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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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bioinformatics biology genomics java next-generation-sequencing ngs science

readme

JVARKIT

Java utilities for Bioinformatics

Build Status

Last commit

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

@yokofakun