commit: e4e256abcf64dccd8c72ad565bd988ef49e740be Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Aug 3 17:39:53 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Aug 3 17:39:53 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4e256ab
sci-biology/samtools: Remove ancient py2 varfilter.py script Closes: https://bugs.gentoo.org/735444 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap <AT> gentoo.org> ...-0.1.20-r3.ebuild => samtools-0.1.20-r4.ebuild} | 36 ++++++++-------------- 1 file changed, 13 insertions(+), 23 deletions(-) diff --git a/sci-biology/samtools/samtools-0.1.20-r3.ebuild b/sci-biology/samtools/samtools-0.1.20-r4.ebuild similarity index 66% rename from sci-biology/samtools/samtools-0.1.20-r3.ebuild rename to sci-biology/samtools/samtools-0.1.20-r4.ebuild index 5cfcfd7f6a7..2c76f0580f8 100644 --- a/sci-biology/samtools/samtools-0.1.20-r3.ebuild +++ b/sci-biology/samtools/samtools-0.1.20-r4.ebuild @@ -1,11 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -PYTHON_COMPAT=( python2_7 ) - -inherit python-single-r1 toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" HOMEPAGE="http://samtools.sourceforge.net/"; @@ -14,23 +12,17 @@ SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.g LICENSE="MIT" SLOT="0.1-legacy" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" -RDEPEND="${PYTHON_DEPS} +RDEPEND=" sys-libs/ncurses:0= dev-lang/perl" -DEPEND="${RDEPEND} - virtual/pkgconfig" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" -PATCHES=( - "${FILESDIR}/${P}-buildsystem.patch" -) +PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) src_prepare() { default - # required, otherwise python_fix_shebang errors out - sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py || die tc-export CC AR } @@ -48,9 +40,9 @@ src_install() { mkdir "${ED%/}"/usr/bin || die mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die - # ... do the same with the python script, but also fix the shebang - mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die - python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py + # remove py2 script, has been removed upstream anyways + # https://github.com/samtools/samtools/issues/1125 + rm "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter.py || die # fix perl shebangs pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die @@ -70,14 +62,12 @@ src_install() { doman ${PN}-${SLOT}.1 einstalldocs - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi + dodoc -r examples + docompress -x /usr/share/doc/${PF}/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." + elog "It is recommended that you use >=sci-biology/samtools-1.10." }
