RAVE:UAB

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Reproducible Analysis and Visualization of iEEG RAVE

How to use RAVE on the UAB Cheaha Cluster

First time only (installs RAVE for an account)

1. Establish Cheaha account with Office of Research Computing. Be sure to request a 16 gb RAM HPC desktop
2. Open Terminal to Cheaha

type

 module load FriBidi/1.0.10-GCCcore-10.3.0
 module load HarfBuzz/2.8.1-GCCcore-10.3.0
 module load R/4.1.0-foss-2021a

type

 R

to start R. Then,

 install.packages('ravemanager', repos = 'https://beauchamplab.r-universe.dev')
 ravemanager::install()

To use RAVE (after installation)

 module load R/4.1.0-foss-2021a
 R

Then, start RAVE within R using the commands

 rave::start_rave()

or

 rave::launch_demo()

This may launch a "graphics device". This can be safely minimized. For analysis of large datasets, you may need to request additional resources. To check on resource usage, type

 seff <jobid>

where <jobid> found on My Interactive sessions or

 sacct -u <blazerid> -X

Set your data directory to point toward shared data

After you have loaded RAVE under your personal account, you may need to set your RAVE data dir and raw dir to point to data stored in a shared project directory.

To view your data dir, run in the R console:

   raveio::raveio_getopt('data_dir')

To set your data dir:

   rave_options(data_dir = 'path/to/shared_data_dir')

To view/set your raw data dir:

   raveio::raveio_getopt('raw_data_dir')
   rave_options(raw_data_dir = 'path/to/shared_raw_data_dir')