Amazon resource for bioinformatics

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Walk through using CloudBioLinux, CloudMan, BioCloudCentral to do custom biological analyses on Amazon EC2 hardware.

Walk through using CloudBioLinux, CloudMan, BioCloudCentral to do custom biological analyses on Amazon EC2 hardware.

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  • 1. Amazon resources for bioinformatics Brad Chapman Bioinformatics Interest Group, 18 Oct 2012
  • 2. Goals Automate: Reduce steps Remove activation energy Increase abstraction Improve: Sharing Reproducibility Teaching
  • 3. Installation
  • 4. Easier installation
  • 5. No installation
  • 6. Challenge Biology computing platform Widely accessible Customizable Community driven
  • 7. General cloud frameworks http://aws.amazon.com/
  • 8. Not only Amazon http://gigaom.com/cloud/what-google-compute- engine-means-for-cloud-computing/
  • 9. CloudBioLinux Amazon image with bioinformatics software and libraries Automated build framework Community eort to maintain and extend http://cloudbiolinux.org
  • 10. CloudMan SGE cluster plus automation Web interface and monitoring Persistence and sharing Powers the Galaxy Cloud oering http://usecloudman.org/
  • 11. BioCloudCentral Automate setup of Amazon instance Launch CloudBioLinux and CloudMan Provide easy ssh access, no key pairs http://biocloudcentral.org
  • 12. Galaxy http://usegalaxy.org
  • 13. Acknowledgments CloudBioLinux: Ntino Krampis, Tim Booth, Dawn Field, Pjotr Prins, John Chilton and CloudBioLinux community. CloudMan: Enis Afgan, James Taylor BioCloudCentral: Enis Afgan, John Chilton, Dannon Baker
  • 14. Documentation http://cda.currentprotocols.com/WileyCDA/CPUnit/ refId-bi1109.html
  • 15. What well do 1 Sign up for Amazon 2 Start a CloudBioLinux/CloudMan instance 3 Add nodes to create a compute cluster 4 Run variant calling pipeline Everything done through the web
  • 16. Getting started Sign up for Amazon Web Services http://aws.amzaon.com Get security credentials: Access Key and Secret Key http://portal.aws.amazon.com/gp/aws/ securityCredentials
  • 17. Launch: http://biocloudcentral.org
  • 18. Ready two minutes later
  • 19. Login to CloudMan
  • 20. Shared CloudMan images Package a complete analysis environment Data Customizations Sharable with other users Share string with NGS analysis platform: cm-b53c6f1223f966914df347687f6fc818/shared/2012-07-23--19-23/
  • 21. Start CloudMan
  • 22. CloudMan console
  • 23. CloudMan admin page
  • 24. CloudMan: managing a cluster
  • 25. Associated Galaxy instance
  • 26. Analysis data on shared instance
  • 27. Graphical variant-calling pipeline
  • 28. Analysis data linked to pipeline
  • 29. Congure pipeline
  • 30. Run pipeline
  • 31. Shut everything down
  • 32. What happened 1 Sign up for Amazon 2 Start a CloudBioLinux/CloudMan instance 3 Add nodes to create a compute cluster 4 Run variant calling pipeline Everything done through the web
  • 33. ssh to the machine $ ssh ubuntu@184.73.104.51 ubuntu@184.73.104.51s password: Welcome to Ubuntu 12.04 LTS (GNU/Linux 3.2.0-23-virtual x86_64) ubuntu@ip-10-72-197-11:~$
  • 34. NX graphical client: login http://www.nomachine.com/download.php
  • 35. NX graphical client: desktop
  • 36. Summary Use cloud resources to build: Machines with standard software Cluster management Analysis pipelines Reproducible, sharable instances Web-based interfaces