Import from Science overlay and version bump

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

4 files changed, 89 insertions, 0 deletions

diff --git a/sci-biology/arb/ChangeLog b/sci-biology/arb/ChangeLog
new file mode 100644
index 000000000000..ec2f3bd7ce75
--- /dev/null
+++ b/sci-biology/arb/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/arb
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/ChangeLog,v 1.1 2009/10/04 00:25:29 weaver Exp $
+
+*arb-5.1 (03 Oct 2009)
+
+  03 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
+  +arb-5.1.ebuild:
+  Import from Science overlay and version bump
+
diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
new file mode 100644
index 000000000000..2d5a11d56e4e
--- /dev/null
+++ b/sci-biology/arb/Manifest
@@ -0,0 +1,4 @@
+DIST arb-5.1.tgz 9727285 RMD160 8757446e7145faf28382c617fc7fe4b57a857baf SHA1 69696e52bf86eea5213ad9d27be30dd74f1255f3 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf
+EBUILD arb-5.1.ebuild 1963 RMD160 91c6b1ba1806dda86f15e0f9849f0f9953ad8000 SHA1 bf8c93d7a64303ca1a4323627d413c3190ff5816 SHA256 f3042d09022690e8b73752038853a477523c631f311b50dbc366d220ea74183f
+MISC ChangeLog 359 RMD160 7364433cec0bd934237fa1cac01a010431e6974f SHA1 e3500c10ffb8286fc6eded4497e23b8b586acc65 SHA256 4c6ef7ebc01220146f53fcc2c1988a31be21f653e35ec5b0d7ba5e6c76c2c612
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/arb/arb-5.1.ebuild b/sci-biology/arb/arb-5.1.ebuild
new file mode 100644
index 000000000000..21a12e1436c8
--- /dev/null
+++ b/sci-biology/arb/arb-5.1.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/arb-5.1.ebuild,v 1.1 2009/10/04 00:25:29 weaver Exp $
+
+EAPI=2
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz"
+MY_TAG=6213
+
+LICENSE="arb"
+SLOT="0"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="app-text/sablotron
+	www-client/lynx
+	x11-libs/openmotif
+	x11-libs/libXpm
+	x11-libs/libXaw
+	media-libs/tiff
+	media-libs/libpng
+	opengl? ( media-libs/glew
+		virtual/glut
+		media-libs/mesa[motif] )"
+RDEPEND="${DEPEND}
+	sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+S="${WORKDIR}/arbsrc_${MY_TAG}"
+
+src_prepare() {
+	sed -i -e 's/getline/arb_getline/' READSEQ/ureadseq.c || die
+	sed -i \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CFLAGS}/" \
+		"${S}/Makefile" || die
+	cp config.makefile.template config.makefile
+	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+	use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+	emake ARBHOME="${S}" links || die
+	# In 5.0; fixed in 5.1
+	# (cd INCLUDE/GL; for i in ../../GL/glAW/*.h; do ln -s $i; done) || die
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die
+	use amd64 && mv arb.tgz arb.64.gentoo.tgz
+	use x86 && mv arb.tgz arb.32.gentoo.tgz
+	ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+	cat <<EOF > "${S}/99${PN}"
+ARBHOME=/opt/arb
+PATH=/opt/arb/bin
+LD_LIBRARY_PATH=/opt/arb/lib
+EOF
+	doenvd "${S}/99${PN}" || die
+}
diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/arb/metadata.xml
@@ -0,0 +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>
+</pkgmetadata>