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https://github.com/aws-samples/aws-batch-genomics
Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.
https://github.com/aws-samples/aws-batch-genomics
Last synced: about 2 months ago
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Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.
- Host: GitHub
- URL: https://github.com/aws-samples/aws-batch-genomics
- Owner: aws-samples
- License: apache-2.0
- Created: 2017-05-24T17:40:46.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2020-06-04T19:10:03.000Z (over 4 years ago)
- Last Synced: 2024-06-14T01:27:49.185Z (7 months ago)
- Language: Python
- Size: 2.03 MB
- Stars: 199
- Watchers: 39
- Forks: 75
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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- top-life-sciences - **aws-samples/aws-batch-genomics** - 2.0 license <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2018-11-29 18:40:42 | (Ranked by starred repositories)
README
This solution has been replaced by the AWS Solution for secondary analysis:
https://aws.amazon.com/solutions/implementations/genomics-secondary-analysis-using-aws-step-functions-and-aws-batch/
# Genomics Research on AWS
This project demonstrates how to run a large-scale, genomics secondary-analysis pipeline on [AWS](https://aws.amazon.com/) using [AWS Step Functions](https://aws.amazon.com/step-functions/) and [AWS Batch](https://aws.amazon.com/batch/). You can learn more about how we used the new AWS Step Functions integration with AWS Batch in our blog post, [Building Simpler Genomics Workflows on AWS Step Functions](https://aws.amazon.com/blogs/compute/building-simpler-genomics-workflows-on-aws-step-functions/).
## PREREQUISITES
* [AWS CLI](https://docs.aws.amazon.com/cli/latest/userguide/installing.html)
* Admin permissions for deployment
## DEPLOY
*Will build and deploy everything needed to run a secondary-analysis pipeline on AWS. This includes:*
1. Custom AMI with 1TB scratch volume using the ECS AMI for your region **(10 min)**
2. Isaac, Strelka, Samtools-Stats and SnpEff as Docker images in ECR **(40 min)**
3. AWS Batch queues, compute environments, job definitions and an AWS Step Functions state machine **(10 min)**
4. Roles and buckets needed.
````bash
$ setup.sh
````
## USAGE
**Run the Workflow**
*Copy the workflow input that was output to the terminal window after the deployment completed. Use that input to run the pipeline in the StepFunctions console. You can also find example workflow inputs in the outputs section of the **batch-genomics-pipeline** Cloudformation stack.*
**Update Pipeline Stack**
*Deploy changes made to local Cloudformation templates.*
````bash
$ update.sh
````
**Teardown Pipeline Stack**
*Deletes everything except the custom AMI and ECR images.*
````bash
$ teardown.sh
````