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| author |   David Seifert <soap@gentoo.org> | 2016-04-10 11:20:56 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2016-04-10 11:21:11 +0200 |
| commit | 5f3acec053c0f95f355f6c4db5e12994555a4b7a (patch) | |
| tree | 74aa9f69bea89f1cb52fd5f950950c47ad8c238d /sci-biology | |
| parent | sys-auth/skey: Stable for HPPA (bug #576366). (diff) | |
| download | gentoo-5f3acec053c0f95f355f6c4db5e12994555a4b7a.tar.gz gentoo-5f3acec053c0f95f355f6c4db5e12994555a4b7a.tar.bz2 gentoo-5f3acec053c0f95f355f6c4db5e12994555a4b7a.zip | |
sci-biology/samtools: Remove lua dep, fix perl shebangs
Package-Manager: portage-2.2.28
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/samtools/samtools-1.3-r1.ebuild (renamed from sci-biology/samtools/samtools-1.3.ebuild) | 17 |
1 files changed, 14 insertions, 3 deletions
diff --git a/sci-biology/samtools/samtools-1.3.ebuild b/sci-biology/samtools/samtools-1.3-r1.ebuild index ec510ec82664..15d6714b0841 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 |