You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
{{ message }}
This repository was archived by the owner on Aug 9, 2023. It is now read-only.
Copy file name to clipboardExpand all lines: docs/tldr.md
+11-11Lines changed: 11 additions & 11 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -1,10 +1,8 @@
1
-
# TL;DR - For the impatient
1
+
# TL;DR - For rapid deployment
2
2
3
-
## Core resources
3
+
## Step 0: Amazon VPC
4
4
5
-
### Amazon VPC
6
-
7
-
While you can use an existing "default" VPC to implement deployment of your genomics environment, we strongly recommend utilizing a VPC with private subnets for the processing sensitive data with AWS Batch. Doing so will restrict access to the instances from the internet, and help meet security and compliance requirements, such as [dbGaP](http://j.mp/aws-dbgap).
5
+
While you can use an existing "default" VPC to implement deployment of your genomics environment, we strongly recommend utilizing a VPC with private subnets for processing sensitive data with AWS Batch. Doing so will restrict access to the instances from the internet, and help meet security and compliance requirements, such as [dbGaP](http://j.mp/aws-dbgap).
8
6
9
7
10
8
!!! tip
@@ -19,13 +17,15 @@ While you can use an existing "default" VPC to implement deployment of your geno
19
17
20
18
| Name | Description | Source | Launch Stack |
21
19
| -- | -- | :--: | :--: |
22
-
{{ cfn_stack_row("VPC", "GenomicsVPC", "https://aws-quickstart.s3.amazonaws.com/quickstart-aws-vpc/templates/aws-vpc.template", "(Optional) Creates a new Virtual Private Cloud to use for your genomics workflow resources.") }}
20
+
{{ cfn_stack_row("VPC (Optional)", "GenomicsVPC", "https://aws-quickstart.s3.amazonaws.com/quickstart-aws-vpc/templates/aws-vpc.template", "Creates a new Virtual Private Cloud to use for your genomics workflow resources.") }}
23
21
24
22
The above template uses the AWS Quickstart reference for a [Modular and Scalable VPC Architecture](https://aws.amazon.com/quickstart/architecture/vpc/) and provides a networking foundation for AWS Cloud infrastructures, deploying an Amazon Virtual Private Cloud (Amazon VPC) according to AWS best practices and guidelines.
25
23
26
24
For architectural details, best practices, step-by-step instructions, and customization options, see the [deployment guide](https://fwd.aws/9VdxN).
27
25
28
-
### Full stack
26
+
## Step 1: Compute Environment
27
+
28
+
### Option A: Full stack
29
29
30
30
The "Full Stack" CloudFormation template below will create all of the AWS resources required - S3 Bucket, EC2 Launch Templates, IAM Roles, Batch Compute Environments, Batch Job Queues - for your genomics workflow environment into an existing VPC.
31
31
@@ -43,20 +43,20 @@ Once completed, click on the `Outputs` tab and copy down the AWS Batch Job Queue
43
43
44
44

45
45
46
-
### Individual components
46
+
### Option B: Individual components
47
47
48
48
The CloudFormation templates above are [nested stacks](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-nested-stacks.html), a hierarchy of templates that pass values from a parent template to dependent templates.
49
49
50
50
Below are the stand-alone CloudFormation templates for S3, IAM, and AWS Batch. These are handy in case you need to modify the individual components, or need to have another individual with elevated privileges to execute one of them (e.g. the IAM template). They are in order of dependency, and you will need to provide output values from one template to the dependent templates.
51
51
52
52
| Name | Description | Source | Launch Stack |
53
53
| -- | -- | :--: | :--: |
54
-
{{ cfn_stack_row("Amazon IAM Roles", "GenomicsWorkflow-IAM", "aws-genomics-iam.template.yaml", "Create the necessary IAM Roles. This is useful to hand to someone with the right permissions to create these on your behalf. _You will need to provide a S3 bucket name_.") }}
54
+
{{ cfn_stack_row("Amazon IAM Roles", "GenomicsWorkflow-IAM", "aws-genomics-iam.template.yaml", "Create the necessary IAM Roles. This is useful to hand to someone with the right permissions to create these on your behalf. _You will need to provide an Amazon S3 bucket name_.") }}
55
55
{{ cfn_stack_row("EC2 Launch Template", "GenomicsWorkflow-LT", "aws-genomics-launch-template.template.yaml", "Creates an EC2 Launch Template that provisions instances on first boot for processing genomics workflow tasks.") }}
56
-
{{ cfn_stack_row("Amazon S3 Bucket", "GenomicsWorkflow-S3", "aws-genomics-s3.template.yaml", "Creates a secure Amazon S3 bucket to read from and write results to.") }}
56
+
{{ cfn_stack_row("Amazon S3 Bucket", "GenomicsWorkflow-S3", "aws-genomics-s3.template.yaml", "Creates a secure Amazon S3 bucket to read inputs and write results.") }}
57
57
{{ cfn_stack_row("AWS Batch", "GenomicsWorkflow-Batch", "aws-genomics-batch.template.yaml", "Creates AWS Batch Job Queues and Compute Environments. You will need to provide the details on IAM roles and instance profiles, and the IDs for a VPC and subnets.") }}
0 commit comments