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Create a bundle for the shiny app in order to run it with shiny server

Source: R/shiny.R
create_bundle.Rd

Generate a 'deployment ready' bundle of the shiny app

Usage

create_bundle(
  mct,
  path,
  hc = NULL,
  overwrite = FALSE,
  self_contained = FALSE,
  branch = "master",
  restart = overwrite,
  permissions = NULL,
  ...
)

Arguments

mct

a MCTracks object

path

Path to the bundle directory

hc

an hclust object with clustering of the metacells (optional, see mct_plot_region)

overwrite

overwrite bundle if already exists

self_contained

include the source code of mcATAC in the bundle and use it to run the app. Use this in order to ensure that the package would always run the same way, regardless of mcATAC changes. When this option is FALSE, the installed version of mcATAC would be loaded, which can be occasionally updated for all the mcATAC apps running from a server. By default, the code of the latest mcATAC release would be used, see branch for other options.

branch

name of the mcATAC branch to include when self_contained=TRUE. By default, the master branch would be used.

restart

add a file named 'restart.txt' to the bundle. This would force shiny-server to restart the app when updated.

permissions

change the file permissions of the bundle after creation, e.g. "777". When NULL - permissions would not be changed.

...

Arguments passed on to gert::git_clone

password

a string or a callback function to get passwords for authentication or password protected ssh keys. Defaults to askpass which checks getOption('askpass').

ssh_key

path or object containing your ssh private key. By default we look for keys in ssh-agent and credentials::ssh_key_info.

verbose

display some progress info while downloading

mirror

use the --mirror flag

url

remote url. Typically starts with https://github.com/ for public repositories, and https://yourname@github.com/ or git@github.com/ for private repos. You will be prompted for a password or pat when needed.

bare

use the --bare flag

Details

Create a minimal shiny app in path directory which would contain:

  • app.R file.

  • mct.rds with the mct object.

The bundle can then be deployed in shiny-server, shinyapps.io or any other environment that supports serving shiny apps.

Note: when deploying to these services - make sure you have the mcATAC package installed with the 'Suggests' dependencies.

Examples

if (FALSE) {
create_bundle(mct, "/path/to/the/bundle/directory")
}