Java utilities for Bioinformatics
Documentation is available at: http://lindenb.github.io/jvarkit/
February 2019. I'm moving to java OpenJdk. See the [[NEWS]] file.
Each tool is compiled independently of each other.
See the documentation for each tool at http://lindenb.github.io/jvarkit/. All the pages should include a paragraph titled 'Download and Compile'
You shouldn't try to compile all the tools because some of them are not tested, deprecated, or just too specific to my lab.
Pierre Lindenbaum PhD