sci-chemistry/theseus: Version Bump

(Portage version: 2.2.0_alpha171/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

3 files changed, 76 insertions, 6 deletions

diff --git a/sci-chemistry/theseus/ChangeLog b/sci-chemistry/theseus/ChangeLog
index bce30627e4d5..a23eb9b25152 100644
--- a/sci-chemistry/theseus/ChangeLog
+++ b/sci-chemistry/theseus/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/theseus
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/theseus/ChangeLog,v 1.4 2012/05/04 07:02:35 jdhore Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/theseus/ChangeLog,v 1.5 2013/04/09 09:57:35 jlec Exp $
+
+*theseus-2.0.1 (09 Apr 2013)
+
+  09 Apr 2013; Justin Lecher <jlec@gentoo.org> +theseus-2.0.1.ebuild,
+  metadata.xml:
+  Version Bump
 
   04 May 2012; Jeff Horelick <jdhore@gentoo.org> theseus-1.6.2-r1.ebuild:
   dev-util/pkgconfig -> virtual/pkgconfig
diff --git a/sci-chemistry/theseus/metadata.xml b/sci-chemistry/theseus/metadata.xml
index dde7ca88a50f..ae9ec7c5f6a4 100644
--- a/sci-chemistry/theseus/metadata.xml
+++ b/sci-chemistry/theseus/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>jlec@gentoo.org</email>
-</maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/theseus/theseus-2.0.1.ebuild b/sci-chemistry/theseus/theseus-2.0.1.ebuild
new file mode 100644
index 000000000000..7c84e3da67b6
--- /dev/null
+++ b/sci-chemistry/theseus/theseus-2.0.1.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/theseus/theseus-2.0.1.ebuild,v 1.1 2013/04/09 09:57:35 jlec Exp $
+
+EAPI=5
+
+inherit multilib toolchain-funcs
+
+DESCRIPTION="maximum likelihood superpositioning and analysis of macromolecular structures"
+HOMEPAGE="http://www.theseus3d.org/"
+SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-libs/gsl
+	|| (
+		sci-biology/probcons
+		sci-biology/mafft
+		sci-biology/t-coffee
+		sci-biology/kalign
+		sci-biology/clustalw
+		sci-biology/muscle
+		)"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}"/${PN}_src/
+
+src_prepare() {
+	cat >> make.inc <<- EOF
+	ARCH = $(tc-getAR)
+	ARCHFLAGS = -rvs
+	RANLIB = $(tc-getRANLIB)
+	LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
+	SYSLIBS = $(pkg-config --libs gsl) -lpthread
+	LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
+	LIBDIR = -L./lib
+	INSTALLDIR = "${ED}"/usr/bin
+	OPT =
+	WARN =
+	CFLAGS = ${CFLAGS} \$(WARN)
+	CC = $(tc-getCC)
+	EOF
+
+	sed \
+		-e 's|theseus:|theseus: libs|g' \
+		-e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
+		-i Makefile || die
+
+	sed \
+		-e 's:/usr/local/bin/::g' \
+		-e 's:/usr/bin/::g' \
+		-i theseus_align || die
+}
+
+src_install() {
+	dobin theseus theseus_align
+	dodoc theseus_man.pdf README AUTHORS
+	use examples && insinto /usr/share/${PN} && doins -r examples
+}