Add more instructions

Author: jfy133

docs/2025/denbi-registration.md

@@ -5,11 +5,17 @@ For the 2025 edition of the summer school, we will again be using cloud computin
 For the use of the computing nodes you will need to sign up for the services.
 
 This is a **multi-step** process, and you will need to complete the registration before the summer school starts!
-If you get stuck at any point following these steps , follow the instructions in walkthrough from deNBI is available here: [https://cloud.denbi.de/wiki/registration/](https://cloud.denbi.de/wiki/registration/).
+There will be be _multiple_ confirmation emails (up to 6!) sent to your email inbox.
+**Make sure to check and click on any that have a confirmation link**!
+These are all due to European data privacy laws.
 
-The final step of the registration process will be to send your registration to the SimpleVM SPAAMSumScho20251 workshop.
+The final step of the registration process will be to send your registration to the SimpleVM SPAAMSumSch25 workshop.
 Make sure to continue the process until you get to this point!
 
+If you get stuck at any point following these steps, follow the instructions in walkthrough from deNBI is available here: [https://cloud.denbi.de/wiki/registration/](https://cloud.denbi.de/wiki/registration/).
+
+## Instructions
+
 1. Open the registration link [here](https://simplevm.denbi.de/portal/webapp/#/workshops/invitation/095dae97d9f14107bce2f965f7bb6358) <!-- This link should come from the SimpleVM workshop overview page - NOT on the central deNBI portal!-->
    1. You will be redirected to the SimpleVM portal to register
 2. Select an identity provider of an existing account (e.g. institutional account, ORCiD, Google)
@@ -20,17 +26,15 @@ Make sure to continue the process until you get to this point!
 
 3. Register/link this account with LifeSciences AAI/Login (this is a centralised EU level single-sign-on service for EU biology related infrastructure)
 
-   > ⚠ Please be aware that there may be _multiple_ confirmation emails (up to 6 emails) sent to your email inbox and you will need to confirm them any that have a confirmation link! This is due to European data privacy laws.
-
-   > ℹ️ If via the Institutional route you get a 'No user account found' error, press 'Proceed to register for an account'
-
-   > ℹ️ If you get a 'Access denied' error, press 'Proceed to register for an account', continue with 'Proceed to registration'
+   1. If via the Institutional route you get a 'No user account found' error, press 'Proceed to register for an account'
+   2. If you get a 'Access denied' error, press 'Proceed to register for an account', continue with 'Proceed to registration'
+      1. This will send happen on the RI Registrar, to register you to the LifeScience Community
+      2. You will have to confirm registration via a confirmation email
+   3. After registering/linking press continue - continue to the next step even if you get a 'Access denied' error - press 'Proceed to registration'
 
 4. Registering with Elixir Community (a European bioinformatics infrastructure)
-   1. This step may now be combined with step 3! See next point if so. Otherwise ask James for help (see bottom of page)
-5. Register with the deNBI Cloud (German bioinformatics infrastructure)
-6. Consenting for login information to be passed from 'SimpleVM Production'
-7. Once registered, the final page should be a 'Workshop Registration' page.
+5. Consenting for login information to be passed from 'SimpleVM Production'
+6. Once registered, the final page should be a 'Workshop Registration' page.
    1. You should see the description of the summer school, and below a button to register.
    2. If you do not see the button (i.e., the description is cut off by the side bar), close the side bar using the box-and-arrow icon at the top right of the sidebar
 

docs/organisers/denbi-nodesetup.md

@@ -7,29 +7,32 @@
 - Have requested and been granted a deNBI project on [deNBI portal](https://cloud.denbi.de/portal/)
 - Create workshop on [SimpleVM portal](https://simplevm.denbi.de)
   - Projects on Side Bar > Select Project > New Workshop
-- Tutor workflow (required extra step to allow access to all nodes)
+- Go to Workshops side bar > SPAAMSumScho25 > Get invitation link (send to participants and tutors)
+- Tutor workflow (this required extra step to allow access to all nodes)
   - On deNBI Portal > Projects > Add Members to see instructions
   - [New tutor] Send deNBI LifeSicnceRI sign up link
   - [New and old tutors] Send deNBI project sign up link
   - [Admin] Check emails for joining, accept requests
+  - DO NOT MAKE ALL TUTOTRS deNBI ADMIN - OTHER THAN PEOPLE FAMILIAR WITH DENBI PORTAL!
+    - Anyone in the deNBI portal project, can act as tutors in the workshop itself
 - Student workflow (send to ALL participants)
   - Go to [SimpleVM portal](https://simplevm.denbi.de)
   - Go to _workshop_ on sidebar
   - Get both Portal and Share invitation links, send to all participants with instructions on website with workflow instructions
     - Go to SimpleVM invite link
     - Pick log-in and/or register with system of choice
-    - Register elixir
+    - Register LifeScienceRI AAI
     - Confirm email
+    - Register elixir
     - T&Cs Elixir
-    - T&Cs Denbi
-    - Email for SPAAMsumScho
-    - Confirm email
+    - T&Cs Denbi / SimplVM release
+    - Send request to join workshop
     - [Admin approve] (SimpleVM Portal -> Project -> <Project Name/> -> Project Member List > See Applications)
-- Once all invited
+- Once all invited and accepted for the _workshop_ (deNBI portal project alone insufficient!), go to SimpleVM portal.
   - [Admin] SimpleVM: Accept all participant requests on project
   - [Admin] SimpleVM: On workspace page, 'show addable Tutors' and add tutors (remember must still be on the deNBI project too!)
 
-## Creating SimplVM workshop
+## Creating SimpleVM workshop
 
 1. On the [SimpleVM portal](https://simplevm.denbi.de/), go to the 'Projects' section on the sidebar and select SPAAMSumSchoXX
 2. Press 'New Workshop'
@@ -48,27 +51,34 @@
 > The snapshot is: SPAAMSumScho24-FinalPatch1
 
 - Log into [SimpleVM portal](https://simplevm.denbi.de)
-- Go to workshops on side bar
-- 'Create new instances' section > 'New Instance' > Follow workflow
-
-Create a machine:
-
-- de.NBI medium + ephemeral: 14 VCPUs - 32 GB RAM - 50 GB root disk + 150 GB ephemeral disk
-- Research environment: [Guacamole](https://cloud.denbi.de/wiki/simple_vm/customization/#apache-guacamole))
-- Add user (yourself)
-- Start VM
-
-Once spun up, log in and clean up desktop environment
-
+- Go to workshops on side bar > Select the SpaamSumScho25 > 'Create new instances' section > 'New Instance' > Follow workflow
+  - Select workshop
+  - Create a machine:
+    - de.NBI medium + ephemeral: 14 VCPUs - 32 GB RAM - 50 GB root disk + 150 GB ephemeral disk
+    - Research environment: [Guacamole](https://cloud.denbi.de/wiki/simple_vm/customization/#apache-guacamole))
+    - New volume
+      - Volume Name: `SPAAMSumScho20250623`
+      - Mountpath: `/vol/volume`
+      - Volume size 80
+    - Add user (yourself)
+    - Start VM
+
+Switch to Instance tab, and wait for VM to spin up
+
+- Once VM is running, expand info of VM
+- Switch to the 'guacamole' tab
+- Open the link
 - Guacamole user: denbi, denbi
-- Select Ubuntu Server US Keyboard Layout (can also be the recent connection one)
+- Select Ubuntu Server UK Keyboard Layout (can also be the recent connection one)
   - If asked to authenticate color managed device use password below
-- Ubuntu user pass: `denbi` (old: `ogvkyf`)
-- Deactivate screensaver/lockscreen & apperance dark mode
-  - X applications (top left menu on desktop) -> Settings -> Screensaver -> (Tab) Screensaver Disable
+- Ubuntu user pass: `denbi`
+- Deactivate screensaver/lockscreen & appearance dark mode
+  - X applications (top left menu on desktop) -> Settings -> Xfce Screensaver > (Tab) Screensaver Disable
   - X applications (top left menu on desktop) -> Settings -> (Tab) Lock Screen -> Disable
   - X applications (top left menu on desktop) -> Appearance -> Greybird-dark
-- Download and set wallpaper from SPAAM summer school website github repo (assets/media/spaam-background-dark.png - 1920 x 965)
+- Download and set wallpaper from SPAAM summer school website github repo
+  - Download from [here](https://github.com/SPAAM-community/spaam-community.github.io/blob/master/assets/media/spaam-background-darkmode.png) (1920 x 965)
+  - Right click on desktop -> Desktop Settings -> Background -> Select the downloaded image > STyle Centered
 - Turn off unsafe paste warnings in terminal
   - Open Terminal -> Edit -> Preferences -> 'Untick Show unsafe paste dialog'
 
@@ -99,28 +109,34 @@ Now install required general software
 
 Install bioinformatics software
 
-- Install Conda & libmamba
+- Install miniforge (conda)
+
   ```bash
    mkdir ~/bin
    cd ~/bin
-   wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  bash Miniconda3-latest-Linux-x86_64.sh
+   wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+  bash Miniforge3-Linux-x86_64.sh
   ```
-  - Install into `/home/ubuntu/bin/miniconda3`
-  - Run init(ialise): Yes
+
+  - Install into `/home/ubuntu/bin/miniforge3`
+  - Run init(ialise): `yes`
   - To load conda into PATH:`source ~/.bashrc`
   - To turn off base: `conda config --set auto_activate_base false`
   - Restart terminal
-  - Delete Miniconda SH
+  - Delete miniforge SH
+
     ```bash
     cd ~/bin
-    rm Miniconda3-latest-Linux-x86_64.sh
+    rm Miniforge3-Linux-x86_64.sh
     ```
+
   - Set up channels
+
     ```bash
     conda config --add channels bioconda
     conda config --add channels conda-forge
     ```
+
 - Create session conda environments
 
   - Download the environment ymls from https://github.com/SPAAM-community/intro-to-ancient-metagenomics-book/tree/main/assets/envs, and create each env
@@ -279,7 +295,7 @@ On simpleVM workspace
 - Need to mount the volumne (to be created)
 
   - Must contain all software, data
-  - bashrc needs to be updated to point to miniconda install on volume
+  - bashrc needs to be updated to point to miniforge install on volume
 
 - Volume for data/software/saving
   - https://cloud.denbi.de/wiki/simple_vm/volumes/#create-the-volume-file-system-once