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author | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2012-01-30 01:57:29 +0100 |
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committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2012-01-30 01:57:29 +0100 |
commit | 2fcbf893286791d9d0139b9250938d57df54c65a (patch) | |
tree | be4c95bce26c961bea3d1343320ad11318bf243b /sci-biology | |
parent | Added first ebuild for k3match, version 1.0 (diff) | |
download | sci-2fcbf893286791d9d0139b9250938d57df54c65a.tar.gz sci-2fcbf893286791d9d0139b9250938d57df54c65a.tar.bz2 sci-2fcbf893286791d9d0139b9250938d57df54c65a.zip |
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)
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/seaview/ChangeLog | 13 | ||||
-rw-r--r-- | sci-biology/seaview/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/seaview/metadata.xml | 16 | ||||
-rw-r--r-- | sci-biology/seaview/seaview-4.3.3.ebuild | 69 |
4 files changed, 99 insertions, 0 deletions
diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog new file mode 100644 index 000000000..cd6851bf0 --- /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/Manifest b/sci-biology/seaview/Manifest new file mode 100644 index 000000000..83381d590 --- /dev/null +++ b/sci-biology/seaview/Manifest @@ -0,0 +1 @@ +DIST seaview_4.3.3.tar.gz 313375 SHA256 632286397b4959ed8e379d6a6c57715a01634a81596ed681bcd87e14e10684b4 SHA512 cc3eb433c807b3482a4e883ffc96e00b8e04b6208561d3e7c7409da25e2171e5db7a0caa252070da904bd672d68f151967133ae0801fe2c6ffdee0d9af7ec8c3 WHIRLPOOL 0310a5e707c7314e3038a7e9467fa854868b691e7f4a82a75808ddf9197c8a98030414be67649c8b6def31a350899faa615c5d38a8f69966dc60080e51964915 diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml new file mode 100644 index 000000000..0c1ebc35d --- /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 000000000..b2cfe65b2 --- /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 +} |