[gentoo-commits] proj/sci:master commit in: sci-biology/seaview/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     2fcbf893286791d9d0139b9250938d57df54c65a
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 30 00:57:29 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 30 00:57:29 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2fcbf893

sci-biology/seaview: version bump; add missing symlink so that the C++ header can be found; remove calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not include path) to /usr/include/fltk-1 so that svg.o gets included during linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*)

(Portage version: 2.1.10.44/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/seaview/ChangeLog            |   13 ++++++
 sci-biology/seaview/metadata.xml         |   16 +++++++
 sci-biology/seaview/seaview-4.3.3.ebuild |   69 ++++++++++++++++++++++++++++++
 3 files changed, 98 insertions(+), 0 deletions(-)

diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog
new file mode 100644
index 0000000..cd6851b
--- /dev/null
+++ b/sci-biology/seaview/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-biology/seaview
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*seaview-4.3.3 (30 Jan 2012)
+
+  30 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +seaview-4.3.3.ebuild, +metadata.xml:
+  version bump; add missing symlink so that the C++ header can be found; remove
+  calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not
+  include path) to /usr/include/fltk-1 so that svg.o gets included during
+  linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*)
+

diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml
new file mode 100644
index 0000000..0c1ebc3
--- /dev/null
+++ b/sci-biology/seaview/metadata.xml
@@ -0,0 +1,16 @@
+<?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>
+	<longdescription>
+		SeaView is a graphical multiple sequence alignment editor developped by
+		Manolo Gouy. SeaView is able to read and write various alignment
+		formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to
+		manually edit the alignment, and also to run DOT-PLOT or CLUSTALW
+		programs to locally improve the alignment.
+	</longdescription>
+</pkgmetadata>

diff --git a/sci-biology/seaview/seaview-4.3.3.ebuild b/sci-biology/seaview/seaview-4.3.3.ebuild
new file mode 100644
index 0000000..b2cfe65
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.3.3.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2012 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 1.5 2011/03/20 20:02:27 jlec 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="+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:^FLTK = /usr/include:FLTK = /usr/include/fltk-1:" \
+		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
+		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+		-e "s:^USE_XFT:#USE_XFT:" \
+		-e "s:^#HELPFILE:HELPFILE:" \
+		-e "s:/usr/share/doc/seaview/seaview.htm:/usr/share/seaview/seaview.htm:" \
+		-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
+	cd FL || die
+	ln -sf . FL
+	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
+}