This is a Command Line Tool that allows for the manipulation of BioCompute Objects. Serveral functionalites are provided (detailed more below in supported modes).
Run the Git Clone command in the location you would like the repostory:
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cd path/to/my/github/repositories
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git clone https://github.com/HadleyKing/bco-tool.git
Add the main bco-tool program to your path
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cd bco-tool
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pip install -r requirements.txt
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cp bco-tool/bco_runner.py /usr/local/bin/bco
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convert - takes a BCO and converts it to the current BCO standard: ieee-2791-schema. Can optionally provide a mapping file to specify mapping fields (template generated through map function), otherwise default mappingis performed.
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validate - takes a BCO and validates it against a schema. Can provide a schema, otherwise ieee-2791-schema is used.
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map - takes a BCO and generates a template mapping file to use for convert method.
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license - takes a BCO and gives a license.
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functions - Lists all functions in app.
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run_cwl - taks a BCO describing a CWL Workflow and runs it
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--help/-h - gives detailed help message
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--version/-v - gives information about version
- --schema/-s - provides schema for the validate, convert, or map functions, to check BCO against. Default schema is ieee-2971-schema.
- --bco/b - URL or path to JSON file of BCO to manipulate.
- --mappingFile/-m - path to mapping file to use for convert function.