Add latest, clean up old.

Package-Manager: portage-2.1.8.3/cvs/Linux x86_64

4 files changed, 87 insertions, 64 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/Manifest b/sci-biology/seaview/Manifest
index 3e840ec541eb..8cb4b7e0afaf 100644
--- a/sci-biology/seaview/Manifest
+++ b/sci-biology/seaview/Manifest
@@ -1,10 +1,10 @@
 AUX seaview-20071113-glibc-2.10.patch 545 RMD160 c8e5f91d20b08a902fc88706a52e6664340f7d1d SHA1 ca1026d79a56ce687bb62237a23a70a9022996ef SHA256 97d670caea6584417851b3da260353043ec73d60349b4a12a2b9fbcbf597f509
 AUX seaview.desktop 207 RMD160 d5b4e57a1866d5f2d384ab1f6acf21292061570f SHA1 38b4a0b0055da291020690e9ac1974d7aed94871 SHA256 314a791477d6059888bce45de2627d58d1b8998a25200d6a9eb8f13c759c7b32
-DIST seaview-20071113.tar.gz 155890 RMD160 1a0b82137e1546eed7e69392a241e7af0e5c3068 SHA1 0928a9729142ebe0fcc32b612150a09ee663eddf SHA256 93335e7e95255a189a5f89cd8fd40a22e3e096727ab30f31b6383c85854c709f
 DIST seaview_4.1.tar.gz 315678 RMD160 de3a7f3e684d73508cf6d9ab0d004549d9abdbf9 SHA1 d8227d0e91dff3221b09ea415e1201d833ead5c5 SHA256 902c6cd8e0f7fb17a4d2849bec3312d9cde94fceb1d7fd02c4242b986f693468
 DIST seaview_4.2.3.tar.gz 323465 RMD160 7b94a5fb14fb664854340e05ac18476a15109974 SHA1 ef28787632ae6c7bdff39e9e0f5ed77e9e43d21c SHA256 b3fb78bc4d3b767f4048231e2ee14944127c88a455ee5d16053cc906760bcf88
-EBUILD seaview-20071113.ebuild 1505 RMD160 d36b5c3a7941dafdaa9be9219aebe04b31c04578 SHA1 79c84456ff1db956d88b011999264941b4839455 SHA256 0649c61169c8d623461bb8697ce7b2d8f7a9821d23c7eb79afd6882962879068
+DIST seaview_4.2.5.tar.gz 319110 RMD160 2aa82be247367790e1b84e4526ac92a98c126551 SHA1 e3ade6b2078aa1b617aad10fb124fe0309084638 SHA256 1d5d555a1afcec0218db99a132942edfdfcb05b7bb93de6c124d7d30315677c9
 EBUILD seaview-4.1.ebuild 2298 RMD160 0a63d56879a4bf2d949610eaa9d80e8bfc3439fa SHA1 e2e1f3f83d349d8ddce2182e85f742bdd1d18532 SHA256 0041378d6075fc18c9e7e4ff2f01e35dcb5817894da18082b9e64def13e19918
 EBUILD seaview-4.2.3.ebuild 2372 RMD160 9a0a715ef4f8b363f48e73114ed92fd5e893f1c2 SHA1 c66839649817ff2a8e364b9622ed8471384d3337 SHA256 23994833e3512cb54f99137409e26d5bd549620ff1cd9def5d04c223724c8b09
-MISC ChangeLog 5794 RMD160 e80573508789f308e1662971542e6b47e1352380 SHA1 df3eb0363ae8175079adb82ee15815e60f384092 SHA256 536e245e4d76ff8c403245904534f348fcb17d08068c7b56aa2b3174951f22ab
+EBUILD seaview-4.2.5.ebuild 2372 RMD160 289f4363c00e36da8da68f93ff1c3d2045f7e3ad SHA1 0a07ab7583ce31826a71182044b369da25ae916a SHA256 24afae12c5f9f9776e11fa86defc2ec82de52eecee7ade18ffd12ad484553054
+MISC ChangeLog 5929 RMD160 8e694837b7368dc10061b2a22c32e75c1e130972 SHA1 85caf420923fe93bb19f9954707337643ed574c7 SHA256 feae77b9c13929a7b7e28c2cc68dbe358d629a6961f0a3fb732153b907cb2980
 MISC metadata.xml 619 RMD160 f7bd8491d8c59372963d3f53e322e52d509c0c81 SHA1 d35f32cd0b1171a837f6c9d0dbeb3e396a44fb90 SHA256 ee63d33ca527ca555056c6bc3a7d89fa9b5f32e5f82b7eae27b1c030c80ced9e
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
+}