Add latest, clean up old.

(Portage version: 2.1.8.3/cvs/Linux x86_64)

3 files changed, 84 insertions, 61 deletions

diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog
index a19a4f9d37e6..1a24bb9e643b 100644
--- a/sci-biology/seaview/ChangeLog
+++ b/sci-biology/seaview/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/seaview
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/ChangeLog,v 1.32 2010/03/20 21:49:12 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/ChangeLog,v 1.33 2010/05/16 17:14:55 je_fro Exp $
+
+*seaview-4.2.5 (16 May 2010)
+
+  16 May 2010; Jeff Gardner <je_fro@gentoo.org> +seaview-4.2.5.ebuild:
+  Latest version, clean out old.
 
 *seaview-4.2.3 (20 Mar 2010)
 
diff --git a/sci-biology/seaview/seaview-20071113.ebuild b/sci-biology/seaview/seaview-20071113.ebuild
deleted file mode 100644
index caff0d04a736..000000000000
--- a/sci-biology/seaview/seaview-20071113.ebuild
+++ /dev/null
@@ -1,60 +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/seaview/seaview-20071113.ebuild,v 1.6 2009/10/07 18:36:07 weaver Exp $
-
-EAPI=1
-inherit eutils toolchain-funcs multilib
-
-DESCRIPTION="A graphical multiple sequence alignment editor"
-HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
-
-MY_PF=${PF/-/_}
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-LICENSE="public-domain"
-
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="x11-libs/fltk:1.1
-	=media-libs/pdflib-7*
-	sci-biology/clustalw
-	sci-biology/muscle"
-
-S=${WORKDIR}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	# Respect CXXFLAGS. Package uses CFLAGS as CXXFLAGS.
-	# Fix invocation of C++ compiler.
-	# Fix include and library paths.
-	sed -i \
-		-e '/^FLTK/d' \
-		-e '/^X11/d' \
-		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
-		-e 's:-I$(FLTK):-I/usr/include/fltk-1.1:' \
-		-e 's:-I$(X11)/include:-I/usr/include/X11R6:' \
-		-e "s:\(^CFLAGS .*\):\1 ${CXXFLAGS}:" \
-		-e "s:-L\$(FLTK)/lib:-L/usr/$(get_libdir)/fltk-1.1:" \
-		-e "s:-L\$(X11)/lib:-L/usr/$(get_libdir)/X11:" \
-		-e "s:^#HELP_NOT_IN_PATH:HELP_NOT_IN_PATH:" \
-		-e "s:bge/mgouy:usr/share:" \
-		Makefile || die "sed Makefile failed"
-
-	epatch "${FILESDIR}"/${P}-glibc-2.10.patch
-}
-
-src_install() {
-	dobin seaview seaview_align.sh
-	insinto /usr/share/${PN}
-	doins protein.mase seaview.help
-
-	insinto /usr/share/pixmaps/
-	doins "${S}/${PN}.xpm"
-
-	insinto /usr/share/applications/
-	doins "${FILESDIR}/${PN}.desktop"
-}
diff --git a/sci-biology/seaview/seaview-4.2.5.ebuild b/sci-biology/seaview/seaview-4.2.5.ebuild
new file mode 100644
index 000000000000..ff5e8b0df302
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.2.5.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/seaview-4.2.5.ebuild,v 1.1 2010/05/16 17:14:55 je_fro Exp $
+
+EAPI="2"
+
+inherit toolchain-funcs multilib eutils base
+
+DESCRIPTION="A graphical multiple sequence alignment editor"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+pdf +xft"
+
+DEPEND="x11-libs/fltk:1.1
+	pdf? ( media-libs/pdflib )
+	xft? (	x11-libs/libXft
+			x11-libs/fltk:1.1[xft] )"
+RDEPEND="${DEPEND}
+	sci-biology/clustalw
+	|| ( sci-libs/libmuscle sci-biology/muscle )
+	sci-biology/phyml"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	# respect CXXFLAGS (package uses them as CFLAGS)
+	sed -i \
+		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
+		-e "s:\$(OPT):${CXXFLAGS}:" \
+		-e "s:^OPT:#OPT:" \
+		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cxxflags):" \
+		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+		-e "s:^USE_XFT:#USE_XFT:" \
+		-e "s:^#HELPFILE:HELPFILE:" \
+		-e "s:^#PHYMLNAME:PHYMLNAME:" \
+		Makefile || die "sed failed while editing Makefile"
+
+	if use pdf; then
+		sed -i \
+			-e "s:PDF_PS_FLAGS = -DNO_PDF:#PDF_PS_FLAGS = -DNO_PDF:" \
+			-e "s:PDF_PS = postscript:#PDF_PS = postscript:" \
+			-e "s:#PDF_INC = \$(HOME)/PDFlibLite:PDF_INC = /usr/include:" \
+			-e "s:#PDF_LIB = \$(HOME)/PDFlibLite:PDF_LIB = /usr/lib:" \
+			-e "s:#PDF_PS = pdf:PDF_PS = pdf:" \
+			-e "s:#PDF_PS_FLAGS = -I\$(PDF_INC):PDF_PS_FLAGS = -I\$(PDF_INC):" \
+			-e "s:#LPDF = -L\$(PDF_LIB) -lpdf:LPDF = -L\$(PDF_LIB) -lpdf:" \
+			Makefile || die "sed failed while editing Makefile to enable pdf output"
+	fi
+
+	if use xft; then
+		sed -i \
+			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $(xft-config --cflags):" \
+			-e "s:-lXft:$(xft-config --libs):" \
+			Makefile || die "sed failed while editing Makefile to enable xft"
+	else
+		sed -i -e "s:-lXft::" Makefile || die
+	fi
+	base_src_prepare
+}
+
+src_install() {
+	dobin seaview || die
+
+	# /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile
+	insinto /usr/share/seaview
+	doins example.nxs seaview.html
+
+	insinto /usr/share/seaview/images
+	doins seaview.xpm || die
+
+	make_desktop_entry seaview Seaview
+
+	doman seaview.1 || die
+}