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Merge branch 'topic-release' into topic-release
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‎.gitignore‎

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.vscode
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*.tar.gz
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rg-deployment-docs
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rg-cft-templates
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.trunk
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.trunk/*
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.isort.cfg
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.markdownlint.yaml
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.flake8
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.shellcheckrc

‎README.md‎

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@@ -69,13 +69,13 @@ If an AMI with the pre-requisites has been shared with you, you can skip this se
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You can create the AMI with pre-requisites yourself by following these steps:
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- Install packer
72-
- Create a Role and attach a policy which permits ECR and EC2 actions and Replace it in builders section
7372
- Export AWS Access Keys and Secret Keys
7473
- export AWS_ACCESS_KEY_ID="your_Access_Key"
7574
- export AWS_SECRET_ACCESS_KEY="your_Secret_Key"
7675
- export AWS_DEFAULT_REGION="Your_Region"
77-
- Download dump.tar.gz to your local rdeploy folder from s3://rg-deployment-docs
78-
- Run packer build package-rg.json.
76+
- Clone this repo on a machine.
77+
- Create a Role and attach a policy which permits ECR and EC2 actions and Replace the "iam-instance_profile" :"<your_rolename>" in builders section which is in the packer-rg.json.
78+
- Run packer build packer-rg.json
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- packer build -var 'awsRegion=your_region' -var 'vpcId=your_VPCID' -var 'subnetId=your_SubnetID' packer-rg.json
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- At Run time pass VPCID, SubnetID, AWSRegion as variables declared in packer-rg.json
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- Note that AMI id from the output

‎cft-templates/Rstudio.yml‎

Lines changed: 63 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,22 @@
1-
AWSTemplateFormatVersion: 2010-09-09
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AWSTemplateFormatVersion: '2010-09-09'
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Description: Sets up RStudio environment on AWS
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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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Type: String
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Description: Instance type for RStudio. Default is t2.medium.
@@ -30,7 +44,39 @@ Parameters:
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Type: "AWS::EC2::KeyPair::KeyName"
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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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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, 'rstudio-role']]
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Path: '/'
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AssumeRolePolicyDocument:
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Version: '2012-10-17'
58+
Statement:
59+
- 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']]
70+
PolicyDocument: !Ref IamPolicyDocument
71+
72+
InstanceProfile:
73+
Type: 'AWS::IAM::InstanceProfile'
74+
Properties:
75+
InstanceProfileName: !Join ['-', [Ref: Namespace, 'rstudio-profile']]
76+
Path: '/'
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Roles:
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- Ref: IAMRole
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RstudioEC2SecurityGroup:
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Type: AWS::EC2::SecurityGroup
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Properties:
@@ -53,30 +99,37 @@ Resources:
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Type: AWS::EC2::Instance
54100
CreationPolicy:
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ResourceSignal:
56-
Timeout: PT9M
102+
Timeout: PT10M
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Properties:
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ImageId : '{{resolve:ssm:/RL/RG/StandardCatalog/RStudio}}'
59105
InstanceType: !Ref 'InstanceType'
60106
SecurityGroups: [!Ref 'RstudioEC2SecurityGroup']
61107
KeyName: !Ref 'KeyPair'
62-
UserData: !Base64
108+
IamInstanceProfile: !Ref InstanceProfile
63109
Tags:
64-
- Key: Name
65-
Value: !Join ["-", [!Ref "AWS::StackName", "RStudio"]]
110+
- Key: Name
111+
Value: !Join ['-', [Ref: Namespace, 'rstudio-server']]
112+
- Key: Description
113+
Value: EC2 linux based Rstudio server
66114
UserData:
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Fn::Base64: !Sub |
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#!/bin/bash
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exec > >(tee /var/log/user-data.log|logger -t user-data -s 2>/dev/console) 2>&1
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trap '/opt/aws/bin/cfn-signal --exit-code 1 --resource RstudioEC2Instance --region ${AWS::Region} --stack ${AWS::StackName}' ERR
119+
sudo yum update -y --security
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71121
#add user(s)
72122
sudo useradd -m -s /bin/bash ${InitialUser}
73123
sudo echo ${InitialUser}:${InitialPassword} | chpasswd
74-
/opt/aws/bin/cfn-signal --exit-code 0 --resource RstudioEC2Instance --region ${AWS::Region} --stack ${AWS::StackName}
124+
125+
#Download and execute bootstrap script
126+
aws s3 cp "${EnvironmentInstanceFiles}/get_bootstrap.sh" "/tmp"
127+
chmod 500 "/tmp/get_bootstrap.sh"
128+
/tmp/get_bootstrap.sh "${EnvironmentInstanceFiles}" '${S3Mounts}'
129+
130+
/opt/aws/bin/cfn-signal --exit-code 0 --resource RstudioEC2Instance --region ${AWS::Region} --stack ${AWS::StackName}
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Outputs:
77-
RStudioURL:
78-
Value: !GetAtt RstudioEC2Instance.PublicDnsName
79-
Description: URL to Access RStudio
80133
InstanceDNSName:
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Value: !GetAtt RstudioEC2Instance.PublicDnsName
82135
Description: Public DNS Name
@@ -85,4 +138,4 @@ Outputs:
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InstanceId:
86139
Value: !Ref 'RstudioEC2Instance'
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ApplicationPort:
88-
Value: '8787'
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Value: '8787'

‎cft-templates/ec2-EIP.yml‎

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@@ -1,14 +1,25 @@
11
Metadata:
22
License: Apache-2.0
33
AWSTemplateFormatVersion: '2010-09-09'
4-
Description: 'AWS CloudFormation Sample Template Sample template EIP_With_Association:
5-
This template shows how to associate an Elastic IP address with an Amazon EC2 instance
6-
- you can use this same technique to associate an EC2 instance with an Elastic IP
7-
Address that is not created inside the template by replacing the EIP reference in
8-
the AWS::EC2::EIPAssoication resource type with the IP address of the external EIP.
4+
Description: 'AWS CloudFormation Template to create an EC2 instance
95
**WARNING** This template creates an Amazon EC2 instance and an Elastic IP Address.
106
You will be billed for the AWS resources used if you create a stack from this template.'
7+
118
Parameters:
9+
Namespace:
10+
Type: String
11+
Description: An environment name that will be prefixed to resource names
12+
S3Mounts:
13+
Type: String
14+
Description: A JSON array of objects with name, bucket, and prefix properties used to mount data
15+
IamPolicyDocument:
16+
Type: String
17+
Description: The IAM policy to be associated with the launched workstation
18+
EnvironmentInstanceFiles:
19+
Type: String
20+
Description: >-
21+
An S3 URI (starting with "s3://") that specifies the location of files to be copied to
22+
the environment instance, including any bootstrap scripts
1223
InstanceType:
1324
Description: Choose the instance type for this instance. e.g. t2.small
1425
Type: String
@@ -30,15 +41,65 @@ Parameters:
3041
LatestAmiId:
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Type: 'AWS::SSM::Parameter::Value<AWS::EC2::Image::Id>'
3243
Default: '/aws/service/ami-amazon-linux-latest/amzn2-ami-hvm-x86_64-gp2'
33-
Resources:
44+
45+
Conditions:
46+
IamPolicyEmpty: !Equals [!Ref IamPolicyDocument, '{}']
47+
48+
Resources:
49+
IAMRole:
50+
Type: 'AWS::IAM::Role'
51+
Properties:
52+
RoleName: !Join ['-', [Ref: Namespace, 'ec2-role']]
53+
Path: '/'
54+
AssumeRolePolicyDocument:
55+
Version: '2012-10-17'
56+
Statement:
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- Effect: 'Allow'
58+
Principal:
59+
Service:
60+
- 'ec2.amazonaws.com'
61+
Action:
62+
- 'sts:AssumeRole'
63+
Policies:
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- !If
65+
- IamPolicyEmpty
66+
- !Ref 'AWS::NoValue'
67+
- PolicyName: !Join ['-', [Ref: Namespace, 's3-studydata-policy']]
68+
PolicyDocument: !Ref IamPolicyDocument
69+
70+
InstanceProfile:
71+
Type: 'AWS::IAM::InstanceProfile'
72+
Properties:
73+
InstanceProfileName: !Join ['-', [Ref: Namespace, 'ec2-profile']]
74+
Path: '/'
75+
Roles:
76+
- Ref: IAMRole
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3478
EC2Instance:
3579
Type: AWS::EC2::Instance
3680
Properties:
37-
UserData: !Base64
81+
UserData:
82+
Fn::Base64: !Sub |
83+
#!/usr/bin/env bash
84+
exec > >(tee /var/log/user-data.log|logger -t user-data -s 2>/dev/console) 2>&1
85+
# Download and execute bootstrap script
86+
aws s3 cp "${EnvironmentInstanceFiles}/get_bootstrap.sh" "/tmp"
87+
chmod 500 "/tmp/get_bootstrap.sh"
88+
/tmp/get_bootstrap.sh "${EnvironmentInstanceFiles}" '${S3Mounts}'
89+
90+
# Signal result to CloudFormation
91+
/opt/aws/bin/cfn-signal -e $? --stack "${AWS::StackName}" --resource "EC2Instance" --region "${AWS::Region}"
3892
InstanceType: !Ref 'InstanceType'
3993
SecurityGroups: [!Ref 'InstanceSecurityGroup']
4094
KeyName: !Ref 'KeyPair'
4195
ImageId: !Ref 'LatestAmiId'
96+
IamInstanceProfile: !Ref InstanceProfile
97+
Tags:
98+
- Key: Name
99+
Value: !Join ['-', [Ref: Namespace, 'ec2-linux']]
100+
- Key: Description
101+
Value: EC2 workspace instance
102+
42103
InstanceSecurityGroup:
43104
Type: AWS::EC2::SecurityGroup
44105
Properties:
@@ -48,6 +109,7 @@ Resources:
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FromPort: '22'
49110
ToPort: '22'
50111
CidrIp: !Ref 'AllowedSSHLocation'
112+
51113
Outputs:
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InstanceId:
53115
Description: InstanceId of the newly created EC2 instance
@@ -57,4 +119,4 @@ Outputs:
57119
Value: !GetAtt [EC2Instance, PublicIp]
58120
InstanceDNSName:
59121
Description: DNS name of the newly created EC2 instance
60-
Value: !GetAtt [EC2Instance, PublicDnsName]
122+
Value: !GetAtt [EC2Instance, PublicDnsName]

‎cft-templates/nextflow-advanced.yaml‎

Lines changed: 3 additions & 2 deletions
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@@ -542,16 +542,17 @@ Resources:
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UserData:
543543
Fn::Base64: !Sub |
544544
#!/bin/bash -xe
545+
exec > >(tee /var/log/user-data.log|logger -t user-data -s 2>/dev/console) 2>&1
545546

546547
sudo yum update -y --security
547-
cd /root/
548+
cd /root/
548549

549550
getOutputData=${OutputDataLocation}
550551
getFirstChar=`echo $getOutputData | cut -c1-1`
551552

552553
if [ "$getFirstChar" == "/" ]
553554
then :
554-
echo "Ngnix URL"
555+
echo "Ngnix URL"
555556
OutputDataLocation=${OutputDataLocation}
556557
echo $OutputDataLocation
557558
else

‎config/app-config.js‎

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@@ -1,25 +1,24 @@
1-
var mkdirp = require('mkdirp');
2-
var fs = require('fs');
1+
var mkdirp = require("mkdirp");
2+
var fs = require("fs");
33
var currentDirectory = __dirname;
4-
var logger = require('../logger/logger')(module);
4+
var logger = require("../logger/logger")(module);
55

66
var configJson;
77
try {
8-
configJson = fs.readFileSync(currentDirectory + '/dashboard-settings.json', {
9-
'encoding': 'utf8'
10-
});
8+
configJson = fs.readFileSync(currentDirectory + "/config.json", {
9+
encoding: "utf8",
10+
});
1111
} catch (err) {
12-
logger.error(err);
13-
configJson = null;
14-
throw err;
12+
logger.error(err);
13+
configJson = null;
14+
throw err;
1515
}
1616

1717
if (configJson) {
18-
var config = JSON.parse(configJson);
18+
var config = JSON.parse(configJson);
1919
}
2020

2121
mkdirp.sync(config.tempDashboardHome);
2222
mkdirp.sync(config.dashboardHome);
2323

2424
module.exports = config;
25-

‎config/bucket-policy.json‎

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1-
{
2-
"Sid": "id-1",
3-
"Effect": "Allow",
4-
"Principal": {
5-
"AWS": ""
6-
},
7-
"Action": "s3:GetObject",
8-
"Resource": "arn:aws:s3:::REPLACE-WITH-S3-BUCKET-NAME/*"
9-
}
1+
[
2+
{
3+
"Sid": "Get:Artifacts",
4+
"Effect": "Allow",
5+
"Principal": {
6+
"AWS": "{principalArns}"
7+
},
8+
"Action": "s3:GetObject",
9+
"Resource": "{artifactObjectsArn}"
10+
},
11+
{
12+
"Sid": "Get:BootstrapScripts",
13+
"Effect": "Allow",
14+
"Principal": {
15+
"AWS": "{accountArns}"
16+
},
17+
"Action": [
18+
"s3:GetObject"
19+
],
20+
"Resource": "{bootstrapObjectsArn}"
21+
},
22+
{
23+
"Sid": "List:BootstrapScripts",
24+
"Effect": "Allow",
25+
"Principal": {
26+
"AWS": "{accountArns}"
27+
},
28+
"Action": [
29+
"s3:ListBucket"
30+
],
31+
"Resource": "{artifactBucketArn}",
32+
"Condition": {
33+
"StringLike": {
34+
"s3:prefix": "{bootstrapPrefix}"
35+
}
36+
}
37+
},
38+
{
39+
"Sid": "Deny requests that do not use TLS",
40+
"Effect": "Deny",
41+
"Principal": "*",
42+
"Action": "s3:*",
43+
"Resource": "{artifactObjectsArn}",
44+
"Condition": {
45+
"Bool": {
46+
"aws:SecureTransport": false
47+
}
48+
}
49+
},
50+
{
51+
"Sid": "Deny requests that do not use SigV4",
52+
"Effect": "Deny",
53+
"Principal": "*",
54+
"Action": "s3:*",
55+
"Resource": "{artifactObjectsArn}",
56+
"Condition": {
57+
"StringNotEquals": {
58+
"s3:signatureversion": "AWS4-HMAC-SHA256"
59+
}
60+
}
61+
}
62+
]

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