first documantation in Read the Docs format

.gitignore

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+#ignore DS_Store files and virtual env
+.DS_Store
+omnicenv/
+docs/build/
+docs/source/_templates/

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/_static/css/custom.css

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+.tight-table td {
+	white-space: normal !important;
+}

docs/source/assembly.rst

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+.. _ASSEMBLY:
+
+Assembly Enhancement
+====================
+
+scaffolding
+-----------
+
+In preparation
+
+Kmer analysis, QV and completness
+---------------------------------
+
+In preparation 
+
+In this section we will not use the long distance infomation that is captured by the Omni-C proximity ligation libraries. Instead, we take advandage of the uniform coverafe of Omni-C libraries and demonstrate how, after trimming, the reads can be used just as shotgun sequencing, for kmer analysis, measuring assembly completness and QV
+
+

docs/source/before_you_begin.rst

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+.. _BYB:
+
+Before you begin
+================
+
+Have a copy of the Omni-C scripts on your machine:
+----------------------------------------------------
+
+Clone this repository:
+
+.. code-block:: console
+
+   git clone https://github.com/dovetail-genomics/Omni-C.git
+
+
+Dependencies
+-------------
+
+Make sure that the following dependencies are installed:
+
+- `pysam <https://pysam.readthedocs.io/en/latest/>`_
+- `tabulate <https://pypi.org/project/tabulate/>`_
+- `bedtools <https://bedtools.readthedocs.io/en/latest/index.html>`_
+- `matplotlib <https://matplotlib.org/>`_
+- `pandas <https://pandas.pydata.org/pandas-docs/stable/dsintro.html>`_
+- `bwa <https://github.com/lh3/bwa>`_
+- `pairtools <https://github.com/open2c/pairtools>`_
+- `preseq <http://smithlabresearch.org/software/preseq/>`_
+- `samtools <https://github.com/samtools/samtools>`_
+
+
+python3 and pip3 are required, if you don't already have them installed, you will need sudo privileges.
+
+* Update and install python3 and pip3:
+
+.. code-block:: console 
+
+   sudo apt-get update
+   sudo apt-get install python3 python3-pip
+
+
+* To set python3 and pip3 as primary alternative:
+
+.. code-block:: console
+
+   sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 1
+   sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
+
+
+If you are working on a new machine and don't have the dependencies, you can use the ``installDep.sh`` script in this repository for updating your instance and installing the dependencies and python3. This process will take approximitly 10' and requiries sudo privileges. The scrit was tested on Ubuntu 18.04 with the latest version as of 04/11/2020
+
+If you choose to run the provided installetion script you will first need to set the permission to the file:
+
+.. code-block:: console
+
+   chmod +x ./Omni-C/installDep.sh
+
+
+And then run the installetion script:
+
+.. code-block:: console
+
+   ./Omni-C/installDep.sh
+
+
+.. admonition:: Remember!
+
+   Once the installetion is completed, sign off and then sign back to your instance to refresh the database of applications.
+
+
+Input files
+-----------
+
+For this tutorial you will need: 
+
+* **fastq files** R1 and R2, either fastq or fastq.gz are acceptable
+* **reference in a fasta file format**, e.g. hg38
+
+If you don't already have your own input files or want to run a test on a small data set, you can download sample fastq files from the :ref:`Omni-C Data Sets section<DATASETS>`. The 2M data set is suitable for a quick testing of the instruction in this tutorial. 
+
+.. code-block:: console
+
+   wget https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_2M_R1.fastq
+   wget https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_2M_R2.fastq
+

docs/source/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = u'Omni-C'
+copyright = u'2021, Dovetail Genomics'
+author = u'Dovetail Genomics'
+
+# The short X.Y version
+version = u''
+# The full version, including alpha/beta/rc tags
+release = u'0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Omni-Cdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'Omni-C.tex', u'Omni-C Documentation',
+     u'Dovetail Genomics', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'omni-c', u'Omni-C Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'Omni-C', u'Omni-C Documentation',
+     author, 'Omni-C', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------

docs/source/data_sets.rst

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+.. _DATASETS:
+
+Omni-C Data Sets
+=================
+
+
+To download one of the data sets, simply use the wget command:
+
+.. code-block:: console
+
+   wget https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_2M_R1.fastq
+   wget https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_2M_R2.fastq
+
+
++---------------------+------------------------------------------------------------------------+
+| Library             | Link                                                                   |
++=====================+========================================================================+
+| GM12878 Omni-C 2M   | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_2M_R1.fastq   |
+|                     | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_2M_R2.fastq   |
++---------------------+------------------------------------------------------------------------+
+| GM12878 Omni-C 100M | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_100M_R1.fastq |
+|                     | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_100M_R2.fastq |
++---------------------+------------------------------------------------------------------------+
+| GM12878 Omni-C 200M | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_200M_R1.fastq |
+|                     | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_200M_R2.fastq |
++---------------------+------------------------------------------------------------------------+
+| GM12878 Omni-C 400M | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_400M_R1.fastq |
+|                     | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_400M_R2.fastq |
++---------------------+------------------------------------------------------------------------+
+| GM12878 Omni-C 800M | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_800M_R1.fastq |
+|                     | - https://s3.amazonaws.com/dovetail.pub/HiC/fastqs/OmniC_800M_R2.fastq |
++---------------------+------------------------------------------------------------------------+