commit: 5f3acec053c0f95f355f6c4db5e12994555a4b7a Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Apr 10 09:20:56 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Apr 10 09:21:11 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5f3acec0
sci-biology/samtools: Remove lua dep, fix perl shebangs Package-Manager: portage-2.2.28 .../{samtools-1.3.ebuild => samtools-1.3-r1.ebuild} | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/sci-biology/samtools/samtools-1.3.ebuild b/sci-biology/samtools/samtools-1.3-r1.ebuild similarity index 83% rename from sci-biology/samtools/samtools-1.3.ebuild rename to sci-biology/samtools/samtools-1.3-r1.ebuild index ec510ec..15d6714 100644 --- a/sci-biology/samtools/samtools-1.3.ebuild +++ b/sci-biology/samtools/samtools-1.3-r1.ebuild @@ -20,8 +20,7 @@ IUSE="examples" REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND="sys-libs/ncurses:0= - >=sci-libs/htslib-${PV} - dev-lang/lua:0 + =sci-libs/htslib-${PV}* dev-lang/perl" DEPEND="${RDEPEND} virtual/pkgconfig" @@ -70,7 +69,19 @@ src_test() { src_install() { dobin samtools $(find misc -type f -executable) - python_replicate_script "${ED}"/usr/bin/varfilter.py + python_replicate_script "${ED}"usr/bin/varfilter.py + + # fix perl shebangs + pushd "${ED}"usr/bin/ >> /dev/null + local i + for i in plot-bamstats *.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.so* insinto /usr/include/bam