# 0.4.2 modified by:
# Adam Huffman
# The Francis Crick Institute
# TODO: deal with the hardcoding of /usr/bin/perl

easyblock = "PackedBinary"

name = 'Trim_Galore'
version = '0.4.4'

homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/'
description = """A wrapper tool around Cutadapt and FastQC to consistently apply 
 quality and adapter trimming to FastQ files, with some extra functionality for 
 MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries."""

toolchain = {'name': 'foss', 'version': '2016b'}

sources = ['%(namelower)s_v%(version)s.zip']
source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s']

install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s"

dependencies = [
    ('FastQC', '0.11.5', '-Java-1.7.0_80', True),
    ('cutadapt', '1.9.1', '-Python-2.7.12'),
]

sanity_check_paths = {
    'files': ["trim_galore"],
    'dirs': [],
}

moduleclass = 'bio'
