Kaessmannlab Wiki

When users work connected to the CiscoVPN it is often the case the connection abruptly ceases after a few hours. This can be rather inconvenient for instance for knitting large scripts that exceed this time.

An alternative approach to circumvent the issue would be as follows:

1. Access Piggeldy or Frederick.
2. Run htop and assess if the server is being intensely used before running.
3. Open a screen with screen -S screen_name.
4. Deactivate your conda base environment and open your conda working environment.
5. Open an R terminal.
6. Load library knitr.
7. Knit your script with the command knit(“path_to_file.Rmd”).
8. Detach from the screen pressing cntrl+a + d.
   • You can check if the screen still exists with screen -list.
9. You can access the screen anytime with screen -r screen_id. It will run on the background without needing the user to be connected to the server.
10. Once the knitting is completed a file called path_to_file.md is created.
11. Open it inside Rstudio and click Preview to quickly generate the html object.
12. Remember to kill your screen. To do so detach as explained above and then run screen -S screen_name -X quit.