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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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<!DOCTYPE html>

<html lang="en" data-content_root="../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; ensembl-anno 0.1 documentation</title>
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
<link rel="stylesheet" type="text/css" href="../_static/agogo.css?v=0438b505" />
<script src="../_static/documentation_options.js?v=2709fde1"></script>
<script src="../_static/doctools.js?v=888ff710"></script>
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
<link rel="canonical" href="https://ensembl.github.io/ensembl-anno/_modules/index.html" />
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
</head><body>
<div class="header-wrapper" role="banner">
<div class="header">
<div class="headertitle"><a
href="../index.html">ensembl-anno 0.1 documentation</a></div>
<div class="rel" role="navigation" aria-label="related navigation">
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |
<a href="../genindex.html" title="General Index"
accesskey="I">index</a>
</div>
</div>
</div>

<div class="content-wrapper">
<div class="content">
<div class="document">

<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">

<h1>All modules for which code is available</h1>
<ul><li><a href="ensembl/tools/anno/protein_annotation/genblast.html">ensembl.tools.anno.protein_annotation.genblast</a></li>
<li><a href="ensembl/tools/anno/repeat_annotation/dust.html">ensembl.tools.anno.repeat_annotation.dust</a></li>
<li><a href="ensembl/tools/anno/repeat_annotation/red.html">ensembl.tools.anno.repeat_annotation.red</a></li>
<li><a href="ensembl/tools/anno/repeat_annotation/repeatmasker.html">ensembl.tools.anno.repeat_annotation.repeatmasker</a></li>
<li><a href="ensembl/tools/anno/repeat_annotation/trf.html">ensembl.tools.anno.repeat_annotation.trf</a></li>
<li><a href="ensembl/tools/anno/simple_feature_annotation/cpg.html">ensembl.tools.anno.simple_feature_annotation.cpg</a></li>
<li><a href="ensembl/tools/anno/simple_feature_annotation/eponine.html">ensembl.tools.anno.simple_feature_annotation.eponine</a></li>
<li><a href="ensembl/tools/anno/snc_rna_annotation/trnascan.html">ensembl.tools.anno.snc_rna_annotation.trnascan</a></li>
<li><a href="ensembl/tools/anno/transcriptomic_annotation/minimap.html">ensembl.tools.anno.transcriptomic_annotation.minimap</a></li>
<li><a href="ensembl/tools/anno/transcriptomic_annotation/scallop.html">ensembl.tools.anno.transcriptomic_annotation.scallop</a></li>
<li><a href="ensembl/tools/anno/transcriptomic_annotation/star.html">ensembl.tools.anno.transcriptomic_annotation.star</a></li>
<li><a href="ensembl/tools/anno/transcriptomic_annotation/stringtie.html">ensembl.tools.anno.transcriptomic_annotation.stringtie</a></li>
</ul>

<div class="clearer"></div>
</div>
</div>
</div>
</div>
<div class="sidebar">

<h3>Table of Contents</h3>
<p class="caption" role="heading"><span class="caption-text">Index</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../install.html">API Setup and installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
<li class="toctree-l1"><a class="reference internal" href="../cpg.html">CpG Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dust.html">DustMasker Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../eponine.html">Eponine Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../genblast.html">Genblast Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../minimap.html">Minimap2 Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../red.html">Red Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../repeatmasker.html">Repeatmasker Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../scallop.html">Scallop Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../star.html">STAR Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../stringtie.html">Stringtie Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../trf.html">TRF Module Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../trnascan.html">tRNAscan-SE Module Documentation</a></li>
</ul>

<div role="search">
<h3 style="margin-top: 1.5em;">Search</h3>
<form class="search" action="../search.html" method="get">
<input type="text" name="q" />
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>modules</a> |
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<div class="footer" role="contentinfo">
&#169; Copyright [2016-2023] EMBL-European Bioinformatics Institute.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.5.
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</html>
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Cmsearch Module Documentation
==============================

.. automodule:: ensembl.tools.anno.snc_rna_annotation.cmsearch
:members:
:undoc-members:
:show-inheritance:

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CpG Module Documentation
==============================

.. automodule:: ensembl.tools.anno.simple_feature_annotation.cpg
:members:
:undoc-members:
:show-inheritance:

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DustMasker Module Documentation
==============================

.. automodule:: ensembl.tools.anno.repeat_annotation.dust
:members:
:undoc-members:
:show-inheritance:

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Eponine Module Documentation
==============================

.. automodule:: ensembl.tools.anno.simple_feature_annotation.eponine
:members:
:undoc-members:
:show-inheritance:

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Genblast Module Documentation
==============================

.. automodule:: ensembl.tools.anno.protein_annotation.genblast
:members:
:undoc-members:
:show-inheritance:

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.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
.. ensembl-anno documentation master file, created by
sphinx-quickstart on Fri Sep 1 12:25:36 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
========================================
Ensembl-anno
===========================================

Anno tool kit


Contents
--------
Check out :ref:`installation <install>` section for further information on how
to install the project.

.. toctree::
:maxdepth: 2
:caption: Index

install
license

_modules/cpg
_modules/dust
_modules/eponine
_modules/genblast
_modules/minimap
_modules/red
_modules/repeatmasker
_modules/scallop
_modules/star
_modules/stringtie
_modules/trf
_modules/trnascan

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
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.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
API Setup and installation
===========================

Requirements
--------------

.. _install:

An Ensembl API checkout including:

- ensembl-production `ensembl-production <https://github.com/Ensembl/ensembl-production>`_.
- ensembl-analysis `ensembl-analysis <https://github.com/Ensembl/ensembl-analysis/tree/dev/hive_master>`_. (on dev/hive_master branch)
- ensembl-taxonomy `ensembl-taxonomy <https://github.com/Ensembl/ensembl-taxonomy>`_.
- ensembl-orm `ensembl-orm <https://github.com/Ensembl/ensembl-orm>`_.

Software
^^^^^^^^

#. Python 3.8+
#. Bioperl 1.6.9+

Python Modules
^^^^^^^^^^^^^^
#. argschema



Installation
------------
Directly from GitHub:

.. code-block:: none
:linenos:
git clone https://github.com/Ensembl/ensembl-analysis -b experimental/gbiab
git clone https://github.com/Ensembl/ensembl-production
git clone https://github.com/Ensembl/ensembl-hive
git clone https://github.com/Ensembl/ensembl-taxonomy
git clone https://github.com/Ensembl/ensembl-orm
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