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authorDavid Seifert <soap@gentoo.org>2016-04-09 21:58:14 +0200
committerDavid Seifert <soap@gentoo.org>2016-04-09 21:58:31 +0200
commit0f059b5eb7e03f75705f623dc74e27842540da40 (patch)
treebf90363664ee396d7caba342a558f66579e38d9c /sci-biology
parentsci-electronics/gazebo: bump to 7.1.0 (diff)
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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-0.1.20-r2.ebuild (renamed from sci-biology/samtools/samtools-0.1.20-r1.ebuild)12
1 files changed, 11 insertions, 1 deletions
diff --git a/sci-biology/samtools/samtools-0.1.20-r1.ebuild b/sci-biology/samtools/samtools-0.1.20-r2.ebuild
index 744d15ff5771..e30ed26ca09f 100644
--- a/sci-biology/samtools/samtools-0.1.20-r1.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r2.ebuild
@@ -20,7 +20,6 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="sys-libs/ncurses:0=
- dev-lang/lua:0
dev-lang/perl"
DEPEND="${RDEPEND}
virtual/pkgconfig"
@@ -50,6 +49,17 @@ src_install() {
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)