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Deploy a Nextflow genomics cluster

Lawrence Gripper 提供
上次更新日期: 2020/4/24

This template deploys a scalable Nextflow cluster with a Jumpbox, n cluster nodes, docker support and shared storage.

此 Azure Resource Manager (ARM) 範本是由社群成員 (而非 Microsoft) 建立。每個 ARM 範本都是由其擁有者 (而非 Microsoft) 依據授權合約授權給您。Microsoft 並不負責社群成員所提供和授權的 ARM 範本,而不會為了安全性、相容性或效能進行篩選。社群 ARM 範本並未依據任何 Microsoft 支援方案或服務提供支援,而且會在沒有任何擔保的情況下依現況提供。

參數

參數名稱 說明
location Location for all resources
dnsNameForJumpBox Unique DNS Name for the Public IP used to access the Docker Virtual Machine (master node).
vmImageReference The image to use for VMs created. This can be marketplace or custom image
vmNodeSku Size of VMs in the VM Scale Set.
vmMasterSku Size of the master node.
vmMasterDiskType Choose between a standard disk for and SSD disk for the master node's NFS fileshare
vmMasterDiskSize The SSD Size to be used for the NFS file share. For pricing details see https://azure.microsoft.com/en-us/pricing/details/managed-disks/
vmAdditionalInstallScriptUrl An additional installs script (bash run as root) to be run after nodes/master are configured. Can be used to mount additional storage or do additional setup
vmAdditionalInstallScriptArgument An argument to be passed to the additional install script
nextflowInstallUrl The install URL for nextflow, this can be used to pin nextflow versions
instanceCount Number of cluster VM instances (100 or less).
adminUsername Admin username on all VMs.
vnetName Name of the virtual network to deploy the scale set into.
subnetName Name of the subnet to deploy the scale set into.
shareName Azure file share name.
mountpointPath Path on VM to mount file shares. '/datadisks/disk1/' is a Premium Managed disk with high iops, this will suit most uses.
nodeMaxCpus Sets the cluster.maxCpus setting on all cluster nodes
forceUpdateTag Determines whether to run the custom script extension on a subsequent deployment. Use the defaultValue.
_artifactsLocation *Advanced* This is best left as default unless you are an advanced user. The base URI where artifacts required by this template are located.
_artifactsLocationSasToken *Advanced* This should be left as default unless you are an advanced user. The sasToken required to access _artifactsLocation. When the template is deployed using the accompanying scripts, a sasToken will be automatically generated.
_diskInitScriptUri *Advanced* This should be left as default unless you are an advanced user. The folder in the artifacts location were shared scripts are stored.
_artifactsNextflowFolder *Advanced* This should be left as default unless you are an advanced user. The folder in the artifacts location were nextflow scripts are stored.
authenticationType Type of authentication to use on the Virtual Machine. SSH key is recommended.
adminPasswordOrKey SSH Key or password for the Virtual Machine. SSH key is recommended.

使用範本

PowerShell

New-AzResourceGroup -Name <resource-group-name> -Location <resource-group-location> #use this command when you need to create a new resource group for your deployment
New-AzResourceGroupDeployment -ResourceGroupName <resource-group-name> -TemplateUri https://raw.githubusercontent.com/Azure/azure-quickstart-templates/master/nextflow-genomics-cluster-ubuntu/azuredeploy.json
安裝和設定 Azure PowerShell

命令列

az group create --name <resource-group-name> --location <resource-group-location> #use this command when you need to create a new resource group for your deployment
az group deployment create --resource-group <my-resource-group> --template-uri https://raw.githubusercontent.com/Azure/azure-quickstart-templates/master/nextflow-genomics-cluster-ubuntu/azuredeploy.json
安裝和設定 Azure 跨平台命令列介面