Running Toolchest asynchronously using the run_id

async_toolchest.py

import time
import toolchest_client as toolchest
toolchest.set_key("YOUR_KEY_HERE")

#
# Toolchest call #1: initiate the run
#
toolchest_run = toolchest.kraken2(
    tool_args="--minimum-base-quality 25",
    read_one="s3://toolchest-demo-data/SRR16201572_R1.fastq",
    custom_database_path="s3://toolchest-fsx-databases/kraken2/k2_viral_20210517/",
    is_async=True,
)

run_id = toolchest_run.run_id

run_status = toolchest.get_status(run_id=run_id)

while run_status != toolchest.Status.READY_TO_TRANSFER_TO_CLIENT:
    print("Current run status: ", run_status)
    print("Run not done yet. Waiting another fifteen seconds before checking again...")
    time.sleep(15)

    #
    # Key Toolchest call #2: check status
    #
    run_status = toolchest.get_status(run_id=run_id)
    if run_status == toolchest.Status.FAILED:
        print("Toolchest run failed. See logs for more details.")


print("Done! Downloading...")
#
# Key Toolchest call #3: download the files
#
toolchest.download(
    output_path='/tmp',
    run_id=run_id,
)

print("Downloaded!")