snakemake-storage-plugin-azure 0.1.6

A Snakemake storage plugin to read and write from Azure Blob Storage

Snakemake Storage Plugin Azure

Azure Blob Storage plugin for snakemake.

Testing

Testing this plugin locally require the azurite storage emulator to be running locally. This can be setup using the following docker run command:

docker run -p 10000:10000 mcr.microsoft.com/azure-storage/azurite azurite-blob --blobHost 0.0.0.0

Then execute the tests:

poetry run coverage run -m pytest tests/tests.py

Example

The below example Snakefile will stream a file, test.txt, containing the text "Hello, World" to the azure blob: https://account.blob.core.windows.net/container/tests.txt

rule touch:
    output: "account/container/test.txt"
    shell:
        "echo 'Hello, World!' > {output}"

Command:

snakemake --default-storage-provider azure --storage-azure-endpoint-url https://account.blob.core.windows.net --verbose --default-storage-prefix "az://"