Galaxy workflow converter: Difference between revisions

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## <code>python bcotool/bco_runner.py validate -b [path to the converted file]</code> (Note: if only run <code>python bcotool/bco_runner.py</code>, more options can be seen.) If passed validation should show as the figure below [[File:Screen Shot 2022-11-09 at 16.38.10.png|800px|thumb|center]]
## <code>python bcotool/bco_runner.py validate -b [path to the converted file]</code> (Note: if only run <code>python bcotool/bco_runner.py</code>, more options can be seen.) If passed validation should show as the figure below [[File:Screen Shot 2022-11-09 at 16.38.10.png|800px|thumb|center]]
## If they encountered errors, will show as the figure below: [[File:Screen Shot 2022-11-09 at 16.46.07.png|800px|thumb|center]]
## If they encountered errors, will show as the figure below: [[File:Screen Shot 2022-11-09 at 16.46.07.png|800px|thumb|center]]
##* Open error log for error description: <code>open error.log</code>

Revision as of 18:58, 10 November 2022

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. cd bcotool/
    3. python -m venv env
    4. . env/bin/activate
    5. pip install -r requirements.txt
    6. 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