easyblock = 'ConfigureMake'

name = 'Stacks'
version = '1.03'

homepage = 'http://creskolab.uoregon.edu/stacks/'
description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on
 the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose
 of building genetic maps and conducting population genomics and phylogeography.
"""

toolchain = {'name': 'ictce', 'version': '5.3.0'}

source_urls = ['http://creskolab.uoregon.edu/stacks/source/']
sources = [SOURCELOWER_TAR_GZ]

runtest = "check"

sanity_check_paths = {
    'files': [
        'bin/%s' %
        binfile for binfile in [
            'clone_filter',
            'denovo_map.pl',
            'exec_velvet.pl',
            'genotypes',
            'index_radtags.pl',
            'load_radtags.pl',
            'populations',
            'process_shortreads',
            'ref_map.pl',
            'sstacks',
            'ustacks',
            'cstacks',
            'estacks',
            'export_sql.pl',
            'hstacks',
            'kmer_filter',
            'load_sequences.pl',
            'process_radtags',
            'pstacks',
            'sort_read_pairs.pl',
            'stacks_export_notify.pl',
        ]],
    'dirs': [],
}

moduleclass = 'bio'
