recipe gbsx

Toolkit for experimental design and demultiplexing genotyping by sequencing experiments

Homepage:

https://github.com/GenomicsCoreLeuven/GBSX

License:

GPL / GPL-3.0

Recipe:

/gbsx/meta.yaml

Links:

doi: 10.1186/s12859-015-0514-3

Genotyping By Sequencing demultipleXing toolkit (GBSX) is a toolkit with an inline barcode demultiplexer for usage in the analysis of single read or paired-end genotyping by sequence (GBS) data, a barcode generator, a barcode discovery tool, and a restriction enzyme predictor. GBSX can easily be incorperated as a preceding analysis step for already deployed SNP pipelines.

package gbsx

(downloads) docker_gbsx

versions:

1.3-1,  1.3-0

depends openjdk:

>=6

depends python:

requirements:

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 gbsx

and update with::

   mamba update gbsx

To create a new environment, run:

mamba create --name myenvname gbsx

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/gbsx:<tag>

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

Notes

GBSX is a Java program that comes with a custom wrapper shell script. This shell wrapper is called "gbsx" 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 "gbsx -Xms512m -Xmx1g"

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