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<!DOCTYPE html>

<html lang="en">
<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=cc331ede" />
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=e031e9a9"></script>
<script src="../_static/doctools.js?v=888ff710"></script>
<script src="../_static/sphinx_highlight.js?v=4825356b"></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">
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<div class="headertitle"><a
href="../index.html">ensembl-anno 0.1 documentation</a></div>
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accesskey="I">index</a>
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</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>

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</div>
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<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>

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&#169; Copyright [2016-2023] EMBL-European Bioinformatics Institute.
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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: 1
:caption: Index

install
license

cpg
dust
eponine
genblast
minimap
red
repeatmasker
scallop
star
stringtie
trf
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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