gatk-3.8

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Queue with IntelliJ IDEA

http://gatkforums.broadinstitute.org/gatk/discussion/1309/queue-with-intellij-idea

We have found it that Queue works best with IntelliJ IDEA Community Edition (free) or Ultimate Edition installed with the Scala Plugin enabled. Once you have downloaded IntelliJ IDEA, follow the instructions below to setup a Sting project with Queue and the Scala Plugin.

File:sting_project_libraries.png File:sting_module_sources.png File:sting_module_dependencies.png File:sting_module_scala_facet.png

1. Build Queue on the Command Line

Build Queue from source from the command line with ant queue, so that:

The lib folder is initialized including the scala jars
The queue-extensions for the GATK are generated to the build folder

2. Add the scala plugin

In IntelliJ, open the menu File > Settings
Under the IDE Settings in the left navigation list select Plugins
Click on the Available tab under plugins
Scroll down in the list of available plugins and install the scala plugin
If asked to retrieve dependencies, click No. The correct scala libraries and compiler are already available in the lib folder from when you built Queue from the command line
Restart IntelliJ to load the scala plugin

3. Creating a new Sting Project including Queue

Select the menu File... > New Project...
On the first page of "New Project" select Create project from scratch Click Next >
On the second page of "New Project" select Set the project Name: to Sting Set the Project files location: to the directory where you checked out the Sting git repository, for example /Users/jamie/src/Sting Uncheck Create Module Click Finish
The "Project Structure" window should open. If not open it via the menu File > Project Structure
Under the Project Settings in the left panel of "Project Structure" select Project Make sure that Project SDK is set to a build of 1.6 If the Project SDK only lists <No SDK> add a New > JSDK pointing to /System/Library/Frameworks/JavaVM.framework/Versions/1.6
Under the Project Settings in the left panel of "Project Structure" select Libraries Click the plus (+) to create a new Project Library Set the Name: to Sting/lib Select Attach Jar Directories Select the path to lib folder under your SVN checkout
Under the Project Settings in the left panel of "Project Structure" select Modules
Click on the + box to add a new module
On the first page of "Add Module" select Create module from scratch Click Next \>
On the second page of "Add Module" select Set the module Name: to Sting Change the Content root to: <directory where you checked out the Sting SVN repository> Click Next \>
On the third page Uncheck all of the other source directories only leaving the java/src directory checked Click Next \>
On fourth page click Finish
Back in the Project Structure window, under the Module 'Sting', on the Sources tab make sure the following folders are selected
- Source Folders (in blue): public/java/src public/scala/src private/java/src (Broad only) private/scala/src (Broad only) build/queue-extensions/src
- Test Source Folders (in green): public/java/test public/scala/test private/java/test (Broad only) private/scala/test (Broad only)
In the Project Structure window, under the Module 'Sting', on the Module Dependencies tab select Click on the button Add... Select the popup menu Library... Select the Sting/lib library Click Add selected
Refresh the Project Structure window so that it becomes aware of the Scala library in Sting/lib Click the OK button Reopen Project Structure via the menu File > Project Structure
In the second panel, click on the Sting module Click on the plus (+) button above the second panel module In the popup menu under Facet select Scala On the right under Facet 'Scala' set the Compiler library: to Sting/lib Click OK

4. Enable annotation processing

Open the menu File > Settings
Under Project Settings [Sting] in the left navigation list select Compiler then Annotation Processors
Click to enable the checkbox Enable annotation processing
Leave the radio button obtain processors from the classpath selected
Click OK

5. Debugging Queue

Adding a Remote Configuration

File:queue_debug.png

In IntelliJ 10 open the menu Run > Edit Configurations.
Click the gold [+] button at the upper left to open the Add New Configuration popup menu.
Select Remote from the popup menu.
With the new configuration selected on the left, change the configuration name from 'Unnamed' to something like 'Queue Remote Debug'.
Set the Host to the hostname of your server, and the Port to an unused port. You can try the default port of 5005.
From the Use the following command line arguments for running remote JVM, copy the argument string.
On the server, paste / modify your command line to run with the previously copied text, for example java -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005 Queue.jar -S myscript.scala ....
If you would like the program to wait for you to attach the debugger before running, change suspend=n to suspend=y.
Back in IntelliJ, click OK to save your changes.

Running with the Remote Configuration

Ensure Queue Remote Debug is selected via the configuration drop down or Run > Edit Configurations.
Set your breakpoints as you normally would in IntelliJ.
Start your program by running the full java path (with the above -Xdebug -Xrunjdwp ...) on the server.
In IntelliJ go to the Run > Debug.

6. Binding javadocs and source

From Stack overflow:

Add javadocs:

Point IntelliJ to http://download.oracle.com/javase/6/docs/api/.
Go to File -> Project Structure -> SDKs -> Apple 1.x -> DocumentationPaths, and the click specify URL.

Add sources:

In IntelliJ, open File -> Project Structure. Click on "SDKs" under "Platform Settings". Add the following path under the Sourcepath tab: /Library/Java/JavaVirtualMachines/1.6.0_29-b11-402.jdk/Contents/Home/src.jar!/src

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