def main():
args = parse_args(sys.argv[1:])
config = read_config(args)
prov = provider.get_provider(args['provider_name'], args['project_dir'])
p = project.Project(args, prov)
p.verify_directory_structure()
p.read_samples()
p.validate_de_input()
generate_scripts(p, config)
print_instructions(p)
def test_generate_sbatch_command():
args = get_default_args()
prov = provider.get_provider(args['provider_name'],
args['project_dir'])
proj = project.Project(args, prov)
proj.samples = [1, 2, 3, 4]
expected = "sbatch --array=1-4%6 run_sample.sh"
assert_equal(pipeline.generate_sbatch_command(proj), expected)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
self.pwd = os.getcwd()
args = get_default_args()
args.update({
'project_dir': self.tmp_root
})
test_dir = os.path.dirname(os.path.abspath(__file__))
template_dir = "{0}/../templates".format(test_dir)
self.env = Environment(loader=FileSystemLoader(template_dir))
prov = provider.get_provider(args['provider_name'],
args['project_dir'])
self.project = project.Project(args, prov)
self.project.samples = [1, 2, 3, 4]
self.config = get_default_config()
def test_get_provider_sll():
project_root = "."
sll_provider = provider.get_provider("sll", project_root)
assert_true(isinstance(sll_provider, sll.SllProvider))
assert_equal(sll_provider.project_root, project_root)
def test_get_provider_gcf():
project_root = "."
gcf_provider = provider.get_provider("gcf", project_root)
assert_true(isinstance(gcf_provider, gcf.GcfProvider))
assert_equal(gcf_provider.project_root, project_root)