##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
# License::   MIT/GPL
# $Id$
#
# This work implements a part of the HPCBIOS project and is a component of the policy:
# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
##

name = 'Cufflinks'
version = '2.0.2'

homepage = 'http://cole-trapnell-lab.github.io/cufflinks/'
description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq"""

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

sources = [SOURCELOWER_TAR_GZ]
source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/']

dependencies = [
    ('Boost', '1.51.0', '-Python-2.7.3'),
    ('SAMtools', '0.1.18'),
    ('Eigen', '3.1.1'),
    ('zlib', '1.2.7'),
]

patches = ['Cufflinks_GCC-4.7.patch']

configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib'
preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" '

sanity_check_paths = {
    'files': ['bin/cufflinks'],
    'dirs': []
}

moduleclass = 'bio'
