From e8212c30bdd8ce069601969a43760808909db739 Mon Sep 17 00:00:00 2001
From: Scott Chamberlain <sachamber@fredhutch.org>
Date: Tue, 27 Aug 2024 15:32:20 -0700
Subject: [PATCH] fix #22 fix install line for rcromwell

---
 vignettes/proofr.Rmd    | 22 +++++++++++-----------
 vignettes/proofr.Rmd.og |  2 +-
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/vignettes/proofr.Rmd b/vignettes/proofr.Rmd
index f295c2f..d46ea98 100644
--- a/vignettes/proofr.Rmd
+++ b/vignettes/proofr.Rmd
@@ -12,7 +12,7 @@ vignette: >
 Load `proofr`
 
 
-```r
+``` r
 library(proofr)
 ```
 
@@ -21,7 +21,7 @@ library(proofr)
 Run the function `proof_authenticate()`, which calls the PROOF API with your username and password, and returns an API token (an alphanumeric string).
 
 
-```r
+``` r
 my_proof_token <- proof_authenticate("username", "password")
 my_proof_token
 #> xyGKibGctQ92rmMKKb39q43XgPxGCmrWoX7NZtamTjDP
@@ -32,7 +32,7 @@ my_proof_token
 Alternatively, save your API token directly as an environment variable named `PROOF_TOKEN` so that it can be used by other `proofr` functions without exposing your token in your code.  To do so, run the following: 
 
 
-```r
+``` r
 Sys.setenv("PROOF_TOKEN" = proof_authenticate("username", "password"))
 ```
 
@@ -41,7 +41,7 @@ Sys.setenv("PROOF_TOKEN" = proof_authenticate("username", "password"))
 Start a PROOF server using the `proof_start()` function:
 
 
-```r
+``` r
 proof_start()
 ```
 Note: `proofr` assumes you only have one server running; if you've started a server using the app, you'll need to stop that server before starting one in R via `proofr`. 
@@ -49,7 +49,7 @@ Note: `proofr` assumes you only have one server running; if you've started a ser
 Get metadata about the PROOF server you have started, including the URL of the API, using `wait=TRUE` so that it doesn't return data until the server is fully ready to use.  
 
 
-```r
+``` r
 metadata <- proof_status(wait = TRUE)
 cromwell_url <- metadata$cromwellUrl
 cromwell_url
@@ -60,10 +60,10 @@ cromwell_url
 Load  `rcromwell`
 
 
-```r
+``` r
 if (!requireNamespace("rcromwell", quietly=TRUE)) {
   install.packages("pak")
-  pak::pak("rcromwell")
+  pak::pak("getwilds/rcromwell")
 }
 library(rcromwell)
 library(httr)
@@ -74,21 +74,21 @@ There are two options for setting the URL in `rcromwell`.
 The first option is to set the Cromwell server URL to be recognized by `rcromwell` with `cromwell_config`
 
 
-```r
+``` r
 cromwell_config(cromwell_url)
 ```
 
 The other option is to pass the url to each function, for example:
 
 
-```r
+``` r
 cromwell_jobs(url = cromwell_url)
 ```
 
 In addition to setting the Cromwell URL, your PROOF API token is also required for HTTP requests to your server. After getting your PROOF token you can set it as the env var `PROOF_TOKEN`, or pass it to the `rcromwell` functions, for example:
 
 
-```r
+``` r
 cromwell_jobs(url = cromwell_url, token = my_proof_token)
 ```
 
@@ -98,7 +98,7 @@ cromwell_jobs(url = cromwell_url, token = my_proof_token)
 As an example, `cromwell_version()` checks the version of your Cromwell server
 
 
-```r
+``` r
 cromwell_version()
 #> $cromwell
 #> [1] "84"
diff --git a/vignettes/proofr.Rmd.og b/vignettes/proofr.Rmd.og
index bb6de78..8dff75b 100644
--- a/vignettes/proofr.Rmd.og
+++ b/vignettes/proofr.Rmd.og
@@ -63,7 +63,7 @@ Load  `rcromwell`
 ```{r setup-rcromwell}
 if (!requireNamespace("rcromwell", quietly=TRUE)) {
   install.packages("pak")
-  pak::pak("rcromwell")
+  pak::pak("getwilds/rcromwell")
 }
 library(rcromwell)
 library(httr)