In Giappo/jappe: Jap

First, specify basic info

account <- jap::your_account()
project_name <- "mbd"
projects_folder_name <- "Projects"
drive <- TRUE # we want to use google drive

A note on using the drive option. The set of tools of that feature use the tidyverse package googledrive, which requires a short set-up. First call googledrive::drive_auth(), this will open a pop-up window asking you to sign-in your Google account, and grant permission to googledrive to access and edit your Drive folders. There is a common issues with the Google API, reported here for example. There is a fix to this on the latest implementation on GitHub, but not yet on CRAN (as of 27/04/2020). So we recommend:

remotes::install_github("tidyverse/googledrive")

Then open a session. We are gonna use this session every time we want to execute tasks on the cluster

library(jap)
session <- jap::open_session(account = account)

Then we setup the entire folder structure on three different places: local, peregrine and google drive

jap::create_folder_structure(
  project_name = project_name,
  projects_folder_name = projects_folder_name,
  drive = drive,
  account = account,
  session = session
)

We can check the structure on the remote folder and on the drive folder

jap::remote_list.files(
  dir = projects_folder_name,
  account = account,
  session = session
)
jap::drive_list.files(
  dir = projects_folder_name
)

We can now install the package we need from Github

jap::remote_install.packages(
  github_name = "Giappo",
  package_name = project_name,
  account = account,
  session = session
)

We can even install any package from CRAN. To do so it suffices to not specify the 'github_name' argument

jap::remote_install.packages(
  package_name = "ape",
  account = account,
  session = session
)

Or we can run a function

cluster_folder <- "data"
jap::run_on_cluster(
  package_name = "ape",
  function_name = "rtree",
  fun_arguments = "n = 10",
  cluster_folder = cluster_folder
)

jap::remote_list.files(dir = "jap_scripts", cluster_folder = cluster_folder)

Giappo/jappe documentation built on Aug. 30, 2020, 2:41 p.m.