galaxy.tools.deps.container_resolvers package

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)

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

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

resolve(enabled_container_types, tool_info)

Find a container explicitly mentioned in tool description.

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

resolver_type = 'explicit'

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')

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

container_type = 'docker'

resolve(enabled_container_types, tool_info)

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 = 'cached_mulled'

class galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver(app_info=None, hash_func='v2', **kwds)

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

container_type = 'singularity'

resolve(enabled_container_types, tool_info)

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 = 'cached_mulled_singularity'

class galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver(app_info=None, namespace='biocontainers', hash_func='v2')

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

Look for mulled images matching tool dependencies.

container_type = 'docker'

resolve(enabled_container_types, tool_info)

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 = 'mulled'

class galaxy.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver(app_info=None, namespace='local', hash_func='v2', **kwds)

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

Build for Docker mulled images matching tool dependencies.

container_type = 'docker'

resolve(enabled_container_types, tool_info)

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 = 'build_mulled'

class galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver(app_info=None, hash_func='v2', **kwds)

Bases: galaxy.tools.deps.container_resolvers.ContainerResolver

Build for Singularity mulled images matching tool dependencies.

container_type = 'singularity'

resolve(enabled_container_types, tool_info)

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 = 'build_mulled_singularity'

Module contents

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

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

Bases: galaxy.util.dictifiable.Dictifiable

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

dict_collection_visible_keys = ['resolver_type']

resolve(tool_info)

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.