:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'biopet-fastqsplitter'
.. highlight: bash

biopet-fastqsplitter
====================

.. conda:recipe:: biopet-fastqsplitter
   :replaces_section_title:
   :noindex:

   This tool divides a fastq file into smaller fastq files\, based on the number of output files specified.

   :homepage: https://github.com/biopet/fastq-splitter
   :license: MIT
   :recipe: /`biopet-fastqsplitter <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biopet-fastqsplitter>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biopet-fastqsplitter/meta.yaml>`_

   This tool divides a fastq file into smaller fastq files\, based on the number of output files specified. For ecample\,
   if one specifies 5 output files\, it will split the fastq into 5 files of equal size. This can be very useful if one
   wants to use the chunking option in a pipeline\: FastqSplitter can generate the exact number of fastq files
   \(chunks\) as needed.

   FastqSplitter will read groups of reads \(100 reads per group\)
   and distribute this evenly over the output FASTQ
   files. FastqSplitter will iterate over all the output files while writing the
   read groups.

   Example\:
   A fastq file is split with a group size of 100 and three output files.
   read 1\-100 will be assigned to output1
   read 101\-200 will be assigned to output2
   read 201\-300 will be assigned to output3
   read 301\-400 will be assigned to output1
   read 401\-500 will be assigned to output2
   etc.

   This will make sure the output fastq files are of equal size and there is no positional bias in each
   output file.

   For documentation and manuals visit our github.io page\: https\:\/\/biopet.github.io\/fastq\-splitter


.. conda:package:: biopet-fastqsplitter

   |downloads_biopet-fastqsplitter| |docker_biopet-fastqsplitter|

   :versions:
      
      

      ``0.1-4``,  ``0.1-3``,  ``0.1-2``,  ``0.1-1``

      

   
   :depends on openjdk: ``>=8,<9``
   :depends on python: 

   :additional platforms:
      

Installation
------------

You need a conda-compatible package manager
(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
and the Bioconda channel already activated (see :ref:`bioconda_setup`).
Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi
""""

With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
to install globally, run::

    pixi global install biopet-fastqsplitter

to add into an existing workspace instead, run::

    pixi add biopet-fastqsplitter

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::

    pixi workspace channel add conda-forge
    pixi workspace channel add bioconda

Conda
"""""

With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::

    conda install biopet-fastqsplitter

Alternatively, to install into a new environment, run::

    conda create -n envname biopet-fastqsplitter

with ``envname`` being the name of the desired environment.

Container
"""""""""

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
For e.g. docker, run::

    docker pull quay.io/biocontainers/biopet-fastqsplitter:<tag>

(see `biopet-fastqsplitter/tags`_ for valid values for ``<tag>``).

Integrated deployment
"""""""""""""""""""""

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency.
Check the documentation of your workflow management system to find out about the integration.

.. _conda: https://conda.io
.. _pixi: https://pixi.sh
.. |downloads_biopet-fastqsplitter| image:: https://img.shields.io/conda/dn/bioconda/biopet-fastqsplitter.svg?style=flat
   :target: https://anaconda.org/bioconda/biopet-fastqsplitter
   :alt:   (downloads)
.. |docker_biopet-fastqsplitter| image:: https://quay.io/repository/biocontainers/biopet-fastqsplitter/status
   :target: https://quay.io/repository/biocontainers/biopet-fastqsplitter
.. _`biopet-fastqsplitter/tags`: https://quay.io/repository/biocontainers/biopet-fastqsplitter?tab=tags


.. raw:: html

    <script>
        var package = "biopet-fastqsplitter";
        var versions = ["0.1","0.1","0.1","0.1"];
    </script>





Notes
-----
biopet\-fastqsplitter 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\-fastqsplitter\'. 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\-fastqsplitter \-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-fastqsplitter/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-fastqsplitter/README.html