recipe jvarkit

Java utilities for Bioinformatics.

Homepage:

https://github.com/lindenb/jvarkit

License:

MIT / MIT License

Recipe:

/jvarkit/meta.yaml

Links:

biotools: jvarkit, doi: 10.6084/m9.figshare.1425030

package jvarkit

versions:

2024.08.25-1,  2024.08.25-0,  2024.08.01-0,  2024.04.20-0,  2023.09.07-0

depends bcftools:

>=1.20

depends openjdk:

>=11

depends samtools:

>=1.20

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install jvarkit

and update with::

   mamba update jvarkit

To create a new environment, run:

mamba create --name myenvname jvarkit

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/jvarkit:<tag>

(see `jvarkit/tags`_ for valid values for ``<tag>``)

Notes

jvarkit is Java program that comes with a custom wrapper shell script. This shell wrapper is called "jvarkit" and is on $PATH by default. By default "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with "jvarkit -Xms512m -Xmx1g"

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