Merge pull request #1 from aws-samples/develop

Major Overhaul

Author: wleepang

README.md

@@ -1,43 +1,26 @@
-## Genomics Workflows
+# Genomics Workflows on AWS
 
-Genomics Workflows on AWS
+This repository is the source code for [Genomics Workflows on AWS](docs.opendata.aws/genomics-workflows).  It contains markdown documents that are used to build the site as well as source code (CloudFormation templates, scripts, etc) that can be used to deploy AWS infrastructure for running genomics workflows.
 
-## License Summary
-
-This sample code is made available under a modified MIT license. See the LICENSE file.
-
-#  Deploying reference architecture for the Cromwell workflow management system on AWS
-
-This reference architecture provides a set of YAML templates for deploying AWS resources, such as [AWS Batch](http://aws.amazon.com/batch/), for use with the [Cromwell](http://cromwell.readthedocs.io) workflow management system.
-
-## [Step 0.](id:step-0) Prerequisites
+## Building the documentation
 
-If you have not already all of the following:
+The documentation is built using mkdocs.
 
-1. Created a AWS account
-2. Created a IAM user with proper permissions
-3. Configured the AWS CLI
-3. Created and downloaded an EC2 Key Pair
-4. Are able to SSH into a Linux host
+Install dependencies:
 
-Follow the [Prerequisites Guide](./doc/prereqs) to create these resources. All further instructions assume the above.
+```bash
+$ conda create --file enviroment.yaml
+```
 
-## [Step 1.](id:step-1) Create a customer AMI for genomics on AWS
+This will create a `conda` environment called `mkdocs`
 
-Genomics, the main use case for Cromwell, is a data-heavy workload and requires some modification to the standard AWS Batch processing environment. In particular, we need to scale underlying instance storage that Tasks/Jobs run on top of to meet unpredictable runtime demands.
+Build the docs:
 
-Follow the directions in the ["Creating a custom AMI for genomics"](./doc/create-custom-ami.md) guide.
+```bash
+$ source activate mkdocs
+$ mkdocs build
+```
 
-## [Step 2.](id:step-2) Launch and configure an AWS reference architecture for use with Cromwell
-
-Once you have a custom AMI ID, such as `ami-a7a242da`, you  can launch the reference architecture CloudFormation stack in your account, using one of the links below. A full description of what is going on is described in the ["Deploying AWS Batch"](./doc/cofigure-aws-batch-start.md) guide.
-
-![AWS Batch environment for genomics](https://d2908q01vomqb2.cloudfront.net/1b6453892473a467d07372d45eb05abc2031647a/2018/04/23/Picture2.png)
-
-## [Step 3.](id:step-3) Configuring Cromwell for AWS
-
-Once you have a suitable AWS Batch environment for genomics workflows, you can leverage it with other systems, such as AWS Step Functions, [Cromwell](LINK), and  [Nextflow.io](https://nextflow.io).
+## License Summary
 
-* **[Configure AWS Lambda and AWS Step Functions](./docs/configure-aws-native.md)**
-* **[Configure Cromwell](./docs/configure-cromwell-aws-batch.md)**
-<!-- * **[Configure Nextflow.io](./configure-nextflow-aws-batch.md)** -->
+This sample code is made available under a modified MIT license. See the LICENSE file.