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

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

tecap
=====

.. conda:recipe:: tecap
   :replaces_section_title:
   :noindex:

   3\' terminal exon capture diagnostics for long\-read scRNA\-seq

   :homepage: https://github.com/FullLengthFanatic/tecap
   :license: MIT / MIT
   :recipe: /`tecap <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/tecap>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/tecap/meta.yaml>`_
   :links: doi: :doi:`10.5281/zenodo.19762736`

   tecap classifies long\-read alignments by where their 3\' end lands relative
   to the terminal exon\, its UTR\, and a polyA site atlas. It decomposes
   capture failures into nine mechanism buckets and measures reference base
   composition downstream of each cleavage site to distinguish classic
   A\-tract internal priming from moderate\-A priming characteristic of
   saturating in\-solution oligo\-dT. Designed for PacBio Iso\-Seq \/ Kinnex
   and Oxford Nanopore cDNA BAMs. Direct\-RNA sequencing is unsupported.



.. conda:package:: tecap

   |downloads_tecap| |docker_tecap|

   :versions:
      
      

      ``0.2.0-0``

      

   
   :depends on intervaltree: ``>=3.1``
   :depends on matplotlib-base: ``>=3.5``
   :depends on numpy: ``>=1.22``
   :depends on pysam: ``>=0.22``
   :depends on python: ``>=3.9``

   :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 tecap

to add into an existing workspace instead, run::

    pixi add tecap

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 tecap

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

    conda create -n envname tecap

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/tecap:<tag>

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


.. raw:: html

    <script>
        var package = "tecap";
        var versions = ["0.2.0"];
    </script>






Download stats
-----------------

.. raw:: html
    :file: ../../templates/package_dashboard.html

Link to this page
-----------------

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
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