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OpenCGA uses ARM template to auto deploy a pool with preconfigured opencga docker image. This pool is "AutoScale" enabled so will scale as number of variant index jobs will grow. These ARM script will also populate the following section in "configuration.yml"  which are enables OpenCGA daemon to submit job (azure task) to Azure Batch Service. Once an OpenGCA index job is created, it ll be prepared and then OpenCGA dameon will submit it to the Azure Batch Service for execution.

Configuration 

....
execution:
  mode: AZURE
	...
  options:
    #Azure Batch Service information
    batchAccount : "batchAccount"
    batchKey : "batchKey"
    batchUri : "https://batchservice.uksouth.batch.azure.com"
    batchPoolId : "poolId"
    dockerImageName : "openCGADockerImageName" # preconfigured docker image
    dockerArgs : "dockerRunOptions"   # e,g; mount points etc.
....

...

./opencga.sh files link -i ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -s "sudy" 
./opencga.sh variant index --file ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --calculate-stats --annotate -o tmp

If OpenCGA daemon is not running, user can start it with the following command:

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