name = 'Trinity'
version = '2012-10-05'

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': 'goolf', 'version': '1.4.10'}
toolchainopts = {'optarch': True}

source_urls = [
    ('http://sourceforge.net/projects/trinityrnaseq/files', 'download')]
sources = ['trinityrnaseq_r%s.tgz' % version]

patches = [
    'chrysalis_commandline_noconsts_2012-10-05.patch',
    'cmd_forker_taskset_2012-10-05.patch',
    'trinitypl_increase_max_cpu_2012-10-05.patch',
    'rsem-plugin_makefile-cxx.patch',
    'trinity_jellyfish-GCC-4.7.patch',
]

java = 'Java'
javaver = '1.7.0_10'

dependencies = [
    (java, javaver, '', True),
    ('ant', '1.8.4', '-%s-%s' % (java, javaver), True),
    ('ncurses', '5.9'),
    ('zlib', '1.2.7'),
]

bwapluginver = "0.5.7"
RSEMmod = True

# required for GCC v4.7, see
# http://forums.bannister.org/ubbthreads.php?ubb=showflat&Number=79791&page=2
import os
os.putenv('CPPONLYFLAGS', '-Wno-narrowing')

moduleclass = 'bio'