A Snakemake storage plugin to read and write from Azure Blob Storage
Project description
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://"
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