Setting up and Accessing R Studio on Virtual Machine

From the previous page, all the neccesary files have been retrieved from the server, and the preparation for analysis has been completed. For subsequent analysis using DADA2, R-Studio environment on Virtual Machine on the AWI server is required.

VM on AWI Confluence page: https://spaces.awi.de/display/DM/Get+virtual+machines

1. Go to https://marketplace.awi.de/vcac/org/awi/

2. There is a new virtual machine blueprint available in the market place called "Bioinformatics VM"

3. Apply for Bioinformatics VM and click the checkbox "R-Studio" which runs R4.0 in the background

4. After success application, an email containing the IP address will be sent. This IP address + the port number 80 are used to access R-Studio server in web browser. (e.g. http://172.18.27.123:80)

[Note]

• The VM can be accessed via a terminal (mobaXterm) through this login command ssh 172.18.27.123 (IP address prvided from your deployment page in the market place)
• The Ollie file systems are not part of the file system of the virtual machine. Therefore, data from Ollie need to be transfered to the Virtual Machine ("isilon" data strage).
  • To transfer data to the "isilon" data storage, one can create a own directory under "/isibhv/projects/FRAMdata/ and copy all the neccesary files there.
  • run scp -r /path/on/ollie/to/your/data/ [email protected]:/isibhv/projects/FRAMdata/maniwano