cwltool.software_requirements

This module handles resolution of SoftwareRequirement hints.

This is accomplished mainly by adapting cwltool internals to galaxy-tool-util’s concept of “dependencies”. Despite the name, galaxy-tool-util is a light weight library that can be used to map SoftwareRequirements in all sorts of ways - Homebrew, Conda, custom scripts, environment modules. We’d be happy to find ways to adapt new packages managers and such as well.

Module Contents

Classes

DependenciesConfiguration

Dependency configuration class, for RuntimeContext.job_script_provider.

Functions

get_dependencies(builder)

get_container_from_software_requirements(use_biocontainers, builder)

ensure_galaxy_lib_available()

Attributes

ToolRequirement

SOFTWARE_REQUIREMENTS_ENABLED

COMMAND_WITH_DEPENDENCIES_TEMPLATE

cwltool.software_requirements.ToolRequirement
cwltool.software_requirements.SOFTWARE_REQUIREMENTS_ENABLED
cwltool.software_requirements.COMMAND_WITH_DEPENDENCIES_TEMPLATE
class cwltool.software_requirements.DependenciesConfiguration(args)

Dependency configuration class, for RuntimeContext.job_script_provider.

Parameters

args (argparse.Namespace) –

build_job_script(self, builder, command)
Parameters
Return type

str

cwltool.software_requirements.get_dependencies(builder)
Parameters

builder (cwltool.utils.HasReqsHints) –

Return type

galaxy.tool_util.deps.requirements.ToolRequirements

cwltool.software_requirements.get_container_from_software_requirements(use_biocontainers, builder)
Parameters
Return type

Optional[str]

cwltool.software_requirements.ensure_galaxy_lib_available()
Return type

None