blob: 8ba4d0cf7d195121205ae5826cc8a7e1fc0951ac (
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
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
|
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit cmake multilib
DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip
https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz
https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz
https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz
"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS=""
DEPEND="
dev-libs/boost:0
dev-libs/jemalloc
dev-libs/libdivsufsort
dev-cpp/tbb
dev-cpp/sparsehash
sci-biology/jellyfish:2
"
RDEPEND="${DEPEND}"
BDEPEND="app-arch/unzip"
# a C++-11 compliant compiler is needs, aka >=gcc-4.7
# TODO: disable running wget/curl during src_compile
# https://github.com/kingsfordgroup/sailfish/issues/80
# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
# contains bundled libdivsufsort
# contains bundled libgff https://github.com/COMBINE-lab/libgff
# contains bundled jellyfish-2.2.5
# contains bundled sparsehash-2.0.2
PATCHES=(
"${FILESDIR}/${PN}-0.9.2-no-boost-static.patch"
"${FILESDIR}/${PN}-no-curl.patch"
"${FILESDIR}/${PN}-allow-newer-boost.patch"
)
src_unpack() {
default
mkdir -p "${S}/external"
cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
mv "${WORKDIR}/RapMap-quasi-mph" "${S}/external/RapMap" || die
mv "${WORKDIR}/jellyfish-2.2.5" "${S}/external/jellyfish-2.2.5" || die
mv "${WORKDIR}/sparsehash-sparsehash-2.0.2" "${S}/external/sparsehash-sparsehash-2.0.2" || die
mv "${WORKDIR}/libgff-1.0" "${S}/external/libgff" || die
mkdir -p "${S}/external/install/lib"
cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
mkdir -p "${S}/external/install/src/rapmap"
cp "${S}/external/RapMap/src/"* "${S}/external/install/src/rapmap" || die
}
src_prepare() {
cmake_src_prepare
# use the dynamic library
sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \
-e 's/libdivsufsort64.a/libdivsufsort64.so/g' \
-e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \
src/CMakeLists.txt || die
}
src_configure() {
JELLYFISH_INCLUDE_DIR="/usr/include/jellyfish2" cmake_src_configure
# jellyfish2 instead of jellyfish
find -type f -name "*.hpp" -exec sed -i -e 's/#include \"jellyfish\//#include \"jellyfish2\//g' {} + || die
find -type f -name "*.hpp" -exec sed -i -e 's/#include <jellyfish\//#include <jellyfish2\//g' {} + || die
}
src_install() {
cmake_src_install
rm -r "${ED}"/usr/tests || die
rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
}
|
GitWeb