Skip to content

COMPILING.md

Latest commit

 

History

History
115 lines (93 loc) · 5.12 KB

COMPILING.md

File metadata and controls

115 lines (93 loc) · 5.12 KB

How to compile

To build the project Maven 3.2+ is required. Maven is a Java tool, so you must have Java 1.8+ installed in order to proceed.

To check your local Maven installation, type the following in a terminal or in a command prompt:

mvn --version

If Maven is installed, it should print out your installed version and configuration:

Apache Maven 3.0.5 (r01de14724cdef164cd33c7c8c2fe155faf9602da; 2013-02-19 14:51:28+0100)
Maven home: /usr/local/Cellar/maven/3.0.5/libexec
Java version: 1.8.0_65, vendor: Oracle Corporation
Java home: /Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "mac os x", version: "10.10.5", arch: "x86_64", family: "mac"

If the version is less than 3.2 or Maven is not installed, you need to install a new version of the tool.

Upgrade your Maven installation

To install a new version of Maven, first, download the software and then follow the installation instructions.

After the installation, check that the new version has been correctly installed:

mvn -version
Apache Maven 3.3.9 (bb52d8502b132ec0a5a3f4c09453c07478323dc5; 2015-11-10T11:41:47-05:00)
Maven home: /usr/local/Cellar/maven/3.3.9/libexec
Java version: 1.8.0_65, vendor: Oracle Corporation
Java home: /Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "mac os x", version: "10.10.5", arch: "x86_64", family: "mac"

Compile from the command line

GitHub allows to download projects as Zip archives. However, in this case, if you try to build the project extracted from the archive, you get an error like the following:

[INFO] --- maven-verifier-plugin:1.1:verify (main) @ somatic ---
[error] [Verifier] File not found [<your path>/variationanalysis/.git]

In order to be properly built, the project must be cloned from the git repository. In a terminal or in a command prompt type the following command to clone:

 git clone https://github.com/CampagneLaboratory/variationanalysis.git <dest folder>

Then, change to the project root folder (the folder where you cloned this git repo) and type the following command:

mvn package

The command line will print out various actions, and end with the following:

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Variation Analysis ................................. SUCCESS [  0.635 s]
[INFO] framework .......................................... SUCCESS [  4.780 s]
[INFO] somatic ............................................ SUCCESS [ 14.967 s]
[INFO] genotype ........................................... SUCCESS [  1.473 s]
[INFO] gpus ............................................... SUCCESS [  0.052 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 22.600 s
[INFO] Finished at: 2016-12-09T16:43:41-05:00
[INFO] Final Memory: 363M/1223M
[INFO] ------------------------------------------------------------------------

You may skip unit tests with the command

mvn clean package -DskipTests

GPU support

You can compile the project for CUDA GPUs by activating the GPU profile:

mvn clean package -PGPU

This will create jar files that include CUDA support for DL4J and activate some GPU specific customizations.

Compile in IntelliJ Idea

If building from within IntelliJ Idea, make sure the IDE is configured to build with Maven 3.2+.

To check/change the Maven Integration settings:

  • go to Preferences...>Build,Execution,Deployment>Build Tools and select Maven
  • in the dialog, check the Version number reported under "Maven home directory"
  • if the version is less than 3.2+, click on the browse button next to the input field and select the "Maven home" folder reported by the mvn --version command

Troubleshooting

If you get an error similar to the following one during the build, it's because you are using an outdated Maven version:

[INFO] ------------------------------------------------------------------------
[INFO] Detecting the operating system and CPU architecture
[INFO] ------------------------------------------------------------------------
[INFO] os.detected.name: osx
[INFO] os.detected.arch: x86_64
[INFO] os.detected.version: 10.11
[INFO] os.detected.version.major: 10
[INFO] os.detected.version.minor: 11
[INFO] os.detected.classifier: osx-x86_64
[WARNING] Failed to inject repository session properties.
java.lang.NoSuchMethodError: org.apache.maven.execution.MavenSession.getRepositorySession()Lorg/eclipse/aether/RepositorySystemSession;
	at kr.motd.maven.os.RepositorySessionInjector.injectRepositorySession(RepositorySessionInjector.java:22)

In this case, review the installation according to what reported above and make sure that you are using Maven 3.2+.