From fa96765022071a6ed303757780e63cf3819eab79 Mon Sep 17 00:00:00 2001
From: Zoe <59600387+zoeschindler@users.noreply.github.com>
Date: Mon, 19 Jan 2026 18:07:18 +0100
Subject: [PATCH 1/5] Update README.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Es gibt die Funktion "galaxy_set_api_key()" nicht. Es gibt nur "galaxy_set_credentials()" und das will unbedingt für alles einen Input und funktioniert bei mir nicht (die Zeile "Sys.setenv(structure(value, names = name))" wirft einen Fehler). Ich würde da auch "https://usegalaxy.eu" als default setzen.
---
 README.md | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index fe24128..1c0eece 100644
--- a/README.md
+++ b/README.md
@@ -42,12 +42,16 @@ You can either:
 
 ### Option 1: Set it once per session
 ```r
-galaxy_set_api_key("YOUR_GALAXY_API_KEY")
+galaxy_set_credentials(
+  api-key = "your-secret-key",
+  username = "your-username",
+  password = "your-secret-password"
+)
 ```
 
 ### Option 2: Add it to `~/.Renviron` (recommended)
 ```
-GALAXY_API_KEY=your-secret-key
+GALAXY_API_KEY = "your-secret-key"
 ```
 
 Restart R after editing `.Renviron`.

From 4887fcbe8900e41758f8f2674a3ba10a64f0062b Mon Sep 17 00:00:00 2001
From: Zoe <59600387+zoeschindler@users.noreply.github.com>
Date: Mon, 19 Jan 2026 18:33:13 +0100
Subject: [PATCH 2/5] Update README.md

---
 README.md | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 1c0eece..8cb053c 100644
--- a/README.md
+++ b/README.md
@@ -42,11 +42,7 @@ You can either:
 
 ### Option 1: Set it once per session
 ```r
-galaxy_set_credentials(
-  api-key = "your-secret-key",
-  username = "your-username",
-  password = "your-secret-password"
-)
+galaxy_set_credentials("your-secret-key")
 ```
 
 ### Option 2: Add it to `~/.Renviron` (recommended)

From f1386e53765ae7565966d32f8d530647fe7a64ab Mon Sep 17 00:00:00 2001
From: Zoe <59600387+zoeschindler@users.noreply.github.com>
Date: Mon, 19 Jan 2026 18:44:06 +0100
Subject: [PATCH 3/5] Update README.md

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 8cb053c..cc5bdfb 100644
--- a/README.md
+++ b/README.md
@@ -47,6 +47,7 @@ galaxy_set_credentials("your-secret-key")
 
 ### Option 2: Add it to `~/.Renviron` (recommended)
 ```
+#usethis::edit_r_environ()
 GALAXY_API_KEY = "your-secret-key"
 ```
 

From 3fccdae29716ff93efb49c9e48b9b96969854a1d Mon Sep 17 00:00:00 2001
From: Zoe <59600387+zoeschindler@users.noreply.github.com>
Date: Mon, 19 Jan 2026 18:45:43 +0100
Subject: [PATCH 4/5] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index cc5bdfb..ca355f2 100644
--- a/README.md
+++ b/README.md
@@ -48,7 +48,7 @@ galaxy_set_credentials("your-secret-key")
 ### Option 2: Add it to `~/.Renviron` (recommended)
 ```
 #usethis::edit_r_environ()
-GALAXY_API_KEY = "your-secret-key"
+GALAXY_API_KEY = your-secret-key
 ```
 
 Restart R after editing `.Renviron`.

From c0c073c2c53a63cdfcbdc2b3607336df3834ef38 Mon Sep 17 00:00:00 2001
From: Zoe <59600387+zoeschindler@users.noreply.github.com>
Date: Mon, 19 Jan 2026 18:56:03 +0100
Subject: [PATCH 5/5] Update README.md

Geht nicht mit file_id$id.
---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index ca355f2..60942aa 100644
--- a/README.md
+++ b/README.md
@@ -103,7 +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
   )
@@ -179,8 +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