CONNECT TO YOUR GALAXY SERVER

Once your VM is up and running, its state indicator turns green.

In addition to the internal IP address (which you will not use), an external IP address is also attributed to your VM (red ellipsis in the above screenshot).

This is the address that you are going to use to reach the web interface of your Galaxy server. All you have to do is to click on it.

When you have started your VM, a lot of events were triggered to activate the Galaxy server, its job manager and its web frontend. This may take 2-3 minutes, even after the instance turned green in the GCE control panel. Thus, if this error web page is returned when you click the external address for the first time,

502 Bad Gateway

nginx/1.24.0 (Ubuntu)

Do not panic. Wait for 30-60 seconds and refresh the page.

First connection to your Galaxy server¶

The first time you land to your Galaxy server home page, you see this:

You are connected as an anonymous user. As so, you may navigate in the Galaxy interface, but your actions will be very limited. For instance, you won't be able to rename histories or to import input datasets the histories of Galaxy.

Thus, the first thing to do is to register. You will even register with all the administration rights, to be able to fully manage your Galaxy server. Don't miss your chance!

Click on the Authentification et Enregistrement top menu (as shown above) and, in the new page that opens, do not fill anything. Instead, click the link Register here.

This link opens a page where you can register as an admin.
Use admin@galaxy.org as email address. This is mandatory to be recognized by galaxy as a true admin. You can copy the email address bellow :
```
admin@galaxy.org
```
Put twice the same password of your choice ( don't forget it)
Put a public name of your choice. Public names must be at least three characters in length and contain only lower-case letters, numbers, dots, underscores, and dashes ('.', '_', '-').

The public name chris is already taken, sorry about that .
Click on the Create button.

Back to the Galaxy home page, you will see that an additional menu is now present in the top menu bar: Admin. In addition, if you click on the menu Utilisateur, you should see your public name.

Congratulations !¶

Your Galaxy admin account is set up and ready to use.

Here, we need to check that you succesfully passed through all the previous steps.

Therefore, we ask you to click the top Admin menu.

In the left Admin Home menu that shows up, click the Install and Uninstall tab (in the bottom section Tool Management).
Check the radio button Installed Only.
Take a limited screenshot (no need for a full screen !) of the top of the list of the installed tools.
Post this "artifact" in https://github.com/ARTbio/AnalyseGenome/discussions/49 (You'll see an an example from my own first connection)
Thank you ! You can now suspend (or stop) your VM (see below).

Ends of Galaxy work sessions¶

Each time you have finished to work with Galaxy, save your Google coupon:

Go to your Google cloud console (web interface))
Click the 3 vertical dots in the line of your VM and select Suspendre (or Suspend with the english interface)
You may also stop it, but it will take more time the next time you start it.

Please, make a last effort by reading the next section which summarize important guidelines about the management of your Virtual Machines (VMs) during the rest of the course.

Pay a particular attention to this part !

The next time you connect to your Galaxy server¶

You can directly enter your account with your login (either admin@galaxy.org or your Public name) and password.

Note that sometimes, you are directly logged in because a cooky remember your recent visit.

The Geek Corner: controlling your Galaxy server through an ssh session

You can control you galaxy server by connecting to a ssh shell session in your VM. To do so :

Click on the ssh menu in the line of your VM and select Ouvrir dans une fenêtre du navigateur
In the ssh session that opens with your VM, type sudo -i

The following commands won't work if you are not logged as root. (sudo -i at your initial connection)

reconnect the slurm node when it is drain state (broken)

scontrol update NodeName=<your-instance-name> State=Resume

Check the state of the Galaxy server
```
galaxyctl status
```
Restart "gently" the Galaxy server
```
galaxyctl graceful 
```
Restart "firmly" the Galaxy server (if for whatever reason it is frozen)
```
galaxyctl restart
```
Follow the activity log of the Galaxy WEB server:
```
galaxyctl follow
```
Type CtrlC to exit.

Follow the slum job manager of Galaxy

watch "squeue --format '%.18i %.9P %.40j %.8u %.2t %.10M %.4C %.6D %R' && sinfo"

Type CtrlC to exit.