def _configure_galaxy_options(env,
option_dict=None,
prefix="galaxy_universe_"):
"""
Read through fabric's environment and make sure any property of
the form galaxy_universe_XXX=YYY lands up in Galaxy's universe_wsgi.ini
options as XXX=YYY using Galaxy configuration directory:
"""
galaxy_conf_directory = env.get("galaxy_conf_directory", None)
if not galaxy_conf_directory:
return False
# By default just read the options from env (i.e. from fabricrc), but
# allow override so the options can come from a YAML file (such as done
# with galaxy-vm-launcher.)
if option_dict is None:
option_dict = env
option_priority = env.get("galaxy_conf_priority", "200")
for key, value in option_dict.iteritems():
if key.startswith(prefix):
key = key[len(prefix):]
conf_file_name = "%s_override_%s.ini" % (option_priority, key)
conf_file = os.path.join(galaxy_conf_directory, conf_file_name)
contents = "[app:main]\n%s=%s" % (key, value)
_write_to_file(contents, conf_file, "0700")
_chown_galaxy(env, conf_file)
def _configure_galaxy_options(env, option_dict=None, prefix="galaxy_universe_"):
"""
Read through fabric's environment and make sure any property of
the form galaxy_universe_XXX=YYY, lands up in Galaxy's universe_wsgi.ini
options as XXX=YYY using John Chilton's configuration directory work:
https://bitbucket.org/galaxy/galaxy-central/pull-request/44/allow-usage-of-directory-of-configuration
Until, the above pull request is accepted, its changeset should be pulled
into the configured Galaxy repository.
"""
galaxy_conf_directory = env.get("galaxy_conf_directory", False)
if not galaxy_conf_directory:
return False
# By default just read the options from env (i.e. from fabricrc), but
# allow override so the options can come from a YAML file (such as done
# with galaxy-vm-launcher.)
if option_dict is None:
option_dict = env
option_priority = env.get("galaxy_conf_priority", "200")
for key, value in option_dict.iteritems():
if key.startswith(prefix):
key = key[len(prefix):]
conf_file_name = "%s_override_%s.ini" % (option_priority, key)
conf_file = os.path.join(galaxy_conf_directory, conf_file_name)
contents = "[app:main]\n%s=%s" % (key, value)
_write_to_file(contents, conf_file, 0700)
_chown_galaxy(env, conf_file)
def _configure_ec2_autorun(env, use_repo_autorun=False):
"""
ec2autorun.py is a script that launches CloudMan on instance boot
and is thus required on an instance. See the script itself for the
details of what it does.
This script also adds a cloudman service to ``/etc/init``, which
actually runs ec2autorun.py as a system-level service at system boot.
"""
script = "ec2autorun.py"
remote = os.path.join(env.install_dir, "bin", script)
if not exists(os.path.dirname(remote)):
sudo('mkdir -p {0}'.format(os.path.dirname(remote)))
if use_repo_autorun:
url = os.path.join(MI_REPO_ROOT_URL, script)
sudo("wget --output-document=%s %s" % (remote, url))
else:
install_file_dir = os.path.join(env.config_dir, os.pardir, "installed_files")
put(os.path.join(install_file_dir, script), remote, mode=0777, use_sudo=True)
# Create upstart configuration file for boot-time script
cloudman_boot_file = 'cloudman.conf'
remote_file = '/etc/init/%s' % cloudman_boot_file
_write_to_file(cm_upstart % (remote, os.path.splitext(remote)[0]), remote_file, mode=0644)
# Setup default image user data (if configured by image_user_data_path or
# image_user_data_template_path). This specifies defaults for CloudMan when
# used with resulting image, normal userdata supplied by user will override
# these defaults.
_setup_conf_file(env, os.path.join(env.install_dir, "bin", "IMAGE_USER_DATA"), "image_user_data", default_source="image_user_data")
env.logger.info("Done configuring CloudMan's ec2_autorun")
def install_nginx(env):
"""Nginx open source web server.
http://www.nginx.org/
"""
version = "1.2.0"
url = "http://nginx.org/download/nginx-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, "nginx")
remote_conf_dir = os.path.join(install_dir, "conf")
# Skip install if already present
if exists(remote_conf_dir) and contains(os.path.join(remote_conf_dir, "nginx.conf"), "/cloud"):
env.logger.debug("Nginx already installed; not installing it again.")
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
modules = _get_nginx_modules(env)
module_flags = " ".join(["--add-module=../%s" % x for x in modules])
run("wget %s" % url)
run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
run("./configure --prefix=%s --with-ipv6 %s "
"--user=galaxy --group=galaxy --with-debug "
"--with-http_ssl_module --with-http_gzip_static_module" %
(install_dir, module_flags))
sed("objs/Makefile", "-Werror", "")
run("make")
sudo("make install")
sudo("cd %s; stow nginx" % env.install_dir)
conf_file_contents = _get_nginx_conf_contents(env)
nginx_conf_file = 'nginx.conf'
_write_to_file(conf_file_contents, os.path.join(remote_conf_dir, nginx_conf_file), mode=0755)
nginx_errdoc_file = 'nginx_errdoc.tar.gz'
url = os.path.join(REPO_ROOT_URL, nginx_errdoc_file)
remote_errdoc_dir = os.path.join(install_dir, "html")
with cd(remote_errdoc_dir):
sudo("wget --output-document=%s/%s %s" % (remote_errdoc_dir, nginx_errdoc_file, url))
sudo('tar xvzf %s' % nginx_errdoc_file)
sudo("mkdir -p %s" % env.install_dir)
if not exists("%s/nginx" % env.install_dir):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, env.install_dir))
# If the guessed symlinking did not work, force it now
cloudman_default_dir = "/opt/galaxy/sbin"
if not exists(cloudman_default_dir):
sudo("mkdir -p %s" % cloudman_default_dir)
if not exists(os.path.join(cloudman_default_dir, "nginx")):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, cloudman_default_dir))
env.logger.debug("Nginx {0} installed to {1}".format(version, install_dir))
def _configure_ec2_autorun(env, use_repo_autorun=False):
"""
ec2autorun.py is a script that launches CloudMan on instance boot
and is thus required on an instance. See the script itself for the
details of what it does.
This script also adds a cloudman service to ``/etc/init``, which
actually runs ec2autorun.py as a system-level service at system boot.
"""
script = "ec2autorun.py"
remote = os.path.join(env.install_dir, "bin", script)
if not exists(os.path.dirname(remote)):
sudo('mkdir -p {0}'.format(os.path.dirname(remote)))
if use_repo_autorun:
# Is this used, can we eliminate use_repo_autorun?
url = os.path.join(MI_REPO_ROOT_URL, script)
sudo("wget --output-document=%s %s" % (remote, url))
else:
install_file_dir = os.path.join(env.config_dir, os.pardir,
"installed_files")
put(os.path.join(install_file_dir, script),
remote,
mode=0777,
use_sudo=True)
# Create upstart configuration file for boot-time script
cloudman_boot_file = 'cloudman.conf'
remote_file = '/etc/init/%s' % cloudman_boot_file
_write_to_file(cm_upstart % (remote, os.path.splitext(remote)[0]),
remote_file,
mode=0644)
# Setup default image user data (if configured by image_user_data_path or
# image_user_data_template_path). This specifies defaults for CloudMan when
# used with resulting image, normal userdata supplied by user will override
# these defaults.
image_user_data_path = os.path.join(env.install_dir, "bin",
"IMAGE_USER_DATA")
if "image_user_data_dict" in env:
# Explicit YAML contents defined in env, just dump them as is.
import yaml
_write_to_file(yaml.dump(env.get("image_user_data_dict")),
image_user_data_path,
mode=0644)
else:
# Else use file or template file.
_setup_conf_file(env,
image_user_data_path,
"image_user_data",
default_source="image_user_data")
env.logger.info("Done configuring CloudMan's ec2_autorun")
def _configure_ec2_autorun(env, use_repo_autorun=False):
script = "ec2autorun.py"
remote = os.path.join(env.install_dir, "bin", script)
if not exists(os.path.dirname(remote)):
sudo('mkdir -p {0}'.format(os.path.dirname(remote)))
if use_repo_autorun:
url = os.path.join(MI_REPO_ROOT_URL, script)
sudo("wget --output-document=%s %s" % (remote, url))
else:
install_file_dir = os.path.join(env.config_dir, os.pardir, "installed_files")
put(os.path.join(install_file_dir, script), remote, mode=0777, use_sudo=True)
# Create upstart configuration file for boot-time script
cloudman_boot_file = 'cloudman.conf'
remote_file = '/etc/init/%s' % cloudman_boot_file
_write_to_file(cm_upstart % (remote, os.path.splitext(remote)[0]), remote_file, mode=777)
env.logger.debug("Done configuring CloudMan ec2_autorun")
def _configure_ec2_autorun(env, use_repo_autorun=False):
script = "ec2autorun.py"
remote = os.path.join(env.install_dir, "bin", script)
if not exists(os.path.dirname(remote)):
sudo('mkdir -p {0}'.format(os.path.dirname(remote)))
if use_repo_autorun:
url = os.path.join(MI_REPO_ROOT_URL, script)
sudo("wget --output-document=%s %s" % (remote, url))
else:
install_file_dir = os.path.join(env.config_dir, os.pardir, "installed_files")
put(os.path.join(install_file_dir, script), remote, mode=0777, use_sudo=True)
# Create upstart configuration file for boot-time script
cloudman_boot_file = 'cloudman.conf'
remote_file = '/etc/init/%s' % cloudman_boot_file
_write_to_file(cm_upstart % (remote, os.path.splitext(remote)[0]), remote_file, mode=777)
env.logger.debug("Done configuring CloudMan ec2_autorun")
def _configure_ec2_autorun(env, use_repo_autorun=False):
"""
ec2autorun.py is a script that launches CloudMan on instance boot
and is thus required on an instance. See the script itself for the
details of what it does.
This script also adds a cloudman service to ``/etc/init``, which
actually runs ec2autorun.py as a system-level service at system boot.
"""
script = "ec2autorun.py"
remote = os.path.join(env.install_dir, "bin", script)
if not env.safe_exists(os.path.dirname(remote)):
env.safe_sudo('mkdir -p {0}'.format(os.path.dirname(remote)))
if use_repo_autorun:
# Is this used, can we eliminate use_repo_autorun?
url = os.path.join(MI_REPO_ROOT_URL, script)
env.safe_sudo("wget --output-document=%s %s" % (remote, url))
else:
install_file_dir = os.path.join(env.config_dir, os.pardir, "installed_files")
tmp_remote = os.path.join("/tmp", os.path.basename(remote))
env.safe_put(os.path.join(install_file_dir, script), tmp_remote)
env.safe_sudo("mv %s %s" % (tmp_remote, remote))
env.safe_sudo("chmod 0777 %s" % remote)
# Create upstart configuration file for boot-time script
cloudman_boot_file = 'cloudman.conf'
remote_file = '/etc/init/%s' % cloudman_boot_file
_write_to_file(cm_upstart % (remote, os.path.splitext(remote)[0]), remote_file, mode="0644")
# Setup default image user data (if configured by image_user_data_path or
# image_user_data_template_path). This specifies defaults for CloudMan when
# used with resulting image, normal userdata supplied by user will override
# these defaults.
image_user_data_path = os.path.join(env.install_dir, "bin", "IMAGE_USER_DATA")
if "image_user_data_dict" in env:
# Explicit YAML contents defined in env, just dump them as is.
import yaml
_write_to_file(yaml.dump(env.get("image_user_data_dict")), image_user_data_path, mode="0644")
else:
# Else use file or template file.
_setup_conf_file(env, image_user_data_path, "image_user_data", default_source="image_user_data")
env.logger.info("Done configuring CloudMan's ec2_autorun")
def _configure_galaxy_options(env, option_dict=None, prefix="galaxy_universe_"):
"""
Read through fabric's environment and make sure any property of
the form galaxy_universe_XXX=YYY lands up in Galaxy's universe_wsgi.ini
options as XXX=YYY using Galaxy configuration directory:
"""
galaxy_conf_directory = env.get("galaxy_conf_directory", None)
if not galaxy_conf_directory:
return False
# By default just read the options from env (i.e. from fabricrc), but
# allow override so the options can come from a YAML file (such as done
# with galaxy-vm-launcher.)
if option_dict is None:
option_dict = env
option_priority = env.get("galaxy_conf_priority", "200")
for key, value in option_dict.iteritems():
if key.startswith(prefix):
key = key[len(prefix):]
conf_file_name = "%s_override_%s.ini" % (option_priority, key)
conf_file = os.path.join(galaxy_conf_directory, conf_file_name)
contents = "[app:main]\n%s=%s" % (key, value)
_write_to_file(contents, conf_file, 0700)
_chown_galaxy(env, conf_file)
