def _validate_target_distribution(dist, dist_name=None):
"""Check target matches environment setting (for sanity)
Throws exception on error
"""
env.logger.debug("Checking target distribution " + env.distribution)
if dist in ["debian", "ubuntu"]:
tag = env.safe_run_output("cat /proc/version")
if tag.lower().find(dist) == -1:
# hmmm, test issue file
tag2 = env.safe_run_output("cat /etc/issue")
if tag2.lower().find(dist) == -1:
raise ValueError("Distribution does not match machine; are you using correct fabconfig for " + dist)
if env.edition.short_name in ["minimal"]:
# "minimal editions don't actually change any of the apt
# source except adding biolinux, so won't cause this
# problem and don't need to match dist_name"
return
if not dist_name:
raise ValueError("Must specify a dist_name property when working with distribution %s" % dist)
# Does this new method work with CentOS, do we need this.
actual_dist_name = env.safe_run_output("cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d =")
if actual_dist_name.lower().find(dist_name) == -1:
raise ValueError("Distribution does not match machine; are you using correct fabconfig for " + dist)
else:
env.logger.debug("Unknown target distro")
def _validate_target_distribution(dist, dist_name=None):
"""Check target matches environment setting (for sanity)
Throws exception on error
"""
env.logger.debug("Checking target distribution " + env.distribution)
if dist in ["debian", "ubuntu"]:
tag = env.safe_run_output("cat /proc/version")
if tag.lower().find(dist) == -1:
# hmmm, test issue file
tag2 = env.safe_run_output("cat /etc/issue")
if tag2.lower().find(dist) == -1:
raise ValueError("Distribution does not match machine; are you using correct fabconfig for " + dist)
if not dist_name:
raise ValueError("Must specify a dist_name property when working with distribution %s" % dist)
# Does this new method work with CentOS, do we need this.
if dist == "debian":
actual_dist_name = _debian_dist_name(env)
else:
actual_dist_name = _ubuntu_dist_name(env)
if actual_dist_name != dist_name:
raise ValueError(
"Distribution does not match machine; are you using correct fabconfig <"
+ actual_dist_name
+ "> for "
+ dist
)
else:
env.logger.debug("Unknown target distro")
def _validate_target_distribution(dist, dist_name=None):
"""Check target matches environment setting (for sanity)
Throws exception on error
"""
env.logger.debug("Checking target distribution " + env.distribution)
if dist in ["debian", "ubuntu"]:
tag = env.safe_run_output("cat /proc/version")
if tag.lower().find(dist) == -1:
# hmmm, test issue file
tag2 = env.safe_run_output("cat /etc/issue")
if tag2.lower().find(dist) == -1:
raise ValueError(
"Distribution does not match machine; are you using correct fabconfig for "
+ dist)
if not dist_name:
raise ValueError(
"Must specify a dist_name property when working with distribution %s"
% dist)
# Does this new method work with CentOS, do we need this.
if dist == 'debian':
actual_dist_name = _debian_dist_name(env)
else:
actual_dist_name = _ubuntu_dist_name(env)
if actual_dist_name != dist_name:
raise ValueError(
"Distribution does not match machine; are you using correct fabconfig <"
+ actual_dist_name + "> for " + dist)
else:
env.logger.debug("Unknown target distro")
def _validate_target_distribution(dist, dist_name=None):
"""Check target matches environment setting (for sanity)
Throws exception on error
"""
env.logger.debug("Checking target distribution " + env.distribution)
if dist in ["debian", "ubuntu"]:
tag = env.safe_run_output("cat /proc/version")
if tag.lower().find(dist) == -1:
# hmmm, test issue file
tag2 = env.safe_run_output("cat /etc/issue")
if tag2.lower().find(dist) == -1:
raise ValueError(
"Distribution does not match machine; are you using correct fabconfig for "
+ dist)
if env.edition.short_name in ["minimal"]:
# "minimal editions don't actually change any of the apt
# source except adding biolinux, so won't cause this
# problem and don't need to match dist_name"
return
if not dist_name:
raise ValueError(
"Must specify a dist_name property when working with distribution %s"
% dist)
# Does this new method work with CentOS, do we need this.
actual_dist_name = _ubuntu_dist_name(env)
if actual_dist_name != dist_name:
raise ValueError(
"Distribution does not match machine; are you using correct fabconfig for "
+ dist)
else:
env.logger.debug("Unknown target distro")
def _connect_native_packages(env, pkg_install, lib_install):
"""Connect native installed packages to local versions.
This helps setup a non-sudo environment to handle software
that needs a local version in our non-root directory tree.
"""
bin_dir = os.path.join(env.system_install, "bin")
path = env.safe_run_output("echo $PATH")
comment_line = "# CloudBioLinux PATH updates"
if not env.safe_contains(env.shell_config, comment_line):
env.safe_append(env.shell_config, "\n" + comment_line)
if bin_dir not in path and env.safe_exists(env.shell_config):
add_path = "export PATH=%s:$PATH" % bin_dir
if not env.safe_contains(env.shell_config, add_path):
env.safe_append(env.shell_config, add_path)
ldlib_path = os.path.join(env.system_install, "lib")
add_ldlibrary = "export LD_LIBRARY_PATH=%s:$LD_LIBRARY_PATH" % ldlib_path
if not env.safe_contains(env.shell_config, add_ldlibrary):
env.safe_append(env.shell_config, add_ldlibrary)
perl_export = (
"export PERL5LIB=%s/lib/perl5:%s/lib/perl5/site_perl:${PERL5LIB}" %
(env.system_install, env.system_install))
if not env.safe_contains(env.shell_config, perl_export):
env.safe_append(env.shell_config, perl_export)
if "python" in pkg_install and "python" in lib_install:
_create_local_virtualenv(env.system_install)
def _connect_native_packages(env, pkg_install, lib_install):
"""Connect native installed packages to local versions.
This helps setup a non-sudo environment to handle software
that needs a local version in our non-root directory tree.
"""
bin_dir = os.path.join(env.system_install, "bin")
path = env.safe_run_output("echo $PATH")
comment_line = "# CloudBioLinux PATH updates"
if not env.safe_contains(env.shell_config, comment_line):
env.safe_append(env.shell_config, "\n" + comment_line)
if bin_dir not in path and env.safe_exists(env.shell_config):
add_path = "export PATH=%s:$PATH" % bin_dir
if not env.safe_contains(env.shell_config, add_path):
env.safe_append(env.shell_config, add_path)
ldlib_path = os.path.join(env.system_install, "lib")
add_ldlibrary = "export LD_LIBRARY_PATH=%s:$LD_LIBRARY_PATH" % ldlib_path
if not env.safe_contains(env.shell_config, add_ldlibrary):
env.safe_append(env.shell_config, add_ldlibrary)
perl_export = ("export PERL5LIB=%s/lib/perl5:%s/lib/perl5/site_perl:${PERL5LIB}"
% (env.system_install, env.system_install))
if not env.safe_contains(env.shell_config, perl_export):
env.safe_append(env.shell_config, perl_export)
if "python" in pkg_install and "python" in lib_install:
_create_local_virtualenv(env.system_install)
def _determine_distribution(env):
"""
Attempt to automatically determine the distribution of the target machine.
Currently works for Ubuntu, CentOS, Debian, Scientific Linux and Mac OS X.
"""
with quiet():
output = env.safe_run_output("cat /etc/*release").lower()
if output.find("distrib_id=ubuntu") >= 0:
return "ubuntu"
elif output.find("centos release") >= 0:
return "centos"
elif output.find("red hat enterprise linux server release") >= 0:
return "centos"
elif output.find("scientific linux release") >= 0:
return "scientificlinux"
elif env.safe_exists("/etc/debian_version"):
return "debian"
# check for file used by Python's platform.mac_ver
elif env.safe_exists("/System/Library/CoreServices/SystemVersion.plist"):
return "macosx"
else:
raise Exception(
"Attempt to automatically determine Linux distribution of target machine failed, please manually specify distribution in fabricrc.txt"
)
def _setup_deb_general():
"""Shared settings for different debian based/derived distributions.
"""
env.logger.debug("Debian-shared setup")
env.sources_file = "/etc/apt/sources.list.d/cloudbiolinux.list"
env.global_sources_file = "/etc/apt/sources.list"
env.apt_preferences_file = "/etc/apt/preferences"
if not hasattr(env, "python_version_ext"):
env.python_version_ext = ""
if not hasattr(env, "ruby_version_ext"):
env.ruby_version_ext = "1.9.1"
if not env.has_key("java_home"):
# Try to determine java location from update-alternatives
java_home = "/usr/lib/jvm/java-7-openjdk-amd64"
with quiet():
java_info = env.safe_run_output("update-alternatives --display java")
for line in java_info.split("\n"):
if line.strip().startswith("link currently points to"):
java_home = line.split()[-1].strip()
java_home = java_home.replace("/jre/bin/java", "")
env.java_home = java_home
shared_sources = [
"deb http://download.virtualbox.org/virtualbox/debian %s contrib", # virtualbox
]
return shared_sources
def _setup_deb_general():
"""Shared settings for different debian based/derived distributions.
"""
env.logger.debug("Debian-shared setup")
env.sources_file = "/etc/apt/sources.list.d/cloudbiolinux.list"
env.global_sources_file = "/etc/apt/sources.list"
env.apt_preferences_file = "/etc/apt/preferences"
if not hasattr(env, "python_version_ext"):
env.python_version_ext = ""
if not hasattr(env, "ruby_version_ext"):
env.ruby_version_ext = "1.9.1"
if not env.has_key("java_home"):
# Try to determine java location from update-alternatives
java_home = "/usr/lib/jvm/java-7-openjdk-amd64"
with quiet():
java_info = env.safe_run_output(
"update-alternatives --display java")
for line in java_info.split("\n"):
if line.strip().startswith("link currently points to"):
java_home = line.split()[-1].strip()
java_home = java_home.replace("/jre/bin/java", "")
env.java_home = java_home
shared_sources = [
"deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux", # Bio-Linux
"deb http://download.virtualbox.org/virtualbox/debian %s contrib", # virtualbox
]
return shared_sources
def _determine_distribution(env):
"""
Attempt to automatically determine the distribution of the target machine.
Currently works for Ubuntu, CentOS, Debian, Scientific Linux and Mac OS X.
"""
with quiet():
output = env.safe_run_output("cat /etc/*release").lower()
if output.find("distrib_id=ubuntu") >= 0:
return "ubuntu"
elif output.find("centos release") >= 0:
return "centos"
elif output.find("centos linux release") >= 0:
return "centos"
elif output.find("red hat") >= 0:
return "centos"
elif output.find("fedora release") >= 0:
return "centos"
elif output.find("amzn") >= 0: # Amazon AMIs are Red-Hat based
return "centos"
elif output.find("suse linux") >= 0:
return "suse"
elif output.find("opensuse") >= 0:
return "suse"
elif output.find("scientific linux") >= 0:
return "scientificlinux"
elif env.safe_exists("/etc/debian_version"):
return "debian"
elif output.find("id=arch") >= 0:
return "arch"
# check for file used by Python's platform.mac_ver
elif env.safe_exists("/System/Library/CoreServices/SystemVersion.plist"):
return "macosx"
else:
raise Exception("Attempt to automatically determine Linux distribution of target machine failed, please manually specify distribution in fabricrc.txt")
def _setup_distribution_environment(ignore_distcheck=False):
"""Setup distribution environment
"""
env.logger.info("Distribution %s" % env.distribution)
if env.hosts == ["vagrant"]:
_setup_vagrant_environment()
elif env.hosts == ["localhost"]:
_setup_local_environment()
if env.distribution == "ubuntu":
_setup_ubuntu()
elif env.distribution == "centos":
_setup_centos()
elif env.distribution == "scientificlinux":
_setup_scientificlinux()
elif env.distribution == "debian":
_setup_debian()
else:
raise ValueError("Unexpected distribution %s" % env.distribution)
configure_runsudo(env)
if not ignore_distcheck:
_validate_target_distribution(env.distribution, env.get('dist_name', None))
_cloudman_compatibility(env)
_setup_nixpkgs()
_setup_fullpaths(env)
# allow us to check for packages only available on 64bit machines
machine = env.safe_run_output("uname -m")
env.is_64bit = machine.find("_64") > 0
def _setup_distribution_environment(ignore_distcheck=False):
"""Setup distribution environment
"""
env.logger.info("Distribution %s" % env.distribution)
if env.hosts == ["vagrant"]:
_setup_vagrant_environment()
elif env.hosts == ["localhost"]:
_setup_local_environment()
if env.distribution == "ubuntu":
_setup_ubuntu()
elif env.distribution == "centos":
_setup_centos()
elif env.distribution == "scientificlinux":
_setup_scientificlinux()
elif env.distribution == "debian":
_setup_debian()
else:
raise ValueError("Unexpected distribution %s" % env.distribution)
configure_runsudo(env)
if not ignore_distcheck:
_validate_target_distribution(env.distribution,
env.get('dist_name', None))
_cloudman_compatibility(env)
_setup_nixpkgs()
_setup_fullpaths(env)
# allow us to check for packages only available on 64bit machines
machine = env.safe_run_output("uname -m")
env.is_64bit = machine.find("_64") > 0
def _setup_fullpaths(env):
home_dir = env.safe_run_output("echo $HOME")
for attr in ["data_files", "galaxy_home", "local_install"]:
if hasattr(env, attr):
x = getattr(env, attr)
if x.startswith("~"):
x = x.replace("~", home_dir)
setattr(env, attr, x)
def _setup_fullpaths(env):
home_dir = env.safe_run_output("echo $HOME")
for attr in ["data_files", "galaxy_home", "local_install"]:
if hasattr(env, attr):
x = getattr(env, attr)
if x.startswith("~"):
x = x.replace("~", home_dir)
setattr(env, attr, x)
def _setup_distribution_environment(ignore_distcheck=False):
"""Setup distribution environment.
In low-level terms, this method attempts to populate various values in the fabric
env data structure for use other places in CloudBioLinux.
"""
if "distribution" not in env:
env.distribution = "__auto__"
if "dist_name" not in env:
env.dist_name = "__auto__"
env.logger.info("Distribution %s" % env.distribution)
if env.hosts == ["vagrant"]:
_setup_vagrant_environment()
elif env.hosts == ["localhost"]:
_setup_local_environment()
configure_runsudo(env)
if env.distribution == "__auto__":
env.distribution = _determine_distribution(env)
if env.distribution == "ubuntu":
## TODO: Determine if dist_name check works with debian.
if env.dist_name == "__auto__":
env.dist_name = _ubuntu_dist_name(env)
_setup_ubuntu()
elif env.distribution == "centos":
_setup_centos()
elif env.distribution == "scientificlinux":
_setup_scientificlinux()
elif env.distribution == "debian":
if env.dist_name == "__auto__":
env.dist_name = _debian_dist_name(env)
_setup_debian()
elif env.distribution == "arch":
pass # No package support for Arch yet
elif env.distribution == "suse":
pass # No package support for SUSE yet
elif env.distribution == "macosx":
_setup_macosx(env)
ignore_distcheck = True
else:
raise ValueError("Unexpected distribution %s" % env.distribution)
if not ignore_distcheck:
_validate_target_distribution(env.distribution,
env.get('dist_name', None))
_cloudman_compatibility(env)
_setup_nixpkgs()
_setup_fullpaths(env)
# allow us to check for packages only available on 64bit machines
machine = env.safe_run_output("uname -m")
env.is_64bit = machine.find("_64") > 0
def _setup_distribution_environment(ignore_distcheck=False):
"""Setup distribution environment.
In low-level terms, this method attempts to populate various values in the fabric
env data structure for use other places in CloudBioLinux.
"""
if "distribution" not in env:
env.distribution = "__auto__"
if "dist_name" not in env:
env.dist_name = "__auto__"
env.logger.info("Distribution %s" % env.distribution)
if env.hosts == ["vagrant"]:
_setup_vagrant_environment()
elif env.hosts == ["localhost"]:
_setup_local_environment()
configure_runsudo(env)
if env.distribution == "__auto__":
env.distribution = _determine_distribution(env)
if env.distribution == "ubuntu":
## TODO: Determine if dist_name check works with debian.
if env.dist_name == "__auto__":
env.dist_name = _ubuntu_dist_name(env)
_setup_ubuntu()
elif env.distribution == "centos":
_setup_centos()
elif env.distribution == "scientificlinux":
_setup_scientificlinux()
elif env.distribution == "debian":
if env.dist_name == "__auto__":
env.dist_name = _debian_dist_name(env)
_setup_debian()
elif env.distribution == "arch":
pass # No package support for Arch yet
elif env.distribution == "suse":
pass # No package support for SUSE yet
elif env.distribution == "macosx":
_setup_macosx(env)
ignore_distcheck = True
else:
raise ValueError("Unexpected distribution %s" % env.distribution)
if not ignore_distcheck:
_validate_target_distribution(env.distribution, env.get('dist_name', None))
_cloudman_compatibility(env)
_setup_nixpkgs()
_setup_fullpaths(env)
# allow us to check for packages only available on 64bit machines
machine = env.safe_run_output("uname -m")
env.is_64bit = machine.find("_64") > 0
def _connect_native_packages(env, pkg_install, lib_install):
"""Connect native installed packages to local versions.
This helps setup a non-sudo environment to handle software
that needs a local version in our non-root directory tree.
"""
bin_dir = os.path.join(env.system_install, "bin")
exports = _get_shell_exports(env)
path = env.safe_run_output("echo $PATH")
comment_line = "# CloudBioLinux PATH updates"
if not env.safe_contains(env.shell_config, comment_line):
env.safe_append(env.shell_config, "\n" + comment_line)
if bin_dir not in path and env.safe_exists(env.shell_config):
if not env.safe_contains(env.shell_config, exports["path"]):
env.safe_append(env.shell_config, exports["path"])
if "python" in pkg_install and "python" in lib_install:
_create_local_virtualenv(env.system_install)
def _determine_distribution(env):
"""
Attempt to automatically determine the distribution of the target machine.
Currently works for Ubuntu, CentOS, Debian, Scientific Linux and Mac OS X.
"""
with quiet():
output = env.safe_run_output("cat /etc/*release").lower()
if output.find("id=ubuntu") >= 0:
return "ubuntu"
elif output.find("centos release") >= 0:
return "centos"
elif output.find("centos linux release") >= 0:
return "centos"
elif output.find("red hat enterprise linux") >= 0:
return "centos"
elif output.find("fedora") >= 0:
return "centos"
# Amazon AMIs are Red-Hat based
elif output.find("amzn") >= 0 or output.find("amazon") >= 0:
return "centos"
elif output.find("suse linux") >= 0:
return "suse"
elif output.find("opensuse") >= 0:
return "suse"
elif output.find("scientific linux") >= 0:
return "scientificlinux"
elif env.safe_exists("/etc/debian_version"):
return "debian"
elif output.find("id=arch") >= 0 or output.find('id_like="arch"') >= 0:
return "arch"
elif output.find("antergos") >= 0:
return "arch"
# check for file used by Python's platform.mac_ver
elif env.safe_exists("/System/Library/CoreServices/SystemVersion.plist"):
return "macosx"
else:
raise Exception(
"Attempt to automatically determine Linux distribution of target machine failed:\n%s"
% output)
def _debian_dist_name(env):
"""
Determine Debian dist name (e.g. squeeze).
"""
return env.safe_run_output("lsb_release -a | grep Codename | cut -f 2")
def _ubuntu_dist_name(env):
"""
Determine Ubuntu dist name (e.g. precise or quantal).
"""
return env.safe_run_output(
"cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d =")
def _debian_dist_name(env):
"""
Determine Debian dist name (e.g. squeeze).
"""
return env.safe_run_output("lsb_release -a | grep Codename | cut -f 2")
def _ubuntu_dist_name(env):
"""
Determine Ubuntu dist name (e.g. precise or quantal).
"""
return env.safe_run_output("cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d =")
