# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# Swiss Institute of Bioinformatics
# Biozentrum - University of Basel
# Modified by: Adam Huffman
# The Francis Crick Institute

easyblock = 'ConfigureMake'

name = 'TopHat'
version = '2.1.1'

homepage = 'http://ccb.jhu.edu/software/tophat/'
description = """TopHat is a fast splice junction mapper for RNA-Seq reads."""

toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'pic': True}

sources = [SOURCELOWER_TAR_GZ]
source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/']

patches = [
    'tophat-2.0.13-zlib.patch',
]

dependencies = [
    ('Boost', '1.61.0'),
    ('zlib', '1.2.8'),
]

configopts = '--with-boost=$EBROOTBOOST'

parallel = 1

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

moduleclass = 'bio'
