From d85a2df40365da5594f8da38a039d2de70afaafd Mon Sep 17 00:00:00 2001
From: Thomas Rauter <rauterthomas0@gmail.com>
Date: Sat, 28 Sep 2024 13:37:11 +0200
Subject: [PATCH] updated dependency version of openxl and Docker instructions
 vignette

---
 DESCRIPTION                       |  2 +-
 vignettes/Docker-instructions.Rmd | 52 ++++++++++++++++++++++++++++++-
 2 files changed, 52 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fc1ae0c..8516938 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,7 @@ Imports:
     ggrepel(>= 0.9.5),
     here(>= 1.0.1),
     limma(>= 3.58.1),
-    openxlsx(>= 4.2.6.1),
+    openxlsx(>= 4.2.5.2),
     patchwork(>= 1.2.0),
     pheatmap(>= 1.0.12),
     progress(>= 1.2.3),
diff --git a/vignettes/Docker-instructions.Rmd b/vignettes/Docker-instructions.Rmd
index 3f45aaa..0f2216b 100755
--- a/vignettes/Docker-instructions.Rmd
+++ b/vignettes/Docker-instructions.Rmd
@@ -9,12 +9,61 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+```{=html}
+<style>
+.sourceCode pre {
+  background-color: #f7f7f7;
+  padding: 10px;
+  border: 1px solid #ccc;
+  border-radius: 5px;
+  overflow-x: auto;
+  position: relative;
+}
+
+.copy-btn {
+  position: absolute;
+  top: 10px;
+  right: 10px;
+  border: none;
+  background: #4CAF50;
+  color: white;
+  padding: 5px 10px;
+  cursor: pointer;
+  border-radius: 5px;
+}
+
+.copy-btn:hover {
+  background: #45a049;
+}
+</style>
+```
+
+<script>
+document.addEventListener("DOMContentLoaded", function() {
+  document.querySelectorAll(".sourceCode pre").forEach(function(block) {
+    var button = document.createElement("button");
+    button.innerHTML = "Copy";
+    button.className = "copy-btn";
+    block.appendChild(button);
+
+    button.addEventListener("click", function() {
+      var code = block.innerText;
+      navigator.clipboard.writeText(code).then(function() {
+        button.innerHTML = "Copied!";
+        setTimeout(function() {
+          button.innerHTML = "Copy";
+        }, 2000);
+      });
+    });
+  });
+});
+</script>
+
 # Pulling the `Docker` Container
 
 Pull `Docker` container:
 
 ```{r eval=FALSE}
-# Docker Hub repo still private, will make it public then
 docker pull thomasrauter/splineomics:0.1.0
 ```
 
@@ -33,6 +82,7 @@ docker run -it -d \
     -v $(pwd)/output:/home/rstudio/output \
     -p 8888:8787 \
     -e PASSWORD=123 \
+    -u $(id -u):$(id -g) \  # Ensure same user/group ID as host
     --name splineomics \
     thomasrauter/splineomics:0.1.0
 ```