def check_binaries(): if not which(MINIMAP_BIN): raise AlignmentException("minimap2 is not installed") if not which(SAMTOOLS_BIN): raise AlignmentException("samtools is not installed") if not which("sort"): raise AlignmentException("UNIX sort utility is not available")
def check_binaries(): if not which(REPEAT_BIN) or not which(CONTIGGER_BIN): raise RepeatException("Repeat/contigger binaries were not found. " "Did you run 'make'?") try: devnull = open(os.devnull, "w") subprocess.check_call([REPEAT_BIN, "repeat", "-h"], stderr=devnull) except subprocess.CalledProcessError as e: raise RepeatException(str(e)) except OSError as e: raise RepeatException(str(e))
def check_binaries(): if not which(POLISH_BIN): raise PolishException("polishing binary was not found. " "Did you run 'make'?") try: devnull = open(os.devnull, "w") subprocess.check_call([POLISH_BIN, "-h"], stderr=devnull) except subprocess.CalledProcessError as e: if e.returncode == -9: logger.error("Looks like the system ran out of memory") raise PolishException(str(e)) except OSError as e: raise PolishException(str(e))