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 @@
 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:
 
@@ -132,6 +134,67 @@
 
 ![alt text](https://github.com/lusingander/stu/raw/master/img/demo.gif)
 
+### Open OnDemand
+
+Read-Only Mode — You can browse and download files but cannot modify or upload from this interface.
+
+1. Go to https://ood.sc.irbbarcelona.org/pun/sys/dashboard/ and log in with your LDAP credentials.
+
+2. Click on "Home Directory System installed App".
+
+![alt text](../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.
+
+![alt text](../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/).
+Here are the instructions for ubuntu, but it is also possible using windows and mac, check
+the official IRB documentation.
+[IRB documentation.](https://irb.app.lumapps.com/home/ls/content/5695990366740739/archive-to-s3-minio)
+
+1. Create a conda enviroment with rclone.
+```
+conda create -n s3 rclone -c conda-forge -y
+conda activate s3
+```
+
+2. Download and run the app from IT
+```
+wget https://github.com/its-irb/irb-storage-public-scripts/releases/latest/download/minio-rclone-copy-GUI-linux
+chmod minio-rclone-copy-GUI-linux
+./minio-rclone-copy-GUI-linux
+```
+
+3. Mount:
+
+Login using your LDAP credentials.
+
+Select the s3:
+
+![alt text](../assets/images/s3-1.png)
+
+If your Minio credentials are not available or expired, it will offer to renew them.
+
+![alt text](../assets/images/s3-2.png)
+
+In the estination path, put the s3 bucket name and click "Mount destination folder":
+
+![alt text](../assets/images/s3-3.png)
+
+And that's it. Now you can access from the file browser and the terminal:
+
+![alt text](../assets/images/s3-4.png)
+
+![alt text](../assets/images/s3-5.png)
+
+This tool can be used also for moving data between the netapp and the s3, **but it still on testing phase**.
+
 ## How to use it
 
 ### Seqera and Nextflow