jvarkit

JVARKIT

Author : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France. Version : 93bf189ea Compilation : 20240606163145 Github : https://github.com/lindenb/jvarkit Issues : https://github.com/lindenb/jvarkit/issues

Usage

  java -jar jvarkit.jar [options]

or

  java -jar jvarkit.jar <command name> (other arguments)

Options

• –help show this screen
• –help-all show all commands, including the private ones.
• –version print version

Compilation

Requirements / Dependencies

• java compiler SDK 17. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download a pre-compiled executable jar

A pre-compiled java executable of jvarkit.jar is available at https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew jvarkit

The java jar file will be installed in the dist directory.

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite jvarkit ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

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