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

.. title:: Package Recipe 'thapbi-pict'
.. highlight: bash

thapbi-pict
===========

.. conda:recipe:: thapbi-pict
   :replaces_section_title:
   :noindex:

   THAPBI Phytophthora ITS1 Classifier Tool \(PICT\).

   :homepage: https://github.com/peterjc/thapbi-pict
   :documentation: https://thapbi-pict.readthedocs.io/en/latest/
   
   :license: MIT / MIT
   :recipe: /`thapbi-pict <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/thapbi-pict>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/thapbi-pict/meta.yaml>`_

   THAPBI Phytophthora ITS1 Classifier Tool \(PICT\) an ITS1\-based
   diagnostic\/profiling tool from the UK BBSRC funded Tree Health
   and Plant Biosecurity Initiative \(THAPBI\) Phyto\-Threats project\,
   focused on identifying Phytophthora species present in Illumina
   sequenced environmental samples.



.. conda:package:: thapbi-pict

   |downloads_thapbi-pict| |docker_thapbi-pict|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.0.22-0</code>,  <code>1.0.21-0</code>,  <code>1.0.20-0</code>,  <code>1.0.19-0</code>,  <code>1.0.18-0</code>,  <code>1.0.17-0</code>,  <code>1.0.16-0</code>,  <code>1.0.15-0</code>,  <code>1.0.14-0</code>,  </span></summary>
      

      ``1.0.22-0``,  ``1.0.21-0``,  ``1.0.20-0``,  ``1.0.19-0``,  ``1.0.18-0``,  ``1.0.17-0``,  ``1.0.16-0``,  ``1.0.15-0``,  ``1.0.14-0``,  ``1.0.13-0``,  ``1.0.12-0``,  ``1.0.11-0``,  ``1.0.10-0``,  ``1.0.9-0``,  ``1.0.8-0``,  ``1.0.7-0``,  ``1.0.6-0``,  ``1.0.5-0``,  ``1.0.4-0``,  ``1.0.3-0``,  ``1.0.2-0``,  ``1.0.1-0``,  ``1.0.0-0``,  ``0.14.1-0``,  ``0.14.0-0``,  ``0.13.6-0``,  ``0.13.5-0``,  ``0.13.4-0``,  ``0.13.3-0``,  ``0.13.2-0``,  ``0.13.1-0``,  ``0.13.0-0``,  ``0.12.9-0``,  ``0.12.8-0``,  ``0.12.7-0``,  ``0.12.6-0``,  ``0.12.5-0``,  ``0.12.4-0``,  ``0.12.3-0``,  ``0.12.2-0``,  ``0.12.1-0``,  ``0.12.0-0``,  ``0.11.6-0``,  ``0.11.5-0``,  ``0.11.4-0``,  ``0.11.3-0``,  ``0.11.2-0``,  ``0.11.1-0``,  ``0.11.0-0``,  ``0.10.6-0``,  ``0.10.5-0``,  ``0.10.4-0``,  ``0.10.3-0``,  ``0.10.2-0``,  ``0.10.1-0``,  ``0.9.9-0``,  ``0.9.8-0``,  ``0.9.7-0``,  ``0.9.6-0``,  ``0.9.5-0``,  ``0.9.4-0``,  ``0.9.3-0``,  ``0.9.2-0``,  ``0.9.1-0``,  ``0.9.0-0``,  ``0.8.4-0``,  ``0.8.2-0``,  ``0.8.1-0``,  ``0.8.0-0``,  ``0.7.11-0``,  ``0.7.10-0``,  ``0.7.9-0``,  ``0.7.8-0``,  ``0.7.7-0``,  ``0.7.6-0``,  ``0.7.5-0``,  ``0.7.4-0``,  ``0.7.3-0``,  ``0.7.2-0``,  ``0.7.1-0``,  ``0.7.0-0``,  ``0.6.15-0``,  ``0.6.14-0``,  ``0.6.13-0``,  ``0.6.11-0``,  ``0.6.10-0``,  ``0.6.9-0``,  ``0.6.8-0``,  ``0.6.7-0``,  ``0.6.6-0``,  ``0.6.5-0``,  ``0.6.4-0``,  ``0.6.3-0``,  ``0.6.1-1``,  ``0.6.1-0``,  ``0.6.0-0``,  ``0.5.8-0``,  ``0.5.7-0``,  ``0.5.6-0``,  ``0.5.5-0``,  ``0.5.4-0``,  ``0.5.1-0``,  ``0.5.0-0``,  ``0.4.19-0``,  ``0.4.18-0``,  ``0.4.17-0``,  ``0.4.15-0``,  ``0.4.13-0``,  ``0.4.12-0``,  ``0.4.11-0``,  ``0.4.9-0``,  ``0.4.8-0``,  ``0.4.7-0``,  ``0.4.6-0``,  ``0.4.4-0``,  ``0.4.2-0``,  ``0.4.1-0``,  ``0.4.0-0``,  ``0.3.11-0``,  ``0.3.10-0``,  ``0.3.9-0``,  ``0.3.8-0``,  ``0.3.7-0``,  ``0.3.4-0``,  ``0.3.1-0``,  ``0.2.5-0``,  ``0.2.3-0``,  ``0.2.2-0``,  ``0.2.1-0``,  ``0.1.12-0``,  ``0.1.10-0``,  ``0.1.6-0``

      
      .. raw:: html

         </details>
      

   
   :depends on biom-format: ``>=2.1.14``
   :depends on biopython: ``>=1.84``
   :depends on blast: 
   :depends on cutadapt: ``>=4.9``
   :depends on flash: ``>=1.2.11``
   :depends on graphviz: 
   :depends on matplotlib-base: ``>=3.9.2``
   :depends on networkx: ``>=3.4.2``
   :depends on pydot: ``>=3.0.1``
   :depends on python: ``>=3.10``
   :depends on rapidfuzz: ``>=3.10.1``
   :depends on sqlalchemy: ``>=2.0.36``
   :depends on vsearch: 
   :depends on xlsxwriter: ``>=3.2``

   :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 thapbi-pict

to add into an existing workspace instead, run::

    pixi add thapbi-pict

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 thapbi-pict

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

    conda create -n envname thapbi-pict

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/thapbi-pict:<tag>

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


.. raw:: html

    <script>
        var package = "thapbi-pict";
        var versions = ["1.0.22","1.0.21","1.0.20","1.0.19","1.0.18"];
    </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/thapbi-pict/README.html)

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