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Class SoftwarePackage

Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage

Hierarchy

  • Saveable
    • SoftwarePackage

Implements

Index

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

package_

package_: string

The name of the software to be made available. If the name is common, inconsistent, or otherwise ambiguous it should be combined with one or more identifiers in the specs field.

Optional specs

specs?: string[]

One or more IRIs identifying resources for installing or enabling the software named in the package field. Implementations may provide resolvers which map these software identifer IRIs to some configuration action; or they can use only the name from the package field on a best effort basis.

For example, the IRI https://packages.debian.org/bowtie could be resolved with apt-get install bowtie. The IRI https://anaconda.org/bioconda/bowtie could be resolved with conda install -c bioconda bowtie.

IRIs can also be system independent and used to map to a specific software installation or selection mechanism. Using RRID as an example: https://identifiers.org/rrid/RRID:SCR_005476 could be fulfilled using the above mentioned Debian or bioconda package, a local installation managed by Environment Modules, or any other mechanism the platform chooses. IRIs can also be from identifer sources that are discipline specific yet still system independent. As an example, the equivalent ELIXIR Tools and Data Service Registry IRI to the previous RRID example is https://bio.tools/tool/bowtie2/version/2.2.8. If supported by a given registry, implementations are encouraged to query these system independent sofware identifier IRIs directly for links to packaging systems.

A site specific IRI can be listed as well. For example, an academic computing cluster using Environment Modules could list the IRI https://hpc.example.edu/modules/bowtie-tbb/1.22 to indicate that module load bowtie-tbb/1.1.2 should be executed to make available bowtie version 1.1.2 compiled with the TBB library prior to running the accompanying Workflow or CommandLineTool. Note that the example IRI is specific to a particular institution and computing environment as the Environment Modules system does not have a common namespace or standardized naming convention.

This last example is the least portable and should only be used if mechanisms based off of the package field or more generic IRIs are unavailable or unsuitable. While harmless to other sites, site specific software IRIs should be left out of shared CWL descriptions to avoid clutter.

Optional version

version?: string[]

The (optional) versions of the software that are known to be compatible.

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>
  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • Used to construct instances of .

    throws

    ValidationException If the document fragment is not a {@link Dictionary} or validation of fields fails.

    Parameters

    • __doc: any

      Document fragment to load this record object from.

    • baseuri: string

      Base URI to generate child document IDs against.

    • loadingOptions: LoadingOptions

      Context for loading URIs and populating objects.

    • Optional docRoot: string

      ID at this position in the document (if available)

    Returns Promise<Saveable>

    An instance of

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