longbow workflow for KI sprint 7D
Setting up Longbow to run analyses:
- Clone sprint 7D longbow and longbow risk factors repositories
- in R, run the following:
- library(devtools)
- install(longbowRiskFactors)
- Ensure you have a GHAP node running.
- Obtain the IP address by logging into the GHAP portal.
- Click on Create Virtual Environment
- Select M&A Linux (for Mac)
- Wait until status says "running"
-
Copy IP address to SSH into this node: ssh GHAP_username@IP_address
-
Obtain a Longbow API token by logging into longbowapp.com (select API token)
-
Create a cluster_credentials.json file according to these instructions:
- https://github.com/tlverse/longbowtools#running-via-longbow-api
- NOTE: If you've stopped/started a new node, you'll need to update the IP address of the node in this JSON file every time you use it.
- If the data has been updated on GHAP, pull the changes from Github:
- cd ~/datasets/UCB-SuperLearner/
- git pull
- Run run_batch.R script
- Change the path in setwd() if needed.
- Add and commit output to Github