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commit: 2fcbf893286791d9d0139b9250938d57df54c65a |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Mon Jan 30 00:57:29 2012 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Mon Jan 30 00:57:29 2012 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2fcbf893 |
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|
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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*) |
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|
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(Portage version: 2.1.10.44/git/Linux x86_64, unsigned Manifest commit) |
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|
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--- |
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sci-biology/seaview/ChangeLog | 13 ++++++ |
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sci-biology/seaview/metadata.xml | 16 +++++++ |
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sci-biology/seaview/seaview-4.3.3.ebuild | 69 ++++++++++++++++++++++++++++++ |
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3 files changed, 98 insertions(+), 0 deletions(-) |
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|
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diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog |
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new file mode 100644 |
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index 0000000..cd6851b |
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--- /dev/null |
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+++ b/sci-biology/seaview/ChangeLog |
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@@ -0,0 +1,13 @@ |
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+# ChangeLog for sci-biology/seaview |
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+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 |
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+# $Header: $ |
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+ |
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+*seaview-4.3.3 (30 Jan 2012) |
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+ |
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+ 30 Jan 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +seaview-4.3.3.ebuild, +metadata.xml: |
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+ version bump; add missing symlink so that the C++ header can be found; remove |
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+ calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not |
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+ include path) to /usr/include/fltk-1 so that svg.o gets included during |
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+ linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*) |
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+ |
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|
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diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml |
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new file mode 100644 |
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index 0000000..0c1ebc3 |
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--- /dev/null |
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+++ b/sci-biology/seaview/metadata.xml |
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@@ -0,0 +1,16 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <maintainer> |
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+ <email>weaver@g.o</email> |
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+ <name>Andrey Kislyuk</name> |
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+ </maintainer> |
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+ <herd>sci-biology</herd> |
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+ <longdescription> |
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+ SeaView is a graphical multiple sequence alignment editor developped by |
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+ Manolo Gouy. SeaView is able to read and write various alignment |
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+ formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to |
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+ manually edit the alignment, and also to run DOT-PLOT or CLUSTALW |
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+ programs to locally improve the alignment. |
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+ </longdescription> |
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+</pkgmetadata> |
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|
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diff --git a/sci-biology/seaview/seaview-4.3.3.ebuild b/sci-biology/seaview/seaview-4.3.3.ebuild |
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new file mode 100644 |
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index 0000000..b2cfe65 |
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--- /dev/null |
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+++ b/sci-biology/seaview/seaview-4.3.3.ebuild |
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@@ -0,0 +1,69 @@ |
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+# Copyright 1999-2012 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/seaview-4.2.5.ebuild,v 1.5 2011/03/20 20:02:27 jlec Exp $ |
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+ |
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+EAPI="2" |
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+ |
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+inherit toolchain-funcs multilib eutils base |
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+ |
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+DESCRIPTION="A graphical multiple sequence alignment editor" |
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+HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" |
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+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" |
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+ |
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+LICENSE="public-domain" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="+xft" |
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+ |
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+DEPEND="x11-libs/fltk:1 |
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+ xft? ( x11-libs/libXft |
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+ x11-libs/fltk:1[xft] )" |
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+RDEPEND="${DEPEND} |
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+ sci-biology/clustalw |
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+ || ( sci-libs/libmuscle sci-biology/muscle ) |
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+ sci-biology/phyml" |
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+ |
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+S="${WORKDIR}/${PN}" |
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+ |
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+src_prepare() { |
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+ # respect CXXFLAGS (package uses them as CFLAGS) |
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+ sed -i \ |
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+ -e "s:^CXX.*:CXX = $(tc-getCXX):" \ |
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+ -e "s:\$(OPT):${CXXFLAGS}:" \ |
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+ -e "s:^OPT:#OPT:" \ |
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+ -e "s:^FLTK = /usr/include:FLTK = /usr/include/fltk-1:" \ |
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+ -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ |
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+ -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ |
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+ -e "s:^USE_XFT:#USE_XFT:" \ |
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+ -e "s:^#HELPFILE:HELPFILE:" \ |
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+ -e "s:/usr/share/doc/seaview/seaview.htm:/usr/share/seaview/seaview.htm:" \ |
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+ -e "s:^#PHYMLNAME:PHYMLNAME:" \ |
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+ Makefile || die "sed failed while editing Makefile" |
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+ |
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+ if use xft; then |
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+ sed -i \ |
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+ -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $(pkg-config --cflags xft):" \ |
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+ -e "s:-lXft:$(pkg-config --libs xft):" \ |
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+ Makefile || die "sed failed while editing Makefile to enable xft" |
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+ else |
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+ sed -i -e "s:-lXft::" Makefile || die |
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+ fi |
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+ cd FL || die |
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+ ln -sf . FL |
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+ base_src_prepare |
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+} |
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+ |
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+src_install() { |
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+ dobin seaview || die |
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+ |
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+ # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile |
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+ insinto /usr/share/seaview |
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+ doins example.nxs seaview.html |
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+ |
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+ insinto /usr/share/seaview/images |
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+ doins seaview.xpm || die |
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+ |
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+ make_desktop_entry seaview Seaview |
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+ |
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+ doman seaview.1 || die |
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+} |