DEPLOY A GALAXY SERVER IN THE VM
1. Installation of the Galaxy server¶
We have automated the installation of Galaxy on your Google Virtual Machine.
All you need is to (i) taking the control of the machine as root and (ii) cloning
a galaxyXpand folder in your VM and running a bash script, using a single
command line (see below).
Recommendations before starting
The creation of your Galaxy server includes the setup of the Galaxy Services and the installations of ~28 bioinformatics tools to analyse sequencing datasets.
Although it is completely scripted and requires minimal intervention from your part, this process takes 1 hour in total, once, and the deployed server will serve you for the rest of the training week.
Therefore, we ask you extra focus on this section as well as preparing your Galaxy server in advance of the Galaxy training week.
Last practical recommendation about internet connection:
The deployment of the Galaxy server and the installation of Galaxy tools in the server involves remote execution of scripts in your Virtual Machine. Therefore, it is mandatory that the internet connection between your local terminal (where you are physically working !) and the remote VM STAYS UP during these two phases.
Some local machines are configured to sleep after a certain amount of time of inactivity. This sleeping process MAY STOP YOUR CONNECTION with the VM and consequently STOP the EXECUTION OF YOUR INSTALLATION SCRIPTS. Should this happen, you will have to re-run the whole interrupted script, with complications stemming from previous incomplete execution.
→ Please, keep an eye on your deployment during its execution and take any action to prevent internet connection breaks.
So let's do this, step by step, typing in the ssh Terminal you have opened in the previous section:
What does sudo -i command ?
This command open a new shell where you are root. You can check this by typing whoami
that should return root, meaning that you are now working as root user.
This is required because installation of new programs as well as manipulations of network interfaces is permitted only to users with administration rights.
git clone https://github.com/artbio/galaxyXpand -b ag2024 && \
screen -d -m sh ~/galaxyXpand/scripts/deploy_ag2024.sh && \
sleep 5 && tail -f ~/install_log.txt
What is git command doing ?
This command is cloning the GitHub repository artbio/galaxyXpand into a
local folder named galaxyXpand.
galaxyXpand is a software developped to quickly and easily install a Galaxy server. It is based upon the ansible framework for software deployment.
What is screen -d -m doing ? (
Linux geek corner)
screen -d -m <command> is starting the
What is sh ~/galaxyXpand/scripts/deploy_ag2024.sh doing ?
This command runs the script deploy_ag2024.sh
2. About monitoring the deployment of the Galaxy server¶
The tasks executed by the deploy_ag2024.sh are displayed in your terminal
(thanks to the tail -f ~/install_log.txt command) as well as logged in the
file install_log.txt.
Although the installation log in your terminal may seem to stop for
several minutes (because of long internal steps), it is only when the following
lines show up that the Galaxy Installation is finished.
Last lines of install_log.txt
changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
TASK [install.galaxy-tools : include_tasks] ************************************
kipping: [localhost]
TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]
PLAY RECAP *********************************************************************
localhost : ok=11 changed=5 unreachable=0 failed=0 skipped=3 rescued=0 ignored=0
Wed Nov 13 18:05:40 UTC 2024
Installation is complete
The main steps of the Galaxy server deployment
- The Ubuntu system is updated at its latest version
- Python dependencies required for the Galaxy server instance are downloaded and installed
- The ansible framework v3.0.0 is installed for running the ansible playbooks
- The Galaxy computing environment (virtualenv) is automatically set up
- The Galaxy web server is installed (nginx reverse proxying gunicorn) and static pages are built
- The Galaxy database Postgresql is installed and upgraded to its latest structure/model
- The package manager Conda, which is heavily used by Galaxy to install its tools, is installed.
- Plus many other tasks : a high-performance server relies on complex software.
- The final step in Galaxy deployment is the automated installation of around 15 tools which you will need for your analyses.
Naturally, this deployment will happen once. The next time you connect to your Galaxy server, you'll be ready to use it !
Your contribution is expected
As a final check that your Galaxy deployment is successful, type CtrlC to get the hand back over your web terminal, and enter the following command line :
Copy the returned output ( copy is not screenshot), and paste it in
this GitHub Discussion
We are reviewing in a section apart how to display the server activity, stop, start or restart it.
3. Connect to your living Galaxy instance¶
You should now be able to access to you Galaxy instance in a web browser window.
- Go back to your Google Cloud Engine control panel.
- Find the
External IP address/Adresse IP externein the 7th column of the dashboard (to the left of the ssh menu that you used before).
- Click on the hyperlink.
- In the new browser window, follow the menu
Authentification et enregistrement→Enregistrement→Don't have an account? Register here.
and register to your instance using the email address
and the password of your choice ( don't forget it)
- After login, you should see the admin tab in the top menu of the Galaxy interface.
You are connected to Galaxy as an admin !