def data(tmpdir_factory, _cookiecutter_config_file, docker_compose):
p = tmpdir_factory.mktemp("data")
compose = p.join("docker-compose.yaml")
compose.write(docker_compose)
snakefile = p.join("Snakefile")
SNAKEFILE.copy(snakefile)
cluster_config = p.join("cluster-config.yaml")
CLUSTERCONFIG.copy(cluster_config)
template = os.path.join(os.path.abspath(os.path.dirname(__file__)),
os.pardir)
output_factory = tmpdir_factory.mktemp
c = Cookies(template, output_factory, _cookiecutter_config_file)
c._new_output_dir = lambda: str(p.join("slurm"))
c.bake(
extra_context={
'partition': 'normal',
'output': 'logs/slurm-%j.out',
'error': 'logs/slurm-%j.err'
})
# Advanced setting
c = Cookies(template, output_factory, _cookiecutter_config_file)
c._new_output_dir = lambda: str(p.join("slurm-advanced"))
c.bake(
extra_context={
'partition': 'normal',
'output': 'logs/slurm-%j.out',
'error': 'logs/slurm-%j.err',
'submit_script': 'slurm-submit-advanced.py'
})
return p
def _cookie_factory(sbatch_defaults=_sbatch_defaults,
advanced="no",
cluster_name=None,
cluster_config=None,
yamlconfig=_yamlconfig_default):
cookie_template = pjoin(os.path.abspath(pytest.dname), os.pardir)
output_factory = tmpdir_factory.mktemp
c = Cookies(cookie_template, output_factory, _cookiecutter_config_file)
c._new_output_dir = lambda: str(datadir)
extra_context = {
"sbatch_defaults": sbatch_defaults,
"advanced_argument_conversion": advanced
}
if cluster_name is not None:
extra_context["cluster_name"] = cluster_name
if cluster_config is not None:
extra_context["cluster_config"] = cluster_config
c.bake(extra_context=extra_context)
config = datadir.join("slurm").join("config.yaml")
config_d = dict([
tuple(line.split(":")) for line in config.read().split("\n")
if line != ""
])
config_d.update(**yamlconfig)
config.write("\n".join(f"{k}: {v}" for k, v in config_d.items()))
def data(tmpdir_factory, _cookiecutter_config_file):
p = tmpdir_factory.mktemp("data")
snakefile = p.join("Snakefile")
SNAKEFILE.copy(snakefile)
cluster_config = p.join("cluster-config.yaml")
CLUSTERCONFIG.copy(cluster_config)
template = os.path.join(os.path.abspath(os.path.dirname(__file__)),
os.pardir)
output_factory = tmpdir_factory.mktemp
defaults = "partition=normal output=logs/slurm-%j.out error=logs/slurm-%j.err"
c = Cookies(template, output_factory, _cookiecutter_config_file)
c._new_output_dir = lambda: str(p.join("slurm"))
c.bake(extra_context={"sbatch_defaults": defaults})
# Advanced setting
c = Cookies(template, output_factory, _cookiecutter_config_file)
c._new_output_dir = lambda: str(p.join("slurm-advanced"))
c.bake(extra_context={
"sbatch_defaults": defaults,
"advanced_argument_conversion": "yes",
})
return p