Snakemake Storage Plugin Azure

Azure Blob Storage plugin for snakemake. For documentation and usage instructions, see the Snakemake Plugin Catalog.

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 and command will stream a file, test.txt, containing the text "Hello, World" to the azure blob: https://accountname.blob.core.windows.net/container/test.txt

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

Command:

The storage account and container that the output file is streamed to is specified using the default-storage-prefix.

snakemake -j1 \
    --default-storage-provider azure \
    --default-storage-prefix "az://container"
    --storage-azure-account-name accountname \
    --verbose