proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

3 files changed, 90 insertions, 0 deletions

diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
new file mode 100644
index 000000000000..6bb12c484533
--- /dev/null
+++ b/sci-biology/seaview/Manifest
@@ -0,0 +1 @@
+DIST seaview_4.3.5.tar.gz 309530 SHA256 38050d6792eb799d61e5e849f76971a9c7d45f467e5c04fbc4363062d8e7100d SHA512 b20c018da9a29d79fe0393fed5d29117729492ea8f36e72d4aeb98044a3de4a13331bd29e76ca552a08f6da764e57e69f9fb0325fc031551514d7a54b56c849a WHIRLPOOL 82fc7324bf1d934d69712629808d6b4178a5f2cdcf25351fb2fe2784f9cea0c1ec0aaaba7a3a08c84795108eb049394ceaab052af8cc0efbb0975064fa4e80e0
diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml
new file mode 100644
index 000000000000..33794f43ab01
--- /dev/null
+++ b/sci-biology/seaview/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <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-4.3.5.ebuild b/sci-biology/seaview/seaview-4.3.5.ebuild
new file mode 100644
index 000000000000..00abeb426064
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.3.5.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils multilib toolchain-funcs
+
+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 ppc x86"
+IUSE="+xft"
+
+CDEPEND="
+	sys-libs/zlib
+	x11-libs/fltk:1
+	x11-libs/libX11
+	xft? (
+		x11-libs/libXft
+		x11-libs/fltk:1[xft] )"
+RDEPEND="${CDEPEND}
+	sci-biology/clustalw
+	|| ( sci-libs/libmuscle sci-biology/muscle )
+	sci-biology/phyml"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	# respect CXXFLAGS (package uses them as CFLAGS)
+	sed \
+		-e "s:^CC.*:CC = $(tc-getCC):" \
+		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
+		-e "s:\$(OPT):${CXXFLAGS}:" \
+		-e "s:^OPT:#OPT:" \
+		-e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \
+		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
+		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+		-e "s:^USE_XFT:#USE_XFT:" \
+		-e "s:^#HELPFILE:HELPFILE:" \
+		-e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \
+		-e "s:^#PHYMLNAME:PHYMLNAME:" \
+		-e 's:-lXinerama::g' \
+		-e 's:-lpng::g' \
+		-e 's:-ljpeg::g' \
+		-e 's:-lfontconfig::g' \
+		-i Makefile || die "sed failed while editing Makefile"
+
+	if use xft; then
+		sed \
+			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \
+			-e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \
+			-i Makefile || die "sed failed while editing Makefile to enable xft"
+	else
+		sed -i -e "s:-lXft::" Makefile || die
+	fi
+}
+
+src_install() {
+	dobin seaview
+
+	# /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
+
+	make_desktop_entry seaview Seaview
+
+	doman seaview.1
+}