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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit flag-o-matic 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="examples"
COMMON_DEPEND="
x11-libs/libX11
x11-libs/motif:0
sci-biology/samtools:0.1-legacy
"
DEPEND="
${COMMON_DEPEND}
virtual/pkgconfig
"
RDEPEND="
${COMMON_DEPEND}
dev-lang/perl
>=sci-biology/phred-071220-r1
>=sci-biology/phrap-1.080812-r2
"
S="${WORKDIR}"
RESTRICT="fetch"
PATCHES=(
"${FILESDIR}/${PN}-29-fix-build-system.patch"
"${FILESDIR}/${PN}-29-fix-c++14.patch"
"${FILESDIR}/${PN}-29-fix-qa.patch"
"${FILESDIR}/${PN}-29-fix-perl-shebang.patch"
)
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 ${DISTDIR}"
}
src_prepare() {
default
sed \
-e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \
-e "s:/usr/local/genome:${EPREFIX}/usr:" \
-e "s:niceExe = \"/bin/nice\":niceExe = \"${EPREFIX}/usr/bin/nice\":" \
-e "s:/wt1/gordon/genome:${EPREFIX}/usr/bin:" \
-i scripts/* contributions/* || die
}
src_configure() {
append-cflags -std=gnu99
append-lfs-flags
}
src_compile() {
emake \
CC="$(tc-getCC)" \
CXX="$(tc-getCXX)" \
CFLAGS="${CFLAGS}" \
CXXFLAGS="${CXXFLAGS}" \
CPPFLAGS="${CPPFLAGS}" \
LDFLAGS="${LDFLAGS}" \
SAMTOOLS_CPPFLAGS="-I${EPREFIX}/usr/include/bam-0.1-legacy" \
LIBS="-L${EPREFIX}/usr/$(get_libdir)" \
X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" \
SAMTOOLS_LIBS="-lbam-0.1-legacy"
}
src_install() {
dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} scripts/* contributions/*
insinto /usr/lib/screenLibs
doins misc/*.{fa*,seq}
if use examples; then
insinto /usr/share/${PN}/examples
doins -r \
standard polyphred autofinish assembly_view 454_newbler \
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer
fi
cat > 99consed <<-_EOF_ || die
CONSED_HOME=${EPREFIX}/usr
CONSED_PARAMETERS=${EPREFIX}/etc/consedrc
_EOF_
doenvd 99consed
dodoc README.txt *_announcement.txt
}
pkg_postinst() {
einfo "Package documentation is available at"
einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
}
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