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

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

modifi
======

.. conda:recipe:: modifi
   :replaces_section_title:
   :noindex:

   DNA modification detection from PacBio SMRT metagenomic data

   :homepage: https://github.com/sachdevalab/MODIFI
   :license: MIT / MIT
   :recipe: /`modifi <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/modifi>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/modifi/meta.yaml>`_

   MODIFI detects DNA base modifications and infers host\-mobile genetic
   element \(MGE\) linkages from PacBio metagenomic sequencing data. It supports
   modification calling\, motif discovery\, and host\-MGE association for both
   subreads and HiFi read types. Native motif finding uses pbmotifmaker \(from
   pbtk\) on Linux if installed\; otherwise use the bundled MultiMotifMaker.jar
   \(OpenJDK\). On macOS\, install PacBio tools separately or rely on the JAR fallback.



.. conda:package:: modifi

   |downloads_modifi| |docker_modifi|

   :versions:
      
      

      ``0.0.3-0``,  ``0.0.1-0``

      

   
   :depends on adjusttext: 
   :depends on bash: 
   :depends on biopython: 
   :depends on h5py: 
   :depends on joblib: 
   :depends on libgcc: ``>=14``
   :depends on libstdcxx: ``>=14``
   :depends on matplotlib-base: 
   :depends on numpy: 
   :depends on openjdk: 
   :depends on pandas: 
   :depends on pbmm2: 
   :depends on pbtk: 
   :depends on psutil: 
   :depends on pysam: 
   :depends on pyyaml: 
   :depends on regex: 
   :depends on samtools: 
   :depends on scikit-learn: 
   :depends on scipy: 
   :depends on seaborn: 
   :depends on statsmodels: 
   :depends on tqdm: 

   :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 modifi

to add into an existing workspace instead, run::

    pixi add modifi

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 modifi

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

    conda create -n envname modifi

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/modifi:<tag>

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


.. raw:: html

    <script>
        var package = "modifi";
        var versions = ["0.0.3","0.0.1"];
    </script>






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/modifi/README.html)

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