Some cleanup and begin working on seaview

svn path=/; revision=320

6 files changed, 67 insertions, 75 deletions

diff --git a/app-cdr/dvd95/Manifest b/app-cdr/dvd95/Manifest
deleted file mode 100644
index 20f9705..0000000
--- a/app-cdr/dvd95/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX dvd95-1.3_p3-desktop-entry.patch 522 RMD160 2994f861bad84e3d5e7b38683d0e763fc0ffaf8d SHA1 8c087041ce7509f7d7041e8e69a772ac82b3362e SHA256 3ec7848b21c9ca64b5656aeed82a2c86c923225195ce6dfb624d5d6be12d9d7e
-DIST dvd95-1.5p3.tar.gz 1068766 RMD160 803e636c96811f6a9e523b4025fb4286a92ff8b2 SHA1 b317c79742111c3cc8c8e39a0292eb6d65e8fcef SHA256 4ef0ed1b122a3688c9ae0737d2658e148318334403fc1ee277b4ff9071ba5ea9
-EBUILD dvd95-1.5_p3.ebuild 1078 RMD160 6a9460870c84694b3dd22bfd32c570b8aada1688 SHA1 87f2b7c3531004f87eef1a3b0b7a434d1cf73d2c SHA256 93bfba95a728e8d9d24886ebc043eb477f96d9a53ea812efae9407d195e4c548
-MISC metadata.xml 166 RMD160 02ca0a5d9279c1b52c3887f5a1f52f3feb002af9 SHA1 b9fccc7c24aa717c30efef068fd544a692f264f6 SHA256 ce62d1e5b04e01d03a732ee6d33b3d500810de8e55af4a527c970e5b475735d8
diff --git a/app-cdr/dvd95/dvd95-1.5_p3.ebuild b/app-cdr/dvd95/dvd95-1.5_p3.ebuild
deleted file mode 100644
index e5cf785..0000000
--- a/app-cdr/dvd95/dvd95-1.5_p3.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $
-
-EAPI=2
-inherit eutils
-
-DESCRIPTION="DVD95 is a Gnome application to convert DVD9 to DVD5."
-HOMEPAGE="http://dvd95.sourceforge.net/"
-SRC_URI="mirror://sourceforge/dvd95/${P/_}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="3dnow nls mmx mpeg sse sse2"
-
-RDEPEND=">=gnome-base/libgnomeui-2
-	dev-libs/libxml2
-	media-libs/libdvdread
-	mpeg? ( media-libs/libmpeg2 )
-	media-video/mplayer"
-DEPEND="${RDEPEND}
-	dev-util/pkgconfig
-	nls? ( sys-devel/gettext
-		dev-util/intltool )
-	sys-apps/sed"
-
-S=${WORKDIR}/${P/_}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-1.3_p3-desktop-entry.patch
-	sed -i -e "s:-O3:${CFLAGS}:" configure || die "sed failed"
-}
-
-src_configure() {
-	econf \
-		--disable-dependency-tracking \
-		$(use_enable nls) \
-		$(use_enable mmx) \
-		$(use_enable 3dnow) \
-		$(use_enable sse) \
-		$(use_enable sse2) \
-		$(use_enable mpeg libmpeg2)
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "emake install failed"
-	dodoc AUTHORS ChangeLog
-}
diff --git a/app-cdr/dvd95/files/dvd95-1.3_p3-desktop-entry.patch b/app-cdr/dvd95/files/dvd95-1.3_p3-desktop-entry.patch
deleted file mode 100644
index 3bdfa30..0000000
--- a/app-cdr/dvd95/files/dvd95-1.3_p3-desktop-entry.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff -ur dvd95-1.3p3.orig/dvd95.desktop dvd95-1.3p3/dvd95.desktop
---- dvd95-1.3p3.orig/dvd95.desktop	2007-04-10 22:53:38.000000000 +0300
-+++ dvd95-1.3p3/dvd95.desktop	2008-06-06 22:53:00.000000000 +0300
-@@ -3,10 +3,9 @@
- Comment=DVD9 to DVD5 converter
- Comment[fr]=Convertisseur DVD9 vers DVD5
- Exec=dvd95
--Icon=dvd95/dvd9548.png
-+Icon=/usr/share/pixmaps/dvd95/dvd9548.png
- Terminal=false
- Type=Application
--Encoding=UTF-8
--Categories=Application;AudioVideo;
-+Categories=AudioVideo;
- X-Desktop-File-Install-Version=0.10
- 
diff --git a/app-cdr/dvd95/metadata.xml b/app-cdr/dvd95/metadata.xml
deleted file mode 100644
index 3ca6ae7..0000000
--- a/app-cdr/dvd95/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>media-optical</herd>
-</pkgmetadata>
diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
index 40dae82..4a9b16b 100644
--- a/sci-biology/seaview/Manifest
+++ b/sci-biology/seaview/Manifest
@@ -1,4 +1,6 @@
 DIST seaview_4.3.0.tar.gz 306756 RMD160 2a16742e46dc46a895ed71c9f09740b3005f0e39 SHA1 db07722f487c234cac57cbd4c26065ec494da435 SHA256 6fe4c0f5b65aaa2c0b6298e07269be476cd22cec0d60628125f43133cf23e702
+DIST seaview_4.3.2.tar.gz 311332 RMD160 9845fa6a9b028923c344b58d92ad6b42489063f4 SHA1 5d79fbb67bac9271c84727f4d91bc6243b706e4a SHA256 1c80a868e5f2fb8ee945e9ae4411a45740689f0884ad2ec3c7beedcab7847fa5
 EBUILD seaview-4.3.0.ebuild 1566 RMD160 6b3d62ac4ec23b616416c2240f1182a544081543 SHA1 730e779628b9c0a0631b5520426d44394ae4c05e SHA256 fe4cc09d30789adc5e95979f1362565837432fffe6cc48965b888fa30a09e48e
+EBUILD seaview-4.3.2.ebuild 1705 RMD160 1f01379fc2723ff296602747d0ee05df07191a87 SHA1 6dc4710ed7e65bfee6f76a4ab7a6d4af02c95850 SHA256 ca482a79ed7511d96328a55e41f4be91ea88659525545545bf7abc7ec43b5626
 MISC ChangeLog 6973 RMD160 595b90e993cbee2d7fb9644966c33803d59cbcb4 SHA1 dceeb60078a285a304b5220155361b20e7d2b1a0 SHA256 9e431d81b1751316b09495f87e7339685279268d728ee677166eb9ffd5c2da58
 MISC metadata.xml 619 RMD160 f7bd8491d8c59372963d3f53e322e52d509c0c81 SHA1 d35f32cd0b1171a837f6c9d0dbeb3e396a44fb90 SHA256 ee63d33ca527ca555056c6bc3a7d89fa9b5f32e5f82b7eae27b1c030c80ced9e
diff --git a/sci-biology/seaview/seaview-4.3.2.ebuild b/sci-biology/seaview/seaview-4.3.2.ebuild
new file mode 100644
index 0000000..cf03cbd
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.3.2.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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="+xft"
+
+DEPEND="x11-libs/fltk:1
+	xft? (	x11-libs/libXft
+			x11-libs/fltk: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 xft; then
+		sed -i \
+			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $(pkg-config --cflags xft):" \
+			-e "s:-lXft:$(pkg-config --libs xft):" \
+			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
+}