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commit: d16351c8ea24af193b4fa3f7cd9321924ceffc40 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sat Apr 1 12:09:16 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sat Apr 1 12:09:58 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d16351c8 |
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|
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sci-biology/tophat: Unbundle python modules |
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|
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Bug: https://bugs.gentoo.org/show_bug.cgi?id=614370 |
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Package-Manager: Portage-2.3.5, Repoman-2.3.2 |
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|
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.../files/tophat-2.1.1-python2-shebangs.patch | 42 ++++++++++++++++++++++ |
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...phat-2.1.1-r3.ebuild => tophat-2.1.1-r4.ebuild} | 19 +++++----- |
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2 files changed, 50 insertions(+), 11 deletions(-) |
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|
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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 |
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new file mode 100644 |
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index 00000000000..5c38bcc072e |
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--- /dev/null |
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+++ b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch |
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@@ -0,0 +1,42 @@ |
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+Make Python 2 explicit in python scripts |
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+ |
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+--- a/src/bed_to_juncs |
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++++ b/src/bed_to_juncs |
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+@@ -1,4 +1,4 @@ |
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+-#!/usr/bin/env python |
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++#!/usr/bin/env python2 |
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+ # encoding: utf-8 |
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+ """ |
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+ bed_to_juncs.py |
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+--- a/src/contig_to_chr_coords |
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++++ b/src/contig_to_chr_coords |
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+@@ -1,4 +1,4 @@ |
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+-#!/usr/bin/env python |
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++#!/usr/bin/env python2 |
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+ # encoding: utf-8 |
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+ """ |
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+ contig_to_chr_coords.py |
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+--- a/src/sra_to_solid |
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++++ b/src/sra_to_solid |
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+@@ -1,4 +1,4 @@ |
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+-#!/usr/bin/env python |
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++#!/usr/bin/env python2 |
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+ |
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+ """ |
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+ sra_to_solid.py |
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+--- a/src/tophat-fusion-post |
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++++ b/src/tophat-fusion-post |
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+@@ -1,4 +1,4 @@ |
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+-#!/usr/bin/env python |
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++#!/usr/bin/env python2 |
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+ |
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+ |
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+ """ |
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+--- a/src/tophat.py |
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++++ b/src/tophat.py |
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+@@ -1,4 +1,4 @@ |
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+-#!/usr/bin/env python |
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++#!/usr/bin/env python2 |
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+ |
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+ # encoding: utf-8 |
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+ """ |
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|
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diff --git a/sci-biology/tophat/tophat-2.1.1-r3.ebuild b/sci-biology/tophat/tophat-2.1.1-r4.ebuild |
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similarity index 81% |
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rename from sci-biology/tophat/tophat-2.1.1-r3.ebuild |
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rename to sci-biology/tophat/tophat-2.1.1-r4.ebuild |
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index cf684593109..590f6eb2d20 100644 |
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--- a/sci-biology/tophat/tophat-2.1.1-r3.ebuild |
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+++ b/sci-biology/tophat/tophat-2.1.1-r4.ebuild |
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@@ -1,4 +1,4 @@ |
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-# Copyright 1999-2016 Gentoo Foundation |
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+# Copyright 1999-2017 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=6 |
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@@ -19,6 +19,8 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
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|
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RDEPEND="${PYTHON_DEPS} |
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dev-libs/boost:=[threads] |
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+ dev-python/intervaltree[${PYTHON_USEDEP}] |
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+ dev-python/sortedcontainers[${PYTHON_USEDEP}] |
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sci-biology/samtools:0.1-legacy |
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sci-biology/bowtie:2" |
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DEPEND="${RDEPEND} |
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@@ -27,8 +29,9 @@ DEPEND="${RDEPEND} |
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>=sys-devel/autoconf-archive-2016.09.16" |
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|
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PATCHES=( |
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- "${FILESDIR}/${P}-unbundle-seqan-samtools.patch" |
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- "${FILESDIR}/${P}-fix-c++14.patch" |
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+ "${FILESDIR}"/${P}-unbundle-seqan-samtools.patch |
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+ "${FILESDIR}"/${P}-fix-c++14.patch |
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+ "${FILESDIR}"/${P}-python2-shebangs.patch |
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) |
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|
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src_prepare() { |
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@@ -66,16 +69,10 @@ src_configure() { |
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src_install() { |
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default |
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|
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+ # delete bundled python modules |
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local i |
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- # install scripts properly |
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- for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do |
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- python_fix_shebang "${ED%/}/usr/bin/${i}" |
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- done |
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- |
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- # install python modules properly |
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for i in intervaltree sortedcontainers; do |
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- python_domodule "${ED%/}/usr/bin/${i}" |
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- rm -rf "${ED%/}/usr/bin/${i}" || die |
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+ rm -r "${ED%/}"/usr/bin/${i} || die |
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done |
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} |