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# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0-r1.ebuild,v 1.2 2010/06/23 12:03:44 jlec Exp $
EAPI="3"
inherit eutils
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
HOMEPAGE="http://emboss.sourceforge.net/"
SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
LICENSE="GPL-2 LGPL-2"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE="X png minimal"
DEPEND="X? ( x11-libs/libXt )
png? (
sys-libs/zlib
media-libs/libpng
media-libs/gd
)
!minimal? (
sci-biology/primer3
sci-biology/clustalw
)"
RDEPEND="${DEPEND}
!sys-devel/cons"
PDEPEND="!minimal? (
sci-biology/aaindex
sci-biology/cutg
sci-biology/prints
sci-biology/prosite
>=sci-biology/rebase-707
sci-biology/transfac
)"
S="${WORKDIR}/EMBOSS-${PV}"
src_prepare() {
epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
local link_string="-lX11";
if use png; then
link_string="${link_string} -lgd -lpng"
fi
sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
|| die "Failed to patch ajax Makefile"
}
src_configure() {
EXTRA_CONF="--includedir=${ED}/usr/include/emboss"
! use X && EXTRA_CONF="${EXTRA_CONF} --without-x"
! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver"
econf ${EXTRA_CONF} || die
# Do not install the JEMBOSS component (the --without-java configure option
# does not work). JEMBOSS will eventually be available as a separate package.
sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
Makefile || die
}
src_install() {
einstall || die "Failed to install program files."
dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \
|| die "Failed to install documentation."
newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \
|| die "Failed to install Gentoo readme file."
# Install env file for setting libplplot and acd files path.
cat <<- EOF > 22emboss
# plplot libs dir
PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/"
# ACD files location
EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
EOF
doenvd 22emboss || die "Failed to install environment file."
# Symlink preinstalled docs to "/usr/share/doc".
dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
# Remove frestdist documentation conflicting with the EMBASSY philypnew
# package.
rm "${ED}"/usr/share/EMBOSS/doc/programs/text/frestdist.txt || \
die "Failed to remove duplicated documentation."
# Remove useless dummy files from the image.
rm "${ED}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \
|| die "Failed to remove dummy files."
# Move the provided codon files to a different directory. This will avoid
# user confusion and file collisions on case-insensitive file systems (see
# bug #115446). This change is documented in "README.Gentoo".
mv "${ED}"/usr/share/EMBOSS/data/CODONS \
"${ED}"/usr/share/EMBOSS/data/CODONS.orig || \
die "Failed to move CODON directory."
# Move the provided restriction enzyme prototypes file to a different name.
# This avoids file collisions with versions of rebase that install their
# own enzyme prototypes file (see bug #118832).
mv "${ED}"/usr/share/EMBOSS/data/embossre.equ \
"${ED}"/usr/share/EMBOSS/data/embossre.equ.orig || \
die "Failed to move enzyme equivalence file."
}
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