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Deploy a Nextflow genomics cluster

Lawrence Gripper 提供
上次更新时间: 2018/6/14

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

此 Azure Resource Manager (ARM) 模板由社区的某个成员(而不是由 Microsoft)创建。每个 ARM 模板都根据其所有者(不是 Microsoft)的许可协议向你授予许可。Microsoft 不对由社区成员提供并授予许可的 ARM 模板负责,并且不针对安全性、兼容性和性能进行筛选。社区 ARM 模板不由任何 Microsoft 支持计划或服务提供支持,按“原样”提供,没有任何种类的担保。

参数

参数名 说明
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 VMs in the VM Scale Set.
vmMasterDiskType Choose between a standard disk for and SSD disk for the master nodes 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.
adminPassword Admin password 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
_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.
_artifactsSharedFolder *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 teh artifacts location were nextflow scripts are stored.

使用模板

PowerShell

New-AzureRmResourceGroupDeployment -Name <deployment-name> -ResourceGroupName <resource-group-name> -TemplateUri https://raw.githubusercontent.com/Azure/azure-quickstart-templates/master/nextflow-genomics-cluster-ubuntu/azuredeploy.json
安装和配置 Azure PowerShell

命令行

azure config mode arm
azure group deployment create <my-resource-group> <my-deployment-name> --template-uri https://raw.githubusercontent.com/Azure/azure-quickstart-templates/master/nextflow-genomics-cluster-ubuntu/azuredeploy.json
安装和配置 Azure 跨平台命令行界面