EPIG-Seq Files

Installation instructions for the EPIGSeqGUI Program

EPIGSeqGUI is a Java application developed for a Windows7 64 bit OS with multicores for parallel processing.

Unzip the EPIGSeqGUI folder to a directory of your choice.
The folder must contain the following files and folder:
	The bin folder: 
		EPIGSeqGUIJavaWinv01.jar:The Java Jar file
		log.txt: A log file of the processisng
		MyAppInstaller_web.exe:  The MATLAB Compiler (version 8.3/R2014a) Runtime (MCR) application binary web installation executable (this consists of the installation for the math and graphics libs)
		EPIGSeqGUILaunch.java:  The Java wrapper to launch the EPIGSeqGUI
		EPIGSeqLogov01.jpg:  The logo for EPIGSeqGUI
	Sample_data folder: 
		simulated_data.txt: A test tab-delimited file with sample data (n_samples = 201, n_groups = 4, n_patterns = 5, n_genes_per_pattern  = 200).  
				The 1st row must contain the labels of the groups that the samples belong to.
				The 2nd row must contain the total mapped reads for each sample.
				The 1st column must contain the unique gene IDs

				**** The data for processing must be tab-delimited.  No other delimiter is supported at this time. ****
					
	A folder with sample output: 
		categorized_genes.txt: categorized genes
		pattern_pvalues.txt: p-values for the patterns
		outfile.txt: Dispersion for each gene
		outfilePValues.txt: p-values for the categorized genes
		EPIG_pattern_data.txt: data to estimate dispersion from the model
		EPIG_pattern_data2.txt: data to compute the p-value from the model
		

	A folder with the R code: R_code containing two files: quasipoisson.R and quasipoisson2.R.  The R_code folder must be located in the directory one level above where EEPIGSeqGUIJavaWinv01.jar is located.
	
	This readme file: readme.txt

Verify that the Matlab Runtime Compiler (MCR) is installed and ensure you have installed version 8.3 (R2014a) 
If the MCR is not installed, do the following:

Double click on the MyAppInstaller_web.exe executable to extract and install Matlab library files.  You 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 <mcr_root>
The install may take a couple of hours depending on your network speed.

Or download the Windows 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
   
 

Once the Matlab libraries are installed, the workstation is ready to run the Java standalone application. 

Ensure you have the version 1.7 of the Java Development Kit (JDK) installed, operable and in your user environment to compile and launch the EPIGSeqGUI components.. 

EPIGSeqGUIJavaWinv01.jar must be included in your CLASSPATH.

javabuilder.jar must be included in your CLASSPATH. javabuilder.jar can be found in: 
  
  <mcr_root>\toolbox\javabuilder\jar\win64\javabuilder.jar

Finally, you must have a Windows installation of R version 3.0.2 or higher installed and in the user's environment path.
  
Create an environment variable for the R home called R_HOME by executing the following at a DOS command prompt 
C:\> set R_HOME="path to the top level of the directory for the version of R you have installed"  ex.: set R_HOME="C:\Program Files\R\R-3.1.2"
Also, add R to your path by executing the following at a DOS command prompt C:\> set PATH=%PATH%;"path to the bin folder with R.exe"  
ex. set PATH=%PATH%;"C:\Program Files\R\R-3.1.2\bin\x64"

Using a Windows command prompt window, navigate to the EPIGSeqGUI bin folder.


Execute the following command to compile the jar file:
>javac -classpath "<mcr_root>\toolbox\javabuilder\jar\win64\javabuilder.jar";.\EPIGSeqGUIJavaWinv01.jar .\EPIGSeqGUILaunch.jar

Execute the following command to launch the EPIGSeqGUI application:
>java -classpath .;"<mcr_root>\toolbox\javabuilder\jar\win64\javabuilder.jar";.\EPIGSeqGUIJavaWinv01.jar EPIGSeqGUILaunch

The GUI splash screen may take a while to appear. 

It is estimated that to run EPIGSeqGUI, 450MB of available RAM is needed per 1 MB of data (sized on the Windows file system) per CPU.  
For example, if the data file on Windows is 8.2MB, 3.7 GB of available RAM is needed per CPU.
It is best that EPIG-Seq run on a Windows 64 bit workstation with the recommended available RAM.  
Otherwise, enable the 3 GB switch on a 32 bit Windows workstation and limit the data file size and processing to one CPU.  
The fewer CPUs used, the longer the procesisng time.


Email Pierre R. Bushel at bushel@niehs.nih.gov if you encounter problems.