Merge pull request #4 from aws-samples/develop

merged copy edits

Author: wleepang

docs/core-env/create-custom-compute-resources.md

@@ -1,7 +1,8 @@
 # Creating Custom Compute Resources
 
 Genomics is a data-heavy workload and requires some modification to the defaults
-used for batch job processing. In particular, instances running the Tasks/Jobs need scalable storage to meet unpredictable runtime demands.
+used for batch job processing. In particular, instances running the Tasks/Jobs 
+need scalable storage to meet unpredictable runtime demands.
 
 By default, AWS Batch relies upon the [Amazon ECS-Optimized AMI](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-optimized_AMI.html)
 to launch container instances for running jobs.  This is sufficient in most cases, but specialized needs, such as the large 
@@ -20,11 +21,13 @@ The simplest method for customizing an instance is to use an EC2 Launch Template
 This works best if your customizations are relatively light - such as installing
 a few small utilities or making specific configuration changes.
 
-This is because Launch Templates run `UserData` when an instance first launches.
+This is because Launch Templates run a `UserData` script when an instance first launches.
 The longer these scripts / customizations take to complete, the longer it will
 be before your instance is ready for work.
 
-Since this will be working with AWS Batch, you only need to supply the `UserData`
+Launch Templates are capable of pre-configuring a lot of EC2 instance options.
+Since this will be working with AWS Batch, which already does a lot of automatic 
+instance configuration on its own, you only need to supply the `UserData`
 script below:
 
 ```text
@@ -49,9 +52,10 @@ runcmd:
 --==BOUNDARY==--
 ```
 
-By default the `ebs-autoscale` monitor will add a 20GB EBS volume to the logical volume
-mounted at `/scratch`.  If you want this volume to be larger initially, you can
-specify a `/dev/sdc` volume in the Launch Template.
+The above will add an `ebs-autoscale` daemon to an instance.  By default it will 
+add a 20GB EBS volume to the logical volume mounted at `/scratch`.  
+If you want this volume to be larger initially, you can specify a bigger one 
+mapped to `/dev/sdc`  the Launch Template.
 
 !!! note
     The mount point is specific to what orchestration method / engine you intend

docs/core-env/images/aws-genomics-workflows-high-level-arch.png

@@ -2,6 +2,8 @@
 
 A high level view of the architecture you will need is below.
 
+![high level architecture](images/aws-genomics-workflows-high-level-arch.png)
+
 To start you will need the following components:
 
 * A place to store your input data and generated results

docs/core-env/introduction.md

@@ -1,5 +1,7 @@
 # Genomics Workflows on AWS
 
+![banner](images/aws-genomics-workflows-banner.png)
+
 ## Introduction
 
 Welcome!

docs/images/aws-genomics-workflows-banner.png

@@ -1,5 +1,7 @@
 # Step Functions Workflow Examples
 
+THIS IS A STUB
+
 ![Example Workflow](./images/example-state-machine.png)
 
 this was created from [this file](./files/example-state-machine.json).

docs/images/custom-ami-storage.png

@@ -6,22 +6,15 @@
 
 In the context of genomics workflows, the combination of AWS Step Functions with Batch and Lambda constitutes a robust, scalable, and serverless task orchestration solution.
 
-<!--// not ready for release yet
-    // TODO: create the example sfn state-machine cfn template
-## TL;DR
-
-If you need something up and running in a hurry, and you've followed all of the 
-steps in the [Getting Started](../../../core-env/introduction/) section, you 
-already have the majority of what you need setup.
-
-The last component you need is an AWS Step Functions state machine for your workflow.
-Below is a CloudFormation template that creates an example state-machine that
-you can modify to suit your needs.
-
-| Name | Description | Source | Launch Stack |
-| -- | -- | :--: | :--: |
-{{ cfn_stack_row("AWS Step Functions", "GenomicsWorkflow-Sfn", "aws-genomics-sfn.template.yaml", "Create IAM roles, Batch job definitions, and an example genomics workflow using an AWS Step Functions state machine") }}
--->
+## Full Stack Deployment (TL;DR)
+
+If you need something up and running in a hurry, a fully automated setup process
+is provided at this GitHub repository:
+
+[AWS Batch Genomics](https://github.com/aws-samples/aws-batch-genomics)
+
+If you are interested in creating your own solution with AWS Step Functions and AWS Batch,
+read through the rest of this page.
 
 ## Prerequisites
 

docs/images/gen-ecs-opt-amis-table.png

@@ -45,9 +45,9 @@ Once completed, click on the `Outputs` tab and copy down the AWS Batch Job Queue
 
 ### Option B: Individual components
 
-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.
+The `Full Stack` CloudFormation template above is a [nested stack](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.
 
-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.
+Below are the stand-alone CloudFormation templates for each of the sub-stacks. 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.
 
 | Name | Description | Source | Launch Stack |
 | -- | -- | :--: | :--: |