Galaxy workflow converter

Workflows can be directly downloaded from Galaxy but file conversion is needed in order to transfer into BCODB successfully. Please follow the following steps to convert the file and validation:

File conversion

1. Download the converter script from GitHub.
2. On the local terminal, run the following command python [converter script's name.py] -b [path to the file that needs to be converted] -o [path to the output file]

Validation

1. Install Validation Package:
   1. On the local terminal, clone the repository first by git clone https://github.com/biocompute-objects/bcotool
   2. Change directory: cd bcotool/
   3. Go to virtual environment: python -m venv env
   4. Activate virtual environment: . env/bin/activate
   5. Install required packages: pip install -r requirements.txt
   6. Run validation: python bcotool/bco_runner.py validate -b [path to the converted file] (Note: if only run python bcotool/bco_runner.py, more options can be seen.) If passed validation should show as the figure below
      
   7. If they encountered errors, will show as the figure below:
      
      • Open error log for error description: open error.log

Upload

1. Converted JSON file can be uploaded to BCODB through copy/pasting the RAW JSON file directly on BCO Builder or through API, refer to API documentation here.