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:

1. Choose location for repository

    cd path/to/my/github/repositories
   

2. Clone repo

    git clone https://github.com/biocompute-objects/bcotool.git
   

To add the main bco-tool program to your path

4. Enter directory

    cd bcotool
   

5. Create and/or activate a python virtual environment:

    virtualenv [path_to_environment]
   

6. Install requirements in the virtual environment

    pip install -r requirements.txt
   

7. Copy the exicutable program file to the user local bin:

    cp bco-tool/bco_runner.py  /usr/local/bin/bco
   

Supported modes

• 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.

• validate - takes a BCO and validates it against a schema. Can provide a schema, otherwise ieee-2791-schema is used.

• map - takes a BCO and generates a template mapping file to use for convert method.

• license - takes a BCO and gives a license.

• functions - Lists all functions in app.

• run_cwl - taks a BCO describing a CWL Workflow and runs it

• --help/-h - gives detailed help message

• --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.