Using the ssh browser window to ssh the Google VM is instable in 2024 (at least for me)

[drosofff]

Problem description

When a Google cloud VM is running, there is at least 3 options to ssh it.

1. Using a standard terminal and passing the Google private key in the ssh command using the -i option
2. Using the CLI gcloud (after installing it locally) in the macOS terminal and a command similar to

   gcloud compute ssh --zone "europe-west9-c" "ansible-galaxy-paris" --project "analyse-genomes-2024-1"

3. using the Google compute dashboard and the menu SSH --> "Ouvrir dans une fenêtre du navigateur"

2 is my favorite option and 3 is the option preferred for AG students since it requires no skill and configuration of a third-party client (Ubuntu terminal, Putty, MacOS terminal)

Until 2023, the option 3 used to work smoothly, but in 2024, the ssh browser window is very unstable for me, with frequent deconnections.

It looks like there is a problem with a ssh key specifically used for this type of connection to the VM, whose time-out is short and trigger a problem of ssh authentication.

I am currently wondering whether it is a "christophe-specific" issue, due to a new network setting at home, or whether the issue will impact (strongly) the students.

Asking for help

@slecrom could you help me to diagnose on that ?

Your mission, if you accept it, would be to:

• spin off a VM with your Google cloud account
• ssh it using the option 3
• and trigger the deployment of Galaxy using the following command pasted in the browser ssh window:

  git clone https://github.com/artbio/galaxyXpand -b ag2024 && \
  cd galaxyXpand && \
  sh scripts/deploy_ag2024.sh

  If you have the same problem as me, you should be kicked out from the ssh window, and the ansible deployment will unfortunately be interrupted 😢

[slecrom]

Hi @drosofff

I tested Galaxy deployment on GCE 6 times since October 28th. Each time I used the option 3 SSH connexion. It always worked without any deconnexion. However, I don't test it with the latest command you request yesterday. Instead, for the last deployment I used:

wget https://raw.githubusercontent.com/ARTbio/AnalyseGenome/refs/heads/ag-2024/GalaxyServer/deploy_galaxy.sh && \
sh deploy_galaxy.sh

In addition, I used the europe-west6-c zone, but I don't think there is an impact of this setting on the SSH connexion. I used Chrome Version 130.0.6723.117 (Build officiel) (arm64) on MacOS Sonoma 14.6.1.

[drosofff]

Thanks @slecrom

I tested Galaxy deployment

From where ? I have definitely an issue from home, because when I use a socks proxy in Sorbonne-U or a VPN, no ssh deconnection anymore ! The point is that students will set up their VM from home this time. Thus, there is a risk that they experience the same problem as me, in particular if they have an Orange livebox (I installed a new one a couple of weeks ago)...

If you run

git clone https://github.com/artbio/galaxyXpand -b ag2024 && \
cd galaxyXpand && \
sh scripts/deploy_ag2024.sh

it should be protected against ssh deconnexion now. However, you will need the updated startbio documentation: I have pushed the ag2024 startbio branch in the main so that you have access to it.

[slecrom]

I tested the deployment from SU and not from home. I will try from home tonight. However, I haven't found the new URL documentation. Can you tell me where is it located ? Thanks @drosofff

[drosofff]

@slecrom Je change de méthode pour la publication des modifications dans Startbio (voir mon email). Dorénavant, les modifications seront affichées sur le site web le plus vite possible