---
title: "Deploy"
linkTitle: "Deploy"
type: docs
weight: 9
---
*****
## How to deploy the application

The easiest way to deploy SPS is [shinyapps.io{blk}](https://www.shinyapps.io/). 
To get started, it is required to create a *shinyapps.io* account. Please follow this [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html) 
with all the instructions to create an account. There are other ways to deploy, like 
AWS or Google Cloud with a custom Shiny server. There are a lot of tutorials to 
deploy the app other than *shinyapps.io*. We only use *shinyapps.io* as the example 
here to discuss how to deploy. 

## Get started

After you have created a `SPS` project, it is in a deploy-ready state, which means 
you can deploy it as soon as you create the project. 

We have created some important helper code in `deploy.R` under the project root for you. 
1. Read the [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html) 
2. After you have the accounts and token set up according to the tutorial, open 
   `deploy.R`.
   - If you have used Bioconductor packages (mostly likely yes, unless you do not use 
     the default modules), run the options line in R console before deploy, which is this
     
     ```r
     options(repos = BiocManager::repositories())
     ```
     
   - If you want to use develop version of Bioconductor packages (not recommended),
     uncomment following lines and follow the instructions in the file.
    
     ```r
     # repos <- BiocManager::repositories()
     # devel <- "3.13"
     # repos[length(repos) + 1] <- paste0("https://bioconductor.org/packages/", devel, "/bioc")
     # names(repos)[length(repos)] <- "BioC"
     # options(repos = repos)
     # getOption("repos")
     ```
     
   - If you wish *shinyapps.io* to install [SPS modules](/sps/modules/), copy and 
     **uncomment** following lines for the modules to `global.R` file below the 
     line `# load additional libraries that you want to use below`.
     ```r
     ## Workflow module
     # requireNamespace("DOT"); requireNamespace("networkD3"); requireNamespace("pushbar")
     # requireNamespace("readr"); requireNamespace("rhandsontable"); requireNamespace("shinyTree")
     # requireNamespace("systemPipeR"); requireNamespace("systemPipeRdata"); requireNamespace("zip")
     
     ## RNA-Seq module
     # requireNamespace("DESeq2"); requireNamespace("Rtsne"); requireNamespace("SummarizedExperiment")
     # requireNamespace("UpSetR"); requireNamespace("ape"); requireNamespace("ggtree")
     # requireNamespace("glmpca"); requireNamespace("pheatmap"); requireNamespace("systemPipeR")
     
     ## Quick ggplot module
     # requireNamespace("esquisse")
     ```
   - The last section in `deploy.R` is some helper code to set up the account and 
     deploy the app programmatically. If you use the 
     [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html),
     there is no need to do this section.
   - Save your changes in the `global.R`.

## Deploy in Rstudio
We recommend you to deploy the app with Rstudio. If you have set up your *shinyapps.io*
account, we are ready to go. 

<center>

![](../img/deploy.png)

</center>

### A 
1. Open `global.R` in Rstudio, use the "Run App" button to make sure your app 
can be run without problems locally. 
2. Run `options(repos = BiocManager::repositories())` and other Bioconductor 
   set up code as listed above.
3. Click the button next to "Run App" and choose "Publish Application..."

### B
4. If you have set up your account correctly, you should see your account to the 
   right panel. 
5. Select all the files of your SPS project. 
6. Change the app "Title" to what you want.
7. hit "Publish".

## RAM requirement

If you wish to load the workflow and/or RNAseq module(s) on *shinyapps.io*, you need 
at least **2GB** of memory. Unfortunately, these 2 modules depend heavily on Bioconductor 
packages and these packages are not light-weighted. The max RAM for free account 
on *shinyapps.io* is 1GB which means you either need to upgrade your account or 
use other server to deploy your app. 

If you decide to not load these modules which will allow you to deploy the app 
with a free account, change the settings to unload these modules in 
[app options](/sps/adv_features/config/#app-options) in `global.R`.