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.
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.
The (optional) versions of the software that are known to be compatible.
Document fragment to load this record object from.
Base URI to generate child document IDs against.
Context for loading URIs and populating objects.
ID at this position in the document (if available)
Generated using TypeDoc
Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage