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December 5, 2012 19:21
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Bioconductor CloudFormation template
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| { | |
| "AWSTemplateFormatVersion":"2010-09-09", | |
| "Description":"Start up a parallel Bioconductor cluster with ssh access. **WARNING** This template creates Amazon EC2 instances. You will be billed for the AWS resources used if you create a stack from this template.", | |
| "Parameters":{ | |
| "BiocVersion" : { | |
| "Description" : "Bioconductor Version. 2.11 is recommended.", | |
| "Type" : "String", | |
| "Default": "2.11", | |
| "AllowedValues": ["2.11"], | |
| "ConstraintDescription": "Must be 2.11" | |
| }, | |
| "KeyName":{ | |
| "Description":"Name of an existing EC2 KeyPair to enable SSH access to the instances", | |
| "Type":"String" | |
| }, | |
| "ClusterInstanceType":{ | |
| "Description":"EC2 instance type for cluster", | |
| "Type":"String", | |
| "Default":"m1.xlarge", | |
| "AllowedValues":[ | |
| "t1.micro", | |
| "m1.small", | |
| "m1.medium", | |
| "m1.large", | |
| "m1.xlarge", | |
| "m2.xlarge", | |
| "m2.2xlarge", | |
| "m2.4xlarge", | |
| "c1.medium", | |
| "c1.xlarge", | |
| "cc1.4xlarge", | |
| "cc2.8xlarge", | |
| "cg1.4xlarge" | |
| ], | |
| "ConstraintDescription":"must be a valid EC2 instance type." | |
| }, | |
| "NumClusterInstances":{ | |
| "Default":"2", | |
| "Description":"Number of worker instances in cluster", | |
| "Type":"Number" | |
| }, | |
| "SpotPriceBid":{ | |
| "Default":"0.10", | |
| "Description":"Spot instance bid price", | |
| "Type":"Number" | |
| } | |
| }, | |
| "Mappings" : { | |
| "BiocAMIMap" : { | |
| "2.8" : { | |
| "AMI" : "ami-4b2fee22" | |
| }, | |
| "2.9" : { | |
| "AMI" : "ami-5f33e536" | |
| }, | |
| "2.10" : { | |
| "AMI" : "ami-cb8e21a2" | |
| }, | |
| "2.11" : { | |
| "AMI" : "ami-0eec5367" | |
| } | |
| } | |
| }, | |
| "Resources":{ | |
| "CfnUser":{ | |
| "Type":"AWS::IAM::User", | |
| "Properties":{ | |
| "Path":"/", | |
| "Policies":[ | |
| { | |
| "PolicyName":"root", | |
| "PolicyDocument":{ | |
| "Statement":[ | |
| { | |
| "Effect":"Allow", | |
| "Action":["cloudformation:DescribeStackResource", "ec2:DescribeInstances", | |
| "ec2:CreateTags"], | |
| "Resource":"*" | |
| } | |
| ] | |
| } | |
| } | |
| ] | |
| } | |
| }, | |
| "HostKeys":{ | |
| "Type":"AWS::IAM::AccessKey", | |
| "Properties":{ | |
| "UserName":{ | |
| "Ref":"CfnUser" | |
| } | |
| } | |
| }, | |
| "MasterInstance" : { | |
| "Type" : "AWS::EC2::Instance", | |
| "Properties" : { | |
| "SecurityGroups" : [ { "Ref" : "InstanceSecurityGroup" } ], | |
| "KeyName" : { "Ref" : "KeyName" }, | |
| "ImageId" : { "Fn::FindInMap" : [ "BiocAMIMap", { "Ref" : "BiocVersion" }, "AMI" ]}, | |
| "InstanceType": {"Ref": "ClusterInstanceType"}, | |
| "UserData":{ | |
| "Fn::Base64":{ | |
| "Fn::Join":[ | |
| "", | |
| [ | |
| "#!/bin/bash\n", | |
| "rm -rf /usr/local/bioc_cloud ", | |
| " && ", | |
| " svn co --no-auth-cache --non-interactive --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocCloud/inst/CloudFormation/ /usr/local/bioc_cloud", | |
| " && ", | |
| "/usr/local/bioc_cloud/bootstrap_plain.rb", | |
| " --secret-key ", | |
| { | |
| "Fn::GetAtt":[ | |
| "HostKeys", | |
| "SecretAccessKey" | |
| ] | |
| }, | |
| " --region ", | |
| { "Ref": "AWS::Region"}, | |
| " --stack-name ", | |
| { "Ref": "AWS::StackName"}, | |
| " --cluster-size ", | |
| { "Ref": "NumClusterInstances"}, | |
| " --access-key ", | |
| { "Ref": "HostKeys"}, | |
| " --wait-handle ", | |
| "\"", | |
| { "Ref": "WaitHandle"}, | |
| "\"", | |
| " --master ", | |
| " > /root/startup.log 2>&1 ", | |
| "\n" | |
| ] | |
| ] | |
| } | |
| } | |
| } | |
| }, | |
| "WebServerGroup":{ | |
| "Type":"AWS::AutoScaling::AutoScalingGroup", | |
| "Properties":{ | |
| "LaunchConfigurationName":{ | |
| "Ref":"LaunchConfig" | |
| }, | |
| "AvailabilityZones":{ | |
| "Fn::GetAZs":{ | |
| "Ref":"AWS::Region" | |
| } | |
| }, | |
| "MinSize": { | |
| "Ref": "NumClusterInstances" | |
| }, | |
| "MaxSize":{ | |
| "Ref":"NumClusterInstances" | |
| }, | |
| "DesiredCapacity":{ | |
| "Ref":"NumClusterInstances" | |
| } | |
| } | |
| }, | |
| "LaunchConfig":{ | |
| "Type":"AWS::AutoScaling::LaunchConfiguration", | |
| "Properties":{ | |
| "SpotPrice" : {"Ref":"SpotPriceBid"}, | |
| "InstanceType":{ | |
| "Ref":"ClusterInstanceType" | |
| }, | |
| "SecurityGroups":[ | |
| { | |
| "Ref":"InstanceSecurityGroup" | |
| } | |
| ], | |
| "ImageId" : { "Fn::FindInMap" : [ "BiocAMIMap", { "Ref" : "BiocVersion" }, "AMI" ]}, | |
| "KeyName":{ | |
| "Ref":"KeyName" | |
| }, | |
| "UserData":{ | |
| "Fn::Base64":{ | |
| "Fn::Join":[ | |
| "", | |
| [ | |
| "#!/bin/bash\n", | |
| "rm -rf /usr/local/bioc_cloud ", | |
| " && ", | |
| " svn co --no-auth-cache --non-interactive --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocCloud/inst/CloudFormation/ /usr/local/bioc_cloud", | |
| " && ", | |
| "/usr/local/bioc_cloud/bootstrap_plain.rb", | |
| " --secret-key ", | |
| { | |
| "Fn::GetAtt":[ | |
| "HostKeys", | |
| "SecretAccessKey" | |
| ] | |
| }, | |
| " --region ", | |
| { "Ref": "AWS::Region"}, | |
| " --stack-name ", | |
| { "Ref": "AWS::StackName"}, | |
| " --cluster-size ", | |
| { "Ref": "NumClusterInstances"}, | |
| " --access-key ", | |
| { "Ref": "HostKeys"}, | |
| " --wait-handle ", | |
| "\"", | |
| { "Ref": "WaitHandle"}, | |
| "\"", | |
| " --workers ", | |
| " > /root/startup.log 2>&1 ", | |
| "\n" | |
| ] | |
| ] | |
| } | |
| } | |
| } | |
| }, | |
| "WaitHandle":{ | |
| "Type":"AWS::CloudFormation::WaitConditionHandle" | |
| }, | |
| "WaitCondition":{ | |
| "Type":"AWS::CloudFormation::WaitCondition", | |
| "DependsOn":"MasterInstance", | |
| "Properties":{ | |
| "Handle":{ | |
| "Ref":"WaitHandle" | |
| }, | |
| "Count": "1", | |
| "Timeout":"10000" | |
| } | |
| }, | |
| "InstanceSecurityGroup" : { | |
| "Type" : "AWS::EC2::SecurityGroup", | |
| "Properties" : { | |
| "GroupDescription" : "Enable HTTP access via port 8787", | |
| "SecurityGroupIngress" : [ | |
| { | |
| "IpProtocol" : "tcp", | |
| "FromPort" : "8787", | |
| "ToPort" : "8787", | |
| "CidrIp" : "0.0.0.0/0" | |
| } , | |
| { | |
| "IpProtocol": "tcp", | |
| "FromPort": "22", | |
| "ToPort": "22", | |
| "CidrIp": "0.0.0.0/0" | |
| } | |
| ] | |
| } | |
| }, | |
| "InstanceSecurityGroupIngress": { | |
| "Type": "AWS::EC2::SecurityGroupIngress", | |
| "Properties": { | |
| "GroupName": { "Ref": "InstanceSecurityGroup" }, | |
| "IpProtocol": "tcp", | |
| "FromPort": "0", | |
| "ToPort": "65535", | |
| "SourceSecurityGroupName": { "Ref": "InstanceSecurityGroup" } | |
| } | |
| } | |
| }, | |
| "Outputs":{ | |
| "URL" : { | |
| "Description" : "URL of RStudio Server", | |
| "Value" : { "Fn::Join" : [ "", [ "http://", | |
| { "Fn::GetAtt" : [ "MasterInstance", "PublicDnsName" ]}, ":8787"]]} | |
| }, | |
| "Username": { | |
| "Description": "Log in with this username", | |
| "Value": "ubuntu" | |
| }, | |
| "Password": { | |
| "Description": "Log in with this password", | |
| "Value": "bioc" | |
| }, | |
| "Info": { | |
| "Description": "Message", | |
| "Value": "Delete stack when done to avoid charges." | |
| }, | |
| "SSHCommand": { | |
| "Description": "SSH Command", | |
| "Value" : { "Fn::Join" : [ "", [ "ssh -i ", { "Ref": "KeyName"}, ".pem root@", | |
| { "Fn::GetAtt" : [ "MasterInstance", "PublicDnsName" ]}]]} | |
| } | |
| } | |
| } |
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Added a SpotPrice entry in LaunchConfig to use spot instances.