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91 lines
2.8 KiB
91 lines
2.8 KiB
10 years ago
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# Copyright 1999-2014 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-27.ebuild,v 1.1 2014/10/26 16:13:23 jlec Exp $
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EAPI=5
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inherit eutils toolchain-funcs
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DESCRIPTION="A genome sequence finishing program"
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HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
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SRC_URI="
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${P}-sources.tar.gz
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${P}-linux.tar.gz"
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LICENSE="phrap"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE=""
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DEPEND=">=x11-libs/motif-2.3:0"
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RDEPEND="${DEPEND}
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sci-biology/samtools
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>=sci-biology/phred-000925
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>=sci-biology/phrap-1.080721
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dev-lang/perl"
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S="${WORKDIR}"
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RESTRICT="fetch"
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pkg_nofetch() {
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einfo "Please visit ${HOMEPAGE} and obtain the file"
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einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
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einfo "and place it in ${DISTDIR},"
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einfo "obtain the file"
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einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
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einfo "and place it in ${DISTDIR}"
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}
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src_prepare() {
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sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
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sed -i \
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-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
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-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
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-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
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-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
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sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
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sed \
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-e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
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-i "${S}"/scripts/* || die
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}
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src_compile() {
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emake
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emake -C misc/mktrace
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emake -C misc/phd2fasta
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(cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
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}
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src_install() {
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dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
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dobin scripts/* contributions/*
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insinto /usr/lib/screenLibs
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doins misc/*.{fa*,seq}
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insinto /usr/share/${PN}/examples
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doins -r \
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standard polyphred autofinish assembly_view 454_newbler \
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align454reads align454reads_answer solexa_example \
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solexa_example_answer selectRegions selectRegionsAnswer
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echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
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echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
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mkdir -p "${ED}"/etc/consedrc || die
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touch "${ED}"/etc/consedrc || die
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doenvd "${S}/99consed" || die
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sed \
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-e "s#/usr/local/genome#${EPREFIX}/usr#" \
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-i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
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sed \
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-e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
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-i "${ED}"/usr/bin/phredPhrap || die
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sed \
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-e 's#/wt1/gordon/genome#/usr/bin#' \
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-i "${ED}"/usr/bin/fastq2Phrap.perl || die
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dodoc README.txt *_announcement.txt || die
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}
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pkg_postinst() {
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einfo "Package documentation is available at"
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einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
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}
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