From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-biology/seaview/Manifest | 1 + sci-biology/seaview/metadata.xml | 12 +++++ sci-biology/seaview/seaview-4.3.5.ebuild | 77 ++++++++++++++++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 sci-biology/seaview/Manifest create mode 100644 sci-biology/seaview/metadata.xml create mode 100644 sci-biology/seaview/seaview-4.3.5.ebuild (limited to 'sci-biology/seaview') 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 @@ + + + + sci-biology + + 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. + + 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 +} -- cgit v1.2.3-65-gdbad