SConstruct.py

import os
import sys
import ConfigParser
from os import path, environ
import glob
import itertools

venv = environ.get('VIRTUAL_ENV')
if not venv:
    sys.exit('--> an active virtualenv is required'.format(venv))

# requirements installed in the virtualenv
from SCons.Script import (
    ARGUMENTS, Variables, Decider, Depends, EnumVariable,
    PathVariable, Help, BoolVariable, Precious, Dir)

# check timestamps before calculating md5 checksums
Decider('MD5-timestamp')

vars = Variables()

# declare variables for the environment
vars.Add(PathVariable('out', 'Path to output directory',
                      'output', PathVariable.PathIsDirCreate))
vars.Add('nproc', 'Number of concurrent processes', default=12)

# Provides access to options prior to instantiation of env object
# below; it's better to access variables through the env object.
varargs = dict({opt.key: opt.default for opt in vars.options}, **vars.args)
truevals = {True, 'yes', 'y', 'True', 'true', 't'}
nproc = varargs['nproc']

#####################################################################
########################  input data  ###############################
#####################################################################


#####################################################################
#########################  end input data  ##########################
#####################################################################

# Explicitly define PATH, giving preference to local executables; it's
# best to use absolute paths for non-local executables rather than add
# paths here to avoid accidental introduction of external
# dependencies. Environment variables are inherited from the parent
# shell from which scons is run.

environment_variables = dict(
    os.environ,
    PATH=':'.join([
        'bin',
        path.join(venv, 'bin'),
        '/app/bin',  # provides R
        '/usr/local/bin', '/usr/bin', '/bin']),
    OMP_NUM_THREADS=nproc,
    R_LIBS_USER=path.join(path.split(venv)[0], 'R', 'R.%v-library'),
)

env = Environment(
    ENV=environment_variables,
    variables=vars,
    use_cluster=False,
    SHELL='bash'
)