def startup_command(self, ctx, **kwds):
"""Return a shell command used to startup this instance.
Among other common planmo kwds, this should respect the
``daemon`` keyword.
"""
daemon = kwds.get("daemon", False)
daemon_str = "" if not daemon else " -d"
docker_run_extras = "-p %s:80%s" % (self.port, daemon_str)
env_directives = ["%s='%s'" % item for item in self.env.items()]
image = kwds.get("docker_galaxy_image", "bgruening/galaxy-stable")
run_command = docker_util.build_docker_run_command(
"", image,
interactive=False,
env_directives=env_directives,
working_directory=None,
name=self.server_name,
run_extra_arguments=docker_run_extras,
set_user=False,
volumes=self.volumes,
**self.docker_target_kwds
)
chmod_command = [
"chmod",
"-R",
"o+rwx",
self.config_directory,
]
if self.export_directory:
chmod_command.append(self.export_directory)
return shell_join(
argv_to_str(chmod_command),
run_command,
)
def startup_command(self, ctx, **kwds):
"""Return a shell command used to startup this instance.
Among other common planmo kwds, this should respect the
``daemon`` keyword.
"""
daemon = kwds.get("daemon", False)
daemon_str = "" if not daemon else " -d"
docker_run_extras = "-p %s:80%s" % (self.port, daemon_str)
env_directives = ["%s='%s'" % item for item in self.env.items()]
image = kwds.get("docker_galaxy_image", "bgruening/galaxy-stable")
run_command = docker_util.build_docker_run_command(
"",
image,
interactive=False,
env_directives=env_directives,
working_directory=None,
name=self.server_name,
run_extra_arguments=docker_run_extras,
set_user=False,
volumes=self.volumes,
**self.docker_target_kwds)
chmod_command = [
"chmod",
"-R",
"o+rwx",
self.config_directory,
]
if self.export_directory:
chmod_command.append(self.export_directory)
return shell_join(
argv_to_str(chmod_command),
run_command,
)
def shell(cmds, **kwds):
if isinstance(cmds, list):
cmd_string = commands.argv_to_str(cmds)
else:
cmd_string = cmds
info(cmd_string)
return commands.shell(cmds, **kwds)
def communicate(cmds, **kwds):
if isinstance(cmds, list):
cmds = commands.argv_to_str(cmds)
info(cmds)
p = commands.shell_process(cmds, **kwds)
if kwds.get("stdout", None) is None and commands.redirecting_io(sys=sys):
output = commands.redirect_aware_commmunicate(p)
else:
output = p.communicate()
if p.returncode != 0:
template = "Problem executing commands {0} - ({1}, {2})"
msg = template.format(cmds, output[0], output[1])
raise RuntimeError(msg)
return output
def communicate(cmds, **kwds):
if isinstance(cmds, list):
cmds = commands.argv_to_str(cmds)
info(cmds)
p = commands.shell_process(cmds, **kwds)
if kwds.get("stdout", None) is None and commands.redirecting_io(sys=sys):
output = commands.redirect_aware_commmunicate(p)
else:
output = p.communicate()
if p.returncode != 0:
template = "Problem executing commands {0} - ({1}, {2})"
msg = template.format(cmds, output[0], output[1])
raise RuntimeError(msg)
return output
def args_to_str(args):
if args is None or isinstance(args, string_types):
return args
else:
return commands.argv_to_str(args)
def args_to_str(args):
if args is None or isinstance(args, string_types):
return args
else:
return commands.argv_to_str(args)