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goog_genomics_pipelines
README.md
README.md~
cmd_generator.R
how_to_dsub.txt
how_to_google_gen_pipeline_v2.txt
stan_logistic_regression.R
task_matrix.txt

README.md

GooglePipelinesRStan

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How to run a custom script with dsub

David L Gibbs

dgibbs@systemsbiology.org

November 7, 2017

https://cloud.google.com/genomics/overview

#################################################################################

In this example, I'm going to be fitting Bayesian logistic regression models using Stan (http://mc-stan.org/). Each job (model fitting) will process a single file, but we could also have each job represent a parameter set, or model, all processing the same data.

This collection of files can be used to demonstrate:

  1. Generating a 'task matrix', each row describing a job in the google cloud. (cmd_generator.R, task_matrix.tsv)

  2. Running a custom R script on user data. (stan_logistic_regression.R, data/*)

  3. Using the Google dsub to automatically start up a VM, run a script, and shutdown. Please see the 'how_to_dsub.txt' file for instructions.