Amazon resource for bioinformatics

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

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Amazon resource for bioinformatics

  1. 1. Amazon resources for bioinformatics Brad Chapman Bioinformatics Interest Group, 18 Oct 2012
  2. 2. Goals Automate: Reduce steps Remove activation energy Increase abstraction Improve: Sharing Reproducibility Teaching
  3. 3. Installation
  4. 4. Easier installation
  5. 5. No installation
  6. 6. Challenge Biology computing platform Widely accessible Customizable Community driven
  7. 7. General cloud frameworks http://aws.amazon.com/
  8. 8. Not only Amazon http://gigaom.com/cloud/what-google-compute- engine-means-for-cloud-computing/
  9. 9. CloudBioLinux Amazon image with bioinformatics software and libraries Automated build framework Community eort to maintain and extend http://cloudbiolinux.org
  10. 10. CloudMan SGE cluster plus automation Web interface and monitoring Persistence and sharing Powers the Galaxy Cloud oering http://usecloudman.org/
  11. 11. BioCloudCentral Automate setup of Amazon instance Launch CloudBioLinux and CloudMan Provide easy ssh access, no key pairs http://biocloudcentral.org
  12. 12. Galaxy http://usegalaxy.org
  13. 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. 14. Documentation http://cda.currentprotocols.com/WileyCDA/CPUnit/ refId-bi1109.html
  15. 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. 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. 17. Launch: http://biocloudcentral.org
  18. 18. Ready two minutes later
  19. 19. Login to CloudMan
  20. 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. 21. Start CloudMan
  22. 22. CloudMan console
  23. 23. CloudMan admin page
  24. 24. CloudMan: managing a cluster
  25. 25. Associated Galaxy instance
  26. 26. Analysis data on shared instance
  27. 27. Graphical variant-calling pipeline
  28. 28. Analysis data linked to pipeline
  29. 29. Congure pipeline
  30. 30. Run pipeline
  31. 31. Shut everything down
  32. 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. 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. 34. NX graphical client: login http://www.nomachine.com/download.php
  35. 35. NX graphical client: desktop
  36. 36. Summary Use cloud resources to build: Machines with standard software Cluster management Analysis pipelines Reproducible, sharable instances Web-based interfaces

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