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

Package-Manager: portage-2.2.28

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 ec510ec826645b987b5d4234e4f0c29d87e924fb..15d6714b0841def0c779570c2fabdd8fa5fb2319 100644 (file)
--- 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