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.container_resolvers package

The module defines the abstract interface for resolving container images for tool execution.

class galaxy.tools.deps.container_resolvers.ContainerResolver(app_info=None, **kwds)[source]

Bases: galaxy.util.dictifiable.Dictifiable, object

Description of a technique for resolving container images for tool execution.

dict_collection_visible_keys = ['resolver_type']
__init__(app_info=None, **kwds)[source]

Default initializer for ContainerResolver subclasses.

resolve(tool_info)[source]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tools.deps.containers.ToolInfo description of the tool and its requirements.

resolver_type

Short label for the type of container resolution.

Submodules

galaxy.tools.deps.container_resolvers.explicit module

This module describes the ExplicitContainerResolver ContainerResolver plugin.

class galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver(app_info=None, **kwds)[source]

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

Find explicit containers referenced in the tool description (e.g. tool XML file) if present.

resolver_type = 'explicit'
resolve(enabled_container_types, tool_info)[source]

Find a container explicitly mentioned in tool description.

This ignores the tool requirements and assumes the tool author crafted a correct container.

galaxy.tools.deps.container_resolvers.mulled module

This module describes the MulledContainerResolver ContainerResolver plugin.

class galaxy.tools.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver(app_info=None, namespace='biocontainers', hash_func='v2')[source]

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

resolver_type = 'cached_mulled'
container_type = 'docker'
__init__(app_info=None, namespace='biocontainers', hash_func='v2')[source]
resolve(enabled_container_types, tool_info)[source]
class galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver(app_info=None, hash_func='v2')[source]

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

resolver_type = 'cached_mulled_singularity'
container_type = 'singularity'
__init__(app_info=None, hash_func='v2')[source]
resolve(enabled_container_types, tool_info)[source]
class galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver(app_info=None, namespace='biocontainers', hash_func='v2')[source]

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

Look for mulled images matching tool dependencies.

resolver_type = 'mulled'
container_type = 'docker'
__init__(app_info=None, namespace='biocontainers', hash_func='v2')[source]
resolve(enabled_container_types, tool_info)[source]
class galaxy.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver(app_info=None, namespace='local', hash_func='v2', **kwds)[source]

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

Build for Docker mulled images matching tool dependencies.

resolver_type = 'build_mulled'
container_type = 'docker'
__init__(app_info=None, namespace='local', hash_func='v2', **kwds)[source]
resolve(enabled_container_types, tool_info)[source]
class galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver(app_info=None, hash_func='v2', **kwds)[source]

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

Build for Singularity mulled images matching tool dependencies.

resolver_type = 'build_mulled_singularity'
container_type = 'singularity'
__init__(app_info=None, hash_func='v2', **kwds)[source]
resolve(enabled_container_types, tool_info)[source]