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Torrent Scout is an interactive tool, which provides users access to raw data generated by the Ion Torrent Personal Genome Machine(TM). It allows users to navigate and view data all the way from the raw signal to the final alignment. Torrent Scout is built using the NetBeans architecture, which enables developers to easily add additional compone…

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To build TorrentScout (release 2.0)  yourself and run it, you will need:

Java 1.6 or higher (Java Download)
NetBeans 7.0 or higher (netbeans.org)
To compile it for the first time:

Open Project TorrentScout in NetBeans 7
Open TorrentScout/important files/Netbeams Platform Config in the Project explorer
(the file TorrentScout/nbproject/platform.properties)
Change the line with harness.dir to the project path/harness
Build and run it!
 
If your developer machine has less than 4 GB of memory available 
and you want to run TorrentScout via NetBeans:
Edit the file harness/run.xml
Go to the line with
<property name="run.args.common" value='--userdir "${test.user.dir}" -J-Dnetbeans.logger.console=true -J-ea -J-Xms512m -J-Xmx4096m'/>
Change the memory setting Xmx4096m to a lower value (such as Xmx2048m)
 
To give NetBeans itself more or less memory:

Open the folder where Netbeans 7 is installed
Go to etc and open the file netbeans.conf
Edit the line with:
netbeans_default_options="-J-client -J-Xss2m -J-Xms512m -J-Xmx3900m -J-XX:PermSize=32m -J-XX:MaxPermSize=384m -J-Dapple.laf.useScreenMenuBar=true -J-Dapple.awt.graphics.UseQuartz=true -J-Dsun.java2d.noddraw=true"
Here again you can change the memory you want to give NetBeans (here: Xmx3900m)
In that same file you can also specify the default location for your jdk
 
If you ever want to deploy it yourself as a web start app, you will also need additional files 
(a modified jnlp-servlet.jar, for instance), which are now in the java folder (inside the TorrentScout project folder)

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Torrent Scout is an interactive tool, which provides users access to raw data generated by the Ion Torrent Personal Genome Machine(TM). It allows users to navigate and view data all the way from the raw signal to the final alignment. Torrent Scout is built using the NetBeans architecture, which enables developers to easily add additional compone…

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