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