def _configure_and_install_native_packages(env, pkg_install):
"""
Setups up native package repositories, determines list
of native packages to install, and installs them.
"""
env.logger.debug("Configure and install native packages for distribution: " + env.distribution)
home_dir = env.safe_run("echo $HOME")
if home_dir:
if env.shell_config.startswith("~"):
nonhome = env.shell_config.split("~/", 1)[-1]
env.shell_config = os.path.join(home_dir, nonhome)
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)
if env.edition.short_name not in ["minimal"]:
_setup_yum_bashrc()
elif env.distribution == "arch":
pass # No package support for Arch yet
elif env.distribution == "macosx":
brew.install_packages(env, pkg_install)
else:
raise NotImplementedError("Unknown target distribution")
def _configure_and_install_native_packages(env, pkg_install):
"""
Setups up native package repositories, determines list
of native packages to install, and installs them.
"""
from fabric.api import env
from cloudbio.package import brew
from cloudbio.package.deb import (_apt_packages, _add_apt_gpg_keys,
_setup_apt_automation, _setup_apt_sources)
from cloudbio.package.rpm import (_yum_packages, _setup_yum_bashrc,
_setup_yum_sources)
home_dir = env.safe_run("echo $HOME")
if home_dir:
if env.shell_config.startswith("~"):
nonhome = env.shell_config.split("~/", 1)[-1]
env.shell_config = os.path.join(home_dir, nonhome)
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()
elif env.distribution in ["arch", "suse"]:
pass # No package support for Arch, SUSE yet
elif env.distribution == "macosx":
brew.install_packages(env, pkg_install)
else:
raise NotImplementedError("Unknown target distribution")
def _configure_and_install_native_packages(env, pkg_install):
"""
Setups up native package repositories, determines list
of native packages to install, and installs them.
"""
home_dir = env.safe_run("echo $HOME")
if home_dir:
if env.shell_config.startswith("~"):
nonhome = env.shell_config.split("~/", 1)[-1]
env.shell_config = os.path.join(home_dir, nonhome)
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)
if env.edition.short_name not in ["minimal"]:
_setup_yum_bashrc()
elif env.distribution == "arch":
pass # No package support for Arch yet
elif env.distribution == "macosx":
brew.install_packages(env, pkg_install)
else:
raise NotImplementedError("Unknown target distribution")
def _configure_and_install_native_packages(env, pkg_install):
"""
Setups up native package repositories, determines list
of native packages to install, and installs them.
"""
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")
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)