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biigle_scripts

Utility scripts that use the BIIGLE API.

Installation

This package requires Python >= 3.7. It's recommended to work under a virtual environment, which could be set as follows:

virtualenv venv-biigle_scripts --python=python3.7
source venv-biigle_scripts/bin/activate

Installation procedure is the following:

git clone https://github.com/charleygros/biigle_scripts.git
cd biigle_scripts
pip install -e .

How to run a script

Type the script's name of interest in your terminal followed by -h to get its usage. For instance:

convert_laser_circle_to_point -h

... gives:

usage: convert_laser_circle_to_point -e EMAIL -t TOKEN -s SURVEY_NAME [-h]

MANDATORY ARGUMENTS:
  -e EMAIL, --email EMAIL
                        Email address used for BIIGLE account.
  -t TOKEN, --token TOKEN
                        BIIGLE API token. To generate one:
                        https://biigle.de/settings/tokens
  -s SURVEY_NAME, --survey-name SURVEY_NAME
                        Survey name, eg NBP1402.

OPTIONAL ARGUMENTS:
  -h, --help            Shows function documentation.