Changes

If you submit a deidentified data request via https://datadirect.precisionhealth.umich.edu, your data will be sent as a 7zip file to the turbo storage in a folder named for your IRB. You will be prompted to enter a password to protect this file, do not lose this password.

=== Accessing the Server - Command Line ===

=== Accessing the Server - Remote Desktop ===

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mkdir bin

To extract your archive move into your working directory and then use the command <code>7zz x '<ARCHIVE>.zip'</code>, entering the password you created in [[#Deidentified Data Request|Deidentified Data Request]]. This should generate a folder containing a series of csv files to be used by your R scripts.

Some R packages may need to be installed in your home folder. To do this go to your home folder <code>cd ~/</code> and enter the following to load the R modules, enter an R shell, install the packages and exit out. You will only have to do this once to install the relevant R packages in your script

Follow the prompts agreeing to make a personal library and using the Michigan mirror (71)

I prefer to generate Rmd scripts on my own computer and then transfer them to the data folder to run (see [[#Transferring Files|Transfering Files]] to move scripts onto the server).

To submit a job to the server you will need to create a batch script to submit your jobs. The Armis2 and Greatlakes servers use slurm to submit jobs.

Details of how to configure a slurm file can be found [https://arc.umich.edu/armis2/slurm-user-guide here]. Each script can include multiple Rmd files. A sample script is below. Make sure to replace <USER> with your slurm user id and entering a name for the job and your email.