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
