def _run_tool(cmd, use_container=True, work_dir=None, log_file=None):
    """Run with injection of bcbio path.

    Place at end for runs without containers to avoid overriding other
    bcbio installations.
    """
    if isinstance(cmd, (list, tuple)):
        cmd = " ".join([str(x) for x in cmd])
    cmd = utils.local_path_export(at_start=use_container) + cmd
    if log_file:
        cmd += " 2>&1 | tee -a %s" % log_file
    try:
        print("Running: %s" % cmd)
        subprocess.check_call(cmd, shell=True)
    finally:
        if use_container and work_dir:
            _chown_workdir(work_dir)
def _run_tool ( cmd , use_container = True , work_dir = None , log_file = None ) : if isinstance ( cmd , ( list , tuple ) ) : cmd = " " . join ( [ str ( x ) for x in cmd ] ) cmd = utils . local_path_export ( at_start = use_container ) + cmd if log_file : cmd += " 2>&1 | tee -a %s" % log_file try : print ( "Running: %s" % cmd ) subprocess . check_call ( cmd , shell = True ) finally : if use_container and work_dir : _chown_workdir ( work_dir )
Run with injection of bcbio path.

    Place at end for runs without containers to avoid overriding other
    bcbio installations.