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:

Choose location for repository
```
 cd path/to/my/github/repositories
```

Clone repo

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

To add the main bco-tool program to your path

Enter directory
```
 cd bcotool
```
Create and/or activate a python virtual environment:
```
 virtualenv [path_to_environment]
```
Install requirements in the virtual environment
```
 pip install -r requirements.txt
```
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.