[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

["David Seifert" <soap@gentoo.org>]

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