Bioconductor CloudFormation template

parallel_cluster_ssh.json

{
   "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" ]}]]}
           
       }
   }
}

Added a SpotPrice entry in LaunchConfig to use spot instances.