S3 section, refactor code structure for readability and maintainability

docs/Cluster_basics/s3.md

@@ -6,7 +6,9 @@
     - [Table of Contents](#table-of-contents)
     - [What is a S3 Storage?](#what-is-a-s3-storage)
     - [How to access](#how-to-access)
-        - [Terminal](#terminal)
+        - [Terminal from IRB cluster](#terminal-from-irb-cluster)
+        - [Open OnDemand](#open-ondemand)
+        - [Mount bucket on local](#mount-bucket-on-local)
     - [How to use it](#how-to-use-it)
         - [Seqera and Nextflow](#seqera-and-nextflow)
         - [Python](#python)
@@ -54,7 +56,7 @@ From now on, access to S3 is only possible via the terminal (e.g., to navigate,
 If you only want to use S3 files in your Nextflow pipelines through [seqera platform](https://cloud.seqera.io/), no
 further setup is needed. Credentials are already configured in the pipelines; you only need to export them.
 
-### Terminal
+### Terminal from IRB cluster
 
 To use it via terminal, once in the IRB cluster:
 
@@ -130,7 +132,74 @@ spack load stu
 stu
 ```
 
-![alt text](https://github.com/lusingander/stu/raw/master/img/demo.gif)
+![stu TUI demo](https://github.com/lusingander/stu/raw/master/img/demo.gif)
+
+### Open OnDemand
+
+In addition to command-line from the IRB cluster, you can also  
+access S3 via Open OnDemand. The Open OnDemand S3 interface is read-only: you can browse and  
+download files, but you cannot modify existing objects or upload new ones from this interface.
+
+1. Go to  
+   [Open OnDemand Dashboard](https://ood.sc.irbbarcelona.org/pun/sys/dashboard/)  
+   and log in with your LDAP credentials.
+2. Click on "Home Directory System installed App".
+
+    ![Open OnDemand Home Directory System app screenshot](../assets/images/ooo-home-directory.png)
+
+3. Select the S3 storage on the left panel and navigate through the folders.  
+   You can read PDFs and text files directly in the browser.  
+   To view Excel or HTML files, you need to download them first.
+
+    ![Open OnDemand S3 storage browser screenshot](../assets/images/ooo-s3.png)
+
+### Mount bucket on local
+
+It is also possible to mount the S3 storage as a local partition (as we do with MacGyver and the workspace/).
+This is a read-only option.
+
+Below are the instructions for Ubuntu. It is also possible on Windows and Mac; see the official IRB documentation:
+[IRB documentation.](https://irb.app.lumapps.com/home/ls/content/5695990366740739/archive-to-s3-minio)
+
+1. Create a conda environment with rclone
+
+    ```bash
+    conda create -n s3 rclone -c conda-forge -y
+    conda activate s3
+    ```
+
+2. Download and run the app from IT
+
+    ```bash
+    wget https://github.com/its-irb/irb-storage-public-scripts/releases/latest/download/minio-rclone-copy-GUI-linux
+    chmod +x minio-rclone-copy-GUI-linux
+    ./minio-rclone-copy-GUI-linux
+    ```
+
+3. Mount:
+
+    Login using your LDAP credentials.
+
+    Select the s3:
+
+![S3 selection screen](../assets/images/s3-1.png)
+
+If your Minio credentials are not available or expired, it will offer to renew them.
+
+![Minio credentials renewal prompt](../assets/images/s3-2.png)
+
+In the destination path, put the s3 bucket name and click "Mount destination folder":
+
+![Mount destination folder dialog](../assets/images/s3-3.png)
+
+And that's it. Now you can access from the file browser and the terminal:
+
+![S3 mounted in file browser](../assets/images/s3-4.png)
+
+![S3 mounted in terminal](../assets/images/s3-5.png)
+
+This tool can be used also for moving data between the netapp and the s3,  
+**but this functionality is still in a testing phase and should be used with caution**.
 
 ## How to use it
 
@@ -139,7 +208,7 @@ stu
 As mentioned, you don’t need to include any credentials explicitly in Seqera to run a job. When accessing S3 data
 from a pipeline, remember to select the secrets and include the info in the config:
 
-![alt text](../assets/images/s3_secrets.png)
+![S3 secrets configuration screenshot](../assets/images/s3_secrets.png)
 
 If using nextflow in a terminal, you can add the credentials to the *nextflow.config*