## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  comment = "#>", collapse = TRUE, fig.align = 'center',
  eval = AnVIL::gcloud_exists()
)

## ----eval = FALSE-------------------------------------------------------------
#  if (!require("BiocManager"))
#      install.packages("BiocManager")
#  BiocManager::install("AnVILWorkflow")

## ----results="hide", message=FALSE, warning=FALSE-----------------------------
#  library(AnVIL)
#  library(AnVILGCP)
#  library(AnVILWorkflow)

## -----------------------------------------------------------------------------
#  gcloud_exists()

## ----eval=FALSE---------------------------------------------------------------
#  devtools::install_github("rstudio/cloudml")
#  cloudml::gcloud_install()

## ----eval=FALSE---------------------------------------------------------------
#  accountEmail <- "YOUR_EMAIL@gmail.com"
#  billingProjectName <- "YOUR_BILLING_ACCOUNT"
#  
#  setCloudEnv(accountEmail = accountEmail,
#              billingProjectName = billingProjectName)

## ----echo=FALSE---------------------------------------------------------------
#  ## In case the environment is set already.
#  accountEmail <- AnVILGCP::gcloud_account()
#  billingProjectName <- AnVILGCP::gcloud_project()
#  
#  setCloudEnv(accountEmail = accountEmail,
#              billingProjectName = billingProjectName,
#              message = FALSE)

## -----------------------------------------------------------------------------
#  analysis <- "salmon"

## -----------------------------------------------------------------------------
#  AnVILBrowse("malaria")
#  AnVILBrowse("resistance")
#  AnVILBrowse("resistance", searchFrom = "workflow")

## ----echo=FALSE, eval=FALSE, error=TRUE---------------------------------------
#  # If you attempt to clone the template workspace using the existing
#  # workspaceName, you will get the error message.
#  cloneWorkspace(workspaceName = "salmon_test", analysis = analysis)

## -----------------------------------------------------------------------------
#  salmonWorkspaceName <- basename(tempfile("salmon_")) # unique workspace name
#  salmonWorkspaceName
#  cloneWorkspace(workspaceName = salmonWorkspaceName, analysis = analysis)

## ----cleanup, echo=FALSE, message=FALSE, error=TRUE, warning=FALSE------------
#  ## Delete test workspaces
#  resp <- AnVIL::Terra()$deleteWorkspace(workspaceNamespace = billingProjectName,
#                                         workspaceName = salmonWorkspaceName)
#  rm(resp)

## ----eval=FALSE---------------------------------------------------------------
#  cnvWorkspaceName <- basename(tempfile("cnv_")) # unique workspace name
#  cnvWorkspaceName
#  cloneWorkspace(workspaceName = cnvWorkspaceName,
#                 templateName = "Tumor_Only_CNV")

## ----echo=FALSE---------------------------------------------------------------
#  ## workspace used in this vignette
#  salmonWorkspaceName <- "salmon_test"

## -----------------------------------------------------------------------------
#  config <- getWorkflowConfig(workspaceName = salmonWorkspaceName)
#  current_input <- currentInput(salmonWorkspaceName, config = config)
#  current_input

## -----------------------------------------------------------------------------
#  new_input <- current_input
#  new_input[4,4] <- "athal_index"
#  new_input
#  
#  updateInput(salmonWorkspaceName, inputs = new_input, config = config)

## ----eval=FALSE---------------------------------------------------------------
#  runWorkflow(slamonWorkspaceName, config = config)
#  # You should provide the inputName from the followings:
#  # [1] "AnVILBulkRNASeq_set"
#  #> Error in runWorkflow(salmonWorkspaceName):

## -----------------------------------------------------------------------------
#  runWorkflow(salmonWorkspaceName,
#              inputName = "AnVILBulkRNASeq_set",
#              config = config)

## -----------------------------------------------------------------------------
#  submissions <- monitorWorkflow(workspaceName = salmonWorkspaceName)
#  submissions

## -----------------------------------------------------------------------------
#  stopWorkflow(salmonWorkspaceName)

## -----------------------------------------------------------------------------
#  submissions <- monitorWorkflow(workspaceName = "Bioconductor-Workflow-DESeq2")
#  submissions

## ----no-run-examples, eval=FALSE----------------------------------------------
#  ## Output from the successfully-done submission
#  successful_submissions <- submissions$submissionId[submissions$succeeded == 1]
#  out <- getOutput(workspaceName = "Bioconductor-Workflow-DESeq2",
#                   submissionId = successful_submissions[1])

## ----echo=FALSE---------------------------------------------------------------
#  ## Save the previous submission results from the above chunk
#  ## write.table(out, "vignettes/salmon_test_outputs.csv")
#  out <- read.table("salmon_test_outputs.csv", header = TRUE) %>%
#      tibble::tibble()

## -----------------------------------------------------------------------------
#  head(out)

## ----eval=TRUE----------------------------------------------------------------
sessionInfo()