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 D2B8A59CAF for ; Sun, 10 Apr 2016 09:21:29 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 500EA21C0CA; Sun, 10 Apr 2016 09:21:28 +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 E064B21C0CA for ; Sun, 10 Apr 2016 09:21:27 +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 F06633407B8 for ; Sun, 10 Apr 2016 09:21:26 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 6243A86 for ; Sun, 10 Apr 2016 09:21:24 +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: <1460280071.5f3acec053c0f95f355f6c4db5e12994555a4b7a.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-1.3-r1.ebuild sci-biology/samtools/samtools-1.3.ebuild X-VCS-Directories: sci-biology/samtools/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 5f3acec053c0f95f355f6c4db5e12994555a4b7a X-VCS-Branch: master Date: Sun, 10 Apr 2016 09:21:24 +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: ca52bdcd-dff6-4aad-82b3-29ed60703df0 X-Archives-Hash: f9c7e893fffbe9a7b4e669c66ee6a4a8 commit: 5f3acec053c0f95f355f6c4db5e12994555a4b7a Author: David Seifert gentoo org> AuthorDate: Sun Apr 10 09:20:56 2016 +0000 Commit: David Seifert gentoo 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