SConstruct template

sconstruct

"""
Short description here
"""

import os

from bioscons.fileutils import Targets
from bioscons.slurm import SlurmEnvironment

from SCons.Script import ARGUMENTS, Variables, Decider

# check timestamps before calculating md5 checksums
# see http://www.scons.org/doc/production/HTML/scons-user.html#AEN929
Decider('MD5-timestamp')

outdir = ARGUMENTS.get('out', 'output')

# Cluster configuration
use_cluster = ARGUMENTS.get('use_cluster', 'false') == 'true'
slurm_queue = ARGUMENTS.get('slurm_queue', 'any')
blast_nproc = ARGUMENTS.get('blast_nproc', 6)

vars = Variables()
vars.Add('out', 
         help = '', 
         default = outdir)

env = SlurmEnvironment(ENV = os.environ,
                       variables = vars,
                       use_cluster=use_cluster,
                       slurm_queue=slurm_queue,
                       blast_nproc=blast_nproc
                       )   
targets = Targets()

command = env.Command(
    target = '', 
    source = '', 
    action = ('')
    )   

targets.update(locals().values())

# identify extraneous files
targets.show_extras(outdir)