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

[David Seifert]

commit:     0f059b5eb7e03f75705f623dc74e27842540da40
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Apr  9 19:58:14 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Apr  9 19:58:31 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0f059b5e

sci-biology/samtools: Remove lua dep, fix perl shebangs

Package-Manager: portage-2.2.28

 .../{samtools-0.1.20-r1.ebuild => samtools-0.1.20-r2.ebuild} | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/sci-biology/samtools/samtools-0.1.20-r1.ebuild 
b/sci-biology/samtools/samtools-0.1.20-r2.ebuild
similarity index 87%
rename from sci-biology/samtools/samtools-0.1.20-r1.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r2.ebuild
index 744d15f..e30ed26 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)