`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`(...[, ...])
`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(builder, command)

Parameters:

builder (cwltool.builder.Builder) –
command (List[str]) –

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, container_image_cache_path='.')