Updated the README file.

README.md

@@ -1,9 +1,5 @@
 # ccd-web
-CCD web is a Java web-based application that allows users to run causal modeling algorithms on their dataset.  The application comes in two flavors, desktop and web version.
-
-The desktop version allows a single user to run the algorithms on the the dataset locally on his/her desktop and run the algorithms remotely over at the Pittsburgh Supercomputing Center (PSC) for more computing power.
-
-The web version allows multiple users to run the algorithms on their dataset on the server.  Like the desktop version, users can also run remotely over at the PSC.
+CCD web is a Java web-based application that allows users to run causal modeling algorithms on their dataset.
 
 ## How Can I Use It?
 ### Required Dependencies
@@ -19,38 +15,37 @@ The web version allows multiple users to run the algorithms on their dataset on
 * xom-1.1.jar
 
 #### Application Dependencies
+* ccd-job-queue-0.1.3.jar
+* ccd-mail-0.1.2.jar
 * ccd-db-0.6.0.jar
 * ccd-commons-0.3.0.jar
-* ccd-ws-dto-0.3.0.jar
-
-#### Building the Application
-Since this is a maven project all the dependencies will be download from the Maven public repository when compiling. There is one dependency that must be built and installed manually, the database component.  
-* Download the [ccd-db-0.6.0](https://github.com/bd2kccd/ccd-db/releases/tag/v0.6.0),[ccd-commons-0.3.0](https://github.com/bd2kccd/ccd-commons/releases/tag/v0.3.0) and [ccd-ws-dto-0.3.0](https://github.com/bd2kccd/ccd-ws-dto/releases/tag/v0.3.0)  project from GitHub.
-* Go to each of these project directory and type **mvn clean install** to build and install the jar libraries.
-* After ccd-db-0.6.0 has been successfully built and installed, go to the **ccd-web** directory and run **mvn package**. This will create a jar file called **ccd-web.jar** in the **/target** folder.
-
 
-## Run As a Desktop Application
-### Configurations
-In order to run as a desktop application you must edit the **application.properties** file in the jar file and change the following properties:
 
-* spring.profiles.active = desktop
-
-* spring.jpa.show-sql = false
-
-* app.webapp = false
+#### Building the Application
+Since this is a maven project all the dependencies will be download from the Maven public repository when compiling.  The following dependencies must be downloaded, built, and installed manually.
 
-* server.port=[port]     *// add this property if you have a conflict with the default port 8080, (e.g,. server.port=8181) *
+* [ccd-algorithm-0.4.3](https://github.com/bd2kccd/ccd-algorithm/releases/tag/v0.4.3) 
+* [ccd-job-queue-0.1.3](https://github.com/bd2kccd/ccd-job-queue/releases/tag/v0.1.3) 
+* [ccd-mail-0.1.2](https://github.com/bd2kccd/ccd-mail/releases/tag/v0.1.2) 
+* [ccd-db-0.6.0](https://github.com/bd2kccd/ccd-db/releases/tag/v0.6.0) 
+* [ccd-commons-0.3.0](https://github.com/bd2kccd/ccd-commons/releases/tag/v0.3.0) 
 
-> *Note: this file follows the standard Spring boot configurations properties. see [here](http://docs.spring.io/spring-boot/docs/current-SNAPSHOT/reference/htmlsingle/#common-application-properties) for more information
+Go to each of these project directory and type **mvn clean install** to build and install the jar libraries.
 
-### Setup Workspace
-Workspace is the directory where the application will be working in.  The application will be working from this directory.
+## Run Web Application
+### Configurations
+There are three property files you must fill in to tell the application where to run, what database to use, etc.
+1. **application-mysql.properties** (MySQL database configurations)
+2. **application.properties** (Spring Boot configurations)
+3. **ccd.properties** (CCD web application related configurations)
 
-1. Create a directory called **workspace** in your home directory.  For an example, ***C:\Users\kevin\workspace***.
+### Setting Up
+First, you need to create a workspace for the application to work in.  Create a directory called **workspace**, for an example ***/home/tuser/workspace***.  Inside the workspace directory, create another folder called **lib**, for an example ***/home/tuser/workspace/lib***.  Put all the algorithm dependencies in the **lib** folder.
 
-2. Create a folder called **lib** in the **workspace** directory.  For an example, ***C:\Users\kevin\workspace\lib***.
+Make sure you set **ccd.server.workspace=/home/tuser/workspace** and **ccd.folder.lib=lib** in the **ccd.properties** file.
 
+### Compile the Program
+Go to the **ccd-web** directory and run the command **mvn clean package**. This will create a jar file called **ccd-web-1.0.0.jar** in the **/target** folder.
 
 ### Launch the Program
 ```java
@@ -96,13 +91,13 @@ Add this launch4j configuarion below to the pom.xml in the build/plugins entity.
 					<maxHeapSize>4096</maxHeapSize>
 				</jre>
 				<versionInfo>
-					<fileVersion>0.5.2.0</fileVersion>
-					<txtFileVersion>0.5.2.0</txtFileVersion>
+					<fileVersion>1.0.0</fileVersion>
+					<txtFileVersion>1.0.0</txtFileVersion>
 					<fileDescription>CCD Desktop Windows
 						Application</fileDescription>
 					<copyright>University of Pittsburgh and Carnegie Mellon University</copyright>
-					<productVersion>0.5.2.0</productVersion>
-					<txtProductVersion>0.5.2.0</txtProductVersion>
+					<productVersion>1.0.0</productVersion>
+					<txtProductVersion>1.0.0</txtProductVersion>
 					<productName>CCD-Desktop</productName>
 					<internalName>ccd-web</internalName>
 					<originalFilename>ccd-desktop-windows-0.5.2.exe</originalFilename>
@@ -111,5 +106,4 @@ Add this launch4j configuarion below to the pom.xml in the build/plugins entity.
 		</execution>
 	</executions>
 </plugin>
-
 ```