For EPIG-Seq development in R, the biggest hurdle is the running speed in R. Therefore, we are investigating using MatLab compiled the executable in R. Pierre developed the MatLab application and compile it into an windows executable.

Here is a screenshot for using this application in Windows:

To measure the execution time, I found this useful web-link here.

Here is timecmd.bat

@echo off
@setlocal 

set start=%time%

:: runs your command
cmd /c %*

set end=%time%
set options="tokens=1-4 delims=:."
for /f %options% %%a in ("%start%") do set start_h=%%a&set /a start_m=100%%b %% 100&set /a start_s=100%%c %% 100&set /a start_ms=100%%d %% 100
for /f %options% %%a in ("%end%") do set end_h=%%a&set /a end_m=100%%b %% 100&set /a end_s=100%%c %% 100&set /a end_ms=100%%d %% 100

set /a hours=%end_h%-%start_h%
set /a mins=%end_m%-%start_m%
set /a secs=%end_s%-%start_s%
set /a ms=%end_ms%-%start_ms%
if %hours% lss 0 set /a hours = 24%hours%
if %mins% lss 0 set /a hours = %hours% - 1 & set /a mins = 60%mins%
if %secs% lss 0 set /a mins = %mins% - 1 & set /a secs = 60%secs%
if %ms% lss 0 set /a secs = %secs% - 1 & set /a ms = 100%ms%
if 1%ms% lss 100 set ms=0%ms%

:: mission accomplished
set /a totalsecs = %hours%*3600 + %mins%*60 + %secs% 
echo command took %hours%:%mins%:%secs%.%ms% (%totalsecs%.%ms%s total)

There are three flavors of EPIG-Seq deployments: windows executable, windows-based java application, and linux-based java application. With either situation, one need to Verify that the Matlab Runtime Compiler (MCR) is installed and ensure you have version 8.3 (R2014a)

If the MCR is not installed, do the following:

Execute the MyAppInstaller_web.install file to extract and install Matlab library files via the web. You will need internet access and may need to be an administrator to do so.

The MCR Installer will launch. Click next, then accept agreement, then indicate the path where you want the runtime environment installed. This will be your
The install may take a couple of hours depending on your network speed.

Or manually download and install the Linux x86-64-bit version of the MCR for R2014a
from the MathWorks Web site by navigating to

http://www.mathworks.com/products/compiler/mcr/index.html