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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-27.ebuild,v 1.1 2014/10/26 16:13:23 jlec Exp $
EAPI=5
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
${P}-linux.tar.gz"
LICENSE="phrap"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND=">=x11-libs/motif-2.3:0"
# it needs samtools-0.18 with khash.h
# This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1
RDEPEND="${DEPEND}
<sci-biology/samtools-1.0
>=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 -lbam -lz/' \
-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${S}/makefile" || die
sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
sed \
-e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
-i "${S}"/scripts/* || die
}
src_compile() {
einfo "consed does not compile with sys-devel/gcc-4.6:* or newer (but 4.4.7 works)"
emake
emake -C misc/mktrace
emake -C misc/phd2fasta
(cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
}
src_install() {
dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
dobin scripts/* contributions/*
insinto /usr/lib/screenLibs
doins misc/*.{fa*,seq}
insinto /usr/share/${PN}/examples
doins -r \
standard polyphred autofinish assembly_view 454_newbler \
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer
echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
mkdir -p "${ED}"/etc/consedrc || die
touch "${ED}"/etc/consedrc || die
doenvd "${S}/99consed" || die
sed \
-e "s#/usr/local/genome#${EPREFIX}/usr#" \
-i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
sed \
-e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
-i "${ED}"/usr/bin/phredPhrap || die
sed \
-e 's#/wt1/gordon/genome#/usr/bin#' \
-i "${ED}"/usr/bin/fastq2Phrap.perl || die
dodoc README.txt *_announcement.txt || die
}
pkg_postinst() {
einfo "Package documentation is available at"
einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
}
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