def _setup_xvfb(env):
_setup_conf_file(env, "/etc/init.d/xvfb", "xvfb_init", default_source="xvfb_init")
_setup_conf_file(env, "/etc/default/xvfb", "xvfb_default", default_source="xvfb_default")
_setup_simple_service("xvfb")
env.safe_sudo("mkdir /var/lib/xvfb; chown root:root /var/lib/xvfb; chmod 0755 /var/lib/xvfb")
display_export = "-v DIPSLAY=:42"
_add_to_profiles(display_export, profiles=["/home/%s/.sge_request" % env.get("galaxy_user", "galaxy")])
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 env.safe_exists(remote_conf_dir) and env.safe_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])
env.safe_run("wget %s" % url)
env.safe_run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
env.safe_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))
env.safe_sed("objs/Makefile", "-Werror", "")
env.safe_run("make")
env.safe_sudo("make install")
env.safe_sudo("cd %s; stow nginx" % env.install_dir)
defaults = {"galaxy_home": "/mnt/galaxy/galaxy-app"}
_setup_conf_file(env,
os.path.join(remote_conf_dir, "nginx.conf"),
"nginx.conf",
defaults=defaults)
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):
env.safe_sudo("wget --output-document=%s/%s %s" %
(remote_errdoc_dir, nginx_errdoc_file, url))
env.safe_sudo('tar xvzf %s' % nginx_errdoc_file)
env.safe_sudo("mkdir -p %s" % env.install_dir)
if not env.safe_exists("%s/nginx" % env.install_dir):
env.safe_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 env.safe_exists(cloudman_default_dir):
env.safe_sudo("mkdir -p %s" % cloudman_default_dir)
if not env.safe_exists(os.path.join(cloudman_default_dir, "nginx")):
env.safe_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 _setup_xvfb(env):
_setup_conf_file(env, "/etc/init.d/xvfb", "xvfb_init", default_source="xvfb_init")
_setup_conf_file(env, "/etc/default/xvfb", "xvfb_default", default_source="xvfb_default")
_setup_simple_service("xvfb")
env.safe_sudo("mkdir /var/lib/xvfb; chown root:root /var/lib/xvfb; chmod 0755 /var/lib/xvfb")
display_export = "-v DIPSLAY=:42"
_add_to_profiles(display_export, profiles=["/home/%s/.sge_request" % env.get("galaxy_user", "galaxy")])
def _setup_service(env):
_setup_conf_file(env,
"/etc/init.d/galaxy",
"galaxy_init",
default_source="galaxy_init")
_setup_conf_file(env, "/etc/default/galaxy", "galaxy_default")
_setup_simple_service("galaxy")
def _setup_protvis_service(env):
_setup_conf_file(env,
os.path.join("/etc/init.d/protvis"),
"protvis_init",
default_source="protvis_init")
_setup_conf_file(env, os.path.join("/etc/default/protvis"),
"protvis_default")
_setup_simple_service("protvis")
def _setup_nginx_service(env):
# Setup system service for nginx, not needed for CloudMan but it is
# useful if CloudMan is not being used (such as galaxy-vm-launcher work).
_setup_conf_file(env,
"/etc/init.d/nginx",
"nginx_init",
default_source="nginx_init")
_setup_simple_service("nginx")
def install_proftpd(env):
"""Highly configurable GPL-licensed FTP server software.
http://proftpd.org/
"""
version = "1.3.4c"
postgres_ver = "9.1"
url = "ftp://ftp.tpnet.pl/pub/linux/proftpd/distrib/source/proftpd-%s.tar.gz" % version
modules = "mod_sql:mod_sql_postgres:mod_sql_passwd"
extra_modules = env.get("extra_proftp_modules", "") # Comma separated list of extra modules
if extra_modules:
modules = "%s:%s" % (modules, extra_modules.replace(",", ":"))
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# Skip install if already available
if env.safe_exists(remote_conf_dir):
env.logger.debug("ProFTPd seems to already be installed in {0}".format(install_dir))
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % url)
with settings(hide('stdout')):
env.safe_run("tar xvzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
env.safe_run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s "
"--disable-auth-file --disable-ncurses --disable-ident --disable-shadow "
"--enable-openssl --with-modules=%s "
"--with-libraries=/usr/lib/postgresql/%s/lib" % (install_dir, modules, postgres_ver))
env.safe_sudo("make")
env.safe_sudo("make install")
env.safe_sudo("make clean")
# Get the init.d startup script
initd_script = 'proftpd.initd'
initd_url = os.path.join(REPO_ROOT_URL, 'conf_files', initd_script)
remote_file = "/etc/init.d/proftpd"
env.safe_sudo("wget --output-document=%s %s" % (remote_file, initd_url))
env.safe_sed(remote_file, 'REPLACE_THIS_WITH_CUSTOM_INSTALL_DIR', install_dir, use_sudo=True)
env.safe_sudo("chmod 755 %s" % remote_file)
# Set the configuration file
conf_file = 'proftpd.conf'
remote_file = os.path.join(remote_conf_dir, conf_file)
if "postgres_port" not in env:
env.postgres_port = '5910'
if "galaxy_ftp_user_password" not in env:
env.galaxy_ftp_user_password = '******'
proftpd_conf = {'galaxy_uid': env.safe_run('id -u galaxy'),
'galaxy_fs': '/mnt/galaxy', # Should be a var but uncertain how to get it
'install_dir': install_dir}
_setup_conf_file(env, remote_file, conf_file, overrides=proftpd_conf,
default_source="proftpd.conf.template")
# Get the custom welcome msg file
welcome_msg_file = 'welcome_msg.txt'
welcome_url = os.path.join(REPO_ROOT_URL, 'conf_files', welcome_msg_file)
env.safe_sudo("wget --output-document=%s %s" %
(os.path.join(remote_conf_dir, welcome_msg_file), welcome_url))
# Stow
env.safe_sudo("cd %s; stow proftpd" % env.install_dir)
env.logger.debug("----- ProFTPd %s installed to %s -----" % (version, install_dir))
def install_proftpd(env):
"""Highly configurable GPL-licensed FTP server software.
http://proftpd.org/
"""
version = "1.3.4c"
postgres_ver = "9.1"
url = "ftp://ftp.tpnet.pl/pub/linux/proftpd/distrib/source/proftpd-%s.tar.gz" % version
modules = "mod_sql:mod_sql_postgres:mod_sql_passwd"
extra_modules = env.get("extra_proftp_modules", "") # Comma separated list of extra modules
if extra_modules:
modules = "%s:%s" % (modules, extra_modules.replace(",", ":"))
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# Skip install if already available
if env.safe_exists(remote_conf_dir):
env.logger.debug("ProFTPd seems to already be installed in {0}".format(install_dir))
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % url)
with settings(hide('stdout')):
env.safe_run("tar xvzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
env.safe_run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s "
"--disable-auth-file --disable-ncurses --disable-ident --disable-shadow "
"--enable-openssl --with-modules=%s "
"--with-libraries=/usr/lib/postgresql/%s/lib" % (install_dir, modules, postgres_ver))
env.safe_sudo("make")
env.safe_sudo("make install")
env.safe_sudo("make clean")
# Get the init.d startup script
initd_script = 'proftpd.initd'
initd_url = os.path.join(REPO_ROOT_URL, 'conf_files', initd_script)
remote_file = "/etc/init.d/proftpd"
env.safe_sudo("wget --output-document=%s %s" % (remote_file, initd_url))
env.safe_sed(remote_file, 'REPLACE_THIS_WITH_CUSTOM_INSTALL_DIR', install_dir, use_sudo=True)
env.safe_sudo("chmod 755 %s" % remote_file)
# Set the configuration file
conf_file = 'proftpd.conf'
remote_file = os.path.join(remote_conf_dir, conf_file)
if "postgres_port" not in env:
env.postgres_port = '5910'
if "galaxy_ftp_user_password" not in env:
env.galaxy_ftp_user_password = '******'
proftpd_conf = {'galaxy_uid': env.safe_run('id -u galaxy'),
'galaxy_fs': '/mnt/galaxy', # Should be a var but uncertain how to get it
'install_dir': install_dir}
_setup_conf_file(env, remote_file, conf_file, overrides=proftpd_conf,
default_source="proftpd.conf.template")
# Get the custom welcome msg file
welcome_msg_file = 'welcome_msg.txt'
welcome_url = os.path.join(REPO_ROOT_URL, 'conf_files', welcome_msg_file)
env.safe_sudo("wget --output-document=%s %s" %
(os.path.join(remote_conf_dir, welcome_msg_file), welcome_url))
# Stow
env.safe_sudo("cd %s; stow proftpd" % env.install_dir)
env.logger.debug("----- ProFTPd %s installed to %s -----" % (version, install_dir))
def _install_nginx(env):
"""Nginx open source web server.
http://www.nginx.org/
"""
if "use_nginx_package" in env and env.use_nginx_package.upper() in ["TRUE", "YES"]:
_install_nginx_package(env)
return
# Install nginx from directly
version = "1.3.8"
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 env.safe_exists(remote_conf_dir) and env.safe_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])
env.safe_run("wget %s" % url)
env.safe_run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
env.safe_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))
env.safe_sed("objs/Makefile", "-Werror", "")
env.safe_run("make")
env.safe_sudo("make install")
env.safe_sudo("cd %s; stow nginx" % env.install_dir)
defaults = {"galaxy_home": "/mnt/galaxy/galaxy-app"}
_setup_conf_file(env, os.path.join(remote_conf_dir, "nginx.conf"), "nginx.conf", defaults=defaults)
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):
env.safe_sudo("wget --output-document=%s/%s %s" % (remote_errdoc_dir, nginx_errdoc_file, url))
env.safe_sudo('tar xvzf %s' % nginx_errdoc_file)
env.safe_sudo("mkdir -p %s" % env.install_dir)
if not env.safe_exists("%s/nginx" % env.install_dir):
env.safe_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 env.safe_exists(cloudman_default_dir):
env.safe_sudo("mkdir -p %s" % cloudman_default_dir)
if not env.safe_exists(os.path.join(cloudman_default_dir, "nginx")):
env.safe_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_desktop(env):
"""
Configure a desktop manager to work with VNC. At the moment, this is tailored
to `JWM` (and `jwm` and `vnc4server` packages need to be installed).
"""
if not _read_boolean(env, "configure_desktop", False):
return
# Create a start script for X
_setup_conf_file(env, "/home/ubuntu/.vnc/xstartup", "xstartup", default_source="xstartup")
# Create jwmrc config file
_setup_conf_file(env, "/home/ubuntu/.jwmrc", "jwmrc.xml",
default_source="jwmrc.xml", mode="0644")
env.logger.info("----- Done configuring desktop -----")
def _configure_novnc(env):
if not _read_boolean(env, "configure_novnc", False):
# Longer term would like this enabled by default. -John
return
if not "novnc_install_dir" in env:
env.novnc_install_dir = "/opt/novnc"
if not "vnc_password" in env:
env.vnc_password = "******"
if not "vnc_user" in env:
env.vnc_user = env.user
if not "vnc_display" in env:
env.vnc_display = "1"
if not "vnc_depth" in env:
env.vnc_depth = "16"
if not "vnc_geometry" in env:
env.vnc_geometry = "1024x768"
_configure_vncpasswd(env)
novnc_dir = env.novnc_install_dir
env.safe_sudo("mkdir -p '%s'" % novnc_dir)
env.safe_sudo("chown %s '%s'" % (env.user, novnc_dir))
clone_cmd = "NOVNC_DIR='%s'; rm -rf $NOVNC_DIR; git clone https://github.com/kanaka/noVNC.git $NOVNC_DIR" % novnc_dir
run(clone_cmd)
## Move vnc_auto.html which takes vnc_password as query argument
## to index.html and rewrite it so that password is autoset, no
## need to specify via query parameter.
run("sed s/password\\ =\\ /password\\ =\\ \\\'%s\\\'\\;\\\\\\\\/\\\\\\\\// '%s/vnc_auto.html' > '%s/index.html'" % (env.vnc_password, novnc_dir, novnc_dir))
_setup_conf_file(env, "/etc/init.d/novnc", "novnc_init", default_source="novnc_init")
_setup_conf_file(env, "/etc/default/novnc", "novnc_default", default_source="novnc_default.template")
_setup_conf_file(env, "/etc/init.d/vncserver", "vncserver_init", default_source="vncserver_init")
_setup_conf_file(env, "/etc/default/vncserver", "vncserver_default", default_source="vncserver_default.template")
_setup_simple_service("novnc")
_setup_simple_service("vncserver")
def _configure_novnc(env):
if not _read_boolean(env, "configure_novnc", False):
# Longer term would like this enabled by default. -John
return
if not "novnc_install_dir" in env:
env.novnc_install_dir = "/opt/novnc"
if not "vnc_password" in env:
env.vnc_password = "******"
if not "vnc_user" in env:
env.vnc_user = env.user
if not "vnc_display" in env:
env.vnc_display = "1"
if not "vnc_depth" in env:
env.vnc_depth = "16"
if not "vnc_geometry" in env:
env.vnc_geometry = "1024x768"
_configure_vncpasswd(env)
novnc_dir = env.novnc_install_dir
env.safe_sudo("mkdir -p '%s'" % novnc_dir)
env.safe_sudo("chown %s '%s'" % (env.user, novnc_dir))
clone_cmd = "NOVNC_DIR='%s'; rm -rf $NOVNC_DIR; git clone https://github.com/kanaka/noVNC.git $NOVNC_DIR" % novnc_dir
run(clone_cmd)
## Move vnc_auto.html which takes vnc_password as query argument
## to index.html and rewrite it so that password is autoset, no
## need to specify via query parameter.
run("sed s/password\\ =\\ /password\\ =\\ \\\'%s\\\'\\;\\\\\\\\/\\\\\\\\// '%s/vnc_auto.html' > '%s/index.html'" % (env.vnc_password, novnc_dir, novnc_dir))
_setup_conf_file(env, "/etc/init.d/novnc", "novnc_init", default_source="novnc_init")
_setup_conf_file(env, "/etc/default/novnc", "novnc_default", default_source="novnc_default.template")
_setup_conf_file(env, "/etc/init.d/vncserver", "vncserver_init", default_source="vncserver_init")
_setup_conf_file(env, "/etc/default/vncserver", "vncserver_default", default_source="vncserver_default.template")
_setup_simple_service("novnc")
_setup_simple_service("vncserver")
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_desktop(env):
"""
Configure a desktop manager to work with VNC. Note that `xfce4` (or `jwm`)
and `vnc4server` packages need to be installed for this to have effect.
"""
if not _read_boolean(env, "configure_desktop", False):
return
# Set nginx PAM module to allow logins for any system user
if env.safe_exists("/etc/pam.d"):
env.safe_sudo('echo "@include common-auth" > /etc/pam.d/nginx')
env.safe_sudo('usermod -a -G shadow galaxy')
# Create a start script for X
_setup_conf_file(env, "/home/ubuntu/.vnc/xstartup", "xstartup", default_source="xstartup")
# Create jwmrc config file (uncomment this if using jwm window manager)
# _setup_conf_file(env, "/home/ubuntu/.jwmrc", "jwmrc.xml",
# default_source="jwmrc.xml", mode="0644")
env.logger.info("----- Done configuring desktop -----")
def _configure_desktop(env):
"""
Configure a desktop manager to work with VNC. Note that `xfce4` (or `jwm`)
and `vnc4server` packages need to be installed for this to have effect.
"""
if not _read_boolean(env, "configure_desktop", False):
return
# Set nginx PAM module to allow logins for any system user
if env.safe_exists("/etc/pam.d"):
env.safe_sudo('echo "@include common-auth" > /etc/pam.d/nginx')
env.safe_sudo('usermod -a -G shadow galaxy')
# Create a start script for X
_setup_conf_file(env, "/home/ubuntu/.vnc/xstartup", "xstartup", default_source="xstartup")
# Create jwmrc config file (uncomment this if using jwm window manager)
# _setup_conf_file(env, "/home/ubuntu/.jwmrc", "jwmrc.xml",
# default_source="jwmrc.xml", mode="0644")
env.logger.info("----- Done configuring desktop -----")
def _install_nginx_package(env):
"""
Install nginx from a custom package; also see
https://github.com/afgane/gvl_flavor/tree/master/playbook
"""
version = "1.4.7-gvl20140507b01-precise"
package_url = "http://cloudman-dev.s3.amazonaws.com/gvl-nginx-%s-amd64.deb" % version
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
env.safe_run("wget %s" % package_url)
env.safe_sudo("dpkg -i %s" % os.path.split(package_url)[1])
# The path for `nginx.conf` depends on how the package was built and
# what's set in `nginx_remote_conf_path` must match that!
defaults = {"galaxy_home": "/mnt/galaxy/galaxy-app"}
_setup_conf_file(env, env.nginx_remote_conf_path, "nginx.conf", defaults=defaults)
env.logger.debug("Nginx v{0} installed from package {1}".format(version, package_url))
def _install_nginx_package(env):
"""
Install nginx from a custom package; also see
https://github.com/afgane/gvl_flavor/tree/master/playbook
"""
version = "1.4.7-gvl20140407b03"
package_url = "http://cloudman-dev.s3.amazonaws.com/gvl-nginx-%s-precise-amd64.deb" % version
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
env.safe_run("wget %s" % package_url)
env.safe_sudo("dpkg -i %s" % os.path.split(package_url)[1])
# The path for `nginx.conf` depends on how the package was built and
# what's set in `nginx_remote_conf_path` must match that!
defaults = {"galaxy_home": "/mnt/galaxy/galaxy-app"}
_setup_conf_file(env, env.nginx_remote_conf_path, "nginx.conf", defaults=defaults)
env.logger.debug("Nginx v{0} installed from package {1}".format(version, package_url))
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 _setup_protvis_service(env):
_setup_conf_file(env, os.path.join("/etc/init.d/protvis"), "protvis_init", default_source="protvis_init")
_setup_conf_file(env, os.path.join("/etc/default/protvis"), "protvis_default")
_setup_simple_service("protvis")
def _setup_nginx_service(env):
# Setup system service for nginx, not needed for CloudMan but it is
# useful if CloudMan is not being used (such as galaxy-vm-launcher work).
_setup_conf_file(env, "/etc/init.d/nginx", "nginx_init", default_source="nginx_init")
_setup_simple_service("nginx")
def _setup_xvfb(env):
_setup_conf_file(env, "/etc/init.d/xvfb", "xvfb_init", default_source="xvfb_init")
_setup_conf_file(env, "/etc/default/xvfb", "xvfb_default", default_source="xvfb_default")
_setup_simple_service("xvfb")
env.safe_sudo("mkdir /var/lib/xvfb; chown root:root /var/lib/xvfb; chmod 0755 /var/lib/xvfb")
def _setup_service(env):
_setup_conf_file(env, "/etc/init.d/galaxy", "galaxy_init", default_source="galaxy_init")
_setup_conf_file(env, "/etc/default/galaxy", "galaxy_default")
_setup_simple_service("galaxy")
def _setup_xvfb(env):
_setup_conf_file(env, "/etc/init.d/xvfb", "xvfb_init", default_source="xvfb_init")
_setup_conf_file(env, "/etc/default/xvfb", "xvfb_default", default_source="xvfb_default")
_setup_simple_service("xvfb")
env.safe_sudo("mkdir /var/lib/xvfb; chown root:root /var/lib/xvfb; chmod 0755 /var/lib/xvfb")