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
84
85
86
87
88
89
90
91
|
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Trinity(MakefilePackage):
"""Trinity, developed at the Broad Institute and the Hebrew University of
Jerusalem, represents a novel method for the efficient and robust de
novo reconstruction of transcriptomes from RNA-seq data. Trinity
combines three independent software modules: Inchworm, Chrysalis, and
Butterfly, applied sequentially to process large volumes of RNA-seq
reads. Trinity partitions the sequence data into many individual de
Bruijn graphs, each representing the transcriptional complexity at a
given gene or locus, and then processes each graph independently to
extract full-length splicing isoforms and to tease apart transcripts
derived from paralogous genes.
"""
homepage = "http://trinityrnaseq.github.io/"
url = "https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz"
version('2.6.6', sha256='868dfadeefaf2d3c6150a88d5e86fbc09466d69bbf4a65f70b4f5a7485668984')
depends_on("java@8:", type=("build", "run"))
depends_on("bowtie2")
depends_on("jellyfish")
depends_on("salmon")
depends_on("perl+threads", type=("build", "run"))
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
# There is no documented list of these deps, but they're in the Dockerfile
# and we have runtime errors without them
# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile
depends_on("blast-plus", type="run")
depends_on("bowtie", type="run")
depends_on("r", type="run")
depends_on("r-tidyverse", type="run")
depends_on("r-edger", type="run")
depends_on("r-deseq2", type="run")
depends_on("r-ape", type="run")
depends_on("r-gplots", type="run")
depends_on("r-biobase", type="run")
depends_on("r-qvalue", type="run")
depends_on("rsem", type="run")
depends_on("kallisto", type="run")
depends_on("fastqc", type="run")
depends_on("samtools", type="run")
depends_on("py-numpy", type="run")
depends_on("express", type="run")
depends_on("perl-dbfile", type="run")
depends_on("perl-uri", type="run")
depends_on("r-fastcluster", type="run")
depends_on("r-ctc", type="run")
depends_on("r-goseq", type="run")
depends_on("r-glimma", type="run")
depends_on("r-rots", type="run")
depends_on("r-goplot", type="run")
depends_on("r-argparse", type="run")
depends_on("r-sm", type="run")
def build(self, spec, prefix):
make()
make("trinity_essentials")
make("plugins")
def install(self, spec, prefix):
install_tree('.', prefix.bin)
force_remove(join_path(prefix.bin, '.gitmodules'))
force_remove(join_path(prefix.bin, 'Butterfly', '.err'))
force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.classpath'))
force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.err'))
force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.project'))
remove_linked_tree(join_path(prefix.bin, 'Butterfly', 'src',
'.settings'))
remove_linked_tree(join_path(prefix.bin, 'Inchworm', 'src', '.deps'))
remove_linked_tree(join_path(prefix.bin, 'trinity-plugins',
'ParaFly-0.1.0', 'src', '.deps'))
force_remove(join_path(prefix.bin, 'trinity-plugins',
'seqtk-trinity-0.0.2', '.gitignore'))
force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin',
'.hidden'))
def setup_environment(self, spack_env, run_env):
run_env.set('TRINITY_HOME', self.prefix.bin)
run_env.prepend_path('PATH', self.prefix.bin.util)
spack_env.append_flags('CXXFLAGS', self.compiler.openmp_flag)
|
