Änderungen Readme & beim Setzen der Systemvariablen

R/2025-10-27_JF_R_Galaxy_functions.R

@@ -953,52 +953,59 @@ galaxy_history_size <- function(history_id,
 #' \dontrun{
 #' galaxy_set_credentials(
 #'   api_key = "your-secret-key",
-#'   galaxy_url = "https://usegalaxy.eu",
 #'   username = "your-username",
-#'   password = "your-password"
+#'   password = "your-password",
+#'   galaxy_url = "https://usegalaxy.eu"
 #' )
 #' }
 #'
 #' @export
 galaxy_set_credentials <- function(api_key = NULL,
-                                   galaxy_url = NULL,
-                                   username = NULL,
-                                   password = NULL,
-                                   overwrite = TRUE) {
+                                  username = NULL,
+                                  password = NULL,
+                                  galaxy_url = "https://usegalaxy.eu",
+                                  overwrite = TRUE) {
 
+  # rename inputs
   values <- list(
     GALAXY_API_KEY = api_key,
     GALAXY_URL = galaxy_url,
     GALAXY_USERNAME = username,
     GALAXY_PASSWORD = password
   )
 
-  if(galaxy_has_key() & overwrite) {
+  # replace previous key
+  if (galaxy_has_key() & overwrite) {
     warning("There was already an API key set which will be overwritten")
   }
 
+  # loop over inputs
   set_values <- list()
-
   for (name in names(values)) {
     value <- values[[name]]
 
+    # skip empty values
     if (is.null(value)) {
       next
     }
 
+    # stop at empty strings
     if (!nzchar(value)) {
       stop(name, " must be a non-empty string.")
     }
 
+    # check whether environmental variable is set already
     existing <- Sys.getenv(name, unset = NA_character_)
     if (!isTRUE(overwrite) && !is.na(existing) && nzchar(existing)) {
       stop(name, " already set; use overwrite = TRUE to replace.")
     }
 
-    Sys.setenv(structure(value, names = name))
+    # sets variable
+    do.call(Sys.setenv, as.list(structure(value, names = name)))
     set_values[[name]] <- value
   }
 
+  # returns list of set variables
   invisible(set_values)
 }
 

README.md

@@ -1,6 +1,6 @@
-# GalaxyRTools
+# GalaxyR
 
-**GalaxyRTools** is an R package for programmatic interaction with the **Galaxy API** (tested primarily against [Galaxy Europe](https://usegalaxy.eu)).  
+**GalaxyR** is an R package for programmatic interaction with the **Galaxy API** (tested primarily against [Galaxy Europe](https://usegalaxy.eu)).  
 It allows you to manage histories, upload data, run tools and workflows, wait for jobs to complete, and download results — all directly from R.
 
 This package is designed for **automation, reproducibility, and scripting**, not UI replacement.
@@ -42,12 +42,13 @@ You can either:
 
 ### Option 1: Set it once per session
 ```r
-galaxy_set_api_key("YOUR_GALAXY_API_KEY")
+galaxy_set_credentials("your-secret-key")
 ```
 
 ### Option 2: Add it to `~/.Renviron` (recommended)
 ```
-GALAXY_API_KEY=your-secret-key
+#usethis::edit_r_environ()
+GALAXY_API_KEY = your-secret-key
 ```
 
 Restart R after editing `.Renviron`.
@@ -102,7 +103,7 @@ job_id <- galaxy_run_tool(
     text_input = "added text",
     infile = list(
       src = "hda",
-      id  = file_id$id
+      id  = file_id
     ),
     options = "header"   # add text at the top of the file
   )
@@ -178,8 +179,8 @@ Terminal states:
 
 ---
 
-Author: 
-Julian Frey
-Chair of Forest Growth and Dendroecology
+Author:<br>
+Julian Frey<br>
+Chair of Forest Growth and Dendroecology<br>
 University of Freiburg
 

inst/CITATION

@@ -0,0 +1,10 @@
+citHeader("To cite GalaxyR in publications use:")
+
+citEntry(
+  entry    = "misc",
+  title    = "GalaxyR",
+  author   = "Julian Frey",
+  year     = "2026",
+  url      = "https://github.com/JulFrey/GalaxyR",
+  textVersion = "Frey, J. (2026) GalaxyR. https://github.com/JulFrey/GalaxyR"
+)