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Merge pull request #71 from narendran1560/topic-release
Added batch compute env parameter in the output section and Update the aws-batch flag for the cromwell advanced and nextflow advanced
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‎cft-templates/cromwell-advanced.yaml‎

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@@ -932,4 +932,6 @@ Outputs:
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EC2 Launch Template ID to use when creating AWS Batch compute environments
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Value: !Ref EC2LaunchTemplate
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WorkDataLocation:
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Value: !Sub ${S3Bucket}
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Value: !Sub ${S3Bucket}
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BatchComputeEnvironment:
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Value: !Ref SpotComputeEnv

‎cft-templates/ec2-linux-docker-mysql.yml‎

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Metadata:
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License: Apache-2.0
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AWSTemplateFormatVersion: '2010-09-09'
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Description: 'AWS CloudFormation Template to create an EC2 instance
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**WARNING** This template creates an Amazon EC2 instance and an Elastic IP Address.
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You will be billed for the AWS resources used if you create a stack from this template.'
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Parameters:
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Namespace:
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Type: String
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Description: An environment name that will be prefixed to resource names
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S3Mounts:
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Type: String
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Description: A JSON array of objects with name, bucket, and prefix properties used to mount data
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IamPolicyDocument:
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Type: String
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Description: The IAM policy to be associated with the launched workstation
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EnvironmentInstanceFiles:
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Type: String
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Description: >-
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An S3 URI (starting with "s3://") that specifies the location of files to be copied to
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the environment instance, including any bootstrap scripts
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InstanceType:
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Description: Choose the instance type for this instance. e.g. t2.small
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Type: String
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Default: t2.small
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AllowedValues: [t2.nano, t2.micro, t2.small, t2.medium]
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ConstraintDescription: must be a valid EC2 instance type.
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KeyPair:
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Description: Name of an existing EC2 KeyPair to enable SSH access to the instance. If no key pairs exist, please create one from the button next to the dropdown. Please contact your Administrator if you are unable to create one.
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Type: AWS::EC2::KeyPair::KeyName
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ConstraintDescription: must be the name of an existing EC2 KeyPair.
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AllowedSSHLocation:
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Description: The IP address range that can be used to SSH to the EC2 instances
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Type: String
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MinLength: '9'
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MaxLength: '18'
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Default: 0.0.0.0/0
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AllowedPattern: (\d{1,3})\.(\d{1,3})\.(\d{1,3})\.(\d{1,3})/(\d{1,2})
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ConstraintDescription: must be a valid IP CIDR range of the form x.x.x.x/x.
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LatestAmiId:
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Type: 'AWS::SSM::Parameter::Value<AWS::EC2::Image::Id>'
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Default: '/aws/service/ecs/optimized-ami/amazon-linux-2/recommended/image_id'
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MasterPassword:
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NoEcho: "true"
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Description : "The database master password"
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Type: "String"
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MinLength: "8"
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MaxLength: "100"
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AllowedPattern : "[a-zA-Z0-9]{8,100}"
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ConstraintDescription : "must contain only alphanumeric characters."
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ConnectFromPort:
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Type: Number
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Description: Required Port mappings
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ConnectToPort:
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Type: Number
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Description: Required Port mappings
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Conditions:
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IamPolicyEmpty: !Equals [!Ref IamPolicyDocument, '{}']
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Resources:
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IAMRole:
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Type: 'AWS::IAM::Role'
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Properties:
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RoleName: !Join ['-', [Ref: Namespace, 'ec2-role']]
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Path: '/'
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AssumeRolePolicyDocument:
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Version: '2012-10-17'
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Statement:
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- Effect: 'Allow'
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Principal:
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Service:
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- 'ec2.amazonaws.com'
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Action:
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- 'sts:AssumeRole'
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Policies:
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- !If
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- IamPolicyEmpty
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- !Ref 'AWS::NoValue'
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- PolicyName: !Join ['-', [Ref: Namespace, 's3-studydata-policy']]
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PolicyDocument: !Ref IamPolicyDocument
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InstanceProfile:
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Type: 'AWS::IAM::InstanceProfile'
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Properties:
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InstanceProfileName: !Join ['-', [Ref: Namespace, 'ec2-profile']]
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Path: '/'
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Roles:
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- Ref: IAMRole
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EC2Instance:
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Type: AWS::EC2::Instance
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CreationPolicy:
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ResourceSignal:
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Timeout: PT5M
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Properties:
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UserData:
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Fn::Base64: !Sub |
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#!/usr/bin/env bash
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# pull mysql version 8
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sudo yum install zip -y
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sudo yum install unzip -y
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# Install AWS CLI version2
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curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
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unzip awscliv2.zip
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sudo ./aws/install
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# Install Mysql Shell
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sudo yum install mysql -y
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# Pull Mysql Image
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docker pull mysql:8
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mkdir docker
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mkdir docker/mysql
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mkdir docker/mysql/conf
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mkdir docker/mysql/data
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docker run -d -p 3306:3306 \
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-v /home/ec2-user/docker/mysql/conf/:/etc/mysql/conf.d \
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-v /home/ec2-user/docker/mysql/data/:/var/lib/mysql \
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-e MYSQL_ROOT_PASSWORD=${MasterPassword} \
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--restart always \
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--name docker_mysql mysql:8 \
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# Download and execute shell script
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cd /home/ec2-user
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aws s3 cp "${EnvironmentInstanceFiles}/alter_rootpassword.sh" "alter_rootpassword.sh"
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chmod +x alter_rootpassword.sh
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./alter_rootpassword.sh ${MasterPassword}
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# Install cfn
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yum install -y aws-cfn-bootstrap
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# Download and execute shell script
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aws s3 cp "${EnvironmentInstanceFiles}/get_bootstrap_mysql.sh" "/tmp"
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chmod 500 "/tmp/get_bootstrap_mysql.sh"
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/tmp/get_bootstrap_mysql.sh "${EnvironmentInstanceFiles}" '${S3Mounts}'
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# Signal result to CloudFormation
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/opt/aws/bin/cfn-signal --exit-code 0 --resource EC2Instance --region ${AWS::Region} --stack ${AWS::StackName}
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InstanceType: !Ref 'InstanceType'
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SecurityGroups: [!Ref 'InstanceSecurityGroup']
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KeyName: !Ref 'KeyPair'
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ImageId: !Ref 'LatestAmiId'
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IamInstanceProfile: !Ref InstanceProfile
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Tags:
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- Key: Name
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Value: !Join ['-', [Ref: Namespace, 'ec2-linux']]
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- Key: Description
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Value: EC2 workspace instance
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InstanceSecurityGroup:
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Type: AWS::EC2::SecurityGroup
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Properties:
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GroupDescription: Enable SSH access
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SecurityGroupIngress:
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- IpProtocol: tcp
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FromPort: '22'
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ToPort: '22'
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CidrIp: !Ref 'AllowedSSHLocation'
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- IpProtocol: tcp
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FromPort: !Ref 'ConnectFromPort'
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ToPort: !Ref 'ConnectToPort'
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CidrIp: !Ref 'AllowedSSHLocation'
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Outputs:
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InstanceId:
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Description: InstanceId of the newly created EC2 instance
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Value: !Ref 'EC2Instance'
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InstanceIPAddress:
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Description: IP address of the newly created EC2 instance
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Value: !GetAtt [EC2Instance, PublicIp]
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InstanceDNSName:
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Description: DNS name of the newly created EC2 instance
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Value: !GetAtt [EC2Instance, PublicDnsName]
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InstancePrivateIPAddress:
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Description: Private IP address of the newly created EC2 instance
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Value: !GetAtt [EC2Instance, PrivateIp]

‎cft-templates/nextflow-advanced.yaml‎

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@@ -88,7 +88,7 @@ Parameters:
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Description: Head Node EC2 instance type
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Type: String
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Default: t2.small
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AllowedValues: [t2.nano, t2.micro, t2.small, t2.medium, t2.large, m5.8xlarge]
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AllowedValues: [t2.nano, t2.micro, t2.small, t2.medium]
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ConstraintDescription: Must be a valid EC2 instance type.
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KeyPair:
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Description: Name of an existing EC2 KeyPair to enable SSH access to the Head Node. If no key pairs exist, please create one from the button next to the dropdown. Please contact your Administrator if you are unable to create one.
@@ -110,7 +110,7 @@ Parameters:
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Description: Specify the instance types to be used to carry out the computation. You can specify one or more family or instance type. The option 'optimal' chooses the best fit of M4, C4, and R4 instance types available in the region.
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Type: String
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Default: optimal
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AllowedValues: [optimal, c4.large, m4.large, r4.large, c4.4xlarge, m4.4xlarge, r4.4xlarge, r5.8xlarge, r5.12xlarge, r5.16xlarge, r5.24xlarge, c6i.32xlarge]
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AllowedValues: [optimal, c4.large, m4.large, r4.large, c4.4xlarge, m4.4xlarge, r4.4xlarge]
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WorkerNodeEBSVolumeSize:
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Description: The initial size of the volume (in GBs) Worker Node EBS will use for storage.
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Type: Number
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Value: !Sub ${S3Bucket}
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BatchQueue:
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Value: !Sub ${DefaultQueue}
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BatchComputeEnvironment:
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Value: !Ref SpotComputeEnv

‎dump/standardcatalogitems.json‎

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}
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],
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"checks_after_assigning_product": [],
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"permission_required": {}
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"permission_required": {},
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"cost_resource": true,
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"aws_batch": true
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}
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},
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{
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],
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"checks_after_assigning_product": [],
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"permission_required": {},
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"cost_resource": true
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"cost_resource": true,
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"aws_batch": true
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}
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}
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]

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