From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id CE794139694 for ; Sat, 1 Apr 2017 12:10:19 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EA97521C038; Sat, 1 Apr 2017 12:10:16 +0000 (UTC) Received: from smtp.gentoo.org (dev.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (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 B7AFB21C038 for ; Sat, 1 Apr 2017 12:10:16 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 2F4D234165E for ; Sat, 1 Apr 2017 12:10:15 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 5E16B73DD for ; Sat, 1 Apr 2017 12:10:13 +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: <1491048598.d16351c8ea24af193b4fa3f7cd9321924ceffc40.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/files/, sci-biology/tophat/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch sci-biology/tophat/tophat-2.1.1-r3.ebuild sci-biology/tophat/tophat-2.1.1-r4.ebuild X-VCS-Directories: sci-biology/tophat/ sci-biology/tophat/files/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: d16351c8ea24af193b4fa3f7cd9321924ceffc40 X-VCS-Branch: master Date: Sat, 1 Apr 2017 12:10:13 +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: c766dff0-8127-4023-b859-83dd0743e72e X-Archives-Hash: 9fd034427963ccf3d0747e77401df4c9 commit: d16351c8ea24af193b4fa3f7cd9321924ceffc40 Author: David Seifert gentoo org> AuthorDate: Sat Apr 1 12:09:16 2017 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Apr 1 12:09:58 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d16351c8 sci-biology/tophat: Unbundle python modules Bug: https://bugs.gentoo.org/show_bug.cgi?id=614370 Package-Manager: Portage-2.3.5, Repoman-2.3.2 .../files/tophat-2.1.1-python2-shebangs.patch | 42 ++++++++++++++++++++++ ...phat-2.1.1-r3.ebuild => tophat-2.1.1-r4.ebuild} | 19 +++++----- 2 files changed, 50 insertions(+), 11 deletions(-) diff --git a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch new file mode 100644 index 00000000000..5c38bcc072e --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch @@ -0,0 +1,42 @@ +Make Python 2 explicit in python scripts + +--- a/src/bed_to_juncs ++++ b/src/bed_to_juncs +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + # encoding: utf-8 + """ + bed_to_juncs.py +--- a/src/contig_to_chr_coords ++++ b/src/contig_to_chr_coords +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + # encoding: utf-8 + """ + contig_to_chr_coords.py +--- a/src/sra_to_solid ++++ b/src/sra_to_solid +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + + """ + sra_to_solid.py +--- a/src/tophat-fusion-post ++++ b/src/tophat-fusion-post +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + + + """ +--- a/src/tophat.py ++++ b/src/tophat.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + + # encoding: utf-8 + """ diff --git a/sci-biology/tophat/tophat-2.1.1-r3.ebuild b/sci-biology/tophat/tophat-2.1.1-r4.ebuild similarity index 81% rename from sci-biology/tophat/tophat-2.1.1-r3.ebuild rename to sci-biology/tophat/tophat-2.1.1-r4.ebuild index cf684593109..590f6eb2d20 100644 --- a/sci-biology/tophat/tophat-2.1.1-r3.ebuild +++ b/sci-biology/tophat/tophat-2.1.1-r4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -19,6 +19,8 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND="${PYTHON_DEPS} dev-libs/boost:=[threads] + dev-python/intervaltree[${PYTHON_USEDEP}] + dev-python/sortedcontainers[${PYTHON_USEDEP}] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2" DEPEND="${RDEPEND} @@ -27,8 +29,9 @@ DEPEND="${RDEPEND} >=sys-devel/autoconf-archive-2016.09.16" PATCHES=( - "${FILESDIR}/${P}-unbundle-seqan-samtools.patch" - "${FILESDIR}/${P}-fix-c++14.patch" + "${FILESDIR}"/${P}-unbundle-seqan-samtools.patch + "${FILESDIR}"/${P}-fix-c++14.patch + "${FILESDIR}"/${P}-python2-shebangs.patch ) src_prepare() { @@ -66,16 +69,10 @@ src_configure() { src_install() { default + # delete bundled python modules local i - # install scripts properly - for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do - python_fix_shebang "${ED%/}/usr/bin/${i}" - done - - # install python modules properly for i in intervaltree sortedcontainers; do - python_domodule "${ED%/}/usr/bin/${i}" - rm -rf "${ED%/}/usr/bin/${i}" || die + rm -r "${ED%/}"/usr/bin/${i} || die done }