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Define buildInstructions in profile
.. as it's not in RO-Crate 1.1
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docs/profiles/0.5-DRAFT/provenance_run_crate/index.md

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@@ -468,7 +468,7 @@ In some workflow systems (e.g., CWL, Galaxy), tools are typically wrappers for a
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## Tool runtime environment
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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.
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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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docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-metadata.json

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{ "@id": "https://w3id.org/ro/terms/workflow-run#ParameterConnection" },
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{ "@id": "https://w3id.org/ro/terms/workflow-run#connection" },
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{ "@id": "https://w3id.org/ro/terms/workflow-run#sourceParameter" },
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{ "@id": "https://w3id.org/ro/terms/workflow-run#targetParameter" }
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{ "@id": "https://w3id.org/ro/terms/workflow-run#targetParameter" },
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{ "@id": "https://codemeta.github.io/terms/buildInstructions" }
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],
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"hasResource": [
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{ "@id": "#hasSpecification" },
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"inDefinedTermSet": { "@id": "https://w3id.org/ro/terms/workflow-run#" },
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"description": "The target (upstream) parameter"
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},
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{
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"@id": "https://codemeta.github.io/terms/buildInstructions",
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"@type": "DefinedTerm",
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"name": "buildInstructions",
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"termCode": "buildInstructions",
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"description": "Build environment file (e.g. for Conda)",
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"inDefinedTermSet": { "@id": "https://codemeta.github.io/terms/" }
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},
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{
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"@id": "https://codemeta.github.io/terms/",
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"@type": "DefinedTermSet",
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"name": "Codemeta Terms",
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"url": "https://codemeta.github.io/terms/",
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"version": "3.0"
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},
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{
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"@id": "https://pypi.org/project/runcrate/",
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"@type": "SoftwareApplication",

docs/profiles/0.5-DRAFT/provenance_run_crate/ro-crate-preview.html

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},
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{
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"@id": "https://w3id.org/ro/terms/workflow-run#targetParameter"
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},
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{
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"@id": "https://codemeta.github.io/terms/buildInstructions"
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}
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],
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"hasResource": [
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},
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"description": "The target (upstream) parameter"
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},
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{
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"@id": "https://codemeta.github.io/terms/buildInstructions",
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"@type": "DefinedTerm",
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"name": "buildInstructions",
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"termCode": "buildInstructions",
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"description": "Build environment file (e.g. for Conda)",
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"inDefinedTermSet": {
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"@id": "https://codemeta.github.io/terms/"
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}
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},
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{
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"@id": "#hasSpecification",
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"@type": "ResourceDescriptor",
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"@type": "Person",
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"name": "Salvador Capella-Gutierrez"
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},
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{
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"@id": "https://codemeta.github.io/terms/",
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"@type": "DefinedTermSet",
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"name": "Codemeta Terms",
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"url": "https://codemeta.github.io/terms/",
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"version": "3.0"
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},
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{
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"@id": "http://schema.org/MediaObject",
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"@type": "DefinedTerm",
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<li><a href="#https%3A//w3id.org/ro/terms/workflow-run%23sourceParameter">source parameter</a></li>
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<li><a href="#https%3A//w3id.org/ro/terms/workflow-run%23targetParameter">target parameter</a></li>
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<li><a href="#https%3A//codemeta.github.io/terms/buildInstructions">buildInstructions</a></li>
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</ul></td>
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</tr><tr>
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<th style="text-align:left;" class="prop">hasResource<span>&nbsp;</span><a href="http://www.w3.org/ns/dx/prof/hasResource">[?]</a></th>
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</table>
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</div>
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</div>
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<hr/><br/><br/>
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<div>
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<h3><a href="https://codemeta.github.io/terms/buildInstructions">Go to: </a> buildInstructions</h3>
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<div id="https://codemeta.github.io/terms/buildInstructions">
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<table class="table metadata table-striped" >
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<tbody><tr>
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<th style="text-align:left;" class="prop">@id</th>
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<td style='text-align:left'><a href="https://codemeta.github.io/terms/buildInstructions">https://codemeta.github.io/terms/buildInstructions</a></td>
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</tr><tr>
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<th style="text-align:left;" class="prop">name<span>&nbsp;</span><a href="http://schema.org/name">[?]</a></th>
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<td style='text-align:left'><span>buildInstructions</span></td>
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</tr><tr>
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<th style="text-align:left;" class="prop">@type</th>
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<td style='text-align:left'><span>DefinedTerm</span></td>
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</tr><tr>
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<th style="text-align:left;" class="prop">description<span>&nbsp;</span><a href="http://schema.org/description">[?]</a></th>
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<td style='text-align:left'><span>Build environment file (e.g. for Conda)</span></td>
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</tr><tr>
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<th style="text-align:left;" class="prop">termCode<span>&nbsp;</span><a href="http://schema.org/termCode">[?]</a></th>
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<td style='text-align:left'><span>buildInstructions</span></td>
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</tr><tr>
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<th style="text-align:left;" class="prop">inDefinedTermSet<span>&nbsp;</span><a href="http://schema.org/inDefinedTermSet">[?]</a></th>
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<td style='text-align:left'><a href="#https%3A//codemeta.github.io/terms/">Codemeta Terms</a></td>
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</tr><tr><th colspan="2" style="text-align:center">Items that reference this one</th><tr><tr>
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<th style="text-align:left;" class="prop">hasPart<span>&nbsp;</span><a href="http://schema.org/hasPart">[?]</a></th>
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<td style='text-align:left'><a href="#https%3A//w3id.org/ro/wfrun/provenance/0.5-DRAFT">Provenance Run Crate profile</a></td>
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</tr></tbody>
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</table>
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</div>
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</div>
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<hr/><br/><br/>
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<div>

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