blob: b5bd8bdfe1a0f8b2ad6c4c064ad551cede991e1d (
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
|
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit cmake multilib
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
"${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
"${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
"${FILESDIR}"/salmon-0.10.2_fix_tests.patch
"${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
RDEPEND="${DEPEND}"
# budled copies of:
# sci-biology/bwa-0.7.12.5
# sci-biology/jellyfish
# sci-biology/staden-1.14.8.1
# sci-biology/gfftools
#
# libgff-1.1 from https://github.com/Kingsford-Group/libgff
# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
# https://github.com/Kingsford-Group/libgff/issues/1
#
# dev-libs/spdlog-0.16.1
# cereal-1.2.2
# see the many curl executions:
# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
#
DEPEND="
sys-libs/zlib
app-arch/bzip2
app-arch/xz-utils
dev-libs/boost:0[threads(-)]
dev-libs/libdivsufsort
sci-biology/bwa
>=dev-libs/jemalloc-5.0.1
>=dev-cpp/tbb-2018.20180312
"
RDEPEND="${DEPEND}"
BDEPEND="
net-misc/curl
app-arch/unzip
"
src_prepare() {
# use system libs
sed -i \
-e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \
-e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \
-e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \
-e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \
src/CMakeLists.txt || die
cmake_src_prepare
}
|
GitWeb
