VariantSpark on AWS
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Slides from Broad Institute SoftEng retreat poster session - moving CSIRO bioinformatics team's VariantSpark algorithm on AWS using EMR or EKS
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VariantSpark on AWS
- 1. Lynn Langit for CSIRO Bioinformatics VariantSpark on AWS
- 2. Denis Bauer, PhD Oscar Luo, PhD Rob Dunne, PhD Piotr SzulAidan O’BrienLaurence Wilson, PhD Adrian White Andy Hindmarch David Levy Dan Andrews Kaitao Lai, PhD Arash Bayat PhD John Hildebrandt Mia Chapman Ian Blair Kelly Williams Jules Damji Gaetan Burgio Lynn Langit Jim Counts Matthew Jones Natalie Twine, PhD Prabha Pillay Transformational Bioinformatics Team www.csiro.au Denis C. Bauer | @allPowerde
- 3. BMC Genomics 2015, 16:1052 PMID: 26651996 (IF=4) Cited 4 Denis C. Bauer | @allPowerde
- 4. VariantSpark works with VCF Data
- 5. Supervised ML: Wide Random Forests
- 6. Custom Splits • Horizontal • Vertical Gini Scoring • Local • Global
- 7. Performance – Faster and More Accurate VariantSpark can scale to 100% of the genome low Accuracy high lowSpeedhigh
- 8. Scaling to 50M variables & 10K samples 100K trees: 5 – 50h AWS: ~$215.50 100K trees: 200 – 2000h AWS: ~ $ 8620.00 • Yarn Cluster • 12 workers • 16 x Intel CPUs • Xeon E5-2660@2.20GHz • 128 GB RAM • Spark 1.6.1 • 128 executors • 6GB / executor 0.75TB • Synthetic dataset Whole Genome Range GWAS Range
- 9. Building a Cloud Data Pipeline Spark •IaaS, PaaS, SaaS Vendors •Alibaba, AWS, GCP…
- 10. True CloudCosts
- 12. Moving to the Cloud – SaaS / Databricks
- 13. Synthetic Phenotype: Who is a Bondi Hipster?
- 15. Hello VariantSpark via Hipster-Index BUILDS Community
- 16. Try it out SaaS: VariantSpark Notebook
- 17. Transformational Bioinformatics | @allPowerde
- 18. Spark Server Cluster Pipeline Pattern Jupyter Notebook Data Lake
- 20. Try it out: VariantSpark on AWS EMR
- 21. Try it out: VariantSpark on AWS EKS
- 22. Apache Spark 2.3+ with Kubernetes
- 23. Try it out: VariantSpark on AWS EKS
- 24. Try it out: VariantSpark on AWS EKS
- 25. CSIRO Team Trains Other Researchers Team creates reproducible cloud environments • AWS CloudFormation Templates for EMR • Setup screencasts for Databricks and AWS • Scripts and recommended parameters
- 26. Next Steps • VariantSpark on GCP • Use GCP DataProc – compare to AWS EMR • Use GCP GKE – compare to AWS EKS (K8) • VariantSpark on Terra.bio • First optimize container for GCP raw compute • Write WDL for VariantSpark tool/workflow • Publish on Dockstore as Tool/Workflow • Publish example Jupyter notebooks • Publish example Terra.bio VariantSpark workflow
- 27. Bioinformatics Tools on AWS Lynn Langit for CSIRO Bioinformatics
Editor's Notes
- VariantSpark - https://bioinformatics.csiro.au/variantspark GT-Scan Suite - https://gt-scan.csiro.au/
- https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2269-7
- http://www.internationalgenome.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40/
- https://github.com/aehrc/VariantSpark
- https://academics.cloud.databricks.com/#notebook/170398/command/170419
- Photo from - http://www.drjasonfox.com/
- https://aehrc.github.io/VariantSpark/notebook-examples/VariantSpark_HipsterIndex.html
- https://docs.databricks.com/applications/genomics/variant-spark.html
- https://aehrc.com/als-genomic-research/
- Quickly access a managed Spark cluster - AWS EC2 / spot instances Link to your data and perform whole genome analysis in real-time
- https://medium.com/@lynnlangit/scaling-custom-machine-learning-on-aws-part-2-emr-6dfc3cd91a1f
- https://databricks.com/blog/2017/07/26/breaking-the-curse-of-dimensionality-in-genomics-using-wide-random-forests.html https://github.com/jamesrcounts/VariantSpark/tree/spark2.3/kubernetes
- https://databricks.com/blog/2017/07/26/breaking-the-curse-of-dimensionality-in-genomics-using-wide-random-forests.html https://github.com/jamesrcounts/VariantSpark/tree/spark2.3/kubernetes