| # Copyright 1999-2014 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| 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 |
| ${P}-linux.tar.gz" |
| |
| LICENSE="phrap" |
| SLOT="0" |
| KEYWORDS="~amd64 ~x86" |
| IUSE="" |
| |
| DEPEND=">=x11-libs/motif-2.3:0" |
| RDEPEND="${DEPEND} |
| sci-biology/samtools |
| >=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= ${CFLAGS} /' \ |
| -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${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() { |
| 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" |
| } |