update ubuntu manual + observable (#129)

* include ubuntu manual

* Update docs/manuals/data-transfer-options.qmd

* Update docs/workspaces/plain/ubuntu.qmd

* Update docs/workspaces/plain/ubuntu.qmd

---------

Co-authored-by: Jelle Treep <40466121+jelletreep@users.noreply.github.com>

Author: ShaivanBhagat

docs/manuals/data-transfer-options.qmd

@@ -43,7 +43,7 @@ html`
 
 // Input: Workspace type
 viewof workspaceType = Inputs.select(
-  ["Python Workbench (Desktop)", "Python Workbench (CLI)", "Jupyter Notebook", "VRE Lab", "Windows"],
+  ["Python Workbench (Desktop)", "Python Workbench (CLI)", "Jupyter Notebook", "VRE Lab", "Ubuntu (Desktop)", "Ubuntu (CLI)", "Windows"],
   {label: "What workspace are you using?", value: "Python Workbench (Desktop)", width: "auto"}
 )
 
@@ -66,12 +66,14 @@ viewof skillLevel = Inputs.radio(
 )
 
 // Helper to check workspace type
-isDesktop = workspaceType === "Python Workbench (Desktop)" || workspaceType === "Windows"
+isDesktop = workspaceType === "Python Workbench (Desktop)" || workspaceType === "Windows" || workspaceType === "Ubuntu (Desktop)"
 isPythonDesktop = workspaceType === "Python Workbench (Desktop)"
 isPythonCLI = workspaceType === "Python Workbench (CLI)"
 isJupyter = workspaceType === "Jupyter Notebook"
 isVRELab = workspaceType === "VRE Lab"
 isWindows = workspaceType === "Windows"
+isUbuntuDesktop = workspaceType === "Ubuntu (Desktop)"
+isUbuntuCLI = workspaceType === "Ubuntu (Server/CLI)"
 
 // Get all applicable tools based on selections
 allOptions = {
@@ -83,6 +85,8 @@ allOptions = {
     if (isDesktop) {
       let ibridgesNote = isWindows ? 
         'Pre-installed on "Windows with iBridges" flavor' : 
+        (isUbuntuDesktop || isUbuntuCLI) ?
+        'iBridges needs to be installed' :
         'Pre-installed';
       
       options.push({
@@ -100,7 +104,7 @@ allOptions = {
       tool: "iBridges CLI",
       link: "ibridges.html",
       skillLevel: "Intermediate (CLI)",
-      pros: ["Pre-installed", "Works on all workspaces", "Supports all file sizes"],
+      pros: ["Pre-installed on most workspaces", "Works on all workspaces", "Supports all file sizes"],
       cons: ["Requires command line knowledge"],
       bestFor: ["Users with CLI experience", "All file sizes"]
     });

docs/workspaces/plain/ubuntu.qmd

@@ -7,8 +7,8 @@ login:
 - cli
 os_flavor: linux
 os:
-- Ubuntu 20.04
 - Ubuntu 22.04
+- Ubuntu 24.04
 data:
 - ResearchDrive
 - irods-icommands
@@ -19,11 +19,27 @@ packages:
 gpu: true
 admin: true
 support: SURF
-workspace_cuda: Ubuntu 2204 with CUDA
+workspace_cuda: Ubuntu 22.04 with CUDA/Ubuntu Desktop 22.04 CUDA
 ---
 
 ## Description
 
+Surf Research Cloud allows you to use Ubuntu workspaces with various configurations:
+
+**Command-line interface:**
+
+- Ubuntu 22.04 - SUDO enabled
+- Ubuntu 24.04 - SUDO enabled  
+- Ubuntu 22.04 with CUDA (GPU support)
+
+**Desktop (Graphical interface):**
+
+- Ubuntu Desktop 22.04
+- Ubuntu Desktop 24.04
+- Ubuntu Desktop 22.04 CUDA (GPU support)
+
+Simply choose one of these [catalog items](../../glossary.qmd#catalog-item) in the workspace creation wizard.
+
 {{< include ../partials/_cuda.qmd >}}
 
 
@@ -33,9 +49,52 @@ workspace_cuda: Ubuntu 2204 with CUDA
 
 ## Access
 
+**Command Line only workspaces:** Access via [SSH](../../first-steps.qmd#ssh). By clicking the yellow Access button for the workspace in the dashboard of SURF Research Cloud, you will be prompted to open a command line interface on your local pc/laptop to connect to your workspace via SSH. If you already have an ssh key pair set up, type `yes` to trust the workspace and you will be connected to your SURF Ubuntu workspace.
+
+To set up an ssh key pair for the first time, see the [setting up SSH access manual](https://servicedesk.surf.nl/wiki/spaces/WIKI/pages/195854434/Workspace+access+with+SSH).
+
+**Desktop workspaces:** You can [access Ubuntu Desktop workspaces as a remote desktop in your browser](../../first-steps.qmd#browser-access-to-a-desktop-environment), authenticating via Single-Sign On with your institutional login details. 
+
 ## Data transfer options
 
+Use this table to find the appropriate data transfer method for your situation:
+
+| Data Source | Recommended Tool | Best For | Skill Level |
+|------------|------------------|----------|-------------|
+| Yoda/iRODS | [iBridges](../../manuals/ibridges.qmd) | All file sizes, GUI (Desktop) and CLI access | Beginner to Intermediate |
+| Yoda/iRODS | [iCommands](../../manuals/icommands.qmd) | Large datasets, transfer automation, CLI | Intermediate (CLI) |
+| SURFdrive, ResearchDrive| [rclone](../../manuals/rclone-researchcloud.qmd) | Cloud storage sync, scheduled transfers | Intermediate (CLI) |
+| Your PC/laptop | [scp](../../manuals/ssh-data-transfer-methods.qmd) | Direct one-time transfers | Intermediate (CLI) |
+| Your PC/laptop | [rsync](../../manuals/ssh-data-transfer-methods.qmd) | Sync or repeated transfers | Intermediate (CLI) |
+| Your PC/laptop (Windows only) | [MobaXterm](https://mobaxterm.mobatek.net/) | Graphical SSH/SFTP client | Intermediate |
+| Your PC/laptop | [Cyberduck](https://servicedesk.surf.nl/wiki/spaces/WIKI/pages/112592488/Upload+data+to+a+workspace+with+Cyberduck)| Graphical SFTP client | Intermediate |
+| GitHub/GitLab | [git clone](../../manuals/git-clone.qmd) | Code repositories, version control | Intermediate (CLI) |
+
+
+::: {.callout-note collapse = "true"}
+## Transferring from OneDrive
+OneDrive is currently not directly supported with rclone for UU accounts. To transfer files from OneDrive:
+
+1. Download (preferably compress/zip) files from OneDrive to your local PC
+2. Transfer from your PC to the workspace using one of the methods above
+:::
+
+{{< include ../partials/_data_transfer.qmd >}}
+
 ## Usage
 
+**Installing software packages**
+
+You can install system packages by running the following command in the terminal:
+
+```bash
+# Update package lists
+sudo apt update
+
+# Install a package
+sudo apt install package-name
+```
+
 ## Tips
 
+[Contact us](../../contact.qmd) if you have any questions or need help with your workspace and with installing additional software packages.