name = 'Trinity'
version = '2.1.1'

homepage = 'http://trinityrnaseq.github.io'
description = """Trinity 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."""
toolchain = {'name': 'intel', 'version': '2015b'}
toolchainopts = {'optarch': True}

source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/']

local_java = 'Java'
local_javaver = '1.8.0_66'

sources = ['v%(version)s.tar.gz']

patches = [
    'chrysalis_commandline_noconsts_2012-10-05.patch',
    'Trinity-%(version)s_jellyfish-Makefile.patch',
]

builddependencies = [
    ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')),
]

dependencies = [
    (local_java, local_javaver, '', True),
    ('ant', '1.9.6', '-%s-%s' % (local_java, local_javaver), True),
    ('Bowtie', '1.1.2'),
    ('Bowtie2', '2.2.6'),
    ('ncurses', '5.9',),
    ('zlib', '1.2.8'),
    ('Perl', '5.20.3'),
]

moduleclass = 'bio'
