Deploying and Managing GVL Analysis platform

Using the Default NeCTAR allocation

1. Access the Australian Research Cloud

1. Login via the Dashboard https://dashboard.rc.nectar.org.au

2. Only members of the Australian Access Federation (AAF) can access Australian Research Cloud resources.  If you are not a member of AAF, GVL Help may be able to provide you with credentials.

3. If this is the first time you have accessed the Australian Research Cloud, you must agree to some Terms and Conditions. You are then presented with your Default Project and Default Allocation.

• The default is fairly limited, but is sufficient for launching a working GVL.
• You can apply for more allocation from http://support.rc.nectar.org.au/dashboard/allocation_request.html.  

2. Get Research Cloud credentials

1. Go to https://dashboard.rc.nectar.org.au

2. Click on 'Access & Security’ link in the left hand panel and then the ‘API Access’ tab

3. Click on ‘Download EC2 Credentials’ at top right to download a zip archive of the credentials for that Project to your desktop.

4. Unzip the downloaded archive. Open the file 'ec2rc.sh' with a text editor (Windows users: open the file with Wordpad)

You will need 'EC2_ACCESS_KEY’ and ‘EC2_SECRET_KEY’ each time you use the Launch page (next Section).

3. Launch the CloudBioLinux/Cloudman image

Go to launch.genome.edu.au, bringing you to the GVL BioCloudCentral launch page.

Cloud: Select default: ‘NeCTAR (Openstack)’

Access key and Secret key:  Obtained in the previous Section.

• Make sure you copy and paste exactly (no extra spaces)

Institutional email: This is important for us to keep track of usage for funding & grant reporting

Cluster Name: Choose a name for your GVL instance. Whatever you want.

• Choose a unique name every time you use the Launch page; unless you are deliberately re-launching an instance that you have previously terminated. (Especially, don’t re-use a name from a previous failed launch).

Password: Choose any password - but please make it not obvious, as you are essentially creating a public server and, if it is up long enough, you will almost certainly get anonymous hacking attempts.  

• Remember your password, as this is the password you will use to log into the CBL/Cloudman instance. You will get another chance to see you password when your server launch is done.

Instance Type: Choose default: Medium (2 vcpu / 8GB RAM) CPU/RAM size.

Press 'Start an Instance'. It will take 1-5 minutes to start.  If you know how, you can use the NeCTAR dashboard to observe the node starting up on the cloud node.

The Launch is finished when an IP address is displayed

Click on the ip-address and you will be presented with the Dashboard of your simple GVL analysis server.

• you can access a lightweight GUI desktop via <ip-address>/vnc^[1]
• you can ssh to the server using user “ubuntu” and the password you selected

4. Start a Galaxy instance

1. Click on the Cloudman link

2. Login, with User Name ubuntu and Password the one you entered on the Launch screen.

3. Cloudman will ask which type of bioinformatics cluster you want to start.

1. Select ‘Galaxy Cluster’ and ‘Transient Storage’
2. Press “Choose Platform Type’.

4. Cloudman will configure Galaxy on your GVL analysis server.

1. The process will take around 2-5 minutes.
2. Once completed, the ‘Access GVL’ button at top right will become available

5. Click on the ‘Access GVL’, button. This will open your GVL analysis server Dashboard in a new browser tab.

6. Click on the Galaxy link

7. Register yourself as a Galaxy User (‘User’ menu option, top right), remembering the email address you use to register.

1. You can use any password here, but you might like to choose the same one as you used for starting your GVL instance.

8. Finished. You have a usable Galaxy server - a single node of 2 cores running Galaxy on CloudBioLinux with SunGridEngine!

5. Other Features

Also see: Galaxy and CloudMan Administration Manual - common administration tasks, including making yourself a Galaxy Administrator and managing your virtual cluster.