Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci

39 files changed, 646 insertions, 215 deletions

diff --git a/sci-biology/clover/ChangeLog b/sci-biology/clover/ChangeLog
index 18775e4df..edcb8dd7d 100644
--- a/sci-biology/clover/ChangeLog
+++ b/sci-biology/clover/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/clover
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -clover-2010.02.19.ebuild,
+  +clover-2011.10.24.ebuild, metadata.xml:
+  Version BUmp; fixed license; respect LDFLAGS
+
 *clover-2010.02.19 (23 Aug 2010)
 
   23 Aug 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de>
diff --git a/sci-biology/clover/Manifest b/sci-biology/clover/Manifest
index 701b84d6e..4a3827eb9 100644
--- a/sci-biology/clover/Manifest
+++ b/sci-biology/clover/Manifest
@@ -1,2 +1,2 @@
-DIST clover-2010-02-19.tar.gz 15641 SHA256 f6de99b9ce5676af8b4179e12c4701f81f0b17ac5dadacfe7affa38ad2a585f5
-DIST jaspar2005core 14913 SHA256 498a560c67411789106b50ccdfd9bc41f571d77c2fe9bfba7e95128c0a122fe4
+DIST clover-2011-10-24.tar.gz 15843 SHA256 52ba95c118a32e6ea1097f356dfb0277be4464b834285f65eaaebcf8f504a93e SHA512 edf773943a33d58b07b7a47ca9e6c0fe08715d7f445ef1283848a14eb72d084b2113a911f23bc484b3229ec14b8eeb50d460c6b9fef89db2fa031ea059b36b93 WHIRLPOOL 785c7273c10bc6e4261e91a9dae224ff595aad3f033fb03edbe403d8cb97b456c0fe285e1a537bde3508e5e4a8f2ea5aa442fb3cb72640464df2a24da8be0ae0
+DIST jaspar2009core 54400 SHA256 a76cd1462e7b9c38f64e2049593d21fa90479b968c7997ca3d83f8489327b981 SHA512 621eac23fb0db78391d3d51471f03eccc791e1b348b23b5d9dae32b082c8301e847ee1eea4a76ac188796b639125a0970e5f0b3c0d3c673ae6f6634856c980a0 WHIRLPOOL c148ee32894ec1bd55a4665fd516eb82e6e5904e6a74bb6248d70ef7fef1a1376888a6fe53bcd959faeb8665b7c2bda3668f6801ed2e07c2c445a241a1ebcc4d
diff --git a/sci-biology/clover/clover-2010.02.19.ebuild b/sci-biology/clover/clover-2010.02.19.ebuild
deleted file mode 100644
index 239cc30e4..000000000
--- a/sci-biology/clover/clover-2010.02.19.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit toolchain-funcs versionator
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Cis-eLement OVERrepresentation: Detection of functional DNA motifs"
-HOMEPAGE="http://zlab.bu.edu/clover/"
-SRC_URI="http://zlab.bu.edu/~mfrith/downloads/${PN}-${MY_PV}.tar.gz http://zlab.bu.edu/clover/jaspar2005core"
-
-LICENSE="as-is"
-SLOT="0"
-IUSE=""
-KEYWORDS="~x86 ~amd64"
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/${PN}-${MY_PV}"
-
-src_unpack() {
-	unpack ${PN}-${MY_PV}.tar.gz
-}
-
-src_compile() {
-	sed -i "s:g++:$(tc-getCXX):; s:-Wall -O3:${CFLAGS}:" Makefile || die "sed failed"
-	emake || die "emake failed"
-}
-
-src_install() {
-	dobin clover
-	dodir "/usr/share/${PN}"
-	insinto "/usr/share/${PN}"
-	doins "${DISTDIR}/jaspar2005core" || die
-}
-
-pkg_postinst() {
-	einfo "The motif library jaspar2005core has been installed in"
-	einfo "    /usr/share/clover/jaspar2005core"
-	einfo "You can pass this library to clover for motif search, or use your own library."
-}
diff --git a/sci-biology/clover/clover-2011.10.24.ebuild b/sci-biology/clover/clover-2011.10.24.ebuild
new file mode 100644
index 000000000..cfb057432
--- /dev/null
+++ b/sci-biology/clover/clover-2011.10.24.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs versionator
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="Cis-eLement OVERrepresentation: Detection of functional DNA motifs"
+HOMEPAGE="http://zlab.bu.edu/clover/"
+SRC_URI="
+	http://zlab.bu.edu/~mfrith/downloads/${PN}-${MY_PV}.tar.gz
+	http://zlab.bu.edu/clover/jaspar2009core"
+
+LICENSE="freedist"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86 ~amd64"
+
+S="${WORKDIR}/${PN}-${MY_PV}"
+
+src_prepare() {
+	sed \
+		-e "s:g++:$(tc-getCXX) \$(LDFLAGS):; s:-Wall -O3:${CFLAGS}:" \
+		-i Makefile || die "sed failed"
+}
+
+src_install() {
+	dobin clover
+	insinto /usr/share/${PN}
+	doins "${DISTDIR}/jaspar2009core"
+}
+
+pkg_postinst() {
+	einfo "The motif library jaspar2009core has been installed in"
+	einfo "    /usr/share/clover/jaspar2009core"
+	einfo "You can pass this library to clover for motif search, or use your own library."
+}
diff --git a/sci-biology/clover/metadata.xml b/sci-biology/clover/metadata.xml
index 622c9ed81..fd501d278 100644
--- a/sci-biology/clover/metadata.xml
+++ b/sci-biology/clover/metadata.xml
@@ -1,6 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
-<maintainer><email>maintainer-wanted@gentoo.org</email></maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>maintainer-wanted@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-biology/erpin/ChangeLog b/sci-biology/erpin/ChangeLog
index f98fe95cc..de94a4865 100644
--- a/sci-biology/erpin/ChangeLog
+++ b/sci-biology/erpin/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/erpin
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> erpin-5.5b.ebuild, metadata.xml:
+  Bump to EAPI=5 and respect FLAGS / AR
+
   23 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
   New package, ebuild written by me
 
diff --git a/sci-biology/erpin/Manifest b/sci-biology/erpin/Manifest
index a5845e4ac..0c7cd75e4 100644
--- a/sci-biology/erpin/Manifest
+++ b/sci-biology/erpin/Manifest
@@ -1,2 +1,2 @@
-DIST ErpinBatch.1.4.tar.gz 2195075 SHA256 5da4c69d88092e79f4f5d73e7d67dfccbb3d4a8cbe38c74169548ef608f25808
-DIST erpin5.5b.serv.tar.gz 1145698 SHA256 0433ed25dd54491ddc4c025bb61d78d36797c2c83c61f260b5663c44cbad4d4d
+DIST ErpinBatch.1.4.tar.gz 2195075 SHA256 5da4c69d88092e79f4f5d73e7d67dfccbb3d4a8cbe38c74169548ef608f25808 SHA512 1fe33a0760e843c1f2096e5fa923275d2109e10ba42ff18d24898d59de7d2e31ae2adee915d35d1afc1b1f41dee1243986878bc6440223a0def372fd0536c261 WHIRLPOOL 82871a1836d3cbe7a271e31ed15a2e2aca29a06262105bf1dd03a7bb64e6167a6dedd6bd56c4832c11579d3ca307706b7493d1b81e5cd2b63c166a74cb7577c2
+DIST erpin5.5b.serv.tar.gz 1145698 SHA256 0433ed25dd54491ddc4c025bb61d78d36797c2c83c61f260b5663c44cbad4d4d SHA512 f6ca25e72e26d98b609b54984bf74e4bdc0ff239e94e7f8851b303022b7399bcdf879589827e2c35763b8547487740832d51b9997a6a230d8f24b4c506d338e5 WHIRLPOOL 188ab1e408bec9a4d484b476aa73cce7acdc340f5c1cd5c31bdce8c511b0864abd0312feb815ae0d28b75de99c0225bb8d4765dd9d584295af37b998f9abfc53
diff --git a/sci-biology/erpin/erpin-5.5b.ebuild b/sci-biology/erpin/erpin-5.5b.ebuild
index 8aafe2078..3673a3225 100644
--- a/sci-biology/erpin/erpin-5.5b.ebuild
+++ b/sci-biology/erpin/erpin-5.5b.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.10.1.ebuild,v 1.3 2009/09/22 11:43:28 maekke Exp $
 
-EAPI="2"
+EAPI=5
 
 inherit toolchain-funcs
 
@@ -10,10 +10,11 @@ ERPIN_BATCH_V=1.4
 
 DESCRIPTION="Easy RNA Profile IdentificatioN, an RNA motif search program"
 HOMEPAGE="http://tagc.univ-mrs.fr/erpin/"
-SRC_URI="http://rna.igmors.u-psud.fr/download/Erpin/erpin${PV}.serv.tar.gz
+SRC_URI="
+	http://rna.igmors.u-psud.fr/download/Erpin/erpin${PV}.serv.tar.gz
 	http://rna.igmors.u-psud.fr/download/Erpin/ErpinBatch.${ERPIN_BATCH_V}.tar.gz"
 
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
 SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~x86"
@@ -29,19 +30,21 @@ src_prepare() {
 	find -name '*.mk' | xargs sed -i \
 		-e 's/strip $@/echo skipping strip $@/' \
 		-e '/CFLAGS =/ d' \
-		-e "s/CC = .*/CC = $(tc-getCC)/" || die
+		-e "s/CC = .*/CC = $(tc-getCC)/" \
+		-e "s: -o : ${LDFLAGS} -o :g" \
+		-e "s:ar :$(tc-getAR) :g" || die
 	sed -i 's/cc -O2/$(tc-getCC) ${CFLAGS}/' erpin${PV}.serv/sum/sum.mk || die
 }
 
 src_compile() {
-	emake -C erpin${PV}.serv -f erpin.mk || die
+	emake -C erpin${PV}.serv -f erpin.mk
 }
 
 src_install() {
-	dobin erpin${PV}.serv/bin/* || die
+	dobin erpin${PV}.serv/bin/*
 	insinto /usr/share/${PN}
-	doins -r erpin${PV}.serv/scripts ErpinBatch.${ERPIN_BATCH_V} || die
+	doins -r erpin${PV}.serv/scripts ErpinBatch.${ERPIN_BATCH_V}
 	exeinto /usr/share/${PN}
-	newexe "${FILESDIR}/erpincommand-${PV}.pl" erpincommand.pl || die
-	dodoc erpin${PV}.serv/doc/doc*.pdf || die
+	newexe "${FILESDIR}/erpincommand-${PV}.pl" erpincommand
+	dodoc erpin${PV}.serv/doc/doc*.pdf
 }
diff --git a/sci-biology/erpin/metadata.xml b/sci-biology/erpin/metadata.xml
index 3302123e5..fc7c76942 100644
--- a/sci-biology/erpin/metadata.xml
+++ b/sci-biology/erpin/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/gap2caf/ChangeLog b/sci-biology/gap2caf/ChangeLog
new file mode 100644
index 000000000..8e35f8604
--- /dev/null
+++ b/sci-biology/gap2caf/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/gap2caf
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> gap2caf-2.1.0.ebuild,
+  metadata.xml:
+  Bump to EAPI=5 and fix license; make it build with eautoreconf
+
diff --git a/sci-biology/gap2caf/Manifest b/sci-biology/gap2caf/Manifest
index 3dbd5c548..7d17476c0 100644
--- a/sci-biology/gap2caf/Manifest
+++ b/sci-biology/gap2caf/Manifest
@@ -1,2 +1,2 @@
-DIST gap2caf-2.1.0.tar.gz 92905 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a
-DIST staden-2.0.0b8.tar.gz 4312143 SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d
+DIST gap2caf-2.1.0.tar.gz 92905 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a SHA512 2a843d861b7be6d656793f4876953596b91a93c3da7d23ee8edc10c4620e33fc96a16beaeaaf4f66c1f5c5084eb8a9a255d4fa8e1ca6e87e96372f2459167c90 WHIRLPOOL f5a3360de7c6b8741e5e85a9bc25198de4dbcbebdee73ba48a7e1460eb4d778648a5c93f0bb44c10e15a4fa46dd0c741fc10c8e33ae8c50e2c7cd9914a56aa81
+DIST staden-2.0.0b8.tar.gz 4312143 SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d SHA512 ddd273d281557595c90b93304cd03205adbe1367845ef43763a8c75d06c2729d99ca8622439ff5c31217595481a9ac4ccedf87c5948821aeaeb73c96133dc411 WHIRLPOOL f086f7f81884091a34c9933a2bb901146eefcd2dc4cb4b940228de3a51daee4c1f9d5613ca34ec345bcce48fc53bed6c4a408f5b5d6e87ac5c4deda222daee24
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
index 861bbc8f0..ca12aedf2 100644
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
 inherit autotools eutils
 
 DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz
-		http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz"
+SRC_URI="
+	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz
+	http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz"
 
-LICENSE="as-is staden"
+LICENSE="GRL staden"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-DEPEND="sci-biology/staden
-		>=dev-lang/tcl-8.5"
+DEPEND="
+	sci-biology/staden
+	>=dev-lang/tcl-8.5"
 RDEPEND="${DEPEND}"
 
 #src_prepare(){
@@ -29,13 +28,14 @@ RDEPEND="${DEPEND}"
 
 src_prepare(){
 	sed -i 's:/include/tcl8.4:/include:' configure.ac || die
-	sed -i 's:libtcl8.4:libtcl8.5:' configure.ac || die
-	sed -i 's:tcl8.4:tcl8.5:' src/Makefile.am || die
-	eaclocal
-	eautomake
-	eautoconf
-	sed -i 's:/include/tcl8.4:/include:' configure
-	sed -i 's:libtcl8.4:libtcl8.5:' configure
+	sed -i 's:libtcl8.4:libtcl:' configure.ac || die
+	sed \
+		-e 's:tcl8.4:tcl:' \
+		-e 's:pkglib_PROGRAMS:pkglibexec_PROGRAMS:g' \
+		-i src/Makefile.am || die
+	eautoreconf
+	sed -i 's:/include/tcl8.4:/include:' configure || die
+	sed -i 's:libtcl8.4:libtcl:' configure || die
 }
 
 src_configure(){
@@ -45,12 +45,13 @@ src_configure(){
 	#LDFLAGS="$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \
 	# STADENROOT=/usr/share/staden \
 	# STADENSRC="${WORKDIR}"/staden-2.0.0b8-src \
-	econf --with-stadenroot=/usr \
-	--with-tcl=/usr \
-	--with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src || die
+	econf \
+		--with-stadenroot=/usr \
+		--with-tcl=/usr \
+		--with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src
 	#sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die
 	#sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die
-	sed -i 's:tcl8.4:tcl8.5:' src/Makefile || die
+	sed -i 's:tcl8.4:tcl:' src/Makefile || die
 
 	# The below tricks in overall do not help, only for -ltk_utils somehow
 	sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die
@@ -68,7 +69,7 @@ src_install(){
 	#
 	# Instead, we rely on sci-biology/staden providind /etc/env.d/99staden file providing LDPATH=/usr/lib/staden
 	dobin src/gap2caf
-	dodoc README || die
+	dodoc README
 }
 
 # BUG #259848
diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/gap2caf/metadata.xml
+++ b/sci-biology/gap2caf/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-biology/quicktree/ChangeLog b/sci-biology/quicktree/ChangeLog
index ba6206456..00e62e40d 100644
--- a/sci-biology/quicktree/ChangeLog
+++ b/sci-biology/quicktree/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/quicktree
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> quicktree-1.1-r1.ebuild,
+  metadata.xml:
+  Bump to EAPI=5 and fix license
+
 *quicktree-1.1-r1 (08 Nov 2010)
 
   08 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -quicktree-1.1.ebuild,
diff --git a/sci-biology/quicktree/Manifest b/sci-biology/quicktree/Manifest
index 3bb33a29d..acb09d64c 100644
--- a/sci-biology/quicktree/Manifest
+++ b/sci-biology/quicktree/Manifest
@@ -1 +1 @@
-DIST quicktree-1.1.tar.gz 39035 SHA256 3b5986a8d7b8e59ad5cdc30bd7c7d91431909c25230e8fed13494f21337da6ef
+DIST quicktree-1.1.tar.gz 39035 SHA256 3b5986a8d7b8e59ad5cdc30bd7c7d91431909c25230e8fed13494f21337da6ef SHA512 1b58b786a5f0c96d7a86280e0349eb48b9a1f11160e0266e6b837dfde20a159de1393ec46bc4cdcaae09ffa59c68e8bbc5a985286133b67d6ab8fa6e248823fb WHIRLPOOL 0837a98f78f2ac56ed1f19d89a6e6fa632de4946d3a8b2fe8ec58347e58cf0cc1bcf52dbfaf63bcbc29a3994dc0f3fb61c447e0dbe4711c00201a5ac8a4b9ae7
diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml
index 3302123e5..fc7c76942 100644
--- a/sci-biology/quicktree/metadata.xml
+++ b/sci-biology/quicktree/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/quicktree/quicktree-1.1-r1.ebuild b/sci-biology/quicktree/quicktree-1.1-r1.ebuild
index 99053dc6f..e32314f97 100644
--- a/sci-biology/quicktree/quicktree-1.1-r1.ebuild
+++ b/sci-biology/quicktree/quicktree-1.1-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.0.1.ebuild,v 1.1 2009/09/10 23:14:22 weaver Exp $
+# $Header: $
 
 EAPI=2
 
@@ -8,9 +8,9 @@ inherit toolchain-funcs
 
 DESCRIPTION="Rapid reconstruction of phylogenies by the Neighbor-Joining method"
 HOMEPAGE="http://www.sanger.ac.uk/Software/analysis/quicktree/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz -> quicktree-${PV}.tar.gz"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${PN}/${PN}.tar.gz -> ${P}.tar.gz"
 
-LICENSE="as-is"
+LICENSE="GRL"
 SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~x86"
@@ -18,15 +18,16 @@ KEYWORDS="~amd64 ~x86"
 S=${WORKDIR}/${PN}_${PV}
 
 src_prepare() {
-	sed -e "s/\-O2 \-Wall/${CFLAGS}/" \
+	sed \
+		-e "s/\-O2 \-Wall/${CFLAGS}/" \
 		-i Makefile || die
 }
 
 src_compile() {
-	emake CC="$(tc-getCC)" LFLAGS="${LDFLAGS}" || die
+	emake CC="$(tc-getCC)" LFLAGS="${LDFLAGS}"
 }
 
 src_install() {
-	dobin bin/quicktree || die
-	dodoc README || die
+	dobin bin/quicktree
+	dodoc README
 }
diff --git a/sci-biology/sequin/ChangeLog b/sci-biology/sequin/ChangeLog
index ca9c2b059..639b7c7a9 100644
--- a/sci-biology/sequin/ChangeLog
+++ b/sci-biology/sequin/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-biology/sequin
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*sequin-20121202 (16 Jun 2013)
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -sequin-20090722.ebuild,
+  +sequin-20121202.ebuild:
+  Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html
+  files into sys path
+
   25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Fixed herd entry in metadata.xml
 
diff --git a/sci-biology/sequin/Manifest b/sci-biology/sequin/Manifest
index 442d7db82..956270595 100644
--- a/sci-biology/sequin/Manifest
+++ b/sci-biology/sequin/Manifest
@@ -1,2 +1,2 @@
-DIST sequin-20090722-x86.tar.gz 5999782 SHA256 f12fe7fa084a1d19a75e67cfcb4027cefb91c819b7c6219499072a87f00bdc51
-DIST sequin-20090722-x86_64.tar.gz 6911415 SHA256 338de057edf9c14e911f69c372c9480675c2b5a4b24efed605dcbdf7e8e4d486
+DIST sequin-20121202-x86.tar.gz 6760477 SHA256 a07bb9ad491b1ef0c7f03381bd73cab4bb6305a0897c117b071ad5a633a4a95e SHA512 a93d79b5a7ed7a42cc02107a0ca87051e3f95554afb103ad9fb17d1c98d4f0f5b3f01b512f63b8902cc9865a38eb10cf65cbae46a2fcf0ed4a9c1b9b697f47e9 WHIRLPOOL 288d75b4426edb9d657fe727a484a8f6009c71eff6f3202b412bbc635f52613f89955120ad0170c18f5e7d4bbf6e7f81a06b2f4b9b7f5166dc97617ee8a1c682
+DIST sequin-20121202-x86_64.tar.gz 8277570 SHA256 fe7d430a32320f22917fa515c3ba13b6fb3c9af42916759a353b9b62c0437b81 SHA512 33664d49cb0b33194d64781086ee27fad65602b6c058c4cc079ce840b6a4774c675b21c82bfcf2648b6b1f95fb0bcacc4f2eddb25d06fb8a363d4993cbb20b32 WHIRLPOOL 3f5c107701755eab1021014f9e9b333a74af42f49a1c6595d15cc38100ba1d5fe4c91fe1eef31083f937aae9bac66d94f21cd253430d1bb68e341ceb7308797b
diff --git a/sci-biology/sequin/sequin-20090722.ebuild b/sci-biology/sequin/sequin-20090722.ebuild
deleted file mode 100644
index b1d419648..000000000
--- a/sci-biology/sequin/sequin-20090722.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-2.0.12.ebuild,v 1.1 2009/10/18 21:14:11 weaver Exp $
-
-EAPI=2
-
-inherit eutils
-
-DESCRIPTION="A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/Sequin/"
-SRC_URI="amd64? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz )
-	x86? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86.tar.gz -> ${P}-x86.tar.gz )"
-
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="x11-libs/libXmu
-	x11-libs/libXp"
-
-S="${WORKDIR}"
-
-src_install() {
-	insinto /opt/${PN}
-	doins -r * || die
-	exeinto /opt/${PN}
-	doexe sequin || die
-	dosym /opt/${PN}/sequin /usr/bin/sequin || die
-	make_desktop_entry sequin Sequin || die
-}
diff --git a/sci-biology/sequin/sequin-20121202.ebuild b/sci-biology/sequin/sequin-20121202.ebuild
new file mode 100644
index 000000000..5e586dcd8
--- /dev/null
+++ b/sci-biology/sequin/sequin-20121202.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-2.0.12.ebuild,v 1.1 2009/10/18 21:14:11 weaver Exp $
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/Sequin/"
+SRC_URI="
+	amd64? ( ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz )
+	x86? ( ftp://ftp.ncbi.nih.gov/sequin/sequin.linux.tar.gz -> ${P}-x86.tar.gz )"
+#	amd64? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz )
+#	x86? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86.tar.gz -> ${P}-x86.tar.gz )"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	x11-libs/libXmu
+	x11-libs/libXp"
+
+S="${WORKDIR}"
+
+QA_PREBUILT="/opt/.*"
+
+src_install() {
+	dohtml -r *htm images
+	rm -rf *htm images || die
+
+	insinto /opt/${PN}
+	doins -r *
+
+	exeinto /opt/${PN}
+	doexe sequin
+
+	dosym /opt/${PN}/sequin /opt/bin/sequin
+
+	make_desktop_entry sequin Sequin
+}
diff --git a/sci-biology/smalt-bin/ChangeLog b/sci-biology/smalt-bin/ChangeLog
index f3268fd32..7f6f91f99 100644
--- a/sci-biology/smalt-bin/ChangeLog
+++ b/sci-biology/smalt-bin/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-biology/smalt-bin
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*smalt-bin-0.7.4 (16 Jun 2013)
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -smalt-bin-0.5.1.ebuild,
+  +smalt-bin-0.7.4.ebuild, metadata.xml:
+  Version Bump; restrict license; add QA_PREBUILT for binaries
+
   25 Jun 2011; Justin Lecher <jlec@gentoo.org> smalt-bin-0.5.1.ebuild:
   Cleaned ebuild and fixed LICENSE
 
diff --git a/sci-biology/smalt-bin/Manifest b/sci-biology/smalt-bin/Manifest
index f9f5194ab..0e8053bb2 100644
--- a/sci-biology/smalt-bin/Manifest
+++ b/sci-biology/smalt-bin/Manifest
@@ -1 +1 @@
-DIST smalt-0.5.1.tgz 534824 SHA256 c8bca18a7ded7ad4b7070be7478bd046cf2d6a0a81054dfd96ebdba65c0a49d0
+DIST smalt-0.7.4.tgz 1437480 SHA256 a6997fcbef746c57f889c3784b2bc9c399ad03562ed8d4a835180ba8cc6822fe SHA512 9c31f358ef4094566bdc67f92b2576e6cf15a010bbf7dc1eb4a66afb2107253dfe4947a529c10c579484ccd7aff6aaae048ea8b17fd468804b08d88fb6588e39 WHIRLPOOL 65c1a52608d26e3411a77137fa03c65ae30cc845d5e9f676ab4c1a53812f1fcbd2300b4e5a0a8839c24c00f526f0a5627b6facbec54cbe86af7d132857b728c1
diff --git a/sci-biology/smalt-bin/metadata.xml b/sci-biology/smalt-bin/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/smalt-bin/metadata.xml
+++ b/sci-biology/smalt-bin/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild b/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild
deleted file mode 100644
index 7566c2097..000000000
--- a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-"${PV}".tgz"
-
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}"/smalt-"${PV}"
-
-src_install(){
-	use x86 && newbin smalt_i386 smalt
-	use amd64 && newbin smalt_x86_64 smalt
-	use ia64 && newbin smalt_ia64
-
-	dodoc NEWS smalt_manual.pdf
-	doman smalt.1
-}
diff --git a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
new file mode 100644
index 000000000..01acc05a9
--- /dev/null
+++ b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+MY_PN="${PN%-bin}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}.tgz"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S="${WORKDIR}"/${MY_P}
+
+QA_PREBUILT="/opt/.*"
+
+src_install(){
+	exeinto /opt/bin
+	use x86 && newexe ${MY_PN}_i386 ${MY_PN}
+	use amd64 && newexe ${MY_PN}_x86_64 ${MY_PN}
+	use ia64 && newexe ${MY_PN}_ia64 ${MY_PN}
+
+	dodoc NEWS ${MY_PN}_manual.pdf
+	doman ${MY_PN}.1
+}
diff --git a/sci-biology/ssaha2-bin/ChangeLog b/sci-biology/ssaha2-bin/ChangeLog
index 914725e6e..8b3f2ffef 100644
--- a/sci-biology/ssaha2-bin/ChangeLog
+++ b/sci-biology/ssaha2-bin/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/ssaha2-bin
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -ssaha2-bin-2.5.3.ebuild,
+  +ssaha2-bin-2.5.5.ebuild, metadata.xml:
+  Version Bump; restrict license; add QA_PREBUILT for binaries
+
   25 Jun 2011; Justin Lecher <jlec@gentoo.org> ssaha2-bin-2.5.3.ebuild:
   Cleaned ebuild and fixed LICENSE
 
diff --git a/sci-biology/ssaha2-bin/Manifest b/sci-biology/ssaha2-bin/Manifest
index 3cd3275a6..f1a6a5db5 100644
--- a/sci-biology/ssaha2-bin/Manifest
+++ b/sci-biology/ssaha2-bin/Manifest
@@ -1,5 +1,4 @@
-DIST samflag.c 2424 SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0
-DIST ssaha2-manual.pdf 163188 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf
-DIST ssaha2_i686.tgz 288481 SHA256 7d173d763d9f685ef3d0075124bf8b763c6d2d3ed1a1f823bc66d6b6b029abed
-DIST ssaha2_ia64.tgz 458507 SHA256 3eb2a31559911f3ee87e11f3b977962da31b60c25ea0c9a064edfd1165b6b5dd
-DIST ssaha2_x86_64.tgz 287790 SHA256 0135ab2e285a898d450744b7c9d643efbeb6048783169a6647f310ce2e7b8138
+DIST samflag.c 2424 SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0 SHA512 50ef4d134e5fab4f1399fd2eb35de0c8ce901c23e360a52ee5cdca117c124c77f432a50a666d655dc0f04089db84d873f9251e68ff6f6f4ac327e23362657aa7 WHIRLPOOL c89abd1bac315aaadfc4456c4ec4252a6ccdd1f42db604b60568d3ee7e367f8ec99ff7915aeaac7dafa594bd29bb11affb3f62ed9d6dd577dd407c2c4c93e7c5
+DIST ssaha2-manual.pdf 163188 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf SHA512 2a43d038684519d3a4e1fca54b75ac731961dc1e9e1034914eff481b303e5b49d11f4d9149e56a6e06292107f5be3ee6357bb9ec508cdb4de1fac677fade5d0e WHIRLPOOL 25040635acf63d874c453d5e2c2bb93dd2f44537c79ce5d3109bd59a345cbf41e4106b05039a8d3e0b00a8e1bd7a66d923161b8f0fe2544f10c37f5a4bfbbaf9
+DIST ssaha2_v2.5.5_i686.tgz 1045230 SHA256 b66ddbf1374cbcf583ff5413cb7c17dd0e63c2372d227c26526fa79597cb39c8 SHA512 e5611a2b382348e84b7cc40496b42d78ca1b5a5d641acfdb1371bff79dbe055f8c22db10b3a428d7943a6824246141e28e71146722a613585d82034187d81e32 WHIRLPOOL 169d316e548a4cc223755534b235163f0356129b6aab44540cbe5eb6083ea46f47ee689097301ecc86974da8a7b21f5887db8e88b772668c3049de31120581de
+DIST ssaha2_v2.5.5_x86_64.tgz 1167987 SHA256 478bdbda9d5fe36278748e571299f5eaf39d5172758cf0d0a85fa750f84667d4 SHA512 483dc726e1ac52020481a5721e0ac870fccdec22d9f7e74bddc76cbb76bd10ceccba57ecab9e2787045cde0e6cb74186bd3769e5c7222eb15e9c445ba7ac2592 WHIRLPOOL dbde27ca5e2eeba1c44fc59cd66f1ac6c6fa52647174c184521cf88b9ae8b05633f2fc1bc93b3be6e07e499832ec0938c4fab1017e53706b51c78060f6590b01
diff --git a/sci-biology/ssaha2-bin/metadata.xml b/sci-biology/ssaha2-bin/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/ssaha2-bin/metadata.xml
+++ b/sci-biology/ssaha2-bin/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
index 34b63dd43..96a183dc7 100644
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
@@ -1,34 +1,40 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
 inherit toolchain-funcs
 
+MY_PN="${PN%-bin}"
+MY_P="${MY_PN}_v${PV}"
+
 DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2"
 SRC_URI="
-	x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz )
-	amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz )
-	ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz )
+	x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_i686.tgz )
+	amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_x86_64.tgz )
 	ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c
 	ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf"
 
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-use x86 && S="${WORKDIR}"/ssaha2_v"${PV}"_i686
-use amd64 && S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64
-use ia64 && S="${WORKDIR}"/ssaha2_v"${PV}"_ia64
+QA_PREBUILT="/opt/.*"
 
+pkg_setup() {
+	use x86 && export S="${WORKDIR}"/${MY_P}_i686
+	use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64
+}
 src_compile() {
 	$(tc-getCC) ${CFLAGS} ${LDFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags"
 }
 
 src_install() {
-	dobin samflag ssaha2 ssaha2Build ssahaSNP
+	dobin samflag
+	exeinto /opt/bin
+	doexe ssaha2 ssaha2Build ssahaSNP
 	dodoc README "${DISTDIR}"/ssaha2-manual.pdf
 }
diff --git a/sci-biology/twinscan/ChangeLog b/sci-biology/twinscan/ChangeLog
index 3914a6070..fedf86e90 100644
--- a/sci-biology/twinscan/ChangeLog
+++ b/sci-biology/twinscan/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/twinscan
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild,
+  metadata.xml:
+  Bump to EAPI=5 and fix license
+
   07 Mar 2011; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild:
   Correct Slots for gtk 3 introduction to tree
 
diff --git a/sci-biology/twinscan/Manifest b/sci-biology/twinscan/Manifest
index e9fea6590..7e7f3adc1 100644
--- a/sci-biology/twinscan/Manifest
+++ b/sci-biology/twinscan/Manifest
@@ -1 +1 @@
-DIST iscan-4.1.2.tar_.gz 5894833 SHA256 30c7e980b2ccbba22a5e2d7ff0d7c1aaeb610cc1cec81432bb30e87f03f7e56a
+DIST twinscan-4.1.2.tar.gz 5894833 SHA256 30c7e980b2ccbba22a5e2d7ff0d7c1aaeb610cc1cec81432bb30e87f03f7e56a SHA512 d216f790f6d0f35a070575d1aa4b5e1866c00132168b381b9177b076b1b2a16f2ecd7a88aa443d7ba6b8f62c3ec2595ba33c4608a674e09d94e9f7dc6a181327 WHIRLPOOL e95df100f970c6cabf9b21a9a6651dcd249fccbfafc908a8766bf26ad5108c08b5de105c5142492bb7b0c13f39bd65836a92be9161cfbbb303147f925e775d99
diff --git a/sci-biology/twinscan/metadata.xml b/sci-biology/twinscan/metadata.xml
index 3302123e5..fc7c76942 100644
--- a/sci-biology/twinscan/metadata.xml
+++ b/sci-biology/twinscan/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/twinscan/twinscan-4.1.2.ebuild b/sci-biology/twinscan/twinscan-4.1.2.ebuild
index 96b1a049c..516aec88c 100644
--- a/sci-biology/twinscan/twinscan-4.1.2.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2.ebuild
@@ -1,14 +1,16 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=2
+EAPI=5
+
+inherit toolchain-funcs
 
 DESCRIPTION="TwinScan, N-SCAN, and Pairagon: A gene structure prediction pipeline"
 HOMEPAGE="http://mblab.wustl.edu/software/twinscan"
-SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz"
+SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz"
 
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
 SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~x86"
@@ -18,14 +20,21 @@ RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/N-SCAN"
 
-src_unpack() {
-	unpack ${A}
-	tar -C "${WORKDIR}" -xf iscan-${PV}.tar_
-}
-
 src_prepare() {
 	sed -i "1 a use lib '/usr/share/${PN}/lib/perl5';" "${S}"/bin/*.pl || die
-	sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl"
+	sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl" || die
+	tc-export CC AR RANLIB
+
+	sed \
+		-e 's:ar :$(AR) :g' \
+		-e 's:ranlib :$(RANLIB) :g' \
+		-e 's: -o : $(LDFLAGS) -o :g' \
+		-i Makefile || die
+
+	sed \
+		-e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \
+		-e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)-DHAS_GLIB:g" \
+		-i Makefile.include || die
 }
 
 src_install() {
@@ -35,5 +44,6 @@ src_install() {
 	doins -r "${S}/lib" || die
 	echo "TWINSCAN=/usr" > "${S}"/99${PN}
 	doenvd "${S}"/99${PN} || die
+	rm -rf examples/tmp
 	dodoc examples/* README*
 }
diff --git a/sci-chemistry/shiftx2/ChangeLog b/sci-chemistry/shiftx2/ChangeLog
new file mode 100644
index 000000000..5aafaf3ca
--- /dev/null
+++ b/sci-chemistry/shiftx2/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-chemistry/shiftx2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx2-1.07_p20120106.ebuild,
+  metadata.xml:
+  Respect FLAGS
+
diff --git a/sci-chemistry/shiftx2/Manifest b/sci-chemistry/shiftx2/Manifest
new file mode 100644
index 000000000..94fd67e47
--- /dev/null
+++ b/sci-chemistry/shiftx2/Manifest
@@ -0,0 +1 @@
+DIST shiftx2-v107-linux-20120106.tgz 114164215 SHA256 47bd11f00c824967738f72a02387b47eafc60a10697aa157e27163f2edbf9927 SHA512 b1fa6ce19e988a938e6645fdbd14f7903b4db13754a476c67da0bf74909675e07b7cec4df63be30d7190ea645e8822eef551e6dd26625172e585da279f1f7396 WHIRLPOOL 20fc5ea052106e2f6f708ba61da2ad9310a50a1c85dfb46d947c919d665835cc43180267094c057b7ce542b59659a1b44940c762c4c8e190cdbb7727dc30c865
diff --git a/sci-chemistry/shiftx2/files/gentoo-fixes.patch b/sci-chemistry/shiftx2/files/gentoo-fixes.patch
new file mode 100644
index 000000000..2baa443c5
--- /dev/null
+++ b/sci-chemistry/shiftx2/files/gentoo-fixes.patch
@@ -0,0 +1,194 @@
+diff --git a/shiftx2-v107-linux/src/LimitedCShift.java b/shiftx2-v107-linux/src/LimitedCShift.java
+index cd27fbf..9e72208 100755
+--- a/shiftx2-v107-linux/src/LimitedCShift.java
++++ b/shiftx2-v107-linux/src/LimitedCShift.java
+@@ -13,8 +13,8 @@ public class LimitedCShift {
+ 	public void loadLimitedCShift () {		
+                 // System.out.println("SHIFTX2_DIR: "+ShiftXp.SHIFTX2_DIR);
+ 
+-		String filename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.dat";
+-		String objFilename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.osf";
++		String filename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.dat";
++		String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.osf";
+ 		
+ 		File f = new File(objFilename);
+ 		if (f.exists()) {
+@@ -44,7 +44,7 @@ public class LimitedCShift {
+ 				br.close();
+ 				
+ 				// save object into object file format for speed up
+-				saveObjectFile(objFilename, limshift);
++				//saveObjectFile(objFilename, limshift);
+ 
+ 			} catch(IOException ex){
+ 				ex.printStackTrace();
+diff --git a/shiftx2-v107-linux/src/ModuleExecutor.java b/shiftx2-v107-linux/src/ModuleExecutor.java
+index 36cfeb1..704451f 100755
+--- a/shiftx2-v107-linux/src/ModuleExecutor.java
++++ b/shiftx2-v107-linux/src/ModuleExecutor.java
+@@ -22,12 +22,12 @@ public class ModuleExecutor {
+ 	// private static final String WORKING_DIR = "./wkdir/";
+ 	private static String WORKING_DIR = "";
+ 
+-	private static final String RESMF_EXE = "/modules/resmf/resmf";
+-	private static final String EFFECTS_EXE = "/modules/effects/caleffect"; 
+-	private static final String ANGLES_EXE = "/modules/angles/get_angles";	
+-	private static final String ANGLES_REDUCE_DIR = "/modules/angles";
++	private static final String RESMF_EXE = "resmf";
++	private static final String EFFECTS_EXE = "caleffect"; 
++	private static final String ANGLES_EXE = "get_angles";	
++	private static final String ANGLES_REDUCE_DIR = "angles";
+ 
+-    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
++//    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
+ 
+ 	private static final String REDUCE_FLAG = "1"; // 1 or 0
+ 
+@@ -80,8 +80,8 @@ public class ModuleExecutor {
+ 		if(DEBUG) System.out.println("> Processing [Major Features] with " + pdbfile);
+         // Update: add pdbdir both input pdbfile and output result, pdbId (2011.03.17)
+ 		// cmd = RESMF_EXE + " -f " + pdbdir +"/"+ pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf";
+-		cmd = SHIFTXP_DIR + RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" 
+-                      + " -d " + SHIFTXP_DIR + "/modules/resmf/lib";
++		cmd = RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" 
++                      + " -d " + ShiftXp.GENTOO_SHARE_PATH + "/vader";
+ 
+ 		if(DEBUG){ System.out.println("\t"+cmd); }
+ 		execCode = execute_command(cmd); 
+@@ -93,7 +93,7 @@ public class ModuleExecutor {
+ 		
+ 		/* call effects for calculating ring current calculator */
+ 		if(DEBUG) System.out.println("> processing [Effects] with " + pdbfile);
+-		cmd = SHIFTXP_DIR + EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy";
++		cmd = EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy";
+ 
+ 		if(DEBUG){ System.out.println("\t"+cmd); }
+ 		execCode = execute_command(cmd); 
+@@ -106,7 +106,7 @@ public class ModuleExecutor {
+ 		/* call angle calculator : output must be redirected to file using PrintStream */
+ 		if(DEBUG) System.out.println("> Processing [Angle] with " + pdbfile);
+ 		// cmd = ANGLES_EXE + " " + ANGLES_REDUCE_DIR + " " + pdbfile ;
+-		cmd = SHIFTXP_DIR + ANGLES_EXE + " " + SHIFTXP_DIR + ANGLES_REDUCE_DIR + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG;
++		cmd = ANGLES_EXE + " " + ShiftXp.GENTOO_SHARE_PATH + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG;
+ 		String outpath = WORKING_DIR + pdbId + ".angles";
+ 
+ 		if(DEBUG){ System.out.println("\t"+cmd); }
+diff --git a/shiftx2-v107-linux/src/PredictionModels.java b/shiftx2-v107-linux/src/PredictionModels.java
+index a77d1cb..fb84666 100755
+--- a/shiftx2-v107-linux/src/PredictionModels.java
++++ b/shiftx2-v107-linux/src/PredictionModels.java
+@@ -13,9 +13,7 @@ public class PredictionModels {
+     private final static String MODEL_FILE_SIDECHAIN_ONLY = "predmodels_sidechain.sobj";
+ 
+     private final static String OBJECT_MODEL_DIRECTORY = "/lib";
+-    private final static String MODEL_DIRECTORY = "/lib/predmodels";
+-
+-    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
++    private final static String MODEL_DIRECTORY = "predmodels";
+ 
+     HashMap<String, Classifier> hsmap_predmodel = new HashMap<String, Classifier>();
+ 
+@@ -36,7 +34,7 @@ public class PredictionModels {
+        // System.out.println("SHIFTXP_DIR:" + SHIFTXP_DIR+"\n\n");
+        // System.out.println("SHIFTX2_DIR:" + ShiftXp.SHIFTX2_DIR+"\n\n");
+ 
+-        String headerfilename = ShiftXp.SHIFTX2_DIR + "/lib/data-header.arff"; 
++        String headerfilename = ShiftXp.GENTOO_SHARE_PATH + "/data-header.arff"; 
+ 
+         try {
+             // assigned instance header from data-header.arff
+@@ -150,7 +148,7 @@ public class PredictionModels {
+             // if option is not sidechain only, put backbone models into modeling file 
+             if ( ! this.prediction_type.equals("SIDECHAIN") ) {
+                 for(int i=0; i < BACKBONE_MODEL_LENGTH; i++)  {
+-                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
++                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
+                     classifier = (Classifier) ois.readObject();
+                     hsmap_predmodel.put(atomNameArray[i],classifier);
+                     ois.close();
+@@ -160,7 +158,7 @@ public class PredictionModels {
+             // if option is not backbone only, put/append sidechain models into modeling file
+             if ( ! this.prediction_type.equals("BACKBONE") ) {
+                 for(int i=BACKBONE_MODEL_LENGTH; i < (BACKBONE_MODEL_LENGTH + SIDECHAIN_MODEL_LENGTH); i++)  {
+-                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
++                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
+                     classifier = (Classifier) ois.readObject();
+                     hsmap_predmodel.put(atomNameArray[i], classifier);
+                     ois.close();
+@@ -185,11 +183,11 @@ public class PredictionModels {
+         */
+ 
+         if ( this.prediction_type.equals("ALL") == true) {
+-            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_ALLATOMS;
++            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_ALLATOMS;
+         } else if ( this.prediction_type.equals("BACKBONE") == true) {
+-            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_BACKBONE_ONLY;
++            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_BACKBONE_ONLY;
+         } else if ( this.prediction_type.equals("SIDECHAIN") == true) {
+-            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_SIDECHAIN_ONLY;
++            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_SIDECHAIN_ONLY;
+         } 
+ 
+         File f = new File( model_file );
+@@ -198,7 +196,7 @@ public class PredictionModels {
+             readHashObjectPredModelFile( model_file );
+         } else {
+             setHashMap(); 
+-            saveHashObjectPredModelFile( model_file ); 
++//            saveHashObjectPredModelFile( model_file ); 
+         }
+     }
+ 
+diff --git a/shiftx2-v107-linux/src/RandomCoil.java b/shiftx2-v107-linux/src/RandomCoil.java
+index 25a8999..7442938 100755
+--- a/shiftx2-v107-linux/src/RandomCoil.java
++++ b/shiftx2-v107-linux/src/RandomCoil.java
+@@ -33,11 +33,9 @@ public class RandomCoil {
+ 	public void loadRandomCoil() {		
+ 
+         // change path as absolute path
+-        String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
+-
+-		String filename = SHIFTXP_DIR + "/lib/RandomCoil.csv";
+-		String objFilename = SHIFTXP_DIR + "/lib/RandomCoil.osf";
+-		String objAtomListname = SHIFTXP_DIR + "/lib/RCoilAtomlist.osf";
++		String filename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.csv";
++		String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.osf";
++		String objAtomListname = ShiftXp.GENTOO_SHARE_PATH + "/RCoilAtomlist.osf";
+ 		
+ 		
+ 		File f = new File(objFilename);
+@@ -85,8 +83,8 @@ public class RandomCoil {
+ 				br.close();
+ 				
+ 				// save object into object file format for speed up
+-				saveObjectFile(objFilename, rcoil);				
+-				saveObjectFile(objAtomListname, restypeAtomStringList);
++//				saveObjectFile(objFilename, rcoil);				
++//				saveObjectFile(objAtomListname, restypeAtomStringList);
+ 
+ 			} catch(IOException ex){
+ 				ex.printStackTrace();
+diff --git a/shiftx2-v107-linux/src/ShiftXp.java b/shiftx2-v107-linux/src/ShiftXp.java
+index 505a3f6..920f420 100755
+--- a/shiftx2-v107-linux/src/ShiftXp.java
++++ b/shiftx2-v107-linux/src/ShiftXp.java
+@@ -27,7 +27,7 @@ public class ShiftXp {
+     static final boolean DEBUG = false; 
+     static boolean RCOIL_PRINTOUT = false;
+     static String SHIFTX2_DIR = ".";  // to support running on other directory
+-
++    public static final String GENTOO_SHARE_PATH = "PUT_GENTOO_SHARE_PATH_HERE";
+     // Loading only one time, that's why these are here 
+     static RandomCoil rcoil = new RandomCoil();
+     static LimitedCShift chkcshift = new LimitedCShift();
+@@ -140,8 +140,7 @@ public class ShiftXp {
+ 
+         // check execute directory 
+         // 2011.08.31 changed shiftx2_main.py --> shiftx2.py
+-        if ( !( new File( SHIFTX2_DIR + "/shiftx2.py").exists() 
+-             &&  new File(SHIFTX2_DIR + "/lib/weka.jar").exists() )  )  {
++        if (!new File(SHIFTX2_DIR + "/shiftx2.py").exists()) {
+ 
+            System.err.println("\n********************************************************************************");
+            System.err.println("[Error]\t Required: When the SHIFTX2 execute on other directory,\n"
diff --git a/sci-chemistry/shiftx2/metadata.xml b/sci-chemistry/shiftx2/metadata.xml
new file mode 100644
index 000000000..80444f44b
--- /dev/null
+++ b/sci-chemistry/shiftx2/metadata.xml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <longdescription>
+		SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical
+		shifts for proteins using their structural (PDB) coordinates as input.
+		SHIFTX2 combines ensemble machine learning methods with sequence
+		alignment-based methods to calculate protein chemical shifts for
+		backbone
+		and side chain atoms. SHIFTX2 has been trained on a carefully selected
+		set of
+		197 proteins and tested on a separate set of 61 proteins. Both the
+		training
+		and testing sets consisted of high resolution X-ray structures (less
+		2.1A)
+		with carefully verified chemical shifts assignments. SHIFTX2 is able to
+		attain
+		correlation coefficients between experimentally observed and predicted
+		backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB),
+		0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412,
+		0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to
+		other
+		chemical shift predictors using the same testing data set indicates that
+		SHIFTX2 is substantially more accurate (up to 26% better by
+		correlation
+		coefficient with an RMS error that is up to 3.3X smaller) than any other
+		program.
+
+		Please cite the following: Beomsoo Han, Yifeng Liu, Simon Ginzinger, and
+		David Wishart. (2011) SHIFTX2: significantly improved protein chemical
+		shift
+		prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57.
+		doi: 10.1007/s10858-011-9478-4.
+	</longdescription>
+  <use>
+    <flag name="debug">Enables debug output in the shiftx2 java part</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
new file mode 100644
index 000000000..5a19e4b0b
--- /dev/null
+++ b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 java-pkg-simple python-r1 versionator
+
+MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))"
+MY_PATCH="20120106"
+MY_P="${PN}-v${MY_PV}-linux"
+
+DESCRIPTION="Predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins"
+HOMEPAGE="http://shiftx2.wishartlab.com/"
+SRC_URI="http://shiftx2.wishartlab.com/download/${MY_P}-${MY_PATCH}.tgz"
+
+SLOT="0"
+LICENSE="all-rights-reserved"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug"
+
+CDEPEND="dev-util/weka"
+
+RDEPEND="${CDEPEND}
+	dev-lang/R
+	sci-chemistry/reduce
+	>=virtual/jre-1.5"
+DEPEND="${CDEPEND}
+	>=virtual/jdk-1.5"
+
+S="${WORKDIR}"/${MY_P}
+
+QA_PREBUILT="/opt/.*"
+
+src_prepare() {
+	epatch "${FILESDIR}/gentoo-fixes.patch"
+	rm "${S}"/src/FeatureRanges.java || die
+
+	shared=$(echo "/usr/share/${PN}" | sed -e 's/\//\\\//g')
+	sed -i -e "s/PUT_GENTOO_SHARE_PATH_HERE/${shared}/g" "${S}/src/ShiftXp.java" || die
+
+	if use debug; then
+		sed -i -e 's/DEBUG = false/DEBUG = true/g' "${S}/src/ShiftXp.java" || die
+	fi
+
+	# hack alert!
+	sed \
+		-e '/-o/s:$(GCC):$(GCC) $(LDFLAGS):g' \
+		-e '/-o/s:$(CC):$(CC) $(LDFLAGS):g' \
+		-i modules/*/Makefile || die
+
+	sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
+}
+
+src_compile() {
+	mkdir "${S}"/build || die
+	ejavac -classpath "$(java-pkg_getjars weka)" -nowarn \
+		-d "${S}"/build $(find src/ -name "*.java")
+	jar cf "${PN}.jar" -C "${S}"/build . || die
+
+	einfo "Building module angles"
+	cd "${S}"/modules/angles || die
+	emake clean
+	emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" get_angles phipsi
+
+	einfo "Building module resmf"
+	cd "${S}"/modules/resmf || die
+	emake clean
+	emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" resmf
+
+	einfo "Building module effects"
+	cd "${S}"/modules/effects || die
+	emake clean
+	emake CFLAGS="${CFLAGS}" CC=$(tc-getCC) LINK="${LDFLAGS}" all
+}
+
+src_install() {
+	java-pkg_dojar "${PN}.jar"
+	java-pkg_dolauncher ${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin"
+
+	insinto /usr/share/${PN}
+	doins "${S}"/lib/{limitedcshift.dat,RandomCoil.csv,data-header.arff}
+	doins -r "${S}"/lib/predmodels
+
+	insinto /usr/share/${PN}/vader
+	doins -r "${S}"/modules/resmf/lib/*
+
+	local instdir="/opt/${PN}"
+	dodoc README 1UBQ.pdb
+	python_parallel_foreach_impl python_doscript "${S}"/*py
+
+	# other modules
+	dobin \
+		"${S}"/modules/angles/{get_angles,phipsi} \
+		"${S}"/modules/resmf/resmf \
+		"${S}"/modules/effects/caleffect
+
+	# script
+	python_scriptinto ${instdir}/script
+	python_parallel_foreach_impl python_doscript "${S}"/script/*py
+	exeinto ${instdir}/script
+	doexe "${S}"/script/*.r
+
+	# shifty3
+	python_scriptinto ${instdir}/shifty3
+	python_parallel_foreach_impl python_doscript "${S}"/shifty3/*py
+	exeinto ${instdir}/shifty3
+	doexe "${S}"/shifty3/xalign_x
+	dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x
+}