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-\documentclass[11pt,fullpage]{article}
-\usepackage[urlcolor=blue,colorlinks=true]{hyperref}
-
-\begin{document}
-
-\title{Using IntelliJ with the Broad Sting Repository}
-\author{Aaron Mckenna}
-\date{\today}
-\maketitle
-
-\section{Overview}
-Using JetBrains IntelliJ with the Broad String repository is a relatively simple process.  
-
-\subsection{Getting the source}
-The source can be checked out from the repository, from the following link: \\ \\
-\url{https://svnrepos/sting}\\ \\
-Using the command:\\ \\
-\texttt{svn co http://svnrepos/sting ./sting} \\ \\ 
-Replacing the second directory with the location you'd like the code to reside in on your local machine.  
-\subsection{Getting IntelliJ}
-Licensing of JetBrains IntelliJ at MIT is done one license at a time, we don't have a site license for it.  You'll need to contact help,
-(help@broad.mit.edu) and they'll retrieve a license for you.  In the the mean time you can download the IntelliJ demo, which is a 
-fully featured 30 day trial that the license can be entered into.  You can download it from their site: \\ \\
-\url{http://www.jetbrains.com/idea/download} \\ \\
-When you do have your license, you can enter the license into IntelliJ by selecting help, and then the register drop down option. 
-\section{Working with the code in IntelliJ}
-
-\subsection{Setting up the project}
-IntelliJ doesn't need to know that the project is an ant project specifically, instead it knows how to build an ant project once it's loaded.  To
-setup a new project, create a new project, selecting the \textit{Create project from existing sources} option.  It's best to work with either the 
-playground or the core sources one at a time, and all development work should be done in the playground.  The best option in IntelliJ is to 
-choose the java directory in playground as your source, and let IntelliJ create the project directory there. 
-\\
-\begin{enumerate}
-\item Choose \textit{New Project} from the file menu \\
-\item Choose the \textit{Create project from existing sources} option.\\
-\item Name your project, something sensical like Playground, and choose the source directory \textit{sting/playground/java}. \\
-\item Choose the .idea (directory format) project storage.  This is just a recommendation, you can do either. \\
-\item After clicking next, IntelliJ should detect that the java directory already has a src directory, click through the next few windows and finally select finish.
-\end{enumerate}
-
-To have IntelliJ recognize that the project is an Ant project, select the Ant tab on the far right of the IntelliJ window.  When the window pane opens, click the
-plus symbol, and select the build.xml in the /playground/java directory.  Now the Ant build target window should have a list of the targets that were loaded
-from the build file.
-
-\subsection{Building the code}
-To build the code, select the compile list options from the Ant window.  Ivy should automatically build the dependancy list, and fetch any libraries that aren't already loaded.  To 
-transfer the code to one of our machines once a jar file is created.  
-
-Useful targets include:
-\input{Ant_Help}
-
-\subsection{Adding external sources}
-To easily debug into third-party dependencies like picard and samtools, add their source to the dependency list as follows:
-
-\begin{enumerate}
-  \item Right-click one of the Sting modules and select 'Module Settings'.
-  \item Select the 'dependencies' tab.
-  \item Right-click your library directory.  Hit 'Edit...'.
-  \item Click 'Attach Sources...'.
-  \item In the 'Choose Source Roots' directory, if the project contains a test directory, unselect it.
-  \item Click 'Okay' or 'Apply' until all dialogs are closed.
-\end{enumerate}
-
-\subsection{Debugging remotely on gsa1 / gsa2}
-To debug remotely on gsa1 or gsa2:
-
-\begin{enumerate}
-  \item Select 'Edit Configurations' from the 'Run' menu.
-  \item Click the '+' button to add a new configuration.  Select 'Remote'.
-  \item Type in 'gsa1' or 'gsa2' in the Host field.  Choose a port randomly (please choose a value >= 1024).
-  \item Before launch, run ant target 'dist'.
-  \item Make a note of the command-line settings required to initiate remote debugging:
-    \begin{verbatim}
-      -Xdebug 
-      -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005
-    \end{verbatim}
-  \item Start the application on gsa1 as follows:
-    \begin{verbatim}
-      java -Xdebug \
-           -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005 \ 
-           -Xmx{mem_required} \ 
-           -jar {your jar} {your options}
-    \end{verbatim}
-  \item Select the 'Debug' icon from the toolbar.  Press the 'Debug' button in the resulting dialog.
-\end{enumerate}
-
-\subsection{Setting up the header to contain the license file}
-
-\section{Platform-specific Notes}
-
-\subsection{Using IntelliJ on Linux}
-If IntelliJ hangs or crashes, try changing the default arguments specified in the \$\{INTELLIJ\_HOME\}/idea.vmoptions file to the following:
-
-\begin{verbatim}
--server
--Xms768m
--Xmx1248m
--Xmn170m
--XX:MaxPermSize=300m
--ea
-\end{verbatim}
-
-
-\end{document}