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)