Galaxy workflow converter

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Revision as of 21:01, 10 November 2022 by Twang9 (talk | contribs) (→‎Validation)
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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
      Screen Shot 2022-11-09 at 16.38.10.png
    7. If they encountered errors, will show as the figure below:
      Screen Shot 2022-11-09 at 16.46.07.png
      • 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.