From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 5212E59CAF for ; Sat, 9 Apr 2016 19:58:47 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 34E7121C01D; Sat, 9 Apr 2016 19:58:44 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id CECDC21C01D for ; Sat, 9 Apr 2016 19:58:43 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 44A9A340AB2 for ; Sat, 9 Apr 2016 19:58:42 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 25D687E for ; Sat, 9 Apr 2016 19:58:38 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1460231911.0f059b5eb7e03f75705f623dc74e27842540da40.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/samtools/samtools-0.1.20-r1.ebuild sci-biology/samtools/samtools-0.1.20-r2.ebuild X-VCS-Directories: sci-biology/samtools/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 0f059b5eb7e03f75705f623dc74e27842540da40 X-VCS-Branch: master Date: Sat, 9 Apr 2016 19:58:38 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: a7e3333a-27ba-4ba4-ba97-2a8f9a7a7aea X-Archives-Hash: a8df988e571e0c0e3caeebc9429c7dd1 commit: 0f059b5eb7e03f75705f623dc74e27842540da40 Author: David Seifert gentoo org> AuthorDate: Sat Apr 9 19:58:14 2016 +0000 Commit: David Seifert gentoo 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)