:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'biopet-scatterregions' .. highlight: bash biopet-scatterregions ===================== .. conda:recipe:: biopet-scatterregions :replaces_section_title: :noindex: This tool breaks a reference or bed file into smaller scatter regions of equal size. :homepage: https://github.com/biopet/scatterregions :license: MIT :recipe: /`biopet-scatterregions `_/`meta.yaml `_ This tool breaks a reference or bed file into smaller scatter regions of equal size. This can be used for processing inside a pipeline. For documentation and manuals visit our github.io page\: https\:\/\/biopet.github.io\/scatterregions .. conda:package:: biopet-scatterregions |downloads_biopet-scatterregions| |docker_biopet-scatterregions| :versions: ``0.2-1``,  ``0.2-0``,  ``0.1-1``,  ``0.1-0`` :depends openjdk: ``>=8,<9`` :depends python: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 biopet-scatterregions and update with:: mamba update biopet-scatterregions To create a new environment, run:: mamba create --name myenvname biopet-scatterregions 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/biopet-scatterregions: (see `biopet-scatterregions/tags`_ for valid values for ````) .. |downloads_biopet-scatterregions| image:: https://img.shields.io/conda/dn/bioconda/biopet-scatterregions.svg?style=flat :target: https://anaconda.org/bioconda/biopet-scatterregions :alt: (downloads) .. |docker_biopet-scatterregions| image:: https://quay.io/repository/biocontainers/biopet-scatterregions/status :target: https://quay.io/repository/biocontainers/biopet-scatterregions .. _`biopet-scatterregions/tags`: https://quay.io/repository/biocontainers/biopet-scatterregions?tab=tags .. raw:: html Notes ----- biopet\-scatterregions is a Java program that comes with a custom wrapper shell script. By default \'no default java option\' is set in the wrapper. The command that runs the program is \'biopet\-scatterregions\'. If you want to overwrite it you can specify memory options directly after your binaries. If you have \_JAVA\_OPTIONS set globally this will take precedence. For example run it with \'biopet\-scatterregions \-Xms512m \-Xmx1g\'. Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/biopet-scatterregions/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/biopet-scatterregions/README.html