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Deploy a Nextflow genomics cluster

Zuletzt aktualisiert: 14.06.2018

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

Diese ARM-Vorlage (Azure-Ressourcen-Manager) wurde von einem Mitglied der Community und nicht von Microsoft erstellt. Jede ARM-Vorlage wird für Sie von dessen Besitzer, nicht von Microsoft, unter einem Lizenzvertrag lizenziert. Microsoft übernimmt keine Zuständigkeiten für ARM-Vorlagen, die von Mitgliedern der Community bereitgestellt und lizenziert werden, und auch nicht für deren Sicherheit, Kompatibilität oder Leistung. ARM-Vorlagen aus der Community werden von keinem Microsoft-Supportprogramm oder -Dienst unterstützt und wie vorhanden ohne jegliche Gewährleistung zur Verfügung gestellt.

Parameter

Parametername Beschreibung
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.

Verwenden der Vorlage

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
Azure PowerShell installieren und konfigurieren

Befehlszeile

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
Installieren und Konfigurieren der plattformübergreifenden Azure-Befehlszeilenschnittstelle