As of version 0.2.82, pip installations of Hail come bundled with a command-line tool,
hdinsight for working with Microsoft Azure HDInsight Spark clusters configured for
This tool requires the Azure CLI.
An HDInsight cluster always consists of two “head” nodes, two or more “worker” nodes, and an Azure
Blob Storage container. The head nodes are automatically configured to serve Jupyter Notebooks at
https://CLUSTER_NAME.azurehdinsight.net/jupyter . The Jupyter server is protected by a
username-password combination. The username and password are printed to the terminal after the
cluster is created.
Every HDInsight cluster is associated with one storage account which your Jupyter notebooks may
access. In addition, HDInsight will create a container within this storage account (sharing a name
with the cluster) for its own purposes. When a cluster is stopped using
hailctl hdinsight stop,
this container will be deleted.
To start a cluster, you must specify the cluster name, a storage account, and a resource group. The storage account must be in the given resource group.
hailctl hdinsight start CLUSTER_NAME STORAGE_ACCOUNT RESOURCE_GROUP
To submit a Python job to that cluster, use:
hailctl hdinsight submit CLUSTER_NAME STORAGE_ACCOUNT HTTP_PASSWORD SCRIPT [optional args to your python script...]
To list running clusters:
hailctl hdinsight list
Importantly, to shut down a cluster when done with it, use:
hailctl hdinsight stop CLUSTER_NAME STORAGE_ACCOUNT RESOURCE_GROUP
Variant Effect Predictor (VEP)¶
The following cluster configuration enables Hail to run VEP in parallel on every variant in a dataset containing GRCh37 variants:
hailctl hdinsight start CLUSTER_NAME STORAGE_ACCOUNT RESOURCE_GROUP \ --vep GRCh37 \ --vep-loftee-uri https://STORAGE_ACCOUNT.blob.core.windows.net/CONTAINER/loftee-GRCh37 \ --vep-homo-sapiens-uri https://STORAGE_ACCOUNT.blob.core.windows.net/CONTAINER/homo-sapiens-GRCh37
Those two URIs must point at directories containing the VEP data files. You can populate them by
downloading the two tar files using
gs://hail-us-vep/homo-sapiens/85_GRCh37.tar, extracting them into a local folder, and uploading
that folder to your storage account using
az storage copy. The hail-us-vep Google Cloud Storage
bucket is a requester pays bucket which means you must pay the cost of transferring them out of
Google Cloud. We do not provide these files in Azure because Azure Blob Storage lacks an equivalent
cost control mechanism.
Hail also supports VEP for GRCh38 variants. The required tar files are located at
A cluster started without the
--vep argument is unable to run VEP and cannot be modified to run
VEP. You must start a new cluster using