BCO-TOOL
This is a Command Line Tool that allows for the manipulation of BioCompute Objects. Serveral functionalites are provided (detailed more below in supported modes).
To install:
Run the Git Clone command in the location you would like the repostory:
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Choose location for repository
cd path/to/my/github/repositories
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Clone repo
git clone https://github.com/biocompute-objects/bcotool.git
To add the main bco-tool program to your path
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Enter directory
cd bcotool
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Create and/or activate a python virtual environment:
virtualenv [path_to_environment]
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Install requirements in the virtual environment
pip install -r requirements.txt
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Copy the exicutable program file to the user local bin:
cp bco-tool/bco_runner.py /usr/local/bin/bco
Supported modes
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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
Optional arguments
- --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.