Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.tools.deps package

Dependency management for tools.

galaxy.tools.deps.build_dependency_manager(config)[source]
class galaxy.tools.deps.DependencyManager(default_base_path, conf_file=None, app_config={})[source]

Bases: object

A DependencyManager attempts to resolve named and versioned dependencies by searching for them under a list of directories. Directories should be of the form:

$BASE/name/version/…

and should each contain a file ‘env.sh’ which can be sourced to make the dependency available in the current shell environment.

__init__(default_base_path, conf_file=None, app_config={})[source]

Create a new dependency manager looking for packages under the paths listed in base_paths. The default base path is app.config.tool_dependency_dir.

set_enabled_container_types(container_types_to_destinations)[source]

Set the union of all enabled container types.

get_destination_info_for_container_type(container_type, destination_id=None)[source]
enabled_container_types

Returns the union of enabled container types.

get_resolver_option(resolver, key, explicit_resolver_options={})[source]

Look in resolver-specific settings for option and then fallback to global settings.

get_app_option(key, default=None)[source]
dependency_shell_commands(requirements, **kwds)[source]
requirements_to_dependencies(requirements, **kwds)[source]

Takes a list of requirements and returns a dictionary with requirements as key and dependencies as value caching these on the tool instance if supplied.

uses_tool_shed_dependencies()[source]
find_dep(name, version=None, type='package', **kwds)[source]
class galaxy.tools.deps.CachedDependencyManager(default_base_path, conf_file=None, app_config={}, tool_dependency_cache_dir=None)[source]

Bases: galaxy.tools.deps.DependencyManager

__init__(default_base_path, conf_file=None, app_config={}, tool_dependency_cache_dir=None)[source]
build_cache(requirements, **kwds)[source]
dependency_shell_commands(requirements, **kwds)[source]

Runs a set of requirements through the dependency resolvers and returns a list of commands required to activate the dependencies. If dependencies are cacheable and the cache does not exist, will try to create it. If cached environment exists or is successfully created, will generate commands to activate it.

hash_dependencies(resolved_dependencies)[source]

Return hash for dependencies

get_hashed_dependencies_path(resolved_dependencies)[source]

Returns the path to the hashed dependencies directory (but does not evaluate whether the path exists).

Parameters:resolved_dependencies (list) – list of resolved dependencies
Returns:path
Return type:str
class galaxy.tools.deps.NullDependencyManager(default_base_path=None, conf_file=None, app_config={})[source]

Bases: galaxy.tools.deps.DependencyManager

__init__(default_base_path=None, conf_file=None, app_config={})[source]
uses_tool_shed_dependencies()[source]
dependency_shell_commands(requirements, **kwds)[source]
find_dep(name, version=None, type='package', **kwds)[source]

Submodules

galaxy.tools.deps.brew_exts module

class galaxy.tools.deps.brew_exts.BrewContext(args=None)[source]

Bases: object

__init__(args=None)[source]
class galaxy.tools.deps.brew_exts.RecipeContext(recipe, version, brew_context=None)[source]

Bases: object

static from_args(args, brew_context=None)[source]
__init__(recipe, version, brew_context=None)[source]
cellar_path
tap_path
galaxy.tools.deps.brew_exts.main()[source]
exception galaxy.tools.deps.brew_exts.CommandLineException(command, stdout, stderr)[source]

Bases: exceptions.Exception

__init__(command, stdout, stderr)[source]
galaxy.tools.deps.brew_exts.versioned_install(recipe_context, package=None, version=None, installed_deps=[])[source]
galaxy.tools.deps.brew_exts.commit_for_version(recipe_context, package, version)[source]
galaxy.tools.deps.brew_exts.print_versioned_deps(recipe_context, recipe, version)[source]
galaxy.tools.deps.brew_exts.load_versioned_deps(cellar_path, relaxed=None)[source]
galaxy.tools.deps.brew_exts.unversioned_install(package)[source]
galaxy.tools.deps.brew_exts.brew_execute(args, env=None)[source]
galaxy.tools.deps.brew_exts.build_env_statements_from_recipe_context(recipe_context, **kwds)[source]
galaxy.tools.deps.brew_exts.build_env_statements(cellar_root, cellar_path, relaxed=None, custom_only=False)[source]
galaxy.tools.deps.brew_exts.build_env_actions(deps, cellar_root, cellar_path, relaxed=None, custom_only=False)[source]
class galaxy.tools.deps.brew_exts.EnvAction(keg_root, action_description)[source]

Bases: object

__init__(keg_root, action_description)[source]
static build_env(env_actions)[source]
modify_environ(environ)[source]
to_statements()[source]
galaxy.tools.deps.brew_exts.brew_head_at_version(*args, **kwds)[source]
galaxy.tools.deps.brew_exts.brew_head_at_commit(*args, **kwds)[source]
galaxy.tools.deps.brew_exts.git_execute(args)[source]
galaxy.tools.deps.brew_exts.execute(cmds, env=None)[source]
galaxy.tools.deps.brew_exts.brew_deps(package)[source]
galaxy.tools.deps.brew_exts.brew_info(recipe)[source]
galaxy.tools.deps.brew_exts.extended_brew_info(recipe)[source]
galaxy.tools.deps.brew_exts.brew_versions_info(package, tap_path)[source]
galaxy.tools.deps.brew_exts.recipe_cellar_path(cellar_path, recipe, version)[source]
galaxy.tools.deps.brew_exts.ensure_brew_on_path(args)[source]
galaxy.tools.deps.brew_exts.which(file)[source]

galaxy.tools.deps.brew_util module

brew_exts defines generic extensions to Homebrew this file builds on those abstraction and provides Galaxy specific functionality not useful to the brew external commands.

class galaxy.tools.deps.brew_util.HomebrewRecipe(recipe, version, tap)[source]

Bases: object

__init__(recipe, version, tap)[source]
galaxy.tools.deps.brew_util.requirements_to_recipes(requirements)[source]
galaxy.tools.deps.brew_util.requirement_to_recipe(requirement)[source]
galaxy.tools.deps.brew_util.requirements_to_recipe_contexts(requirements, brew_context)[source]

galaxy.tools.deps.commands module

Generic I/O and shell processing code used by Galaxy tool dependencies.

galaxy.tools.deps.commands.redirecting_io(sys=<module 'sys' (built-in)>)[source]

Predicate to determine if we are redicting stdout in process.

galaxy.tools.deps.commands.redirect_aware_commmunicate(p, sys=<module 'sys' (built-in)>)[source]

Variant of process.communicate that works with in process I/O redirection.

galaxy.tools.deps.commands.shell(cmds, env=None, **kwds)[source]

Run shell commands with shell_process and wait.

galaxy.tools.deps.commands.shell_process(cmds, env=None, **kwds)[source]

A high-level method wrapping subprocess.Popen.

Handles details such as environment extension and in process I/O redirection.

galaxy.tools.deps.commands.execute(cmds)[source]

Execute commands and throw an exception on a non-zero exit.

Return the standard output if the commands are successful

galaxy.tools.deps.commands.argv_to_str(command_argv, quote=True)[source]

Convert an argv command list to a string for shell subprocess.

If None appears in the command list it is simply excluded.

Arguments are quoted with shlex_quote. That said, this method is not meant to be used in security critical paths of code and should not be used to sanitize code.

galaxy.tools.deps.commands.download_command(url, to='-', quote_url=False)[source]

Build a command line to download a URL.

By default the URL will be downloaded to standard output but a specific file can be specified with the to argument.

exception galaxy.tools.deps.commands.CommandLineException(command, stdout, stderr, returncode)[source]

Bases: exceptions.Exception

An exception indicating a non-zero command-line exit.

__init__(command, stdout, stderr, returncode)[source]

Construct a CommandLineException from command and standard I/O.

galaxy.tools.deps.commands.which(file)[source]

galaxy.tools.deps.conda_compat module

Compat. layer with conda_build/verify if Galaxy/galaxy-lib not installed through conda.

In general there are utilities available for Conda building and parsing that are high-quality and should be utilized when available but that are only available in conda channels and not in PyPI. This module serves as a PyPI capable interface to these utilities.

galaxy.tools.deps.conda_compat.raw_metadata(recipe_dir)[source]

Evaluate Conda template if needed and return raw metadata for supplied recipe directory.

galaxy.tools.deps.conda_compat.MetaData

alias of galaxy.tools.deps.conda_compat._MetaData

galaxy.tools.deps.conda_util module

class galaxy.tools.deps.conda_util.CondaContext(conda_prefix=None, conda_exec=None, shell_exec=None, debug=False, ensure_channels='', condarc_override=None, use_path_exec=False, copy_dependencies=False, use_local=False)[source]

Bases: galaxy.tools.deps.installable.InstallableContext

installable_description = 'Conda'
__init__(conda_prefix=None, conda_exec=None, shell_exec=None, debug=False, ensure_channels='', condarc_override=None, use_path_exec=False, copy_dependencies=False, use_local=False)[source]
conda_version
conda_build_available
ensure_conda_build_installed_if_needed()[source]
conda_info()[source]
is_conda_installed()[source]

Check if conda_exec exists

can_install_conda()[source]

If conda_exec is set to a path outside of conda_prefix, there is no use installing conda into conda_prefix, since it can’t be used by galaxy. If conda_exec equals conda_prefix/bin/conda, we can install conda if either conda_prefix does not exist or is empty.

exec_command(operation, args, stdout_path=None)[source]

Execute the requested command.

Return the process exit code (i.e. 0 in case of success).

exec_create(args, allow_local=True, stdout_path=None)[source]

Return the process exit code (i.e. 0 in case of success).

exec_remove(args)[source]

Remove a conda environment using conda env remove -y –name args.

Return the process exit code (i.e. 0 in case of success).

exec_install(args, allow_local=True, stdout_path=None)[source]

Return the process exit code (i.e. 0 in case of success).

exec_clean(args=[], quiet=False)[source]

Clean up after conda installation.

Return the process exit code (i.e. 0 in case of success).

export_list(name, path)[source]

Return the process exit code (i.e. 0 in case of success).

env_path(env_name)[source]
envs_path
has_env(env_name)[source]
deactivate
activate
is_installed()[source]
can_install()[source]
parent_path
class galaxy.tools.deps.conda_util.CondaTarget(package, version=None, channel=None)[source]

Bases: object

__init__(package, version=None, channel=None)[source]
package_specifier

Return a package specifier as consumed by conda install/create.

install_environment

The dependency resolution and installation frameworks will expect each target to be installed it its own environment with a fixed and predictable name given package and version.

galaxy.tools.deps.conda_util.install_conda(conda_context, force_conda_build=False)[source]
galaxy.tools.deps.conda_util.install_conda_target(conda_target, conda_context, skip_environment=False)[source]

Install specified target into a its own environment.

Return the process exit code (i.e. 0 in case of success).

galaxy.tools.deps.conda_util.requirements_to_conda_targets(requirements)[source]

galaxy.tools.deps.containers module

class galaxy.tools.deps.containers.ContainerFinder(app_info)[source]

Bases: object

__init__(app_info)[source]
find_best_container_description(enabled_container_types, tool_info)[source]

Regardless of destination properties - find best container for tool.

Given container types and container.ToolInfo description of the tool.

find_container(tool_info, destination_info, job_info)[source]
class galaxy.tools.deps.containers.NullContainerFinder[source]

Bases: object

find_container(tool_info, destination_info, job_info)[source]
class galaxy.tools.deps.containers.ContainerRegistry(app_info)[source]

Bases: object

Loop through enabled ContainerResolver plugins and find first match.

__init__(app_info)[source]
find_best_container_description(enabled_container_types, tool_info)[source]

Yield best container description of supplied types matching tool info.

galaxy.tools.deps.dependencies module

class galaxy.tools.deps.dependencies.AppInfo(galaxy_root_dir=None, default_file_path=None, outputs_to_working_directory=False, container_image_cache_path=None, library_import_dir=None, enable_beta_mulled_containers=False, containers_resolvers_config_file=None, involucro_path=None, involucro_auto_init=True, mulled_channels=['conda-forge', 'bioconda'])[source]

Bases: object

__init__(galaxy_root_dir=None, default_file_path=None, outputs_to_working_directory=False, container_image_cache_path=None, library_import_dir=None, enable_beta_mulled_containers=False, containers_resolvers_config_file=None, involucro_path=None, involucro_auto_init=True, mulled_channels=['conda-forge', 'bioconda'])[source]
class galaxy.tools.deps.dependencies.ToolInfo(container_descriptions=[], requirements=[], requires_galaxy_python_environment=False, env_pass_through=['GALAXY_SLOTS'])[source]

Bases: object

__init__(container_descriptions=[], requirements=[], requires_galaxy_python_environment=False, env_pass_through=['GALAXY_SLOTS'])[source]
class galaxy.tools.deps.dependencies.JobInfo(working_directory, tool_directory, job_directory, tmp_directory, job_directory_type)[source]

Bases: object

__init__(working_directory, tool_directory, job_directory, tmp_directory, job_directory_type)[source]
class galaxy.tools.deps.dependencies.DependenciesDescription(requirements=[], installed_tool_dependencies=[])[source]

Bases: object

Capture (in a readily serializable way) context related a tool dependencies - both the tool’s listed requirements and the tool shed related context required to resolve dependencies via the ToolShedPackageDependencyResolver.

This is meant to enable remote resolution of dependencies, by the Pulsar or other potential remote execution mechanisms.

__init__(requirements=[], installed_tool_dependencies=[])[source]
to_dict()[source]
static from_dict(as_dict)[source]

galaxy.tools.deps.docker_util module

Utilities for building up Docker commands…

…using common defaults and configuration mechanisms.

galaxy.tools.deps.docker_util.kill_command(container, signal=None, **kwds)[source]
galaxy.tools.deps.docker_util.logs_command(container, **kwds)[source]
galaxy.tools.deps.docker_util.build_command(image, docker_build_path, **kwds)[source]
galaxy.tools.deps.docker_util.build_save_image_command(image, destination, **kwds)[source]
galaxy.tools.deps.docker_util.build_pull_command(tag, **kwds)[source]
galaxy.tools.deps.docker_util.build_docker_cache_command(image, **kwds)[source]
galaxy.tools.deps.docker_util.build_docker_images_command(truncate=True, **kwds)[source]
galaxy.tools.deps.docker_util.build_docker_load_command(**kwds)[source]
galaxy.tools.deps.docker_util.build_docker_run_command(container_command, image, interactive=False, terminal=False, tag=None, volumes=[], volumes_from=None, memory=None, env_directives=[], working_directory=None, name=None, net=None, run_extra_arguments=None, docker_cmd='docker', sudo=True, sudo_cmd='sudo', auto_rm=True, set_user='$UID', host=None)[source]
galaxy.tools.deps.docker_util.command_list(command, command_args=[], **kwds)[source]

Return Docker command as an argv list.

galaxy.tools.deps.docker_util.command_shell(command, command_args=[], **kwds)[source]

Return Docker command as a string for a shell or command-list.

galaxy.tools.deps.dockerfiles module

galaxy.tools.deps.dockerfiles.docker_host_args(**kwds)[source]
galaxy.tools.deps.dockerfiles.dockerfile_build(path, dockerfile=None, error=<bound method CBLogger.error of <cloudbridge.CBLogger object>>, **kwds)[source]

galaxy.tools.deps.installable module

Abstractions for installing local software managed and required by Galaxy/galaxy-lib.

class galaxy.tools.deps.installable.InstallableContext[source]

Bases: object

Represent a directory/configuration of something that can be installed.

is_installed()[source]

Return bool indicating if the configured software is installed.

can_install()[source]

Check preconditions for installation.

installable_description

Short description of thing being installed for log statements.

parent_path

Return parent path of the location the installable will be created within.

galaxy.tools.deps.installable.ensure_installed(installable_context, install_func, auto_init)[source]

Make sure target is installed - handle multiple processes potentially attempting installation.

galaxy.tools.deps.requirements module

class galaxy.tools.deps.requirements.ToolRequirement(name=None, type=None, version=None, specs=[])[source]

Bases: object

Represents an external requirement that must be available for the tool to run (for example, a program, package, or library). Requirements can optionally assert a specific version.

__init__(name=None, type=None, version=None, specs=[])[source]
to_dict()[source]
copy()[source]
static from_dict(dict)[source]
class galaxy.tools.deps.requirements.RequirementSpecification(uri, version=None)[source]

Bases: object

Refine a requirement using a URI.

__init__(uri, version=None)[source]
specifies_version
short_name
to_dict()[source]
static from_dict(dict)[source]
class galaxy.tools.deps.requirements.ToolRequirements(tool_requirements=None)[source]

Bases: object

Represents all requirements (packages, env vars) needed to run a tool.

__init__(tool_requirements=None)[source]
static from_list(requirements)[source]
resolvable
packages
to_list()[source]
append(requirement)[source]
exception galaxy.tools.deps.requirements.ToolRequirementsException[source]

Bases: exceptions.Exception

class galaxy.tools.deps.requirements.ContainerDescription(identifier=None, type='docker', resolve_dependencies=False, shell='/bin/sh')[source]

Bases: object

__init__(identifier=None, type='docker', resolve_dependencies=False, shell='/bin/sh')[source]
to_dict()[source]
static from_dict(dict)[source]
galaxy.tools.deps.requirements.parse_requirements_from_dict(root_dict)[source]
galaxy.tools.deps.requirements.parse_requirements_from_xml(xml_root)[source]
>>> from xml.etree import ElementTree
>>> def load_requirements( contents ):
...     contents_document = '''<tool><requirements>%s</requirements></tool>'''
...     root = ElementTree.fromstring( contents_document % contents )
...     return parse_requirements_from_xml( root )
>>> reqs, containers = load_requirements('''<requirement>bwa</requirement>''')
>>> reqs[0].name
'bwa'
>>> reqs[0].version is None
True
>>> reqs[0].type
'package'
>>> reqs, containers = load_requirements('''<requirement type="binary" version="1.3.3">cufflinks</requirement>''')
>>> reqs[0].name
'cufflinks'
>>> reqs[0].version
'1.3.3'
>>> reqs[0].type
'binary'
galaxy.tools.deps.requirements.container_from_element(container_elem)[source]

galaxy.tools.deps.singularity_util module

galaxy.tools.deps.singularity_util.pull_mulled_singularity_command(docker_image_identifier, cache_directory, namespace=None, singularity_cmd='singularity', sudo=False, sudo_cmd='sudo')[source]
galaxy.tools.deps.singularity_util.build_singularity_run_command(container_command, image, volumes=[], env=[], working_directory=None, singularity_cmd='singularity', run_extra_arguments=None, sudo=False, sudo_cmd='sudo')[source]

galaxy.tools.deps.views module

class galaxy.tools.deps.views.DependencyResolversView(app)[source]

Bases: object

Provide a RESTfulish/JSONy interface to a galaxy.tools.deps.DependencyResolver object. This can be adapted by the Galaxy web framework or other web apps.

__init__(app)[source]
index()[source]
show(index)[source]
reload()[source]
manager_requirements()[source]
resolver_requirements(index)[source]
manager_dependency(**kwds)[source]
resolver_dependency(index, **kwds)[source]
show_dependencies(tool_requirements_d, installed_tool_dependencies=None)[source]

Resolves dependencies to build a requirements status in the admin panel/API

uninstall_dependencies(index=None, resolver_type=None, **payload)[source]

Attempt to uninstall requirements. Returns 0 if successfull, else None.

unused_dependency_paths

List dependencies that are not currently installed.

remove_unused_dependency_paths(envs)[source]

Remove dependencies that are not currently used.

Returns a list of all environments that have been successfully removed.

install_dependencies(requirements, **kwds)[source]
install_dependency(index=None, **payload)[source]

Installs dependency using highest priority resolver that supports dependency installation (Currently only the conda resolver supports this). If index is given, attempt installation directly using the corresponding resolver. Returns True on success, False on failure. payload is dictionary that must container name, version and type, e.g. {‘name’: ‘numpy’, version=‘1.9.1’, type=’package’}

installable_resolvers

List index for all active resolvers that have the ‘install_dependency’ attribute.

uninstallable_resolvers

List index for all active resolvers that can uninstall dependencies that have been installed through this resolver.

tool_ids_by_requirements

Dictionary with requirements as keys, and tool_ids as values.

toolbox_requirements_status
get_requirements_status(tool_requirements_d, installed_tool_dependencies=None)[source]
clean(index=None, **kwds)[source]