commit: 6cd0461e803e777a0b1d91569a25a91b05edc4b1 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Oct 3 19:50:27 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Oct 3 20:21:21 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6cd0461e
sci-biology/samtools: Use 'python-single-r1' instead of 'python-r1' Package-Manager: portage-2.3.1 ...-0.1.20-r2.ebuild => samtools-0.1.20-r3.ebuild} | 38 ++++++++++++---------- 1 file changed, 21 insertions(+), 17 deletions(-) diff --git a/sci-biology/samtools/samtools-0.1.20-r2.ebuild b/sci-biology/samtools/samtools-0.1.20-r3.ebuild similarity index 60% rename from sci-biology/samtools/samtools-0.1.20-r2.ebuild rename to sci-biology/samtools/samtools-0.1.20-r3.ebuild index e30ed26..787add8 100644 --- a/sci-biology/samtools/samtools-0.1.20-r2.ebuild +++ b/sci-biology/samtools/samtools-0.1.20-r3.ebuild @@ -6,7 +6,7 @@ EAPI=6 PYTHON_COMPAT=( python2_7 ) -inherit eutils python-r1 toolchain-funcs +inherit python-single-r1 toolchain-funcs DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" HOMEPAGE="http://samtools.sourceforge.net/"; @@ -16,10 +16,10 @@ LICENSE="MIT" SLOT="0.1-legacy" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" IUSE="examples" - REQUIRED_USE="${PYTHON_REQUIRED_USE}" -RDEPEND="sys-libs/ncurses:0= +RDEPEND="${PYTHON_DEPS} + sys-libs/ncurses:0= dev-lang/perl" DEPEND="${RDEPEND} virtual/pkgconfig" @@ -30,7 +30,8 @@ PATCHES=( src_prepare() { default - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + # required, otherwise python_fix_shebang errors out + sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py || die tc-export CC AR } @@ -41,24 +42,24 @@ src_compile() { } 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 + # install executables and hide them away from sight + dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \ + misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck} + 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-${SLOT}.py + # ... do the same with the python script, but also fix the shebang + mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die + python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py # fix perl shebangs - pushd "${ED}"usr/bin/"${PN}-${SLOT}"/ >> /dev/null + pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die local i for i in plot-bamcheck *.pl; do sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die done - - # remove lua scripts - rm -f r2plot.lua vcfutils.lua || die - popd >> /dev/null + popd >/dev/null || die dolib.so libbam-${SLOT}$(get_libname 1) dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) @@ -68,9 +69,12 @@ src_install() { mv ${PN}{,-${SLOT}}.1 || die doman ${PN}-${SLOT}.1 - dodoc AUTHORS NEWS + einstalldocs - use examples && dodoc -r examples + if use examples; then + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi } pkg_postinst() {
