def udev_trigger(subsystem=None, action="add", name=None):
argv = ["trigger", "--action=%s" % action]
if subsystem:
argv.append("--subsystem-match=%s" % subsystem)
if name:
argv.append("--sysname-match=%s" % name)
util.run_program(["udevadm"] + argv)
udev_settle()
def run_rates(command):
global _tiger_binary
if _tiger_binary is None:
_tiger_binary = util.find_program(_binary_name)
try:
util.run_program(_tiger_binary, command)
except util.ExternalProgramError:
log.error("fast_TIGER did not execute successfully")
log.error("fast_TIGER output follows, in case it's helpful for \
finding the problem")
log.error("You probably just need to recompile the fast_TIGER \
code for your system. But please note that this is an \
unsupported option. For empirical work we recommend using \
entropy calculations for site rates, which is the default \
behaviour for the kmeans algorithm in PF2.")
raise
def run_raxml_pthreads(command, cpus):
global _raxml_pthreads_binary
if _raxml_pthreads_binary is None:
_raxml_pthreads_binary = util.find_program(_binary_name_pthreads)
command = " ".join([command, "-T", str(cpus), " "])
util.run_program(_raxml_pthreads_binary, command)
def run_raxml(command):
global _raxml_binary
if _raxml_binary is None:
_raxml_binary = util.find_program(_binary_name)
util.run_program(_raxml_binary, command)
def run_raxml_pthreads(command, cpus):
global _raxml_pthreads_binary
if _raxml_pthreads_binary is None:
_raxml_pthreads_binary = util.find_program(_binary_name_pthreads)
command = " ".join([command, "-T", str(cpus), " "])
util.run_program(_raxml_pthreads_binary, command)
def run_raxml(command):
global _raxml_binary
if _raxml_binary is None:
_raxml_binary = util.find_program(_binary_name)
util.run_program(_raxml_binary, command)
def udev_settle():
# wait maximal 300 seconds for udev to be done running blkid, lvm,
# mdadm etc. This large timeout is needed when running on machines with
# lots of disks, or with slow disks
util.run_program(["udevadm", "settle", "--timeout=300"])