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Add spec on software dependencies #67

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Nov 23, 2023
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Add spec on software dependencies #67

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0adcb78
add spec on software dependencies
simleo Nov 23, 2023
79e4977
Update process_run_crate.md
stain Nov 23, 2023
130bd75
Update process_run_crate.md
stain Nov 23, 2023
bf68f1f
Update provenance_run_crate.md
stain Nov 23, 2023
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21 changes: 21 additions & 0 deletions docs/profiles/0.4-DRAFT/process_run_crate.md
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Expand Up @@ -466,3 +466,24 @@ Alternatively, the `containerImage` could point to a `URL`. For instance:
"containerImage": "https://example.com/samtools.sif"
}
```


## Specifying software dependencies

Software dependencies MAY be specified using `softwareRequirements` to a `SoftwareApplication`:

```json
{
"@id": "script.py",
"@type": "SoftwareApplication",
"name": "Analysis Script",
"version": "0.1",
"softwareRequirements": {"@id": "https://pypi.org/project/numpy/1.26.2/"}
},
{
"@id": "https://pypi.org/project/numpy/1.26.2/",
"@type": "SoftwareApplication",
"name": "NumPy",
"version": "1.26.2"
}
```
28 changes: 28 additions & 0 deletions docs/profiles/0.4-DRAFT/provenance_run_crate.md
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Expand Up @@ -426,6 +426,34 @@ A workflow engine may support configuration through a configuration file. In thi
See also the [section on referencing configuration files of executed tools](process_run_crate#referencing-configuration-files).


## Tool wrapper dependencies

In some workflow systems (e.g., CWL, Galaxy), tools are typically wrappers for an executable written in a scripting programming language. This MAY be represented by listing the wrapped tool and its dependencies as described in [Specifying software dependencies](process_run_crate#specifying-software-dependencies). The wrapped tool can be highlighted by using `mainEntity`:

```json
{
"@id": "data_analysis_tool.cwl",
"@type": "SoftwareApplication",
"softwareRequirements": [
{"@id": "scripts/data_analysis_script.py"},
{"@id": "https://pypi.org/project/numpy/1.26.2/"}
],
"mainEntity": {"@id": "scripts/data_analysis_script.py"}
},
{
"@id": "scripts/data_analysis_script.py",
"@type": "SoftwareApplication",
"version": "0.1"
},
{
"@id": "https://pypi.org/project/numpy/1.26.2/",
"@type": "SoftwareApplication",
"name": "NumPy",
"version": "1.26.2"
}
```


## Requirements

The requirements of this profile are those of [Workflow Run Crate](workflow_run_crate) plus the ones listed below.
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