Awesome
JVARKIT
Java utilities for Bioinformatics
Documentation
Documentation is available at: https://jvarkit.readthedocs.io/
Download
A pre-compiled jar is available at https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH .
Compilation
Since 2023, most tools (but not all) are now packaged into one application jvarkit.jar. Tools that were executed like java -jar toolname.jar are now executed as java -jar jvarkit.jar toolname. The documentation is not always up to date on this point.
See the documentation at https://jvarkit.readthedocs.io/.
Conda / Bioconda
A conda package created by DrYak is available at https://bioconda.github.io/recipes/jvarkit/README.html
Containers
jvarkit is available as a Docker container at https://hub.docker.com/r/lindenb/jvarkit . The jar is compiled under /opt/jvarkit/dist/jvarkit.jar so a command should be docker run java -jar /opt/jvarkit/dist/jvarkit.jar . Nevertheless GUI/Swing applications don't work.
Author
Pierre Lindenbaum PhD