name = 'Trinity'
version = '2013-02-25'

homepage = 'http://trinityrnaseq.sourceforge.net/'
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': 'ictce', 'version': '4.1.13'}
toolchainopts = {'optarch': True}

source_urls = [
    ('http://sourceforge.net/projects/trinityrnaseq/files', 'download'),
    'http://www.cbcb.umd.edu/software/jellyfish/',
]

java = 'Java'
javaver = '1.7.0_15'
jellyfishver = '1.1.10'

versionsuffix = '-jellyfish-%s' % jellyfishver

sources = [
    'trinityrnaseq_r%s.tgz' % version,
    'jellyfish-%s.tar.gz' % jellyfishver,
]

patches = [
    'chrysalis_commandline_noconsts_2012-10-05.patch',
    'cmd_forker_taskset_2012-10-05.patch',
    'trinitypl_increase_max_cpu_2013-02-25.patch',
    'rsem-plugin_makefile-cxx-2013-02-25.patch',
    'trinity_ictce-no-jellyfish-2013-02-25.patch',
]


dependencies = [
    (java, javaver, '', True),
    ('ant', '1.9.0', '-%s-%s' % (java, javaver), True),
    ('ncurses', '5.9'),
    ('zlib', '1.2.7'),
]

bwapluginver = "0.5.7"
RSEMmod = True

moduleclass = 'bio'
