def check_binaries():
if not which(MINIMAP_BIN):
raise AlignmentException("Minimap2 is not installed")
if not which(GRAPHMAP_BIN):
raise AlignmentException("GraphMap is not installed")
if not which("sort"):
raise AlignmentException("UNIX sort utility is not available")
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:
raise PolishException(
"Some error inside native {0} module: {1}".format(POLISH_BIN, e))
def check_binaries():
if not which(ASSEMBLE_BIN):
raise AssembleException("Assemble binary was not found. "
"Did you run 'make'?")
try:
devnull = open(os.devnull, "w")
subprocess.check_call([ASSEMBLE_BIN, "-h"], stderr=devnull)
except subprocess.CalledProcessError as e:
raise AssembleException(
"Some error inside native {0} module: {1}".format(ASSEMBLE_BIN, e))
def check_binaries():
if not which(ASSEMBLE_BIN):
raise AssembleException("Assemble binary was not found. "
"Did you run 'make'?")
try:
devnull = open(os.devnull, "w")
subprocess.check_call([ASSEMBLE_BIN, "-h"], stderr=devnull)
except (subprocess.CalledProcessError, OSError) as e:
if e.returncode == -9:
logger.error("Looks like the system ran out of memory")
raise AssembleException(str(e))
def check_binaries():
if not which(BLASR_BIN):
raise AlignmentException("BLASR is not installed")
def check_binaries():
if not which(BLASR_BIN):
raise AlignmentException("BLASR is not installed")
if not which("sort"):
raise AlignmentException("UNIX sort utility is not available")
