Version: 23.1.0

Manual AWS Batch configuration

This document describes how to set up AWS roles and Batch queues manually for the deployment of Nextflow workloads using Tower Enterprise.

These steps are only needed if you want to create the AWS Batch resources manually. If you use the Batch Forge option, these steps are not needed, because Tower will automatically create the required Batch queues.

Create a user policy

Create the policy for the user launching Nextflow jobs:

Go to the IAM Console
Go to the Policy page

Create a new policy with the following content:

{
  "Version": "2012-10-17",
  "Statement": [
    {
      "Sid": "Stmt1530313170000",
      "Effect": "Allow",
      "Action": [
        "batch:CancelJob",
        "batch:RegisterJobDefinition",
        "batch:DescribeComputeEnvironments",
        "batch:DescribeJobDefinitions",
        "batch:DescribeJobQueues",
        "batch:DescribeJobs",
        "batch:ListJobs",
        "batch:SubmitJob",
        "batch:TerminateJob"
      ],
      "Resource": ["*"]
    }
  ]
}

Save with it the name nf-tower-user.

Create the instance role policy

Go to the IAM Console
Go to the Policy page

Create a new policy with the following content:

{
  "Version": "2012-10-17",
  "Statement": [
    {
      "Sid": "VisualEditor0",
      "Effect": "Allow",
      "Action": [
        "batch:DescribeJobQueues",
        "batch:CancelJob",
        "batch:SubmitJob",
        "batch:ListJobs",
        "batch:DescribeComputeEnvironments",
        "batch:TerminateJob",
        "batch:DescribeJobs",
        "batch:RegisterJobDefinition",
        "batch:DescribeJobDefinitions",
        "ecs:DescribeTasks",
        "ec2:DescribeInstances",
        "ec2:DescribeInstanceTypes",
        "ec2:DescribeInstanceAttribute",
        "ecs:DescribeContainerInstances",
        "ec2:DescribeInstanceStatus",
        "logs:Describe*",
        "logs:Get*",
        "logs:List*",
        "logs:StartQuery",
        "logs:StopQuery",
        "logs:TestMetricFilter",
        "logs:FilterLogEvents"
      ],
      "Resource": "*"
    }
  ]
}

Finally, save it with the name nf-tower-batchjob.

Create the Batch Service Role

This is a role used by AWS Batch to launch EC2 instances on your behalf.

Go to the IAM Console
Click on "Roles"
Click on "Create role"
Select "AWS service" as the trusted entity
Choose "Batch" as the service to use the role
Click "Next: Permissions"
In Attached permissions policies, the AWSBatchServiceRole will already be attached
Click "Next: Tags" (adding tags is optional)
Click "Next: Review"
Set the Role Name to nf-tower-servicerole
Finally, Click "Create role"

Create an EC2 Instance Role

This is a role that controls which AWS Resources EC2 instances launched by AWS Batch have access to. In this case, you will limit S3 access to just the bucket you created earlier.

Go to the IAM Console
Click on "Roles"
Click on "Create role"
Select "AWS service" as the trusted entity
Choose EC2 from the larger services list
Choose "EC2 - Allows EC2 instances to call AWS services on your behalf" as the use case.
Click "Next: Permissions"
- Type "ContainerService" in the search field for policies
- Click the checkbox next to AmazonEC2ContainerServiceforEC2Role to attach the policy
- Type "S3" in the search field for policies
- Click the checkbox next to AmazonS3FullAccess to attach the policy (you may want to use to use a custom policy to allow the access only on specific S3 buckets)
Search and attach the custom policy nf-tower-batchjob
Click "Next: Tags". (adding tags is optional)
Click "Next: Review"
Set the Role Name to nf-tower-instancerole
Finally, Click "Create role"

Create an EC2 SpotFleet Role

This is a role that allows creation and launch of Spot fleets - Spot instances with similar compute capabilities (i.e. vCPUs and RAM). This is for using Spot instances when running jobs in AWS Batch.

Go to the IAM Console
Click on "Roles"
Click on "Create role"
Select "AWS service" as the trusted entity
Choose EC2 from the larger services list
Choose "EC2 - Spot Fleet Tagging" as the use case
- In Attached permissions policies, the AmazonEC2SpotFleetTaggingRole will already be attached.
Click "Next: Tags". (adding tags is optional)
Click "Next: Review"
Set the Role Name to nf-tower-fleetrole
Click "Create role".

Create a launch template

Required to configure the EC2 instance deployed by the Batch jobs.

Go to the EC2 Console
Click Launch template

Create a new launch template which uses the User Data (in the Advanced details section) shown below:

MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="//"

--//
Content-Type: text/x-shellscript; charset="us-ascii"

#!/bin/sh
su - root << 'EOF'
(
set -x
## install awscli
USER=/home/ec2-user
export PATH=/usr/local/bin:$PATH
yum install -y jq python27-pip sed wget bzip2
pip install -U boto3
wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $USER/miniconda
$USER/miniconda/bin/conda install -c conda-forge -y awscli
rm Miniconda3-latest-Linux-x86_64.sh
chown -R ec2-user:ec2-user $USER/miniconda
) &>> ~/boot.log
EOF
cp ~/boot.log ~ec2-user/boot.log

--//--

Finally, save it with name nf-tower-launchtemplate.

Create the Batch compute environments

Go to the Batch Console
Create a new compute environment specifying the Instance profile, Service role, Fleet role and Launch template created previously.
Save it with a name of your choice.

Create the Batch Queue

Go to the Batch Console
Create a new queue
Associate to the compute environment created in the previous step.
Finally, save it with a name of your choice.

Create a user policy​

Create the instance role policy​

Create the Batch Service Role​

Create an EC2 Instance Role​

Create an EC2 SpotFleet Role​

Create a launch template​

Create the Batch compute environments​

Create the Batch Queue​