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update README.md
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AlexDo1 committed Nov 14, 2022
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Expand Up @@ -16,15 +16,15 @@ Each container needs at least the following structure:
```
/
|- in/
| |- tool.json
| |- parameters.json
|- out/
| |- ...
|- src/
| |- tool.yml
| |- run.py
```

* `tool.json` are parameters. Whichever framework runs the container, this is how parameters are passed.
* `parameters.json` are parameters. Whichever framework runs the container, this is how parameters are passed.
* `tool.yml` is the tool specification. It contains metadata about the scope of the tool, the number of endpoints (functions) and their parameters
* `run.py` is the tool itself, or a Python script that handles the execution. It has to capture all outputs and either `print` them to console or create files in `/out`

Expand All @@ -45,9 +45,9 @@ in the repository secrets in order to run properly.

## How to run?

This template installs the toolbox-runner python package to parse the parameters in the `/in/tool.json`. This assumes that
This template installs the json2args python package to parse the parameters in the `/in/parameters.json`. This assumes that
the files are not renamed and not moved and there is actually only one tool in the container. For any other case, the environment variables
`PARAM_FILE` can be used to specify a new location for the `tool.json` and `TOOL_RUN` can be used to specify the tool to be executed.
`PARAM_FILE` can be used to specify a new location for the `parameters.json` and `TOOL_RUN` can be used to specify the tool to be executed.
The `run.py` has to take care of that.

To invoke the docker container directly run something similar to:
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