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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=3
inherit eutils toolchain-funcs
DESCRIPTION="A genome sequence finishing program"
HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
SRC_URI="${P}-sources.tar.gz
${P}-linux.tar.gz"
LICENSE="phrap"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND=">=x11-libs/motif-2.3:0"
RDEPEND="${DEPEND}
>=sci-biology/phred-000925
>=sci-biology/phrap-1.080721
dev-lang/perl"
S="${WORKDIR}"
RESTRICT="fetch"
pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
einfo "and place it in ${DISTDIR},"
einfo "obtain the file"
einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
einfo "and place it in ${DISTDIR}"
}
src_prepare() {
sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
sed -i \
-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
epatch "${FILESDIR}"/nextPhredPipeline.cpp.patch || die
epatch "${FILESDIR}"/nLine.h.patch || die
}
src_compile() {
emake || die "If you have gcc-4.5 please use <=4.4 or visit bug #351152"
emake -C misc/mktrace || die
emake -C misc/phd2fasta || die
(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
}
src_install() {
dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
dobin scripts/* contributions/* || die
insinto /usr/lib/screenLibs
doins misc/*.{fa*,seq} || die
insinto /usr/share/${PN}/examples
doins -r standard polyphred autofinish assembly_view 454_newbler \
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
doenvd "${S}/99consed" || die
dodoc README.txt *_announcement.txt || die
}
pkg_postinst() {
einfo "Package documentation is available at"
einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
}
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