blob: 6625162e21b7ee59da15990a0521bfa290fa0171 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
|
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
AUTOTOOLS_AUTORECONF=yes
PYTHON_COMPAT=( python2_7 )
inherit autotools-utils python-single-r1
DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
HOMEPAGE="http://ccb.jhu.edu/software/tophat"
# https://github.com/infphilo/tophat
# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz
SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS=""
IUSE="debug"
DEPEND="dev-libs/boost"
# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
# boost and seqan is needed for tophat_reporter
# tophat.py calls
# samtools_0.1.18 view -h -
# samtools_0.1.18 sort
# samtools_0.1.18 merge -f -h -u -Q --sam-header
RDEPEND="${DEPEND}
>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
src_prepare() {
sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* || die
sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die
# rm -rf src/SeqAn* || die
eautoreconf
autotools-utils_src_prepare
}
src_configure() {
local myeconfargs=(
--disable-optim
$(use_enable debug)
)
autotools-utils_src_configure
cd ../"${P}"_build/src || die
ln -s ../"${P}"/src/SeqAn-1.3 . || die
ln -s ../../"${P}"/src/samtools-0.1.18 . || die
sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* || die
}
src_install() {
# introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die
autotools-utils_src_install
python_fix_shebang "${ED}"/usr/bin/tophat
}
|
GitWeb
