eggs Package

eggs Package

Manage Galaxy eggs

class galaxy.eggs.CaseSensitiveConfigParser(defaults=None, dict_type=<class 'collections.OrderedDict'>, allow_no_value=False)

Bases: ConfigParser.SafeConfigParser

optionxform(optionstr)

class galaxy.eggs.Crate(galaxy_config_file=None, platform=None)

Bases: object

Reads the eggs.ini file for use with checking and fetching.

all_eggs

Return a list of all eggs in the crate.

all_missing

Return true if any eggs in the eggs config file are missing.

all_names

Return a list of names of all eggs in the crate.

config_eggs

Return a list of all eggs in the crate that are needed based on the options set in the Galaxy config file.

config_file = '/var/build/user_builds/jmchilton-galaxy/checkouts/latest/eggs.ini'

config_missing

Return true if any eggs are missing, conditional on options set in the Galaxy config file.

config_names

Return a list of names of all eggs in the crate that are needed based on the options set in the Galaxy config file.

parse()

parse_egg_section(eggs, tags, full_platform=False, egg_class=<class 'galaxy.eggs.Egg'>)

resolve(all=False)

Try to resolve (e.g. fetch) all eggs in the crate.

class galaxy.eggs.Egg(name=None, version=None, tag=None, url=None, platform=None, crate=None)

Bases: object

Contains information about locating and downloading eggs.

fetch() serves as the install method to pkg_resources.working_set.resolve()

path

Return the path of the egg, if it exists, or None

remove_doppelgangers()

require()

resolve()

set_dir()

set_distribution()

Stores a pkg_resources Distribution object for reference later

unpack_if_needed()

version_conflict(conflict_dist, conflict_req)

exception galaxy.eggs.EggNotFetchable(eggs)

Bases: exceptions.Exception

class galaxy.eggs.GalaxyConfig(config_file)

Bases: object

always_conditional = ('pysam', 'ctypes', 'python_daemon')

check_conditional(egg_name)

class galaxy.eggs.URLRetriever(*args, **kwargs)

Bases: urllib.FancyURLopener

http_error_default(*args)

galaxy.eggs.get_env()

galaxy.eggs.remove_file_or_path(f)

galaxy.eggs.require(req_str)

galaxy.eggs.string_as_bool(string)

galaxy.eggs.unpack_zipfile(filename, extract_dir, ignores=[])

dist Module

Manage Galaxy eggs

class galaxy.eggs.dist.DistScrambleCrate(galaxy_config_file, build_on='all')

Bases: galaxy.eggs.scramble.ScrambleCrate

Holds eggs with info on how to build them for distribution.

dist_config_file = '/var/build/user_builds/jmchilton-galaxy/checkouts/latest/dist-eggs.ini'

get_platforms(wanted)

parse()

parse_egg_section(eggs, tags, full_platform=False)

class galaxy.eggs.dist.DistScrambleEgg(*args, **kwargs)

Bases: galaxy.eggs.scramble.ScrambleEgg

path

run_scramble_script()

set_dir()

unpack_if_needed()

scramble Module

Manage Galaxy eggs

class galaxy.eggs.scramble.ScrambleCrate(galaxy_config_file=None, platform=None)

Bases: galaxy.eggs.__init__.Crate

Reads the eggs.ini file for use with scrambling eggs.

parse()

parse_egg_section(*args, **kwargs)

scramble(all=False)

class galaxy.eggs.scramble.ScrambleEgg(*args, **kwargs)

Bases: galaxy.eggs.__init__.Egg

Contains information about scrambling eggs.

archive_dir = '/var/build/user_builds/jmchilton-galaxy/checkouts/latest/scripts/scramble/archives'

build_dir = '/var/build/user_builds/jmchilton-galaxy/checkouts/latest/scripts/scramble/build'

copy_build_script()

ez_setup = '/var/build/user_builds/jmchilton-galaxy/checkouts/latest/scripts/scramble/lib/ez_setup.py'

ez_setup_url = 'http://peak.telecommunity.com/dist/ez_setup.py'

fetch_one(urls)

Fetches the first available archive out of a list.

fetch_source()

Get egg (and dependent) source

get_tld(names)

run_scramble_script()

scramble()

scramble_dir = '/var/build/user_builds/jmchilton-galaxy/checkouts/latest/scripts/scramble'

script_dir = '/var/build/user_builds/jmchilton-galaxy/checkouts/latest/scripts/scramble/scripts'

unpack_source()

unpack_tar()

unpack_zip()

exception galaxy.eggs.scramble.ScrambleFailure(eggs, msg=None)

Bases: exceptions.Exception