ${FILESDIR}/clean ${WORKDIR}
-    cd ${WORKDIR}
-    for lib in ${REPLIBRARIES}
-    do
-      einfo Cleaning library file ${lib/=*/} to ${lib/*=/}
-      ./clean ${MY_P}/${lib/=*/} ${lib/*=/} 
-    done
-}
-
-src_install() 
-{
-    cd ${WORKDIR}
-    install -m 755 -d ${D}/usr/share/${PN}/
-    for lib in ${REPLIBRARIES}
-    do
-      install -m 644 ${lib/*=/} ${D}/usr/share/${PN}/
-    done
-}
diff --git a/sci-biology/repbase/repbase-9.12.ebuild b/sci-biology/repbase/repbase-9.12.ebuild
deleted file mode 100644
index 32f0e4f..0000000
--- a/sci-biology/repbase/repbase-9.12.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-CATEGORY="sci-biology"
-
-MY_P="RepBase${PV}.fasta"
-
-DESCRIPTION="A database of repetetive genetic elements in various organisms."
-HOMEPAGE="http://www.girinst.org"
-SRC_URI="${MY_P}.tar.gz"
-
-LICENSE="repbase-agreement"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-RESTRICT="fetch"
-
-REPBASELOC="${HOMEPAGE}/server/RepBase/"
-
-REPLIBRARIES="
-angrep.ref=repeat_lib_A.gambiae
-cbrrep.ref=repeat_lib_C.briggsae
-celrep.ref=repeat_lib_C.elegans
-drorep.ref=repeat_lib_D.melanogaster
-fugrep.ref=repeat_lib_F.rubripes
-humrep.ref=repeat_lib_H.sapiens
-prirep.ref=repeat_lib_P.troglodyte
-rodrep.ref=repeat_lib_M.musculus
-rodrep.ref=repeat_lib_R.norvegicus
-zebrep.ref=repeat_lib_D.rerio
-"
-
-pkg_nofetch() 
-{
-    einfo "Please download ${SRC_URI}"
-    einfo "from ${REPBASELOC} and place it in ${DISTDIR}."
-    einfo "You will need to register as an academic user at"
-    einfo "${HOMEPAGE} in order to be"
-    einfo "allowed to download the file."
-}
-
-src_compile() 
-{
-    cp ${FILESDIR}/clean ${WORKDIR}
-    cd ${WORKDIR}
-    for lib in ${REPLIBRARIES}
-    do
-      einfo Cleaning library file ${lib/=*/} to ${lib/*=/}
-      ./clean ${MY_P}/${lib/=*/} ${lib/*=/} 
-    done
-}
-
-src_install() 
-{
-    cd ${WORKDIR}
-    install -m 755 -d ${D}/usr/share/${P}/
-    for lib in ${REPLIBRARIES}
-    do
-      install -m 644 ${lib/*=/} ${D}/usr/share/${P}/
-    done
-}