def _perform_install(target=None, flavor=None):
"""
Once CBL/fabric environment is setup, this method actually
runs the required installation procedures.
See `install_biolinux` for full details on arguments
`target` and `flavor`.
"""
pkg_install, lib_install, custom_ignore, custom_add = _read_main_config()
if target is None or target == "packages":
# can only install native packages if we have sudo access.
if env.use_sudo:
_configure_and_install_native_packages(env, pkg_install)
else:
_connect_native_packages(env, pkg_install, lib_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore, custom_add)
if target is None or target == "chef_recipes":
_provision_chef_recipes(pkg_install, custom_ignore)
if target is None or target == "puppet_classes":
_provision_puppet_classes(pkg_install, custom_ignore)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install(pkg_install=pkg_install)
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if "is_ec2_image" in env and env.is_ec2_image.upper() in ["TRUE", "YES"]:
_cleanup_ec2(env)
def _perform_install(target=None, flavor=None):
"""
Once CBL/fabric environment is setup, this method actually
runs the required installation procedures.
See `install_biolinux` for full details on arguments
`target` and `flavor`.
"""
pkg_install, lib_install, custom_ignore, custom_add = _read_main_config()
if target is None or target == "packages":
# can only install native packages if we have sudo access.
if env.use_sudo:
_configure_and_install_native_packages(env, pkg_install)
else:
_connect_native_packages(env, pkg_install, lib_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore, custom_add)
if target is None or target == "chef_recipes":
_provision_chef_recipes(pkg_install, custom_ignore)
if target is None or target == "puppet_classes":
_provision_puppet_classes(pkg_install, custom_ignore)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install(pkg_install=pkg_install)
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if "is_ec2_image" in env and env.is_ec2_image.upper() in [
"TRUE", "YES"
]:
_cleanup_ec2(env)
def _perform_install(target=None, flavor=None):
"""
Once CBL/fabric environment is setup, this method actually
runs the required installation procedures.
See `install_biolinux` for full details on arguments
`target` and `flavor`.
"""
pkg_install, lib_install, custom_ignore = _read_main_config()
if target is None or target == "packages":
_configure_and_install_native_packages(env, pkg_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
_update_biolinux_log(env, target, flavor)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install(pkg_install=pkg_install)
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if env.has_key("is_ec2_image") and env.is_ec2_image.upper() in ["TRUE", "YES"]:
if env.distribution in ["ubuntu"]:
# For the time being (Dec 2012), must install development version
# of cloud-init because of a boto & cloud-init bug:
# https://bugs.launchpad.net/cloud-init/+bug/1068801
sudo('wget --output-document=cloud-init_0.7.1-0ubuntu4_all.deb ' +
'https://launchpad.net/ubuntu/+archive/primary/+files/cloud-init_0.7.1-0ubuntu4_all.deb')
sudo("dpkg -i cloud-init_0.7.1-0ubuntu4_all.deb")
sudo("rm -f cloud-init_0.7.1-0ubuntu4_all.deb")
_cleanup_ec2(env)
def _perform_install(target=None, flavor=None, more_custom_add=None):
"""
Once CBL/fabric environment is setup, this method actually
runs the required installation procedures.
See `install_biolinux` for full details on arguments
`target` and `flavor`.
"""
pkg_install, lib_install, custom_ignore, custom_add = _read_main_config()
if more_custom_add:
if custom_add is None:
custom_add = {}
for k, vs in more_custom_add.iteritems():
if k in custom_add:
custom_add[k].extend(vs)
else:
custom_add[k] = vs
if target is None or target == "packages":
env.keep_isolated = getattr(env, "keep_isolated",
"false").lower() in ["true", "yes"]
# Only touch system information if we're not an isolated installation
if not env.keep_isolated:
# can only install native packages if we have sudo access or are root
if env.use_sudo or env.safe_run_output("whoami").strip() == "root":
_configure_and_install_native_packages(env, pkg_install)
else:
_connect_native_packages(env, pkg_install, lib_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore, custom_add)
if target is None or target == "chef_recipes":
_provision_chef_recipes(pkg_install, custom_ignore)
if target is None or target == "puppet_classes":
_provision_puppet_classes(pkg_install, custom_ignore)
if target is None or target == "brew":
install_brew(flavor=flavor, automated=True)
if target is None or target == "conda":
install_conda(flavor=flavor, automated=True)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.flavor.post_install()
if "is_ec2_image" in env and env.is_ec2_image.upper() in [
"TRUE", "YES"
]:
_freenx_scripts(env)
if pkg_install is not None and 'cloudman' in pkg_install:
_configure_cloudman(env)
if target is None or target == "cleanup":
if env.use_sudo:
_cleanup_space(env)
if "is_ec2_image" in env and env.is_ec2_image.upper() in [
"TRUE", "YES"
]:
_cleanup_ec2(env)
def _perform_install(target=None, flavor=None, more_custom_add=None):
"""
Once CBL/fabric environment is setup, this method actually
runs the required installation procedures.
See `install_biolinux` for full details on arguments
`target` and `flavor`.
"""
pkg_install, lib_install, custom_ignore, custom_add = _read_main_config()
if more_custom_add:
if custom_add is None:
custom_add = {}
for k, vs in more_custom_add.iteritems():
if k in custom_add:
custom_add[k].extend(vs)
else:
custom_add[k] = vs
if target is None or target == "packages":
env.keep_isolated = getattr(env, "keep_isolated", "false").lower() in ["true", "yes"]
# Only touch system information if we're not an isolated installation
if not env.keep_isolated:
# can only install native packages if we have sudo access or are root
if env.use_sudo or env.safe_run_output("whoami").strip() == "root":
_configure_and_install_native_packages(env, pkg_install)
else:
_connect_native_packages(env, pkg_install, lib_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore, custom_add)
if target is None or target == "chef_recipes":
_provision_chef_recipes(pkg_install, custom_ignore)
if target is None or target == "puppet_classes":
_provision_puppet_classes(pkg_install, custom_ignore)
if target is None or target == "brew":
install_brew(flavor=flavor, automated=True)
if target is None or target == "conda":
install_conda(flavor=flavor, automated=True)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.flavor.post_install()
if "is_ec2_image" in env and env.is_ec2_image.upper() in ["TRUE", "YES"]:
_freenx_scripts(env)
if pkg_install is not None and 'cloudman' in pkg_install:
_configure_cloudman(env)
if target is None or target == "cleanup":
if env.use_sudo:
_cleanup_space(env)
if "is_ec2_image" in env and env.is_ec2_image.upper() in ["TRUE", "YES"]:
_cleanup_ec2(env)
def _perform_install(target=None, flavor=None, more_custom_add=None):
"""
Once CBL/fabric environment is setup, this method actually
runs the required installation procedures.
See `install_biolinux` for full details on arguments
`target` and `flavor`.
"""
pkg_install, lib_install, custom_ignore, custom_add = _read_main_config()
if more_custom_add:
if custom_add is None:
custom_add = {}
for k, vs in more_custom_add.iteritems():
if k in custom_add:
custom_add[k].extend(vs)
else:
custom_add[k] = vs
if target is None or target == "packages":
env.keep_isolated = getattr(env, "keep_isolated",
"false").lower() in ["true", "yes"]
# can only install native packages if we have sudo access.
if env.use_sudo:
_configure_and_install_native_packages(env, pkg_install)
elif not env.keep_isolated:
_connect_native_packages(env, pkg_install, lib_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore, custom_add)
if target is None or target == "chef_recipes":
_provision_chef_recipes(pkg_install, custom_ignore)
if target is None or target == "puppet_classes":
_provision_puppet_classes(pkg_install, custom_ignore)
if target is None or target == "brew":
install_brew(flavor=flavor)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install(pkg_install=pkg_install)
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if "is_ec2_image" in env and env.is_ec2_image.upper() in [
"TRUE", "YES"
]:
_cleanup_ec2(env)
def _perform_install(target=None, flavor=None):
"""
Once CBL/fabric environment is setup, this method actually
runs the required installation procedures.
See `install_biolinux` for full details on arguments
`target` and `flavor`.
"""
pkg_install, lib_install, custom_ignore = _read_main_config()
if target is None or target == "packages":
# can only install native packages if we have sudo access.
if env.use_sudo:
_configure_and_install_native_packages(env, pkg_install)
else:
_connect_native_packages(env, pkg_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore)
if target is None or target == "chef_recipes":
_provision_chef_recipes(pkg_install, custom_ignore)
if target is None or target == "puppet_classes":
_provision_puppet_classes(pkg_install, custom_ignore)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install(pkg_install=pkg_install)
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if "is_ec2_image" in env and env.is_ec2_image.upper() in [
"TRUE", "YES"
]:
if env.distribution in ["ubuntu"]:
# For the time being (Dec 2012), must install development version
# of cloud-init because of a boto & cloud-init bug:
# https://bugs.launchpad.net/cloud-init/+bug/1068801
sudo(
'wget --output-document=cloud-init_0.7.1-0ubuntu4_all.deb '
+
'https://launchpad.net/ubuntu/+archive/primary/+files/cloud-init_0.7.1-0ubuntu4_all.deb'
)
sudo("dpkg -i cloud-init_0.7.1-0ubuntu4_all.deb")
sudo("rm -f cloud-init_0.7.1-0ubuntu4_all.deb")
_cleanup_ec2(env)
def _perform_install(target=None, flavor=None, more_custom_add=None):
"""
Once CBL/fabric environment is setup, this method actually
runs the required installation procedures.
See `install_biolinux` for full details on arguments
`target` and `flavor`.
"""
pkg_install, lib_install, custom_ignore, custom_add = _read_main_config()
if more_custom_add:
if custom_add is None:
custom_add = {}
for k, vs in more_custom_add.iteritems():
if k in custom_add:
custom_add[k].extend(vs)
else:
custom_add[k] = vs
if target is None or target == "packages":
env.keep_isolated = getattr(env, "keep_isolated", "false").lower() in ["true", "yes"]
# can only install native packages if we have sudo access.
if env.use_sudo:
_configure_and_install_native_packages(env, pkg_install)
elif not env.keep_isolated:
_connect_native_packages(env, pkg_install, lib_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore, custom_add)
if target is None or target == "chef_recipes":
_provision_chef_recipes(pkg_install, custom_ignore)
if target is None or target == "puppet_classes":
_provision_puppet_classes(pkg_install, custom_ignore)
if target is None or target == "brew":
install_brew(flavor=flavor)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install(pkg_install=pkg_install)
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if "is_ec2_image" in env and env.is_ec2_image.upper() in ["TRUE", "YES"]:
_cleanup_ec2(env)
def install_biolinux(target=None, flavor=None):
"""Main entry point for installing BioLinux on a remote server.
`flavor` allows customization of CloudBioLinux behavior. It can either
be a flavor name that maps to a corresponding directory in contrib/flavor
or the path to a custom directory. This can contain:
- alternative package lists (main.yaml, packages.yaml, custom.yaml)
- custom python code (nameflavor.py) that hooks into the build machinery
`target` allows running only particular parts of the build process. Valid choices are:
- packages Install distro packages
- custom Install custom packages
- libraries Install programming language libraries
- post_install Setup CloudMan, FreeNX and other system services
- cleanup Remove downloaded files and prepare images for AMI builds
"""
_setup_logging(env)
time_start = _print_time_stats("Config", "start")
_check_fabric_version()
_configure_fabric_environment(env, flavor)
env.logger.debug("Target is '%s'" % target)
pkg_install, lib_install, custom_ignore = _read_main_config()
if target is None or target == "packages":
_configure_and_install_native_packages(env, pkg_install)
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
_update_biolinux_log(env, target, flavor)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install(pkg_install=pkg_install)
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if env.has_key("is_ec2_image") and env.is_ec2_image.upper() in ["TRUE", "YES"]:
_cleanup_ec2(env)
_print_time_stats("Config", "end", time_start)
def install_biolinux(target=None, packagelist=None, flavor=None, environment=None):
"""Main entry point for installing Biolinux on a remote server.
This allows a different main package list (the main YAML file is passed in),
and/or use of Flavor. So you can say:
install_biolinux:packagelist=contrib/mylist/main.yaml,flavor=specialflavor
Both packagelist and flavor, as well as the Edition, can also be passed in
through the fabricrc file.
target can also be supplied on the fab CLI. Special targets are:
- packages Install distro packages
- custom Install custom packages
- libraries Install programming language libraries
- post_install Setup CloudMan, FreeNX and other system services
- cleanup Remove downloaded files and prepare images for AMI builds
environment allows adding additional information on the command line -
usually for defining environments, for example environment=testing, or
environment=production, will set the deployment environment and tune
post-installation settings.
"""
_setup_logging(env)
time_start = _print_time_stats("Config", "start")
_check_fabric_version()
_parse_fabricrc()
_setup_edition(env)
_setup_flavor(flavor, environment)
_setup_distribution_environment() # get parameters for distro, packages etc.
_create_local_paths()
env.logger.info("packagelist=%s" % packagelist)
pkg_install, lib_install = _read_main_config(packagelist) # read yaml
env.logger.info("Target=%s" % target)
if target is None or target == "packages":
if env.distribution in ["debian", "ubuntu"]:
_setup_apt_sources()
_setup_apt_automation()
_add_apt_gpg_keys()
_apt_packages(pkg_install)
elif env.distribution in ["centos", "scientificlinux"]:
_setup_yum_sources()
_yum_packages(pkg_install)
_setup_yum_bashrc()
else:
raise NotImplementedError("Unknown target distribution")
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
_update_biolinux_log(env, target, flavor)
if target is None or target == "custom":
_custom_installs(pkg_install)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install()
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if env.has_key("is_ec2_image") and env.is_ec2_image.upper() in ["TRUE", "YES"]:
_cleanup_ec2(env)
_print_time_stats("Config", "end", time_start)
def install_biolinux(target=None, packagelist=None, flavor=None, environment=None,
pkg_config_file_path=None):
"""
Main entry point for installing BioLinux on a remote server.
``packagelist`` should point to a top level file (eg, ``main.yaml``) listing
all the package categories that should be installed. This allows a different
package list and/or use of Flavor. So you can say::
install_biolinux:packagelist=contrib/mylist/main.yaml,flavor=specialflavor
``pkg_config_file_path`` can be used to specify a path where a custom
``packages.yaml`` and ``packages-[dist].yaml`` are located, allowing fine-
grained (i.e., individual package) customization. Otherwise, default
to ``./contrib`` where the CBL files are defined.
Both ``packagelist`` and ``flavor``, as well as the Edition, can also be
passed in through the ``fabricrc`` file.
target can also be supplied on the fab CLI. Special targets are:
- packages Install distro packages
- custom Install custom packages
- libraries Install programming language libraries
- post_install Setup CloudMan, FreeNX and other system services
- cleanup Remove downloaded files and prepare images for AMI builds
``environment`` allows adding additional information on the command line -
usually for defining environments, for example ``environment=testing``, or
``environment=production``, will set the deployment environment and tune
post-installation settings.
"""
_setup_logging(env)
time_start = _print_time_stats("Config", "start")
_check_fabric_version()
_parse_fabricrc()
_setup_edition(env)
_setup_flavor(flavor, environment)
_setup_distribution_environment() # get parameters for distro, packages etc.
_create_local_paths()
env.logger.debug("Meta-package list is '%s'" % packagelist)
env.logger.debug("File path for explicit packages is '%s'" % pkg_config_file_path)
env.logger.debug("Target is '%s'" % target)
pkg_install, lib_install, custom_ignore = _read_main_config(packagelist) # read main yaml
if target is None or target == "packages":
if env.distribution in ["debian", "ubuntu"]:
_setup_apt_sources()
_setup_apt_automation()
_add_apt_gpg_keys()
_apt_packages(pkg_install, pkg_config_file_path=pkg_config_file_path)
elif env.distribution in ["centos", "scientificlinux"]:
_setup_yum_sources()
_yum_packages(pkg_install)
_setup_yum_bashrc()
else:
raise NotImplementedError("Unknown target distribution")
if env.nixpkgs: # ./doc/nixpkgs.md
_setup_nix_sources()
_nix_packages(pkg_install)
_update_biolinux_log(env, target, flavor)
if target is None or target == "custom":
_custom_installs(pkg_install, custom_ignore)
if target is None or target == "libraries":
_do_library_installs(lib_install)
if target is None or target == "post_install":
env.edition.post_install(pkg_install=pkg_install)
env.flavor.post_install()
if target is None or target == "cleanup":
_cleanup_space(env)
if env.has_key("is_ec2_image") and env.is_ec2_image.upper() in ["TRUE", "YES"]:
_cleanup_ec2(env)
_print_time_stats("Config", "end", time_start)