Skip to contents

Generate a 'deployment ready' bundle of the a project app

Source: R/project.R
create_bundle.Rd

Generate a 'deployment ready' bundle of the a project app

Usage

create_bundle(
  project,
  path = getwd(),
  name = "MCView_bundle",
  overwrite = FALSE,
  self_contained = FALSE,
  branch = "latest_release",
  restart = overwrite,
  permissions = NULL,
  light_version = FALSE,
  excluded_tabs = c("Gene modules", "Annotate", "Inner-fold", "Stdev-fold"),
  shiny_cache_dir = NULL,
  shiny_cache_max_size = NULL,
  ...
)

Arguments

project

path to the project directory

path

path in which to create the bundle.

name

name of the folder in which to create the bundle. The bundle would be created at path/name

overwrite

overwrite bundle if already exists

self_contained

include the source code of MCView 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 MCView changes. When this option is FALSE, the version of MCView which is installed on the server would be loaded, which can be occasionally be different than the one used when creating the app. By default, the code uses the latest MCView release would be used, see branch for other options.

branch

name of the MCView branch to include when self_contained=TRUE. By default, the latest release would be used. You can set this parameter to NULL in order to include the current development version ('master' branch), or set it to any other branch in the 'tanaylab/MCView' github repository.

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.

light_version

create a light version of the bundle, which would not include features that require heavy computation (e.g. changing Marker genes, Gene modules etc.)

excluded_tabs

a character vector of tabs to exclude from the light version of the bundle.

shiny_cache_dir

a path to a directory in which to store shiny cache, can be relative to the bundle, e.g. "./shiny_cache". If set to TRUE, a temporary directory would be set. If NULL - shiny would cache objects in memory.

shiny_cache_max_size

maximum size of the shiny cache in bytes. Default is 200e6.

...

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/name directory which would contain:

  • app.R file.

  • project config and cache.

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 MCView package installed.

Examples

if (FALSE) { # \dontrun{
MCView::create_bundle(project = "PBMC", path = getwd(), name = "PBMC")

# latest release
MCView::create_bundle(project = "PBMC", path = getwd(), name = "PBMC", self_contained = TRUE)

# development version
MCView::create_bundle(
    project = "PBMC",
    path = getwd(),
    name = "PBMC",
    self_contained = TRUE,
    branch = NULL
)

# specific branch
MCView::create_bundle(
    project = "PBMC",
    path = getwd(),
    name = "PBMC",
    self_contained = TRUE,
    branch = "feat@atlas-projection"
)
} # }