blob: 30bd4ca62c1a1dd0deb4d71bd6a92378ef76d512 (
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
|
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit perl-module toolchain-funcs
# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
DESCRIPTION="Transcriptome assembler for RNA-seq reads"
HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
>=sci-biology/jellyfish-2.2.6:2
>=sci-libs/htslib-1.2.1
>=sci-biology/samtools-1.3:0
>=sci-biology/trimmomatic-0.36
>=sci-biology/GAL-0.2.1
dev-perl/IO-All
sci-biology/seqtools"
# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
# has the following "plugins" (aka bundled 3rd-party code)
# slclust
# DEXseq_util
# COLLECTL
# ParaFly-0.1.0
S="${WORKDIR}/${PN}-v${PV}"
PATCHES=(
"${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
)
src_compile(){
emake all
emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
}
src_install(){
dodoc Chrysalis/chrysalis.notes
dodoc Changelog.txt
perl_set_version
dobin Trinity
perl_domodule util/*.pl
dobin Inchworm/bin/*
cd Chrysalis/bin || die
dobin BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta QuantifyGraph ReadsToTranscripts
cd ../../util/R || die
insinto /usr/share/"${PN}"/R
doins *.R
cd ../PBS || die
insinto /usr/share/"${PN}"/PBS
doins *
cd .. || die
cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die
cd "${S}" || die
perl_domodule util/misc/PerlLib/*.pm PerlLib/*.pm
perl_domodule PerlLib/KmerGraphLib/*.pm
perl_domodule PerlLib/CDNA/*.pm
perl_domodule PerlLib/Simulate/*.pm
perl_domodule PerlLib/CanvasXpress/*.pm
chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
}
|
GitWeb
