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Switch to the region intended to deploy Partek ^® Flow^®  software. This tutorial uses US East (N. Virginia) as an example. 

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Click the Select button next to Ubuntu Server 16.04 LTS (HVM), SSD Volume Type - ami-f4cc1de2. NOTE: Please use the latest Ubuntu AMI. It is likely that the AMI listed here will be out of date.

Choose an Instance Type, the selection depends on your budget and the size of the Partek Flow deployment. We recommend m4.large for testing or cluster front-end operation, m4.xlarge for standard deployments, and m4.2xlarge for alignment-heavy workloads with a large user-base. See the section AWS instance type resources and costs for assistance with choosing the right instance. In most cases, the instance type and associated resources can be changed after deployment, so one is not locked into the choices made for this step. 

NOTE: New instance types will become available. Please use the latest mX instance type provided as it will likely perform better and be more cost effective than older instance types. 

On the Configure Instance Details page, make the following selections:

Set the number of instances to 1. An autoscaling group is not necessary for single-node deployments

Purchasing optionOption: Leave Request Spot instancesInstances unchecked. This is relevant for cost-minimization of Partek Flow cluster deployments.

Network: If you do not have a virtual private cloud (VPC) already created for Partek Flow, click Create new New VPC. This will open a new browser tab for VPC management. 

Use the following settings for the VPC:

Name tagTag: Flow-VPC

IPv4 CIDR block: 10.0.0.0/16

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Click Yes, Create. You may be asked to select a DHCP option Option set. If so, then make sure the DHCP option dynamic host configuration protocol (DHCP) option set has the following properties:

Options: domain-name = ec2.internal;domain-name-servers = AmazonProvidedDNS;

DNS resolutionResolution: leave the defaults set to yes

DNS hostnameHostname: change this to yes as internal DNS resolution may be necessary depending on the Partek Flow deployment

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Make sure the DHCP option set is set to the one created above. If it is not, right-click on the row containing Flow-VPC and select Edit DHCP option setsOption Sets.

Close the VPC managementManagement tab and go back to the EC2 management consoleManagement Console.

Click the refresh arrow next to Create new New VPC and select Flow-VPC.

Click Create new subnetNew Subnet and a new browser tab will open with a list of existing subnets. Click Create Subnet and set the following options:

Name tagTag: Flow-Subnet

VPC: Flow-VPC

VPC CIDRs: This should be automatically populated with the information from Flow-VPC

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IPv4 CIDR block: 10.0.1.0/24

Stay on the VPC dashboard tabDashboard Tab and on the left navigation menu, click Internet gatewaysGateways, then click Create Internet Gateway and use the following options:

Name tagTag: Flow-IGW

Click Yes, createCreate

The new gateway will be displayed as detached Detached. Right click on the Flow-IGW gateway and select Attach to VPC, then select Flow-VPC and click Yes, Attach.

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Click the refresh arrow next to Create new subnetNew Subnet and select Flow-Subnet.

Auto-assign public ipPublic IP: Use subnet setting (Disable)

Placement groupGroup: No placement group

IAM role: None.

Note: For multi-node Partek Flow deployments or instances where you would like Partek to manage AWS resources on your behalf, please see Partek AWS support and set up an IAM role for your Partek Flow EC2 instance. In most cases a specialized IAM role is unnecessary and we only need instance ssh keys.

Shutdown behaviourBehaviour: Stop

Enable termination protectionTermination Protection: select Protect against accidental termination

Monitoring: leave Enable CloudWatch detailed monitoringDetailed Monitoring disabled

EBS-optimized instanceInstance: Make sure Launch as EBS-optimized instanceInstance is enabled. Given the recommended choice of an m4 instance type, EBS optimization should be enabled at no extra cost. 

Tenancy: Shared - Run a shared hardware instance

Network interfacesInterfaces: leave as-is

Advanced detailsDetails: leave as-is

Click Next: Add storageStorage. You should be on Step 4: Add Storage

For the existing root volume, set the following options:

Size: 8 GB

Volume typeType: Magnetic

Select Delete on terminationTermination

Note: All Partek Flow data is stored on a non-root EBS volume. Since only the OS is on the root volume and not frequently re-booted, a fast root volume is probably not necessary or worth the cost. For more information about EBS volumes and their performance, see the section EBS volumes.

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Click Next: Configure Security Group

For Assign a security groupSecurity Group select Create a new security groupNew Security Group

Security group nameGroup Name: Flow-SG

Description: Security group for Partek Flow server

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The server should be assigned a fixed IP address. To do this, click on Elastic IPs on the left navigation menu from the EC2 management consoleManagement Console.

Click Allocate new addressNew Address

Assign Scope to VPC

Click Allocate

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Attach, format, and move the ubuntu home directory onto the large ST1 Elastic Block Store elastic block store (EBS) volume. All Partek Flow data will live in this volume. Consult the AWS EC2 documentation for further information about attaching EBS volumes to your instance.

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Note: Under Volumes in the EC2 management console, inspect Attachment informationInformation. It will likely list the large ST1 EBS volume as attached to /dev/sdb. Replace "s" with "xv" to find the device name to use for this mkfs command.

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Before beginning, send the media access control (MAC) address of the EC2 instance to MAC address of the EC2 instance to licensing@partek.com. The output of ifconfig will suffice. Given this information, Partek employees will create a license for your AWS server. MAC addresses will remain the same after stopping and starting the Partek Flow EC2 instance. If the MAC address does change, let our licensing department know and we can add your license to our floating license server or suggest other workarounds.

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$ sudo apt-get update

$ sudo apt-get install python perl install software-properties-common

$ sudo add-apt-repository -y ppa:openjdk-r/ppa

$ sudo apt-get install openjdk-8-jdk python python-pip python-dev zlib1g-dev python-matplotlib r-base python-htseq libxml2-dev perl make gcc g++ zlib1g libbz2-1.0 libstdc++6 libgcc1 libncurses5 libsqlite3-0 libfreetype6 libpng12-0 zip unzip libgomp1 libxrender1 libxtst6 libxi6 debconfdebconf 

$ sudo pip install --upgrade pip && pip install --upgrade --upgrade-strategy eager --force-reinstall virtualenv numpy pysam cnvkit

Install Partek Flow:

Note: Make sure you are running as the ubuntu user.

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Partek Flow has finished loading when you see INFO: Server startup in xxxxxxx ms in the partek_flow/logs/catalina.out log file. This takes ~30 seconds.

Alternative: Install Flow with Docker. Our base packages are located here: https://hub.docker.com/r/partekinc/flow/tags

Open Partek Flow with a web browser: http://elastic.ip:8080/

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After the EC2 instance is provisioned, we are happy to assist with setting up Partek Flow or address other issues you encounter with the usage of Partek Flow. The quickest way to receive help is to allow us remote access to your server by sending us Flow-Key.pem and amending the SSH rule for Flow-SG to include access from IP 97.84.41.194 (Partek HQ). We recommend sending us us the Flow-Key.pem via secure means. The easiest way to do this is with the following command:

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We also provide live assistance via GoTo meeting or TeamViewer if you are uncomfortable with us accessing your EC2 instance directly. Before contacting us, please run $ ./partek_flow/flowstatus.sh to send us logs and other information that will assist us with your support request.

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Note that EBS volumes can be grown or performance characteristics changed. To minimize costs, start with a smaller EBS volume allocation of 0.5 - 2 TB as most mature Partek Flow installations generate roughly this amount of data. When necessary, the EBS volume and the underlying file system can be grown on-line (making ext4 a good choice). Shrinking is also possible but may require the Partek Flow server to be offline. 

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