auto-irida-uploader

Automated upload of sequence data into an IRIDA instance. Intended as a companion to the auto-irida-azure-upload tool.

Usage

usage: auto-irida-uploader [-h] [-c CONFIG] [--log-level LOG_LEVEL]

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
  --log-level LOG_LEVEL

The config file should have the following format:

{
    "excluded_runs_list": "/path/to/excluded_runs.csv",
    "runs_to_upload_dir": "/path/to/irida_runs_to_upload",
    "scan_interval_seconds": 60,
    "irida_base_url": "https://your.irida.server.ca/irida/api/",
    "irida_username": "uploader",
    "irida_password": "s3cr3tpa$$w0rd",
    "irida_client_id": "uploader",
    "irida_client_secret": "cli3nts3cr3t",
    "parser": "directory"
}

...where the excluded_runs_list is simply a list of sequencing run IDs that should be excluded from uploads:

230812_M00123_126_000000000-AG4BE
230930_VH00234_45_AAE46WTN0

the runs_to_upload_dir should be the directory where azure-based uploads are deposited.