Added sci-biology back into the stable overlay

svn path=/stable/; revision=749

28 files changed, 647 insertions, 0 deletions

diff --git a/sci-biology/autoprime/Manifest b/sci-biology/autoprime/Manifest
new file mode 100644
index 0000000..8550d31
--- /dev/null
+++ b/sci-biology/autoprime/Manifest
@@ -0,0 +1,6 @@
+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
new file mode 100644
index 0000000..659d86c
--- /dev/null
+++ b/sci-biology/autoprime/autoprime-2.0.0.ebuild
@@ -0,0 +1,37 @@
+# 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
new file mode 100644
index 0000000..f6b2708
--- /dev/null
+++ b/sci-biology/autoprime/autoprime-2.0.1.ebuild
@@ -0,0 +1,37 @@
+# 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
new file mode 100644
index 0000000..cfac2ec
--- /dev/null
+++ b/sci-biology/autoprime/autoprime-2.0.ebuild
@@ -0,0 +1,35 @@
+# 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
new file mode 100644
index 0000000..3d38458
--- /dev/null
+++ b/sci-biology/autoprime/files/digest-autoprime-2.0
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000..bdee895
--- /dev/null
+++ b/sci-biology/autoprime/files/digest-autoprime-2.0.0
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000..1a4558b
--- /dev/null
+++ b/sci-biology/autoprime/files/digest-autoprime-2.0.1
@@ -0,0 +1 @@
+MD5 70b857e0563898db9ad15acf8babd014 AutoPrime-2.0.1.tar.gz 25737
diff --git a/sci-biology/autoprimeweb/Manifest b/sci-biology/autoprimeweb/Manifest
new file mode 100644
index 0000000..db785a4
--- /dev/null
+++ b/sci-biology/autoprimeweb/Manifest
@@ -0,0 +1,2 @@
+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
new file mode 100644
index 0000000..e2f427d
--- /dev/null
+++ b/sci-biology/autoprimeweb/autoprimeweb-2.0.0.ebuild
@@ -0,0 +1,42 @@
+# 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
new file mode 100644
index 0000000..fa17cb1
--- /dev/null
+++ b/sci-biology/autoprimeweb/files/digest-autoprimeweb-2.0.0
@@ -0,0 +1 @@
+MD5 580b9c0665889a1ababd05f3f14415be AutoPrimeWeb-2.0.0.tar.bz2 30337
diff --git a/sci-biology/ensembl-perl/Manifest b/sci-biology/ensembl-perl/Manifest
new file mode 100644
index 0000000..cc791f2
--- /dev/null
+++ b/sci-biology/ensembl-perl/Manifest
@@ -0,0 +1,7 @@
+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
new file mode 100644
index 0000000..d00116e
--- /dev/null
+++ b/sci-biology/ensembl-perl/ensembl-perl-31.ebuild
@@ -0,0 +1,45 @@
+# 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 ${WORKDIR}
+
+	perl-module_src_install
+}
diff --git a/sci-biology/ensembl-perl/ensembl-perl-32.ebuild b/sci-biology/ensembl-perl/ensembl-perl-32.ebuild
new file mode 100644
index 0000000..bcd7ff4
--- /dev/null
+++ b/sci-biology/ensembl-perl/ensembl-perl-32.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+inherit cvs perl-module
+
+CATEGORY="sci-biology"
+
+DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database"
+HOMEPAGE="http://www.ensembl.org/"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+ECVS_LOCALNAME="EnsEMBL"
+ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster"
+ECVS_MODULE="ensembl/modules/Bio/EnsEMBL"
+ECVS_BRANCH="branch-ensembl-${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 ${WORKDIR}
+
+	perl-module_src_install
+}
diff --git a/sci-biology/ensembl-perl/ensembl-perl-33.ebuild b/sci-biology/ensembl-perl/ensembl-perl-33.ebuild
new file mode 100644
index 0000000..bcd7ff4
--- /dev/null
+++ b/sci-biology/ensembl-perl/ensembl-perl-33.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+inherit cvs perl-module
+
+CATEGORY="sci-biology"
+
+DESCRIPTION="Additional perl modules for bioperl that can be used to easily access the EnsEMBL database"
+HOMEPAGE="http://www.ensembl.org/"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+ECVS_LOCALNAME="EnsEMBL"
+ECVS_SERVER="cvsro.sanger.ac.uk:/cvsroot/CVSmaster"
+ECVS_MODULE="ensembl/modules/Bio/EnsEMBL"
+ECVS_BRANCH="branch-ensembl-${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
new file mode 100644
index 0000000..cafb2aa
--- /dev/null
+++ b/sci-biology/ensembl-perl/files/Makefile.PL
@@ -0,0 +1,10 @@
+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
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/sci-biology/ensembl-perl/files/digest-ensembl-perl-31
diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-32 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-32
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/sci-biology/ensembl-perl/files/digest-ensembl-perl-32
diff --git a/sci-biology/ensembl-perl/files/digest-ensembl-perl-33 b/sci-biology/ensembl-perl/files/digest-ensembl-perl-33
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/sci-biology/ensembl-perl/files/digest-ensembl-perl-33
diff --git a/sci-biology/repbase/Manifest b/sci-biology/repbase/Manifest
new file mode 100644
index 0000000..f727e94
--- /dev/null
+++ b/sci-biology/repbase/Manifest
@@ -0,0 +1,9 @@
+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
new file mode 100755
index 0000000..37ee59c
--- /dev/null
+++ b/sci-biology/repbase/files/clean
@@ -0,0 +1,59 @@
+#!/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
+    {
+	$sequence .= uc($_);
+	$sequence =~ s/\n//g;
+    }
+}
diff --git a/sci-biology/repbase/files/digest-repbase-10.03 b/sci-biology/repbase/files/digest-repbase-10.03
new file mode 100644
index 0000000..c718f4e
--- /dev/null
+++ b/sci-biology/repbase/files/digest-repbase-10.03
@@ -0,0 +1 @@
+MD5 c530ff51d4f60a8ae2114f3185b0235f RepBase10.03.fasta.tar.gz 3530082
diff --git a/sci-biology/repbase/files/digest-repbase-10.04 b/sci-biology/repbase/files/digest-repbase-10.04
new file mode 100644
index 0000000..ede3594
--- /dev/null
+++ b/sci-biology/repbase/files/digest-repbase-10.04
@@ -0,0 +1 @@
+MD5 76b1ac539ad79a64ab48904027631cea RepBase10.04.fasta.tar.gz 3562104
diff --git a/sci-biology/repbase/files/digest-repbase-10.07 b/sci-biology/repbase/files/digest-repbase-10.07
new file mode 100644
index 0000000..1a0810a
--- /dev/null
+++ b/sci-biology/repbase/files/digest-repbase-10.07
@@ -0,0 +1 @@
+MD5 54669e3eb561fa101903c681a594e2c7 RepBase10.07.fasta.tar.gz 4061677
diff --git a/sci-biology/repbase/files/digest-repbase-9.12 b/sci-biology/repbase/files/digest-repbase-9.12
new file mode 100644
index 0000000..3188ee7
--- /dev/null
+++ b/sci-biology/repbase/files/digest-repbase-9.12
@@ -0,0 +1 @@
+MD5 fdf7cf4befd28b6b902da0f4a9263c72 RepBase9.12.fasta.tar.gz 3271264
diff --git a/sci-biology/repbase/repbase-10.03.ebuild b/sci-biology/repbase/repbase-10.03.ebuild
new file mode 100644
index 0000000..32f0e4f
--- /dev/null
+++ b/sci-biology/repbase/repbase-10.03.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+CATEGORY="sci-biology"
+
+MY_P="RepBase${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
new file mode 100644
index 0000000..90cfaa9
--- /dev/null
+++ b/sci-biology/repbase/repbase-10.04.ebuild
@@ -0,0 +1,65 @@
+# 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
new file mode 100644
index 0000000..50549fd
--- /dev/null
+++ b/sci-biology/repbase/repbase-10.07.ebuild
@@ -0,0 +1,65 @@
+# 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
new file mode 100644
index 0000000..32f0e4f
--- /dev/null
+++ b/sci-biology/repbase/repbase-9.12.ebuild
@@ -0,0 +1,65 @@
+# 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
+}