Difference between revisions of "Analysing Data on Armis or Great Lakes using Rmd Files"
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=== Configuring R === | === Configuring R === | ||
| − | 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 | + | 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 |
| − | < | + | <pre>module load R |
R | R | ||
install.packages("PACKAGE_NAME") | install.packages("PACKAGE_NAME") | ||
| − | </ | + | exit() |
| + | </pre> | ||
Follow the prompts agreeing to make a personal library and using the Michigan mirror (71) | Follow the prompts agreeing to make a personal library and using the Michigan mirror (71) | ||
| + | |||
| + | === Creating a R script === | ||
| + | I prefer to generate Rmd scripts on my own computer and then transfer them to the data folder to run | ||
== Transferring Results == | == Transferring Results == | ||
Revision as of 17:06, 10 July 2023
Contents
Software
On OSX
- Install Filezilla for file transfers https://filezilla-project.org/
On Windows
- Install Putty for command line access https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html
Access
At Michigan there are two clusters, one for human data (Armis) and one for non-PHI data (Great Lakes). Both of these are connected to a storage service called Turbo. These are available as part of the UM Research Computing Package.
Permissions
- For access to https://datadirect.precisionhealth.umich.edu/, you need to complete these two online classes and have the VPN installed on your device. For more details on access follow these instructions.
- PEERS - Human Subjects Research Protections
- HIPAA Training for Self Service Tools.
- You also need an approved IRB noting that you will use the data direct self-service tools.
- To get access to Armis2 fill out this form.
You can access the server either through the command line or through a remote desktop if you prefer a GUI. There a limited functionality to Armis2 here that can also be used (see these instructions).
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.
Accessing the Server - Command Line
On OSX open a terminal and enter ssh <UNIQNAME>@armis2.arc-ts.umich.edu replacing with your uniqname. Enter your level 1 password. Authenticate using Duo following the instructions. You will be placed in your home folder. Your data should be in /nfs/turbo/precision-health/DataDirect/<YOUR-IRB>. I find it convenient to make symlinks to quickly navigate to your data folder so first find your folder name
ls /nfs/turbo/precision-health/DataDirect/
locate the name of your folder <FOLDER_NAME>
create the symlink
ln -s /nfs/turbo/precision-health/DataDirect/<FOLDER_NAME> <LINK_NAME>
Now you can navigate from your home folder to your data folder by typing
cd <LINK_NAME>
Accessing the Server - Remote Desktop
Extracting Data
Submitting Scripts to the Server
Configuring R
Some R packages may need to be installed in your home folder. To do this go to your home folder cd ~/ 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
module load R
R
install.packages("PACKAGE_NAME")
exit()
Follow the prompts agreeing to make a personal library and using the Michigan mirror (71)
Creating a R script
I prefer to generate Rmd scripts on my own computer and then transfer them to the data folder to run
