recipe je-suite

Je is a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter read duplicates using these UMIs

Homepage:

https://gbcs.embl.de/Je

License:

MIT / MIT License

Recipe:

/je-suite/meta.yaml

package je-suite

(downloads) docker_je-suite

versions:

2.0.RC-0,  1.2-2,  1.2-1,  1.2-0

depends openjdk:

>=8

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 je-suite

and update with::

   mamba update je-suite

To create a new environment, run:

mamba create --name myenvname je-suite

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/je-suite:<tag>

(see `je-suite/tags`_ for valid values for ``<tag>``)

Notes

Je is Java program that comes with a wrapper shell script. By default "-Xmx4G -Xms256m" 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 "je -Xms512m -Xmx1g"

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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