Merge pull request #3 from mshakya/master

readme instruction changes

.gitignore

@@ -25,4 +25,5 @@ thirdParty/messages.log
 thirdParty/evolver.out
 thirdParty/errors.log
 messages.log
-*.log
+*.log
+docs/_build/*

README.md

@@ -4,6 +4,8 @@
 [![Waffle.io - Columns and their card count](https://badge.waffle.io/mshakya/PhaME-1.svg?columns=all)](https://waffle.io/mshakya/PhaME-1)
 [![Documentation Status](https://readthedocs.org/projects/phame/badge/?version=latest)](https://phame.readthedocs.io/en/latest/?badge=latest)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/phame/README.html)
+[![docker](https://quay.io/repository/biocontainers/phame/status)](https://quay.io/repository/biocontainers/phame)
+![phame-downloads](https://anaconda.org/bioconda/phame/badges/downloads.svg)
 
 Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. 
 Uses SNP multiple sequence alignment to construct a phylogenetic tree. 

docs/conf.py

@@ -0,0 +1,178 @@
+# -*- 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 = 'phame'
+copyright = '2018, migun'
+author = 'migun'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = ''
+
+
+# -- 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 = [
+]
+
+# 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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+# 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_logo = 'img/logo.png'
+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 = {
+    'logo_only': True,
+    'display_version': False,
+}
+
+# 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 = 'phame'
+
+
+# -- 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, 'phame.tex', 'phame Documentation',
+     'migun', '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, 'phame', 'phame 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, 'phame', 'phame Documentation',
+     author, 'phame', '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']

docs/index.rst

@@ -1,23 +1,39 @@
 PhaME: **Ph**\ylogenetics **a**\nd **M**\olecular **E**\volution analysis tool
-##########################################################################
+##############################################################################
+
+Phylogenetic and Molecular Evolution (PhaME) analysis tool allows suite of analysis pertaining to phylogeny and moleuclar evolution.
+
+
+
+.. toctree::
+    :maxdepth: 2
+    :caption: INTRODUCTION
+
+    introduction/introduction
+    introduction/runphame
+
+.. toctree::
+    :maxdepth: 2
+    :caption: INSTALL
+
+    install/conda
+    install/docker
+    install/web-interface
 
 .. toctree::
-   :numbered:
-   :maxdepth: 2
-
-   introduction
-   installation
-   runphame
-   cases
-   docker
-   gui
-   commandline
-   output
-   database
-   third_party
-   troubleshooting
-   copyright
-   citation
-   contact
+    :maxdepth: 2
+    :caption: USAGE
+
+    usage/cases
+
+
+.. .. toctree::
+..     :maxdepth: 2
+..     :caption: CITATION
+
+..     citation.rst
+
+
+
 
 

docs/install/conda.rst

@@ -0,0 +1,25 @@
+Conda
+############################
+
+PhaME can be installed using [conda](https://conda.io/docs/index.html). If you do not have anaconda or miniconda installed, please do so. Installation of miniconda or anaconda is rather straight forward. After installtion of conda, add channels for bioconda and conda-forge using:
+
+ .. code-block:: console
+ 
+    $ conda config --add channels r
+    $ conda config --add channels defaults
+    $ conda config --add channels conda-forge
+    $ conda config --add channels bioconda
+
+
+Then simply run
+
+.. code-block:: console
+
+    conda install phame
+
+We recommend creating a separate conda environment for PhaME. You can create a conda environment by:
+
+.. code-block:: console
+
+    $ conda create -n my_env
+    $ conda install phame -n my_env