| # Copyright 1999-2016 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI=6 |
| |
| PYTHON_COMPAT=( python2_7 ) |
| |
| inherit eutils python-r1 toolchain-funcs |
| |
| DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| HOMEPAGE="http://samtools.sourceforge.net/" |
| SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" |
| |
| LICENSE="MIT" |
| SLOT="0.1-legacy" |
| KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| IUSE="examples" |
| |
| REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| |
| RDEPEND="sys-libs/ncurses:0= |
| dev-lang/perl" |
| DEPEND="${RDEPEND} |
| virtual/pkgconfig" |
| |
| PATCHES=( |
| "${FILESDIR}/${P}-buildsystem.patch" |
| ) |
| |
| src_prepare() { |
| default |
| sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| tc-export CC AR |
| } |
| |
| src_compile() { |
| local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| emake dylib LIBCURSES="${_ncurses}" |
| emake LIBCURSES="${_ncurses}" |
| } |
| |
| src_install() { |
| dobin samtools $(find bcftools misc -type f -executable) |
| mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die |
| mkdir "${ED}"/usr/bin || die |
| mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die |
| |
| mv "${ED}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die |
| python_replicate_script "${ED}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py |
| |
| # fix perl shebangs |
| pushd "${ED}"usr/bin/"${PN}-${SLOT}"/ >> /dev/null |
| local i |
| for i in plot-bamcheck *.pl; do |
| sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die |
| done |
| |
| # remove lua scripts |
| rm -f r2plot.lua vcfutils.lua || die |
| popd >> /dev/null |
| |
| dolib.so libbam-${SLOT}$(get_libname 1) |
| dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) |
| |
| insinto /usr/include/bam-${SLOT} |
| doins *.h |
| |
| mv ${PN}{,-${SLOT}}.1 || die |
| doman ${PN}-${SLOT}.1 |
| dodoc AUTHORS NEWS |
| |
| use examples && dodoc -r examples |
| } |
| |
| pkg_postinst() { |
| elog "This version of samtools should *not* be your first choice for working" |
| elog "with NGS data. It is installed solely for programs requiring it." |
| elog "It is recommended that you use >=sci-biology/samtools-1.2." |
| } |