from nestly import Nest
from nestly.scons import SConsWrap, name_targets
import os
import os.path
import appconfig
config = appconfig.read('config.yaml')
# Base folder
nest = Nest()
wrap = SConsWrap(
nest,
os.path.join(config['cluster']['folder'],
config['cluster']['algorithms']['louvain']['folder']))
env = Environment(ENV=os.environ)
# Used for resolving what type of execution environment will be used.
exec_env = appconfig.ExecutionEnvironment(
ARGUMENTS, supported_env=['pbs', 'sge', 'local'])
# don't include root as we don't want it embedded in this nest hierarchy
hic_paths = appconfig.get_precedents(config['map_folder'],
config['hic2ctg'],
prepend_root=False,
tips_only=True)
wrap.add('hic_path', hic_paths)
@wrap.add_target('make_graph')
@name_targets
def make_graph(outdir, c):
