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sci-biology/tophat: Unbundle python modules

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Bug: https://bugs.gentoo.org/show_bug.cgi?id=614370
Package-Manager: Portage-2.3.5, Repoman-2.3.2
This commit is contained in:
David Seifert
2017-04-01 14:09:16 +02:00
parent ae05c37e2b
commit d16351c8ea
2 changed files with 50 additions and 11 deletions
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42
sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch Normal file
View File

@@ -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
"""

19
sci-biology/tophat/tophat-2.1.1-r3.ebuild → sci-biology/tophat/tophat-2.1.1-r4.ebuild
View File

@@ -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
}