def _configure(self):
"""
Configure the Pulsar application.
"""
self.state = service_states.CONFIGURING
misc.make_dir(self.pulsar_home)
# Write out app.yml
token = ''.join(random.SystemRandom().choice(string.ascii_uppercase +
string.lowercase + string.digits) for _ in range(25))
app_template = Template(app_yml)
app_yml_file = os.path.join(self.pulsar_home, 'app.yml')
misc.write_template_file(app_template, {'token': token}, app_yml_file)
# Write out server.ini
srvr_template = Template(server_ini)
server_ini_file = os.path.join(self.pulsar_home, 'server.ini')
misc.write_template_file(srvr_template, {'pulsar_port': self.pulsar_port},
server_ini_file)
# Write out local_env.sh
lcl_template = Template(local_env_sh)
lcl_file = os.path.join(self.pulsar_home, 'local_env.sh')
misc.write_template_file(lcl_template, {'galaxy_home': '/mnt/galaxy/galaxy-app'},
lcl_file)
# Set the owner to 'galaxy' system user
attempt_chown_galaxy(self.pulsar_home, recursive=True)
if self.supervisor:
# Create a supervisor conf file
supervisor_conf_file = os.path.join(self.supervisor.conf_dir,
'{0}.conf'.format(self.supervisor_prog_name))
template = Template(supervisor_conf)
misc.write_template_file(template, None, supervisor_conf_file)
else:
log.warning("No supervisor service?")
def configure_proftpd(self):
"""
Configure environment for running ProFTPd service.
"""
log.debug("Configuring ProFTPd")
# Because we're rewriting the proftpd config file below, update the
# password for PostgreSQL galaxyftp user
gftp_pwd = self.app.path_resolver.proftpd_galaxyftp_user_pwd
log.debug("Setting psql password for galaxyftp role to {0}".format(gftp_pwd))
# Check if galaxtftp role already exists
cmd = ('{0} - postgres -c"{1} -p {2} -tAc\\\"SELECT 1 FROM pg_roles WHERE rolname=\'galaxyftp\'\\\""'
.format(paths.P_SU, self.app.path_resolver.psql_cmd,
self.app.path_resolver.psql_db_port))
role = 'ALTER' if misc.getoutput(cmd) == '1' else 'CREATE'
# Now either CREATE or ALTER the galaxyftp role to set the permissions
cmd = ('{0} - postgres -c"{1} -p {4} -c\\\"{2} ROLE galaxyftp LOGIN PASSWORD \'{3}\'\\\""'
.format(paths.P_SU, self.app.path_resolver.psql_cmd, role,
gftp_pwd, self.app.path_resolver.psql_db_port))
misc.run(cmd)
# Update the config to match the current environment
proftpd_tmplt = conf_manager.PROFTPD_CONF_TEMPLATE
proftpd_conf_template = conf_manager.load_conf_template(proftpd_tmplt)
params = {
'galaxy_user_name': paths.GALAXY_USER_NAME,
'galaxyftp_user_name': 'galaxyftp',
'psql_galaxyftp_password': gftp_pwd,
'galaxy_db_port': self.app.path_resolver.psql_db_port,
'galaxyFS_base_path': self.app.path_resolver.galaxy_data,
'public_ip_address': self.app.cloud_interface.get_public_ip()
}
template = proftpd_conf_template.substitute(params)
# Write out the config file
with open(self.app.path_resolver.proftpd_conf_file, 'w') as f:
print >> f, template
log.debug("Updated ProFTPd conf file {0}".format(
self.app.path_resolver.proftpd_conf_file))
# Place the FTP welcome message file
urllib.urlretrieve("https://s3.amazonaws.com/cloudman/files/proftpd_welcome.txt",
"/usr/proftpd/etc/welcome_msg.txt")
# Setup the Galaxy data dir for FTP
ftp_data_dir = '%s/tmp/ftp' % self.app.path_resolver.galaxy_data
if not os.path.exists(ftp_data_dir):
os.makedirs(ftp_data_dir)
attempt_chown_galaxy(ftp_data_dir)
# Some images have vsFTPd server included so stop it first
vsFTPd_exists = misc.run('status vsftpd', quiet=True)
if vsFTPd_exists and 'start/running' in vsFTPd_exists:
log.debug("Stopping vsFTPd")
misc.run('stop vsftpd')
# Start the server now
if misc.run('/etc/init.d/proftpd start'):
self.state = service_states.RUNNING
return True
else:
log.error("Trouble starting ProFTPd")
self.state = service_states.ERROR
return False
def _setup(self):
log.debug("Running GalaxyReportsService _setup")
# WORKAROUND: The run_reports.sh command refers to a parameter
# named --safe-pidfile which is not supported by the uwsgi binary.
# Replace it with --pidfile instead.
patch_start_command = ("sudo sed -i \"s/--safe-pidfile/--pidfile/g"
"\" %s/scripts/common_startup_functions.sh"
% self.galaxy_home)
misc.run(patch_start_command)
# Create default output dir for files
file_path = os.path.join(self.app.path_resolver.galaxy_home, "database/files")
misc.make_dir(file_path, owner='galaxy')
tmp_file_path = os.path.join(self.app.path_resolver.galaxy_home, "database/tmp")
misc.make_dir(tmp_file_path, owner='galaxy')
# Create the new reports config
params = {
'galaxy_db_port': self.app.path_resolver.psql_db_port
}
template = conf_manager.load_conf_template(conf_manager.GALAXY_REPORTS_TEMPLATE)
misc.write_template_file(template, params, self.conf_file)
attempt_chown_galaxy(self.conf_file)
def _configure(self):
"""
Configure the Pulsar application.
"""
self.state = service_states.CONFIGURING
misc.make_dir(self.pulsar_home)
# Write out app.yml
token = ''.join(
random.SystemRandom().choice(string.ascii_uppercase +
string.lowercase + string.digits)
for _ in range(25))
app_template = Template(app_yml)
app_yml_file = os.path.join(self.pulsar_home, 'app.yml')
misc.write_template_file(app_template, {'token': token}, app_yml_file)
# Write out server.ini
srvr_template = Template(server_ini)
server_ini_file = os.path.join(self.pulsar_home, 'server.ini')
misc.write_template_file(srvr_template,
{'pulsar_port': self.pulsar_port},
server_ini_file)
# Write out local_env.sh
lcl_template = Template(local_env_sh)
lcl_file = os.path.join(self.pulsar_home, 'local_env.sh')
misc.write_template_file(lcl_template,
{'galaxy_home': '/mnt/galaxy/galaxy-app'},
lcl_file)
# Set the owner to 'galaxy' system user
attempt_chown_galaxy(self.pulsar_home, recursive=True)
if self.supervisor:
# Create a supervisor conf file
supervisor_conf_file = os.path.join(
self.supervisor.conf_dir,
'{0}.conf'.format(self.supervisor_prog_name))
template = Template(supervisor_conf)
misc.write_template_file(template, None, supervisor_conf_file)
else:
log.warning("No supervisor service?")
def configure_proftpd(self):
"""
Configure environment for running ProFTPd service.
"""
# In the config, set the port on which postgres is running
log.debug("Configuring ProFTPd")
# This is a bit dodgy but ports are hardcoded in CBL so shoudl be a pretty
# safe bet for the time being
misc.replace_string('/usr/proftpd/etc/proftpd.conf',
'galaxy@localhost:5840',
'galaxy@localhost:{0}'.format(paths.C_PSQL_PORT))
misc.replace_string('/usr/proftpd/etc/proftpd.conf',
'/mnt/galaxyData',
self.app.path_resolver.galaxy_data)
# Verify that the expected config path exists. This is expected to be
# /mnt/galaxy/tools/proftpd
# TODO just use /usr/proftpd. Should be a simple update to the init.d
expected_config_path = os.path.join(self.app.path_resolver.galaxy_data, 'tools', 'proftpd')
if not os.path.exists(expected_config_path):
misc.run('ln -s /usr/profpd %s' % expected_config_path)
# Setup the data dir for FTP
ftp_data_dir = '%s/tmp/ftp' % self.app.path_resolver.galaxy_data
if not os.path.exists(ftp_data_dir):
os.makedirs(ftp_data_dir)
attempt_chown_galaxy(ftp_data_dir)
# Some images have vsFTPd server included so stop it first
vsFTPd_exists = misc.run('status vsftpd', quiet=True)
if vsFTPd_exists and 'start/running' in vsFTPd_exists:
log.debug("Stopping vsFTPd")
misc.run('stop vsftpd')
# Start the server now
if misc.run('/etc/init.d/proftpd start'):
self.state = service_states.RUNNING
return True
else:
log.debug("Trouble starting ProFTPd")
return False
def manage_galaxy(self, to_be_started=True):
if self.app.TESTFLAG is True and self.app.LOCALFLAG is False:
log.debug("Attempted to manage Galaxy, but TESTFLAG is set.")
return
log.debug("Using Galaxy from '{0}'".format(self.galaxy_home))
os.putenv("GALAXY_HOME", self.galaxy_home)
os.putenv("TEMP", self.app.path_resolver.galaxy_temp)
os.putenv("TMPDIR", self.app.path_resolver.galaxy_temp)
self.env_vars["GALAXY_HOME"] = self.galaxy_home
self.env_vars["TEMP"] = self.app.path_resolver.galaxy_temp
self.env_vars["TMPDIR"] = self.app.path_resolver.galaxy_temp
conf_dir = self.option_manager.setup()
if conf_dir:
self.env_vars["GALAXY_UNIVERSE_CONFIG_DIR"] = conf_dir
if self._multiple_processes():
self.env_vars["GALAXY_RUN_ALL"] = "TRUE"
# HACK: Galaxy has a known problem when starting from a fresh configuration
# in multiple process mode. Each process attempts to create the same directories
# and one or more processes can fail to start because it "failed" to create
# said directories (because another process created them first). This hack staggers
# the process starts in an attempt to circumvent this problem.
patch_run_sh_command = "sudo sed -i -e \"s/server.log \\$\\@$/\\0; sleep 4/\" %s/run.sh" % self.galaxy_home
misc.run(patch_run_sh_command)
self.extra_daemon_args = ""
else:
# Instead of sticking with default paster.pid and paster.log, explicitly
# set pid and log file to ``main.pid`` and ``main.log`` to bring single
# process case inline with defaults for for multiple process case (i.e.
# when GALAXY_RUN_ALL is set and multiple servers are defined).
self.extra_daemon_args = "--pid-file=main.pid --log-file=main.log"
if to_be_started and self.remaining_start_attempts > 0:
self.status()
# If not provided as part of user data, update nginx conf with
# current paths
if self.app.ud.get('nginx_conf_contents', None) is None:
self.configure_nginx()
if not self.configured:
log.debug("Setting up Galaxy application")
s3_conn = self.app.cloud_interface.get_s3_connection()
if not os.path.exists(self.galaxy_home):
log.error("Galaxy application directory '%s' does not exist! Aborting." %
self.galaxy_home)
log.debug("ls /mnt/: %s" % os.listdir('/mnt/'))
self.state = service_states.ERROR
self.last_state_change_time = datetime.utcnow()
return False
# If a configuration file is not already in Galaxy's dir,
# retrieve it from a persistent data repository (i.e., S3)
if s3_conn:
for f_name in ['universe_wsgi.ini',
'tool_conf.xml',
'tool_data_table_conf.xml',
'shed_tool_conf.xml',
'datatypes_conf.xml',
'shed_tool_data_table_conf.xml']:
f_path = os.path.join(self.galaxy_home, f_name)
if not os.path.exists(f_path):
if not misc.get_file_from_bucket(s3_conn, self.app.ud['bucket_cluster'],
'{0}.cloud'.format(f_name), f_path):
# We did not get the config file from cluster's
# bucket so get it from the default bucket
log.debug("Did not get Galaxy configuration file " +
"'{0}' from cluster bucket '{1}'"
.format(f_name, self.app.ud['bucket_cluster']))
log.debug("Trying to retrieve one ({0}.cloud) "
"from the default '{1}' bucket."
.format(f_name, self.app.ud['bucket_default']))
local_file = os.path.join(self.galaxy_home, f_name)
misc.get_file_from_bucket(s3_conn,
self.app.ud['bucket_default'], '{0}.cloud'.format(f_name),
local_file)
attempt_chown_galaxy_if_exists(local_file)
# Make sure the temporary job_working_directory exists on user
# data volume (defined in universe_wsgi.ini.cloud)
if not os.path.exists('%s/tmp/job_working_directory' % self.app.path_resolver.galaxy_data):
os.makedirs('%s/tmp/job_working_directory/' % self.app.path_resolver.galaxy_data)
attempt_chown_galaxy('%s/tmp/job_working_directory/' % self.app.path_resolver.galaxy_data)
# Make sure the default shed_tools directory exists
if not os.path.exists('%s/../shed_tools' % self.app.path_resolver.galaxy_data):
os.makedirs('%s/../shed_tools/' % self.app.path_resolver.galaxy_data)
attempt_chown_galaxy('%s/../shed_tools/' % self.app.path_resolver.galaxy_data)
# TEMPORARY ONLY - UNTIL SAMTOOLS WRAPPER IS CONVERTED TO USE
# DATA TABLES
if os.path.exists('/mnt/galaxyIndices/locfiles/sam_fa_indices.loc'):
shutil.copy(
'/mnt/galaxyIndices/locfiles/sam_fa_indices.loc',
'%s/tool-data/sam_fa_indices.loc' % self.galaxy_home)
# Ensure the environment is setup for running Galaxy
# This can also be setup on the tools snapshot and thus avoid these patches
# try:
# subprocess.call( "sed 's/cd `dirname $0`/cd `dirname $0`; export TEMP=\/mnt\/galaxyData\/tmp/; export DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0' %s/run.sh > %s/run.sh.custom" % (self.galaxy_home, self.galaxy_home), shell=True )
# misc.run("cd %s; sed 's/python/python -ES/g' run.sh.custom > run.sh" % self.galaxy_home, "Failed to adjust run.sh", "Successfully adjusted run.sh")
# shutil.copy( self.galaxy_home + '/run.sh.custom', self.galaxy_home + '/run.sh' )
# os.chown( self.galaxy_home + '/run.sh', pwd.getpwnam( "galaxy" )[2], grp.getgrnam( "galaxy" )[2] )
# except Exception, e:
# log.debug("Problem customizing Galaxy's run.sh: %s" % e)
# try:
# misc.run("cd %s; sed 's/pyhton/python -ES/g' setup.sh > setup.sh.custom" % self.galaxy_home, "Failed to edit setup.sh", "Successfully adjusted setup.sh")
# shutil.copy( self.galaxy_home + '/setup.sh.custom', self.galaxy_home + '/setup.sh' )
# os.chown( self.galaxy_home + '/setup.sh', pwd.getpwnam( "galaxy" )[2], grp.getgrnam( "galaxy" )[2] )
# except Exception, e:
# log.error("Error adjusting setup.sh: %s" % e)
# subprocess.call( 'sed "s/#start_job_runners = pbs/start_job_runners = sge/" $GALAXY_HOME/universe_wsgi.ini > $GALAXY_HOME/universe_wsgi.ini.custom', shell=True )
# shutil.move( self.galaxy_home + '/universe_wsgi.ini.custom', self.galaxy_home + '/universe_wsgi.ini' )
# subprocess.call( 'sed "s/#default_cluster_job_runner = pbs:\/\/\//default_cluster_job_runner = sge:\/\/\//" $GALAXY_HOME/universe_wsgi.ini > $GALAXY_HOME/universe_wsgi.ini.custom', shell=True )
# shutil.move( self.galaxy_home + '/universe_wsgi.ini.custom', self.galaxy_home + '/universe_wsgi.ini' )
# Configure PATH in /etc/profile because otherwise some tools do not work
# with open('/etc/profile', 'a') as f:
# f.write('export PATH=/mnt/galaxyTools/tools/bin:/mnt/galaxyTools/tools/pkg/fastx_toolkit_0.0.13:/mnt/galaxyTools/tools/pkg/bowtie-0.12.5:/mnt/galaxyTools/tools/pkg/samtools-0.1.7_x86_64-linux:/mnt/galaxyTools/tools/pkg/gnuplot-4.4.0/bin:/opt/PostgreSQL/8.4/bin:$PATH\n')
# os.chown(self.galaxy_home + '/universe_wsgi.ini',
# pwd.getpwnam("galaxy")[2], grp.getgrnam("galaxy")[2])
self.remaining_start_attempts -= 1
self.configured = True
if self.state != service_states.RUNNING:
log.debug("Starting Galaxy...")
# Make sure admin users get added
self.update_galaxy_config()
start_command = self.galaxy_run_command(
"%s --daemon" % self.extra_daemon_args)
log.debug(start_command)
if not misc.run(start_command, "Error invoking Galaxy",
"Successfully initiated Galaxy start from {0}.".format(self.galaxy_home)):
if self.remaining_start_attempts > 0:
self.state = service_states.UNSTARTED
self.last_state_change_time = datetime.utcnow()
else:
self.state = service_states.ERROR
self.last_state_change_time = datetime.utcnow()
else:
log.debug("Galaxy already running.")
else:
log.info("Shutting down Galaxy...")
self.state = service_states.SHUTTING_DOWN
stop_command = self.galaxy_run_command("%s --stop-daemon" % self.extra_daemon_args)
if misc.run(stop_command):
self.state = service_states.SHUT_DOWN
self.last_state_change_time = datetime.utcnow()
# Move all log files
subprocess.call("bash -c 'for f in $GALAXY_HOME/{main,handler,manager,web}*.log; do mv \"$f\" \"$f.%s\"; done'"
% datetime.utcnow().strftime('%H_%M'), shell=True)
def configure_proftpd(self):
"""
Configure environment for running ProFTPd service.
"""
log.debug("Configuring ProFTPd")
# Because we're rewriting the proftpd config file below, update the
# password for PostgreSQL galaxyftp user
gftp_pwd = self.app.path_resolver.proftpd_galaxyftp_user_pwd
log.debug(
"Setting psql password for galaxyftp role to {0}".format(gftp_pwd))
# Check if galaxtftp role already exists
cmd = (
'{0} - postgres -c"{1} -p {2} -tAc\\\"SELECT 1 FROM pg_roles WHERE rolname=\'galaxyftp\'\\\""'
.format(paths.P_SU, self.app.path_resolver.psql_cmd,
self.app.path_resolver.psql_db_port))
role = 'ALTER' if misc.getoutput(cmd) == '1' else 'CREATE'
# Now either CREATE or ALTER the galaxyftp role to set the permissions
cmd = (
'{0} - postgres -c"{1} -p {4} -c\\\"{2} ROLE galaxyftp LOGIN PASSWORD \'{3}\'\\\""'
.format(paths.P_SU, self.app.path_resolver.psql_cmd, role,
gftp_pwd, self.app.path_resolver.psql_db_port))
misc.run(cmd)
# Update the config to match the current environment
proftpd_tmplt = conf_manager.PROFTPD_CONF_TEMPLATE
proftpd_conf_template = conf_manager.load_conf_template(proftpd_tmplt)
params = {
'galaxy_user_name': paths.GALAXY_USER_NAME,
'galaxyftp_user_name': 'galaxyftp',
'psql_galaxyftp_password': gftp_pwd,
'galaxy_db_port': self.app.path_resolver.psql_db_port,
'galaxyFS_base_path': self.app.path_resolver.galaxy_data,
'public_ip_address': self.app.cloud_interface.get_public_ip()
}
template = proftpd_conf_template.substitute(params)
# Write out the config file
with open(self.app.path_resolver.proftpd_conf_file, 'w') as f:
print >> f, template
log.debug("Updated ProFTPd conf file {0}".format(
self.app.path_resolver.proftpd_conf_file))
# Place the FTP welcome message file
urllib.urlretrieve(
"https://s3.amazonaws.com/cloudman/files/proftpd_welcome.txt",
"/usr/proftpd/etc/welcome_msg.txt")
# Setup the Galaxy data dir for FTP
ftp_data_dir = '%s/tmp/ftp' % self.app.path_resolver.galaxy_data
if not os.path.exists(ftp_data_dir):
os.makedirs(ftp_data_dir)
attempt_chown_galaxy(ftp_data_dir)
# Some images have vsFTPd server included so stop it first
vsFTPd_exists = misc.run('status vsftpd', quiet=True)
if vsFTPd_exists and 'start/running' in vsFTPd_exists:
log.debug("Stopping vsFTPd")
misc.run('stop vsftpd')
# Start the server now
if misc.run('/etc/init.d/proftpd start'):
self.state = service_states.RUNNING
return True
else:
log.error("Trouble starting ProFTPd")
self.state = service_states.ERROR
return False
def manage_galaxy(self, to_be_started=True):
"""
Use this method to start and stop Galaxy application.
:type to_be_started: bool
:param to_be_started: If set, this method will attempt to start the
Galaxy application process. If not set, the
method will attempt to shut down the application
process.
"""
log.debug("Using Galaxy from '{0}'".format(self.galaxy_home))
os.putenv("GALAXY_HOME", self.galaxy_home)
os.putenv("TEMP", self.app.path_resolver.galaxy_temp)
os.putenv("TMPDIR", self.app.path_resolver.galaxy_temp)
self.env_vars["GALAXY_HOME"] = self.galaxy_home
self.env_vars["TEMP"] = self.app.path_resolver.galaxy_temp
self.env_vars["TMPDIR"] = self.app.path_resolver.galaxy_temp
conf_dir = self.option_manager.setup()
if conf_dir:
self.env_vars["GALAXY_UNIVERSE_CONFIG_DIR"] = conf_dir
if self.multiple_processes():
self.env_vars["GALAXY_RUN_ALL"] = "TRUE"
# HACK: Galaxy has a known problem when starting from a fresh
# configuration in multiple process mode. Each process attempts to
# create the same directories and one or more processes can fail to
# start because it "failed" to create said directories (because
# another process created them first). This hack staggers
# the process starts in an attempt to circumvent this problem.
patch_run_sh_command = (
"sudo sed -i -e \"s/server.log \\$\\@$/\\0; "
"sleep 4/\" %s/run.sh" % self.galaxy_home)
misc.run(patch_run_sh_command)
self.extra_daemon_args = ""
else:
# Instead of sticking with default paster.pid and paster.log,
# explicitly set pid and log file to ``main.pid`` and ``main.log``
# to bring single process case inline with defaults for for multiple
# process case (i.e. when GALAXY_RUN_ALL is set and multiple servers
# are defined).
# self.extra_daemon_args = "--pid-file=main.pid --log-file=main.log"
# No longer required
pass
if to_be_started and self.remaining_start_attempts > 0:
self.status()
if not self.configured:
log.debug("Setting up Galaxy application")
# Set job manager configs if necessary
for job_manager_svc in self.app.manager.service_registry.active(
service_role=ServiceRole.JOB_MANAGER):
if ServiceRole.SGE in job_manager_svc.svc_roles:
log.debug("Running on SGE; setting env_vars")
self.env_vars[
"SGE_ROOT"] = self.app.path_resolver.sge_root,
self.env_vars[
"DRMAA_LIBRARY_PATH"] = self.app.path_resolver.drmaa_library_path
# Make sure Galaxy home dir exists
if not os.path.exists(self.galaxy_home):
log.error("Galaxy application directory '%s' does not "
"exist! Aborting." % self.galaxy_home)
log.debug("ls /mnt/: %s" % os.listdir('/mnt/'))
self.state = service_states.ERROR
self.last_state_change_time = datetime.utcnow()
return False
# Ensure the necessary directories exist
for dir_name in [
paths.P_GALAXY_INDICES,
('%s/tmp/job_working_directory' %
self.app.path_resolver.galaxy_data)
]:
misc.make_dir(dir_name, 'galaxy')
self.configured = True
if not self._is_galaxy_running():
log.debug("Starting Galaxy...")
self.update_galaxy_config()
start_command = self.galaxy_run_command("%s --daemon" %
self.extra_daemon_args)
attempt_chown_galaxy(self.galaxy_home)
if misc.run(start_command):
self.remaining_start_attempts -= 1
elif self.remaining_start_attempts > 0:
log.debug(
"It seems Galaxy failed to start; will atempt to "
"auto-restart (up to {0} more time(s)).".format(
self.remaining_start_attempts))
self.state = service_states.UNSTARTED
self.last_state_change_time = datetime.utcnow()
else:
log.debug(
"It seems Galaxy failed to start; setting service "
"state to {0}.".format(service_states.ERROR))
self.state = service_states.ERROR
self.last_state_change_time = datetime.utcnow()
else:
log.debug("Galaxy already running.")
else:
log.info("Shutting down Galaxy...")
self.state = service_states.SHUTTING_DOWN
stop_command = self.galaxy_run_command("%s --stop-daemon" %
self.extra_daemon_args)
if self._is_galaxy_running():
misc.run(stop_command)
if not self._is_galaxy_running():
log.debug(
"Galaxy not running; setting service state to SHUT_DOWN.")
self.state = service_states.SHUT_DOWN
self.last_state_change_time = datetime.utcnow()
# Move all log files
subprocess.call(
"bash -c 'for f in $GALAXY_HOME/{main,handler,manager,web}*.log; "
"do mv \"$f\" \"$f.%s\"; done'" %
datetime.utcnow().strftime('%H_%M'),
shell=True)
