Screenshot

Requirements

BridgePRS depends on R, plink, and runs using a Python3 wrapper.

R

BridgePRS requires the following R [version 3.6.3+] (Download) packages:
BEDMatrix, boot, data.table, doMC, glmnet, MASS, optparse, parallel, and R.utils

R Packages

These packages can be installed from inside an R terminal using the command: 

$ R 
install.packages(c("BEDMatrix","boot","data.table","doMC","glmnet","MASS","optparse","parallel","R.utils"))

BridgePRS requires a version of plink compatible with your machine. (download)

By default BridgePRS includes versions of plink for Linux and MacOs and will attempt to locate the correct version. To override this behavior and use a specific version of plink please use the flag --plinkPath $PLINKPATH to direct BridgePRS to the file location.

Extra MacOs Security:

MacOs often block executables if they are not approved from the app store. You may have to change your settings to allow Plink to be called
For instructions on how to do so, please click here.

Python

The BridgePRS wrapper requires python3+ (download) and the matplotlib library (download) is required to create plots (options).

If Python3+ is not available, BridgePRS can be ran using shell scripts, as described in the README file.
If Python3+ is available, all other dependencies can be ran using the BridgePRS

BridgePRS check requirements

If BridgePRS has been downloaded and made executable (as described previousely) then the following command can be used to allow bridgePRS to check system compatibility and prompt you to install missing software: 

BridgePRS Begins at Sat Sep 30 23:45:46 2023 
Bridge Command-Line:  ../bridgePRS check requirements
Checking Requirements:
           System:  platform=linux,  cores(available)=8,          cores(used)=1       (TIP: Using More Than One Core Will Improve Performace (e.g. ---cores 7))
            Plink:  found=true,      path=/home/tade/Bin/plink
                R:  found=true,      path=/usr/bin/R,             version=3.6.3       (packages=up to date)                                            
          Python3:  found=true,      path=/usr/bin/python3,     matplotlib=true
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