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))
