BerkeleyBiostats/tl-app-experiments

Name: tl-app-experiments

Owner: BerkeleyBiostats

Description: Easy-to-use web app for Targeted Learning

Created: 2017-07-20 02:12:45.0

Updated: 2017-08-10 19:33:42.0

Pushed: 2017-07-30 08:00:28.0

Homepage: null

Size: 10

Language: Shell

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README

Demonstration CLI for multi-target R scripts

The everywhere directory demonstrates the design of an R library and Python harness for writing a single R script that can be run locally and on a cluster.

Install:

pip install fabric

Configure a hosts.ini file in the everywhere directory

[ghap]
ip=...
username=...
password=...

Run:

cd everywhere
python cli.py pi_everywhere.r hosts.ini ghap

Also try locally:

Rscript pi_everywhere.r local

Batchtools on Savio

Create

pi.R
batchtools.slurm.tmpl

Replace the hardcoded paths (e.g. /home/marcpare/…)

Install

load r
R
install.packages('batchtools')

Then,

Rscript pi.R

Batchtools on GHAP

cd /torquefs
rm -rf pitorque # complains if this already exists

Create

pitorque.R
torque.tmpl

Install

R
install.packages('batchtools', dependencies=TRUE, repos='http://cran.rstudio.com/')

Run,

Rscript pitorque.R

Misc

qstat -q # list queues