Module Expr Str Import alias ImportFrom alias alias ImportFrom alias ImportFrom alias ImportFrom alias alias alias alias ImportFrom alias alias alias FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr Str If NameLoad body If Call AttributeLoad AttributeLoad NameLoad attr attr Str body Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Str Num Index Num Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad If CompareIn AttributeLoad NameLoad attr ListLoad Str Str body Expr Call NameLoad Expr Call NameLoad Expr Call NameLoad Expr Call NameLoad NameLoad orelse If CompareIn AttributeLoad NameLoad attr ListLoad Str Str body Expr Call NameLoad Expr Call NameLoad NameLoad Expr Call NameLoad orelse If CompareIn AttributeLoad NameLoad attr ListLoad Str Str body Pass orelse If CompareEq AttributeLoad NameLoad attr Str body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad orelse Raise Call NameLoad Str decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str Assign NameStore Str If UnaryOpNot Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpAdd Str NameLoad If BoolOpAnd CompareNotIn NameLoad NameLoad Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body If UnaryOpNot Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str If BoolOpAnd CompareIn Str NameLoad CompareIn Str NameLoad body Expr Call NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Str Return Dict Str BinOpMod Str NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad NameLoad Print Str For NameStore ListLoad Str body Print SubscriptLoad NameLoad Index NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Str If UnaryOpNot Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Str body With Call NameLoad NameStore body With Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr BinOpMod Str NameLoad Expr Call AttributeLoad NameLoad attr BinOpMod Str NameLoad decorator_list
N/A N/A Install software and configure package managers.
 N/A os fabric.api env cd cloudbio.custom.shared _make_tmp_dir cloudbio.package brew cloudbio.package.deb _apt_packages _add_apt_gpg_keys _setup_apt_automation _setup_apt_sources cloudbio.package.rpm _yum_packages _setup_yum_bashrc _setup_yum_sources _configure_and_install_native_packages N/A N/A env pkg_install N/A N/A N/A 
    Setups up native package repositories, determines list
    of native packages to install, and installs them.
     N/A home_dir N/A N/A env safe_run echo $HOME N/A home_dir N/A N/A N/A N/A N/A env shell_config startswith ~ N/A N/A nonhome N/A N/A N/A N/A env shell_config split ~/ 1 N/A -1 N/A N/A env shell_config N/A N/A N/A os path join home_dir nonhome N/A N/A N/A env distribution N/A debian ubuntu N/A N/A N/A _setup_apt_sources N/A N/A _setup_apt_automation N/A N/A _add_apt_gpg_keys N/A N/A _apt_packages pkg_install N/A N/A N/A N/A env distribution N/A centos scientificlinux N/A N/A N/A _setup_yum_sources N/A N/A _yum_packages pkg_install N/A N/A _setup_yum_bashrc N/A N/A N/A N/A env distribution N/A arch suse N/A N/A N/A N/A N/A N/A env distribution macosx N/A N/A N/A N/A brew install_packages env pkg_install N/A N/A N/A NotImplementedError Unknown target distribution N/A _connect_native_packages N/A N/A env pkg_install lib_install N/A N/A N/A 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.
     N/A bin_dir N/A N/A N/A os path join N/A env system_install bin N/A exports N/A _get_shell_exports env N/A path N/A N/A env safe_run_output echo $PATH N/A comment_line # CloudBioLinux PATH updates N/A N/A N/A N/A env safe_contains N/A env shell_config comment_line N/A N/A N/A N/A env safe_append N/A env shell_config N/A comment_line N/A N/A N/A bin_dir path N/A N/A env safe_exists N/A env shell_config N/A N/A N/A N/A N/A env safe_contains N/A env shell_config N/A exports N/A path N/A N/A N/A N/A env safe_append N/A env shell_config N/A exports N/A path N/A N/A N/A python pkg_install N/A python lib_install N/A N/A N/A _create_local_virtualenv N/A env system_install N/A _get_shell_exports N/A N/A env N/A N/A N/A bin_dir N/A N/A N/A os path join N/A env system_install bin N/A N/A path N/A export PATH=%s:$PATH bin_dir N/A _print_shell_exports N/A N/A env N/A N/A N/A Print a set of exports to add to shell in isolated installations.
     N/A exports N/A _get_shell_exports env N/A 
Isolated installation: add the following to your shell to include installed files: N/A e N/A path N/A N/A N/A exports N/A e N/A _create_local_virtualenv N/A N/A target_dir N/A N/A N/A Create virtualenv in target directory for non-sudo installs.
     N/A url https://raw.github.com/pypa/virtualenv/master/virtualenv.py N/A N/A N/A N/A N/A os path exists N/A N/A N/A os path join target_dir bin python N/A N/A N/A _make_tmp_dir work_dir N/A N/A N/A cd work_dir N/A N/A N/A N/A env safe_run N/A wget --no-check-certificate %s url N/A N/A N/A env safe_run N/A python virtualenv.py %s target_dir N/A