Add Tripal JBrowse submodule documentation.

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+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/_static/theme_overrides.css

@@ -0,0 +1,143 @@
+/* override table width restrictions
+See: https://rackerlabs.github.io/docs-rackspace/tools/rtd-tables.html
+ */
+@media screen and (min-width: 767px) {
+
+   .wy-table-responsive table td {
+      white-space: normal !important;
+   }
+
+   .wy-table-responsive {
+      overflow: visible !important;
+   }
+}
+
+
+/** 
+ * BRANDING
+ */
+ 
+/* Sidebar Title */
+.wy-side-nav-search {
+  background: none !important;
+}
+.wy-side-nav-search input[type="text"] {
+  border-color: black;
+}
+.wy-nav-side {
+  color: #CCCCCC !important;
+  background: #2D2D34 !important;
+  background-image: url("hexagon_pattern.png") !important;
+  background-repeat: repeat !important;
+  background: -webkit-linear-gradient(left, $light-grey , $gray-base) !important;
+  background: linear-gradient(to right, $light-grey , $gray-base) !important;
+}
+/* Logo */
+.fa-home::before, .icon-home::before {
+  content: url('small_logoonly.png')
+}
+/* Sidebar TOC */
+.wy-menu-vertical li.current {
+  color: #CCCCCC;
+  border-color: black;
+  background: rgba(0,0,0,0.5);
+}
+.wy-menu-vertical li.toctree-l1.current > a {
+  color: black;
+  border-color: whitesmoke;
+  background-color: whitesmoke;
+}
+.wy-menu-vertical li.toctree-l2.current > a,
+  .wy-menu-vertical li.toctree-l2.current li.toctree-l3 > a,
+  .wy-menu-vertical li.toctree-l3.current li.toctree-l4 > a {
+    color: #CCCCCC;
+    border-color: black;
+    background-color: rgba(0,0,0,0.05);
+}
+.wy-menu-vertical li.current a:hover,
+  .wy-menu-vertical li.toctree-l1.current > a:hover,
+  .wy-menu-vertical li.toctree-l2.current > a:hover,
+  .wy-menu-vertical li.toctree-l2.current li.toctree-l3 > a:hover,
+  .wy-menu-vertical li.toctree-l3.current li.toctree-l4 > a:hover {
+    color: white;
+    border-color: black;
+    font-weight: bold;
+    background-color: rgba(0,0,0);
+}
+.wy-menu-vertical li.toctree-l1 a,
+  .wy-menu-vertical li.toctree-l2 a, 
+  .wy-menu-vertical li.toctree-l3 a, 
+  .wy-menu-vertical li.toctree-l4 a {
+    color: #CCCCCC;
+    border-color: black;
+}
+/* Main Content */
+.wy-nav-content-wrap {
+  background: whitesmoke;
+}
+a, a:hover {
+  color: #990000;
+}
+a:visited {
+  color: #cc0000;
+}
+a.icon-home:visited {
+  color: #ffffff;
+}
+/* Code blocks */
+.highlight {
+  background: #e1f0db;
+}
+/* Default Notes */
+.wy-alert.wy-alert-info, 
+  .rst-content .note, 
+  .rst-content .wy-alert-info.attention, 
+  .rst-content .wy-alert-info.caution, 
+  .rst-content .wy-alert-info.danger, 
+  .rst-content .wy-alert-info.error, 
+  .rst-content .wy-alert-info.hint, 
+  .rst-content .wy-alert-info.important, 
+  .rst-content .wy-alert-info.tip, 
+  .rst-content .wy-alert-info.warning, 
+  .rst-content .seealso, .rst-content 
+  .wy-alert-info.admonition-todo, 
+  .rst-content .wy-alert-info.admonition {
+    background: #d9d9d9;
+}
+.wy-alert.wy-alert-info 
+  .wy-alert-title, 
+  .rst-content .note .wy-alert-title, 
+  .rst-content .wy-alert-info.attention .wy-alert-title, 
+  .rst-content .wy-alert-info.caution .wy-alert-title, 
+  .rst-content .wy-alert-info.danger .wy-alert-title, 
+  .rst-content .wy-alert-info.error .wy-alert-title, 
+  .rst-content .wy-alert-info.hint .wy-alert-title, 
+  .rst-content .wy-alert-info.important .wy-alert-title, 
+  .rst-content .wy-alert-info.tip .wy-alert-title, 
+  .rst-content .wy-alert-info.warning .wy-alert-title, 
+  .rst-content .seealso .wy-alert-title, 
+  .rst-content .wy-alert-info.admonition-todo .wy-alert-title, 
+  .rst-content .wy-alert-info.admonition .wy-alert-title, 
+  .wy-alert.wy-alert-info .rst-content .admonition-title, 
+  .rst-content .wy-alert.wy-alert-info .admonition-title, 
+  .rst-content .note .admonition-title, 
+  .rst-content .wy-alert-info.attention .admonition-title, 
+  .rst-content .wy-alert-info.caution .admonition-title, 
+  .rst-content .wy-alert-info.danger .admonition-title, 
+  .rst-content .wy-alert-info.error .admonition-title, 
+  .rst-content .wy-alert-info.hint .admonition-title, 
+  .rst-content .wy-alert-info.important .admonition-title, 
+  .rst-content .wy-alert-info.tip .admonition-title, 
+  .rst-content .wy-alert-info.warning .admonition-title, 
+  .rst-content .seealso .admonition-title, .rst-content 
+  .wy-alert-info.admonition-todo .admonition-title, 
+  .rst-content .wy-alert-info.admonition .admonition-title {
+    background: #737373;
+}
+/* Note Warnings */
+.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title {
+  background: #e6b800;
+}
+.wy-alert.wy-alert-warning, .rst-content .wy-alert-warning.note, .rst-content .attention, .rst-content .caution, .rst-content .wy-alert-warning.danger, .rst-content .wy-alert-warning.error, .rst-content .wy-alert-warning.hint, .rst-content .wy-alert-warning.important, .rst-content .wy-alert-warning.tip, .rst-content .warning, .rst-content .wy-alert-warning.seealso, .rst-content .admonition-todo, .rst-content .wy-alert-warning.admonition {
+  background: #FcFde6;
+}

docs/conf.py

@@ -0,0 +1,171 @@
+# -*- 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
+
+
+#PHP stuff
+#see: https://www.sitepoint.com/using-sphinx-for-php-project-documentation/
+
+from sphinx.highlighting import lexers
+from pygments.lexers.web import PhpLexer
+lexers["php"] = PhpLexer(startinline=True, linenos=1)
+lexers["php-annotations"] = PhpLexer(startinline=True, linenos=1)
+
+
+# -- 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'Tripal JBrowse'
+copyright = u'2018, UofS Pulse Bioinformatics and Hardwood Genomics'
+author = u''
+
+# The short X.Y version
+version = u''
+# The full version, including alpha/beta/rc tags
+release = u''
+
+
+# -- 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 = [u'_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- 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']
+
+# Override the base theme.
+# We add the stylesheet this way so that it's loaded after the default.css
+# See https://docs.readthedocs.io/en/latest/guides/adding-custom-css.html
+def setup(app):
+    app.add_stylesheet('theme_overrides.css');
+
+# 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 = 'Tripaldoc'
+
+
+# -- 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, 'Tripal.tex', u'Tripal Documentation',
+     u'Stephen Ficklin, Lacey Sanderson, Bradford Condon et al', '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, 'tripal', u'Tripal 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, 'Tripal', u'Tripal Documentation',
+     author, 'Tripal', 'One line description of project.',
+     'Miscellaneous'),
+]

docs/index.rst

@@ -0,0 +1,9 @@
+
+Tripal JBrowse Documentation
+=============================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   tripal_jbrowse

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/tripal_jbrowse.rst

@@ -0,0 +1,13 @@
+
+Tripal JBrowse Page Integration
+================================
+
+.. note::
+
+   The following functionality is provided by the **Tripal JBrowse Integration** sub-module.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Functionality:
+
+   tripal_jbrowse/instance_page

docs/tripal_jbrowse/instance_page.rst

@@ -0,0 +1,39 @@
+
+JBrowse Instance Page
+======================
+
+This guide will show you **how to create a page within your Tripal site for an existing JBrowse instance**. This ensures a *consistent user experience* by making the menu system of the Tripal site available to the user while browsing. If the user needs more space they can choose the *FullScreen option* to remove the menus.
+
+.. warning::
+
+   This requires you already have a JBrowse instance. Both local (hosted on the same machine as your Tripal site) or external JBrowse instances are supported.
+
+.. note::
+
+   The Tripal JBrowse Management sub-module provides a user interface to ease setup of multiple JBrowse instances. It is a great option but is not required.
+
+You create a JBrowse Instance page by navigating to **Content > Add Content > JBrowse Instance** on the Administration Toolbar. Then just fill out the form and click save!
+
+.. image:: instancepage.1.addcontent.png
+
+.. image:: instancepage.2.addinstance.png
+
+The **title** will become the title of the page and the **description** will be shown above the JBrowse instances. The description is a good place to add any warnings or instructions.
+
+.. image:: instancepage.3.createtop.png
+
+The **Existing JBrowse URL** is the URL to the JBrowse instance you want to embed. You should be able to put this URL into your browser and access the JBrowse instance directly, even in the case of local instances.
+
+The **Start Locations** allows you to specify where you want the JBrowse to navigate to for first time users. Keep in mind that JBrowse caches user location and thus all subsequent times a user accesses the instance it will start at their last browsed location.
+
+.. image:: instancepage.4.createbottom.png
+
+The **Tracks** allows you to set which tracks you want shown by default. You should enter the machine name of the tracks here with multiple tracks separated by comma's.
+
+.. note::
+
+    Depending on how your Drupal site is configured, you may be presented with a **Preview** button instead of a **Save** button. In this case, simply click Preview and then on the next page, click Save.
+
+    The preview for the JBrowse may not load properly. Do not be concerned as this is not an indication that you have incorrectly configured the page.
+
+    To disable the preview button, navigate to Structure > Content Types > JBrowse Instance > edit and set the "Submission for settings" > "Preview before submitting" to "Disabled".