commit: d16351c8ea24af193b4fa3f7cd9321924ceffc40 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Apr 1 12:09:16 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> 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 }
