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docs/profiles/0.5-DRAFT/provenance_run_crate/index.md

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@@ -470,15 +470,15 @@ In some workflow systems (e.g., CWL, Galaxy), tools are typically wrappers for a
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While the `softwareRequirements` of a tool can [specify software dependencies](../process_run_crate#specifying-software-dependencies) (as above) in terms of naming software, a more reproducible definition of a tool's runtime environment may need to include a particular set of binaries that are compiled and/or distributed to work together. (Note that _runtime environment_ here refers to a set of software, configuration and other dependency files, not [environment variables](../workflow_run_crate#environment-variables-as-formal-parameters)).
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Some workflow engines support such package systems as a way to distribute tool dependencies, typically by referring to an _environment file_ which can be programmatically instansiated to retrieve and install a given set of binaries. In a Provenance Crate, environment files are indicated as `buildInstructions` for either the `HowToStep` (for a given step) or the `HowTo` (for the whole workflow).
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Some workflow engines support such package systems as a way to distribute tool dependencies, typically by referring to an _environment file_ which can be programmatically instantiated to retrieve and install a given set of binaries. In a Provenance Crate, environment files are indicated as `buildInstructions` for either the `HowToStep` (for a given step) or the `HowTo` (for the whole workflow).
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For instance, to indicate a [Conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) for a Nextflow workflow:
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```json
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{
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"@id": "main.nf",
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"@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow", "HowTo"],
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"name": "Hello world in Nexflow",
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"name": "Hello world in Nextflow",
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"programmingLanguage": {
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"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
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},
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```
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The `encodingFormat` and/or contextual identifier for `conformsTo` SHOULD be provided for machine-readable build/dependency environment fileds, but it is currently out of scope for this profile to list all possible package environment systems.
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The `encodingFormat` and/or contextual identifier for `conformsTo` SHOULD be provided for machine-readable build/dependency environment files, but it is currently out of scope for this profile to list all possible package environment systems.
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The term `buildInstructions` is taken from [CodeMeta terms](https://codemeta.github.io/terms/), which are [scheduled to be included](https://github.com/ResearchObject/ro-crate/pull/276) in the RO-Crate 1.2 JSON-LD context. For RO-Crate 1.1, the term must be added to the `@context` as:
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