a few change in galaxy management doc (simplification)

docs/AnalyseGenomes_2023/Install_tools.md

@@ -24,7 +24,7 @@ Select `Manage API Key`, click `Create a new Key`, and copy the current API key
 
 and press the ++return++ key
 
-The tool installation should start immediately and last for about 11 minutes (you should
+The tool installation should start immediately and last for about 15 minutes (you should
 see tools installing one at a time)
 
 ---

docs/AnalyseGenomes_2023/deploy-galaxy-server.md

@@ -44,7 +44,7 @@ Naturally, the nextime you start Galaxy, the process will be quickly skipped.
 
 <center>
 
-![](images/coffee_time.png)
+![](images/coffee_time.png){width="200"}
 </center>
 
 When deployment is finished, you will see the following log in the console:

docs/AnalyseGenomes_2023/manage_VM.md

@@ -4,19 +4,17 @@ If you read this, you have probably launched at least one time a Google Virtual
 
 A few rules to get your life easier during the rest of this training:
 
-- ==**Never** stop your VM, instead **suspend** it==
+- ==**Avoid** stopping your VM, instead **suspend** it==
 
   Stopping your VM is like stopping your PC or you laptop.
 
   You will stop everything and will have to literally reboot everything, including
-  the Galaxy server. It is not that difficult actually (see below). However, you have
-  many things to learn these days and it better not use your time and memory just to do
-  that.
+  the Galaxy server. It is not that difficult actually, but it takes a bit more time.
 
   Instead, **Suspending** your VM is like putting your PC in sleeping mode, or closing
   the lid of your laptop.
 
-  Thus, remember, at the end of the day or whenever you will not use your VM for a long
+  Thus, remember, at the end of the day or whenever you are not going to use your VM for a long
   time, use:
 
   ![suspend](images/suspend.png)

docs/AnalyseGenomes_2023/manage_galaxy.md

@@ -1,86 +1,26 @@
-??? info "Galaxy server commands, quick reminder"
-    Check that the server is running
+!!! info "Galaxy server commands, quick reminder"
+    Check that the server is running and see last logs
     ```
-    galaxyctl status
+    systemctl status galaxy*.service
+
+    # the three services Galaxy celery-beat, celery and gunicorn must be
+    # active and running (green)
     ```
     Restart the server
     ```
-    galaxyctl restart
+    systemctl restart galaxy.target
     ```
     Start the Galaxy server, if for any reason it is down
     ```
-    galaxyctl start
+    systemctl start galaxy.target
     ```
-    Follow the activity of Galaxy
+    Follow the activity of the web part only (gunicorn) of the Galaxy server:
     ```
-    galaxyctl follow
-    ```
-    Follow the activity of the web part only of the Galaxy server:
-    ```
-    tail -f /root/galaxy/database/gravity/log/gunicorn.log
+    systemctl status galaxy-gunicorn.service
     ```
 
 ## A graphical view of the Galaxy server states and the commands to control them
 
 ![Galaxy server states](images/GalaxyStates-AG2022.png){width="1200"}
 
-## Commands to control the Galaxy server
-
-### The Galaxy server virtual environment
-
-First of all, you must keep in mind that the next commands are only accessible through
-the virtual environment that has been installed during the Galaxy deployment.
-
-It is easy to remember that you are actually working through this virtual environment,
-because it is indicated in you shell prompt as `(.venv)` when you connect as the admin
-user:
-
-Thus, when you execute `sudo -i`, you immediately see:
-```
-(.venv) root@bare-galaxy:~#
-```
-
-You don't have to worry about activating the .venv environment because during the
-deployment we automated this activation as soon as you log in to the admin account.
-
-However, if for any reason you were disconnected from the virtual environment (loosing
-the `.venv` in the prompt), you can always reactivate it by typing:
-
-```
-source ~/galaxy/.venv/bin/activate
-```
-
-You can experiment this by
-
-1. Deactivating the virtual environment
-  ```
-  deactivate
-  ```
-2. Reactivating it:
-  ```
-  source ~/galaxy/.venv/bin/activate
-  ```
-
-### The useful commands to control the Galaxy server
-
-1. Check that the server is running
-  ```
-  galaxyctl status
-  ```
-2. Restart the server
-  ```
-  galaxyctl restart
-  ```
-3. Start the Galaxy server, if for any reason it is down
-  ```
-  galaxyctl start
-  ```
-4. Follow the activity of Galaxy
-  ```
-  galaxyctl follow
-  ```
-5. Follow the activity of the web part only of the Galaxy server:
-  ```
-  tail -f /root/galaxy/database/gravity/log/gunicorn.log
-  ```
-
+---