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galaxy.tools.deps.container_resolvers package¶
The module defines the abstract interface for resolving container images for tool execution.
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class
galaxy.tools.deps.container_resolvers.
ContainerResolver
(app_info=None, **kwds)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
Description of a technique for resolving container images for tool execution.
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dict_collection_visible_keys
= ['resolver_type', 'can_uninstall_dependencies']¶
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can_uninstall_dependencies
= False¶
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resolve
(enabled_container_types, tool_info, **kwds)[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.
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resolver_type
¶ Short label for the type of container resolution.
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Submodules¶
galaxy.tools.deps.container_resolvers.explicit module¶
This module describes the ExplicitContainerResolver
ContainerResolver plugin.
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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.
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resolver_type
= 'explicit'¶
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class
galaxy.tools.deps.container_resolvers.explicit.
ExplicitSingularityContainerResolver
(app_info=None, **kwds)[source]¶ Bases:
galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver
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resolver_type
= 'explicit_singularity'¶
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container_type
= 'singularity'¶
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resolve
(enabled_container_types, tool_info, **kwds)[source]¶ Find a container explicitly mentioned in tool description.
This ignores the tool requirements and assumes the tool author crafted a correct container. We use singularity here to fetch docker containers, hence the container_description hack here.
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galaxy.tools.deps.container_resolvers.mulled module¶
This module describes the MulledContainerResolver
ContainerResolver plugin.
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class
galaxy.tools.deps.container_resolvers.mulled.
CachedMulledDockerContainerResolver
(app_info=None, namespace='biocontainers', hash_func='v2', **kwds)[source]¶ Bases:
galaxy.tools.deps.container_resolvers.ContainerResolver
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resolver_type
= 'cached_mulled'¶
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container_type
= 'docker'¶
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shell
= '/bin/bash'¶
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class
galaxy.tools.deps.container_resolvers.mulled.
CachedMulledSingularityContainerResolver
(app_info=None, hash_func='v2', **kwds)[source]¶ Bases:
galaxy.tools.deps.container_resolvers.ContainerResolver
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resolver_type
= 'cached_mulled_singularity'¶
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container_type
= 'singularity'¶
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shell
= '/bin/bash'¶
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class
galaxy.tools.deps.container_resolvers.mulled.
MulledDockerContainerResolver
(app_info=None, namespace='biocontainers', hash_func='v2', auto_install=True, **kwds)[source]¶ Bases:
galaxy.tools.deps.container_resolvers.ContainerResolver
Look for mulled images matching tool dependencies.
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resolver_type
= 'mulled'¶
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container_type
= 'docker'¶
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shell
= '/bin/bash'¶
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protocol
= None¶
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class
galaxy.tools.deps.container_resolvers.mulled.
MulledSingularityContainerResolver
(app_info=None, namespace='biocontainers', hash_func='v2', auto_install=True, **kwds)[source]¶ Bases:
galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver
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resolver_type
= 'mulled_singularity'¶
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container_type
= 'singularity'¶
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protocol
= 'docker://'¶
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class
galaxy.tools.deps.container_resolvers.mulled.
BuildMulledDockerContainerResolver
(app_info=None, namespace='local', hash_func='v2', auto_install=True, **kwds)[source]¶ Bases:
galaxy.tools.deps.container_resolvers.ContainerResolver
Build for Docker mulled images matching tool dependencies.
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resolver_type
= 'build_mulled'¶
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container_type
= 'docker'¶
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shell
= '/bin/bash'¶
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class
galaxy.tools.deps.container_resolvers.mulled.
BuildMulledSingularityContainerResolver
(app_info=None, hash_func='v2', auto_install=True, **kwds)[source]¶ Bases:
galaxy.tools.deps.container_resolvers.ContainerResolver
Build for Singularity mulled images matching tool dependencies.
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resolver_type
= 'build_mulled_singularity'¶
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container_type
= 'singularity'¶
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shell
= '/bin/bash'¶
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