This project is a clone of Picard library http://picard.sourceforge.net/, a useful tool for managing SAM/BAM format data in Java/Scala. Unfortunately, however, Picard has not been available from Maven's central repository. In order to use Picard with Maven (Java) and sbt (Scala) projects, we created a new build script for Picard, and now the Picard library becomes available in Maven and sbt projects.

To use picard, add the folloing settings to your project files:

    <dependency>
        <groupId>org.utgenome.thirdparty</groupId>
        <artifactId>picard</artifactId>
        <version>1.102.0</version>
    </dependency>

libraryDependencies += "org.utgenome.thirdparty" % "picard" % "1.102.0"

The version number has a suffix like ".0" following the original Picard version.

$ git clone git://github.com/utgenome/picard.git
$ cd picard
$ bin/sbt pack
$ cd target/pack
$ make install

Picard comamnd-line tools will be installed to $(HOME)/local/bin. Configure your PATH environment vaiable in your shell profile (e.g., .bash_profile, .zprofile, etc.):

   export PATH = $HOME/local/bin:$PATH

Although I recommend you to use Maven (or sbt, Ivy etc.), you can download picard.jar by hand:

• Maven repository: http://repo1.maven.org/maven2/org/utgenome/thirdparty/picard/

Install svn2git, then do:

svn2git --rebase