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

.. title:: Package Recipe 'scramble'
.. highlight: bash

scramble
========

.. conda:recipe:: scramble
   :replaces_section_title:
   :noindex:

   Soft Clipped Read Alignment Mapper

   :homepage: https://github.com/GeneDx/scramble
   :license: CC
   :recipe: /`scramble <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/scramble>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/scramble/meta.yaml>`_
   :links: doi: :doi:`10.1038/s41436-020-0749-x`

   SCRAMble identifies clusters of soft clipped reads in a BAM file\, builds consensus sequences\,
   aligns to representative L1Ta\, AluYa5\, and SVA\-E sequences\, and outputs MEI calls



.. conda:package:: scramble

   |downloads_scramble| |docker_scramble|

   :versions:
      
      

      ``1.0.2-1``,  ``1.0.2-0``,  ``1.0.1-2``,  ``1.0.1-1``,  ``1.0.1-0``

      

   
   :depends on bioconductor-rsamtools: ``>=2.4.0``
   :depends on htslib: ``>=1.17,<1.24.0a0``
   :depends on libgcc-ng: ``>=12``
   :depends on r-base: ``>=4.0.3``
   :depends on r-optparse: ``>=1.6.6``
   :depends on r-rblast: ``>=0.99.1``
   :depends on r-stringr: ``>=1.4.0``

   :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 scramble

to add into an existing workspace instead, run::

    pixi add scramble

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 scramble

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

    conda create -n envname scramble

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/scramble:<tag>

(see `scramble/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_scramble| image:: https://img.shields.io/conda/dn/bioconda/scramble.svg?style=flat
   :target: https://anaconda.org/bioconda/scramble
   :alt:   (downloads)
.. |docker_scramble| image:: https://quay.io/repository/biocontainers/scramble/status
   :target: https://quay.io/repository/biocontainers/scramble
.. _`scramble/tags`: https://quay.io/repository/biocontainers/scramble?tab=tags


.. raw:: html

    <script>
        var package = "scramble";
        var versions = ["1.0.2","1.0.2","1.0.1","1.0.1","1.0.1"];
    </script>





Notes
-----
SCRAMble runs as a two\-step process. First cluster\_identifier is used to generate soft\-clipped
read cluster consensus sequences. Second\, SCRAMble.R analyzes the cluster file for likely MEIs.
Custom wrapper script scramble.sh is provided to help setting location of SCRAMble.R script\,
and values for \-\-install\-dir and \-\-mei\-refs params.


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/scramble/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/scramble/README.html