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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild,v 1.3 2014/11/03 13:53:41 titanofold Exp $
EAPI="4"
inherit autotools eutils
MY_PATCH="4"
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
HOMEPAGE="http://emboss.sourceforge.net/"
SRC_URI="
ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz
ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz"
LICENSE="GPL-2 LGPL-2"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE="doc minimal mysql pdf png postgres static-libs X"
DEPEND="
dev-libs/expat
dev-libs/libpcre:3
sci-libs/plplot
sys-libs/zlib
mysql? ( virtual/mysql )
pdf? ( media-libs/libharu )
png? (
sys-libs/zlib
media-libs/libpng
media-libs/gd
)
postgres? ( virtual/postgresql )
!minimal? (
sci-biology/primer3
sci-biology/clustalw
)
X? ( x11-libs/libXt )"
RDEPEND="${DEPEND}
!sys-devel/cons"
PDEPEND="
!minimal? (
sci-biology/aaindex
sci-biology/cutg
sci-biology/prints
sci-biology/prosite
sci-biology/rebase
sci-biology/transfac
)"
S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}"
src_prepare() {
epatch "${WORKDIR}"/${P}.patch
epatch \
"${FILESDIR}"/${PV}-unbundle-libs.patch \
"${FILESDIR}/${PF}_plcol.patch"
eautoreconf
}
src_configure() {
econf \
$(use_with X x) \
$(use_with png pngdriver "${EPREFIX}/usr") \
$(use_with doc docroot "${EPREFIX}/usr") \
$(use_with pdf hpdf "${EPREFIX}/usr") \
$(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \
$(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \
$(use_enable amd64 64) \
$(use_enable static-libs static) \
--without-java \
--enable-large \
--enable-systemlibs \
--includedir="${ED}/usr/include/emboss"
}
src_install() {
einstall || die "Failed to install program files."
dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
dodoc README.Gentoo
# Install env file for setting libplplot and acd files path.
cat <<- EOF > 22emboss
# plplot libs dir
PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/"
# ACD files location
EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
EOF
doenvd 22emboss
# Symlink preinstalled docs to "/usr/share/doc".
dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html
# Clashes #330507
mv "${ED}"/usr/bin/{digest,pepdigest} || die
# Remove useless dummy files from the image.
find emboss/data -name dummyfile -delete || 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 "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
die "Failed to move CODON directory."
# Move the provided restriction enzyme prototypes file to a different name.
# This avoids file collisions with versions of rebase that install their
# own enzyme prototypes file (see bug #118832).
mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
die "Failed to move enzyme equivalence file."
}
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