1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/77ceb114bf57/
changeset: 77ceb114bf57
user: dannon
date: 2012-06-13 17:31:00
summary: Initial commit of Galaxy Documentation.
affected #: 75 files
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/Makefile
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,153 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = build
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex
latexpdf text man changes linkcheck doctest gettext
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or
PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " texinfo to make Texinfo files"
+ @echo " info to make Texinfo files and run them through makeinfo"
+ @echo " gettext to make PO message catalogs"
+ @echo " changes to make an overview of all changed/added/deprecated
items"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if
enabled)"
+
+clean:
+ -rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with
the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Galaxy.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Galaxy.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/Galaxy"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Galaxy"
+ @echo "# devhelp"
+
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+ "(use \`make info' here to do that automatically)."
+
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/conf.py
--- /dev/null
+++ b/doc/source/conf.py
@@ -0,0 +1,254 @@
+# -*- coding: utf-8 -*-
+#
+# Galaxy documentation build configuration file, created by
+# sphinx-quickstart on Tue Mar 6 10:44:44 2012.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+
+####### REQUIRED GALAXY INCLUDES
+
+sys.path.append(os.path.join(os.getcwd(), '../../lib'))
+import galaxy
+from galaxy import eggs
+
+#######
+
+# 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.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- 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', 'sphinx.ext.doctest',
'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+#configure default autodoc's action
+autodoc_default_flags = ['members', 'undoc-members']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Galaxy'
+copyright = u'2012, Galaxy Team'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+# version = '1'
+# The full version, including alpha/beta/rc tags.
+# release = '1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- 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 = 'default'
+
+# 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 themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# 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']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page
bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is
True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Galaxydoc'
+
+
+# -- 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': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('index', 'Galaxy.tex', u'Galaxy Documentation',
+ u'Galaxy Team', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ ('index', 'galaxy', u'Galaxy Documentation',
+ [u'Galaxy Team'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- 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 = [
+ ('index', 'Galaxy', u'Galaxy Documentation',
+ u'Galaxy Team', 'Galaxy', 'Data intensive biology for
everyone.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/index.rst
--- /dev/null
+++ b/doc/source/index.rst
@@ -0,0 +1,29 @@
+Galaxy Documentation
+********************
+
+Galaxy is an open, web-based platform for accessible, reproducible, and
+transparent computational biomedical research.
+ - Accessible: Users without programming experience can easily specify
+ parameters and run tools and workflows.
+ - Reproducible: Galaxy captures information so that any user can repeat and
+ understand a complete computational analysis.
+ - Transparent: Users share and publish analyses via the web and create
+ Pages, interactive, web-based documents that describe a complete
+ analysis.
+
+Contents
+========
+.. toctree::
+ :maxdepth: 4
+
+ API Documentation <lib/galaxy.web.api>
+
+ Application Documentation <lib/galaxy>
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/fpconst.rst
--- /dev/null
+++ b/doc/source/lib/fpconst.rst
@@ -0,0 +1,7 @@
+fpconst Module
+==============
+
+.. automodule:: fpconst
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.actions.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.actions.rst
@@ -0,0 +1,11 @@
+actions Package
+===============
+
+:mod:`admin` Module
+-------------------
+
+.. automodule:: galaxy.actions.admin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.datatypes.converters.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.datatypes.converters.rst
@@ -0,0 +1,251 @@
+converters Package
+==================
+
+:mod:`bed_to_genetrack_converter` Module
+----------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.bed_to_genetrack_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`bed_to_gff_converter` Module
+----------------------------------
+
+.. automodule:: galaxy.datatypes.converters.bed_to_gff_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`bedgraph_to_array_tree_converter` Module
+----------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.bedgraph_to_array_tree_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`bgzip` Module
+-------------------
+
+.. automodule:: galaxy.datatypes.converters.bgzip
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`fasta_to_len` Module
+--------------------------
+
+.. automodule:: galaxy.datatypes.converters.fasta_to_len
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`fasta_to_tabular_converter` Module
+----------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`fastq_to_fqtoc` Module
+----------------------------
+
+.. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`fastqsolexa_to_fasta_converter` Module
+--------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`fastqsolexa_to_qual_converter` Module
+-------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`gff_to_bed_converter` Module
+----------------------------------
+
+.. automodule:: galaxy.datatypes.converters.gff_to_bed_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`gff_to_interval_index_converter` Module
+---------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`interval_to_bed_converter` Module
+---------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.interval_to_bed_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`interval_to_bedstrict_converter` Module
+---------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`interval_to_coverage` Module
+----------------------------------
+
+.. automodule:: galaxy.datatypes.converters.interval_to_coverage
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`interval_to_interval_index_converter` Module
+--------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`interval_to_summary_tree_converter` Module
+------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.interval_to_summary_tree_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`interval_to_tabix_converter` Module
+-----------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`lped_to_fped_converter` Module
+------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.lped_to_fped_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`lped_to_pbed_converter` Module
+------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`maf_to_fasta_converter` Module
+------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`maf_to_interval_converter` Module
+---------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.maf_to_interval_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`pbed_ldreduced_converter` Module
+--------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`pbed_to_lped_converter` Module
+------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`picard_interval_list_to_bed6_converter` Module
+----------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.picard_interval_list_to_bed6_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sam_or_bam_to_summary_tree_converter` Module
+--------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.sam_or_bam_to_summary_tree_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sam_to_bam` Module
+------------------------
+
+.. automodule:: galaxy.datatypes.converters.sam_to_bam
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`vcf_to_interval_index_converter` Module
+---------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`vcf_to_summary_tree_converter` Module
+-------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.vcf_to_summary_tree_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`vcf_to_vcf_bgzip` Module
+------------------------------
+
+.. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`wiggle_to_array_tree_converter` Module
+--------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.wiggle_to_array_tree_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`wiggle_to_simple_converter` Module
+----------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.datatypes.display_applications.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.datatypes.display_applications.rst
@@ -0,0 +1,27 @@
+display_applications Package
+============================
+
+:mod:`application` Module
+-------------------------
+
+.. automodule:: galaxy.datatypes.display_applications.application
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`parameters` Module
+------------------------
+
+.. automodule:: galaxy.datatypes.display_applications.parameters
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`util` Module
+------------------
+
+.. automodule:: galaxy.datatypes.display_applications.util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.datatypes.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.datatypes.rst
@@ -0,0 +1,156 @@
+datatypes Package
+=================
+
+:mod:`assembly` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.assembly
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`binary` Module
+--------------------
+
+.. automodule:: galaxy.datatypes.binary
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`checkers` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.checkers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`chrominfo` Module
+-----------------------
+
+.. automodule:: galaxy.datatypes.chrominfo
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`coverage` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.coverage
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`data` Module
+------------------
+
+.. automodule:: galaxy.datatypes.data
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`genetics` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.genetics
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`images` Module
+--------------------
+
+.. automodule:: galaxy.datatypes.images
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`interval` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.interval
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`metadata` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.metadata
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`ngsindex` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.ngsindex
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`qualityscore` Module
+--------------------------
+
+.. automodule:: galaxy.datatypes.qualityscore
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`registry` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.registry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sequence` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.sequence
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sniff` Module
+-------------------
+
+.. automodule:: galaxy.datatypes.sniff
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tabular` Module
+---------------------
+
+.. automodule:: galaxy.datatypes.tabular
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tracks` Module
+--------------------
+
+.. automodule:: galaxy.datatypes.tracks
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`xml` Module
+-----------------
+
+.. automodule:: galaxy.datatypes.xml
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.datatypes.converters
+ galaxy.datatypes.display_applications
+ galaxy.datatypes.util
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.datatypes.util.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.datatypes.util.rst
@@ -0,0 +1,27 @@
+util Package
+============
+
+:mod:`util` Package
+-------------------
+
+.. automodule:: galaxy.datatypes.util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`gff_util` Module
+----------------------
+
+.. automodule:: galaxy.datatypes.util.gff_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`image_util` Module
+------------------------
+
+.. automodule:: galaxy.datatypes.util.image_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.eggs.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.eggs.rst
@@ -0,0 +1,27 @@
+eggs Package
+============
+
+:mod:`eggs` Package
+-------------------
+
+.. automodule:: galaxy.eggs
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`dist` Module
+------------------
+
+.. automodule:: galaxy.eggs.dist
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`scramble` Module
+----------------------
+
+.. automodule:: galaxy.eggs.scramble
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.exceptions.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.exceptions.rst
@@ -0,0 +1,11 @@
+exceptions Package
+==================
+
+:mod:`exceptions` Package
+-------------------------
+
+.. automodule:: galaxy.exceptions
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.external_services.result_handlers.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.external_services.result_handlers.rst
@@ -0,0 +1,11 @@
+result_handlers Package
+=======================
+
+:mod:`basic` Module
+-------------------
+
+.. automodule:: galaxy.external_services.result_handlers.basic
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.external_services.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.external_services.rst
@@ -0,0 +1,34 @@
+external_services Package
+=========================
+
+:mod:`actions` Module
+---------------------
+
+.. automodule:: galaxy.external_services.actions
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`parameters` Module
+------------------------
+
+.. automodule:: galaxy.external_services.parameters
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`service` Module
+---------------------
+
+.. automodule:: galaxy.external_services.service
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.external_services.result_handlers
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.forms.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.forms.rst
@@ -0,0 +1,11 @@
+forms Package
+=============
+
+:mod:`forms` Module
+-------------------
+
+.. automodule:: galaxy.forms.forms
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.actions.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.actions.rst
@@ -0,0 +1,19 @@
+actions Package
+===============
+
+:mod:`actions` Package
+----------------------
+
+.. automodule:: galaxy.jobs.actions
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`post` Module
+------------------
+
+.. automodule:: galaxy.jobs.actions.post
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.deferred.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.deferred.rst
@@ -0,0 +1,51 @@
+deferred Package
+================
+
+:mod:`deferred` Package
+-----------------------
+
+.. automodule:: galaxy.jobs.deferred
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`data_transfer` Module
+---------------------------
+
+.. automodule:: galaxy.jobs.deferred.data_transfer
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`genome_transfer` Module
+-----------------------------
+
+.. automodule:: galaxy.jobs.deferred.genome_transfer
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`liftover_transfer` Module
+-------------------------------
+
+.. automodule:: galaxy.jobs.deferred.liftover_transfer
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`manual_data_transfer` Module
+----------------------------------
+
+.. automodule:: galaxy.jobs.deferred.manual_data_transfer
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`pacific_biosciences_smrt_portal` Module
+---------------------------------------------
+
+.. automodule:: galaxy.jobs.deferred.pacific_biosciences_smrt_portal
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.rst
@@ -0,0 +1,45 @@
+jobs Package
+============
+
+:mod:`jobs` Package
+-------------------
+
+.. automodule:: galaxy.jobs
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`handler` Module
+---------------------
+
+.. automodule:: galaxy.jobs.handler
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`manager` Module
+---------------------
+
+.. automodule:: galaxy.jobs.manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`transfer_manager` Module
+------------------------------
+
+.. automodule:: galaxy.jobs.transfer_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.jobs.actions
+ galaxy.jobs.deferred
+ galaxy.jobs.runners
+ galaxy.jobs.splitters
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.runners.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.runners.rst
@@ -0,0 +1,59 @@
+runners Package
+===============
+
+:mod:`runners` Package
+----------------------
+
+.. automodule:: galaxy.jobs.runners
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`drmaa` Module
+-------------------
+
+.. automodule:: galaxy.jobs.runners.drmaa
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`local` Module
+-------------------
+
+.. automodule:: galaxy.jobs.runners.local
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`lwr` Module
+-----------------
+
+.. automodule:: galaxy.jobs.runners.lwr
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`pbs` Module
+-----------------
+
+.. automodule:: galaxy.jobs.runners.pbs
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sge` Module
+-----------------
+
+.. automodule:: galaxy.jobs.runners.sge
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tasks` Module
+-------------------
+
+.. automodule:: galaxy.jobs.runners.tasks
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.splitters.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.jobs.splitters.rst
@@ -0,0 +1,19 @@
+splitters Package
+=================
+
+:mod:`basic` Module
+-------------------
+
+.. automodule:: galaxy.jobs.splitters.basic
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`multi` Module
+-------------------
+
+.. automodule:: galaxy.jobs.splitters.multi
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.model.migrate.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.model.migrate.rst
@@ -0,0 +1,11 @@
+migrate Package
+===============
+
+:mod:`check` Module
+-------------------
+
+.. automodule:: galaxy.model.migrate.check
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.model.orm.ext.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.model.orm.ext.rst
@@ -0,0 +1,19 @@
+ext Package
+===========
+
+:mod:`ext` Package
+------------------
+
+.. automodule:: galaxy.model.orm.ext
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`assignmapper` Module
+--------------------------
+
+.. automodule:: galaxy.model.orm.ext.assignmapper
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.model.orm.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.model.orm.rst
@@ -0,0 +1,26 @@
+orm Package
+===========
+
+:mod:`orm` Package
+------------------
+
+.. automodule:: galaxy.model.orm
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`logging_connection_proxy` Module
+--------------------------------------
+
+.. automodule:: galaxy.model.orm.logging_connection_proxy
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.model.orm.ext
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.model.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.model.rst
@@ -0,0 +1,51 @@
+model Package
+=============
+
+:mod:`model` Package
+--------------------
+
+.. automodule:: galaxy.model
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`custom_types` Module
+--------------------------
+
+.. automodule:: galaxy.model.custom_types
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`item_attrs` Module
+------------------------
+
+.. automodule:: galaxy.model.item_attrs
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`mapping` Module
+---------------------
+
+.. automodule:: galaxy.model.mapping
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`mapping_tests` Module
+---------------------------
+
+.. automodule:: galaxy.model.mapping_tests
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.model.migrate
+ galaxy.model.orm
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.objectstore.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.objectstore.rst
@@ -0,0 +1,19 @@
+objectstore Package
+===================
+
+:mod:`objectstore` Package
+--------------------------
+
+.. automodule:: galaxy.objectstore
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`s3_multipart_upload` Module
+---------------------------------
+
+.. automodule:: galaxy.objectstore.s3_multipart_upload
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.openid.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.openid.rst
@@ -0,0 +1,19 @@
+openid Package
+==============
+
+:mod:`openid` Package
+---------------------
+
+.. automodule:: galaxy.openid
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`providers` Module
+-----------------------
+
+.. automodule:: galaxy.openid.providers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.quota.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.quota.rst
@@ -0,0 +1,11 @@
+quota Package
+=============
+
+:mod:`quota` Package
+--------------------
+
+.. automodule:: galaxy.quota
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.rst
@@ -0,0 +1,54 @@
+galaxy Package
+==============
+
+:mod:`galaxy` Package
+---------------------
+
+.. automodule:: galaxy
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`app` Module
+-----------------
+
+.. automodule:: galaxy.app
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`config` Module
+--------------------
+
+.. automodule:: galaxy.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.actions
+ galaxy.datatypes
+ galaxy.eggs
+ galaxy.exceptions
+ galaxy.external_services
+ galaxy.forms
+ galaxy.jobs
+ galaxy.model
+ galaxy.objectstore
+ galaxy.openid
+ galaxy.quota
+ galaxy.sample_tracking
+ galaxy.security
+ galaxy.tags
+ galaxy.tool_shed
+ galaxy.tools
+ galaxy.util
+ galaxy.visualization
+ galaxy.web
+ galaxy.webapps
+ galaxy.workflow
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.sample_tracking.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.sample_tracking.rst
@@ -0,0 +1,35 @@
+sample_tracking Package
+=======================
+
+:mod:`data_transfer` Module
+---------------------------
+
+.. automodule:: galaxy.sample_tracking.data_transfer
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`external_service_types` Module
+------------------------------------
+
+.. automodule:: galaxy.sample_tracking.external_service_types
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`request_types` Module
+---------------------------
+
+.. automodule:: galaxy.sample_tracking.request_types
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sample` Module
+--------------------
+
+.. automodule:: galaxy.sample_tracking.sample
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.security.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.security.rst
@@ -0,0 +1,19 @@
+security Package
+================
+
+:mod:`security` Package
+-----------------------
+
+.. automodule:: galaxy.security
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`validate_user_input` Module
+---------------------------------
+
+.. automodule:: galaxy.security.validate_user_input
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tags.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tags.rst
@@ -0,0 +1,19 @@
+tags Package
+============
+
+:mod:`tags` Package
+-------------------
+
+.. automodule:: galaxy.tags
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tag_handler` Module
+-------------------------
+
+.. automodule:: galaxy.tags.tag_handler
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tool_shed.migrate.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tool_shed.migrate.rst
@@ -0,0 +1,19 @@
+migrate Package
+===============
+
+:mod:`check` Module
+-------------------
+
+.. automodule:: galaxy.tool_shed.migrate.check
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`common` Module
+--------------------
+
+.. automodule:: galaxy.tool_shed.migrate.common
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tool_shed.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tool_shed.rst
@@ -0,0 +1,51 @@
+tool_shed Package
+=================
+
+:mod:`tool_shed` Package
+------------------------
+
+.. automodule:: galaxy.tool_shed
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`encoding_util` Module
+---------------------------
+
+.. automodule:: galaxy.tool_shed.encoding_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`install_manager` Module
+-----------------------------
+
+.. automodule:: galaxy.tool_shed.install_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tool_shed_registry` Module
+--------------------------------
+
+.. automodule:: galaxy.tool_shed.tool_shed_registry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`update_manager` Module
+----------------------------
+
+.. automodule:: galaxy.tool_shed.update_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.tool_shed.migrate
+ galaxy.tool_shed.tool_dependencies
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.tool_shed.tool_dependencies.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tool_shed.tool_dependencies.rst
@@ -0,0 +1,27 @@
+tool_dependencies Package
+=========================
+
+:mod:`common_util` Module
+-------------------------
+
+.. automodule:: galaxy.tool_shed.tool_dependencies.common_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`fabric_util` Module
+-------------------------
+
+.. automodule:: galaxy.tool_shed.tool_dependencies.fabric_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`install_util` Module
+--------------------------
+
+.. automodule:: galaxy.tool_shed.tool_dependencies.install_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.actions.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.actions.rst
@@ -0,0 +1,51 @@
+actions Package
+===============
+
+:mod:`actions` Package
+----------------------
+
+.. automodule:: galaxy.tools.actions
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`history_imp_exp` Module
+-----------------------------
+
+.. automodule:: galaxy.tools.actions.history_imp_exp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`index_genome` Module
+--------------------------
+
+.. automodule:: galaxy.tools.actions.index_genome
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`metadata` Module
+----------------------
+
+.. automodule:: galaxy.tools.actions.metadata
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`upload` Module
+--------------------
+
+.. automodule:: galaxy.tools.actions.upload
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`upload_common` Module
+---------------------------
+
+.. automodule:: galaxy.tools.actions.upload_common
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.data.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.data.rst
@@ -0,0 +1,11 @@
+data Package
+============
+
+:mod:`data` Package
+-------------------
+
+.. automodule:: galaxy.tools.data
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.deps.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.deps.rst
@@ -0,0 +1,19 @@
+deps Package
+============
+
+:mod:`deps` Package
+-------------------
+
+.. automodule:: galaxy.tools.deps
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tests` Module
+-------------------
+
+.. automodule:: galaxy.tools.deps.tests
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.genome_index.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.genome_index.rst
@@ -0,0 +1,19 @@
+genome_index Package
+====================
+
+:mod:`genome_index` Package
+---------------------------
+
+.. automodule:: galaxy.tools.genome_index
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`index_genome` Module
+--------------------------
+
+.. automodule:: galaxy.tools.genome_index.index_genome
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.imp_exp.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.imp_exp.rst
@@ -0,0 +1,27 @@
+imp_exp Package
+===============
+
+:mod:`imp_exp` Package
+----------------------
+
+.. automodule:: galaxy.tools.imp_exp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`export_history` Module
+----------------------------
+
+.. automodule:: galaxy.tools.imp_exp.export_history
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`unpack_tar_gz_archive` Module
+-----------------------------------
+
+.. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.parameters.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.parameters.rst
@@ -0,0 +1,67 @@
+parameters Package
+==================
+
+:mod:`parameters` Package
+-------------------------
+
+.. automodule:: galaxy.tools.parameters
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`basic` Module
+-------------------
+
+.. automodule:: galaxy.tools.parameters.basic
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`dynamic_options` Module
+-----------------------------
+
+.. automodule:: galaxy.tools.parameters.dynamic_options
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`grouping` Module
+----------------------
+
+.. automodule:: galaxy.tools.parameters.grouping
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`input_translation` Module
+-------------------------------
+
+.. automodule:: galaxy.tools.parameters.input_translation
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`output` Module
+--------------------
+
+.. automodule:: galaxy.tools.parameters.output
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sanitize` Module
+----------------------
+
+.. automodule:: galaxy.tools.parameters.sanitize
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`validation` Module
+------------------------
+
+.. automodule:: galaxy.tools.parameters.validation
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.rst
@@ -0,0 +1,41 @@
+tools Package
+=============
+
+:mod:`tools` Package
+--------------------
+
+.. automodule:: galaxy.tools
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`exception_handling` Module
+--------------------------------
+
+.. automodule:: galaxy.tools.exception_handling
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`test` Module
+------------------
+
+.. automodule:: galaxy.tools.test
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.tools.actions
+ galaxy.tools.data
+ galaxy.tools.deps
+ galaxy.tools.genome_index
+ galaxy.tools.imp_exp
+ galaxy.tools.parameters
+ galaxy.tools.search
+ galaxy.tools.util
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.search.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.search.rst
@@ -0,0 +1,11 @@
+search Package
+==============
+
+:mod:`search` Package
+---------------------
+
+.. automodule:: galaxy.tools.search
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.util.galaxyops.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.util.galaxyops.rst
@@ -0,0 +1,11 @@
+galaxyops Package
+=================
+
+:mod:`galaxyops` Package
+------------------------
+
+.. automodule:: galaxy.tools.util.galaxyops
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.util.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.tools.util.rst
@@ -0,0 +1,34 @@
+util Package
+============
+
+:mod:`util` Package
+-------------------
+
+.. automodule:: galaxy.tools.util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`hyphy_util` Module
+------------------------
+
+.. automodule:: galaxy.tools.util.hyphy_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`maf_utilities` Module
+---------------------------
+
+.. automodule:: galaxy.tools.util.maf_utilities
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.tools.util.galaxyops
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.util.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.util.rst
@@ -0,0 +1,139 @@
+util Package
+============
+
+:mod:`util` Package
+-------------------
+
+.. automodule:: galaxy.util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`aliaspickler` Module
+--------------------------
+
+.. automodule:: galaxy.util.aliaspickler
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`bunch` Module
+-------------------
+
+.. automodule:: galaxy.util.bunch
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`expressions` Module
+-------------------------
+
+.. automodule:: galaxy.util.expressions
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`hash_util` Module
+-----------------------
+
+.. automodule:: galaxy.util.hash_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`heartbeat` Module
+-----------------------
+
+.. automodule:: galaxy.util.heartbeat
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`inflection` Module
+------------------------
+
+.. automodule:: galaxy.util.inflection
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`json` Module
+------------------
+
+.. automodule:: galaxy.util.json
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`lrucache` Module
+----------------------
+
+.. automodule:: galaxy.util.lrucache
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`memdump` Module
+---------------------
+
+.. automodule:: galaxy.util.memdump
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`none_like` Module
+-----------------------
+
+.. automodule:: galaxy.util.none_like
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`odict` Module
+-------------------
+
+.. automodule:: galaxy.util.odict
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sanitize_html` Module
+---------------------------
+
+.. automodule:: galaxy.util.sanitize_html
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`shed_util` Module
+-----------------------
+
+.. automodule:: galaxy.util.shed_util
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`streamball` Module
+------------------------
+
+.. automodule:: galaxy.util.streamball
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`template` Module
+----------------------
+
+.. automodule:: galaxy.util.template
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`topsort` Module
+---------------------
+
+.. automodule:: galaxy.util.topsort
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.visualization.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.visualization.rst
@@ -0,0 +1,26 @@
+visualization Package
+=====================
+
+:mod:`visualization` Package
+----------------------------
+
+.. automodule:: galaxy.visualization
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`genomes` Module
+---------------------
+
+.. automodule:: galaxy.visualization.genomes
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.visualization.tracks
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.visualization.tracks.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.visualization.tracks.rst
@@ -0,0 +1,35 @@
+tracks Package
+==============
+
+:mod:`tracks` Package
+---------------------
+
+.. automodule:: galaxy.visualization.tracks
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`data_providers` Module
+----------------------------
+
+.. automodule:: galaxy.visualization.tracks.data_providers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`summary` Module
+---------------------
+
+.. automodule:: galaxy.visualization.tracks.summary
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`visual_analytics` Module
+------------------------------
+
+.. automodule:: galaxy.visualization.tracks.visual_analytics
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.api.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.web.api.rst
@@ -0,0 +1,352 @@
+Galaxy API Documentation
+************************
+
+Background
+==========
+In addition to being accessible through a web interface, Galaxy can now also be
+accessed programmatically, through shell scripts and other programs. The web
+interface is appropriate for things like exploratory analysis, visualization,
+construction of workflows, and rerunning workflows on new datasets.
+
+The web interface is less suitable for things like
+ - Connecting a Galaxy instance directly to your sequencer and running
+ workflows whenever data is ready
+ - Running a workflow against multiple datasets (which can be done with the
+ web interface, but is tedious)
+ - When the analysis involves complex control, such as looping and
+ branching.
+
+The Galaxy API addresses these and other situations by exposing Galaxy
+internals through an additional interface, known as an Application Programming
+Interface, or API.
+
+Quickstart
+==========
+
+Set the following option in universe_wsgi.ini and start the server::
+
+ enable_api = True
+
+Log in as your user, navigate to the API Keys page in the User menu, and
+generate a new API key. Make a note of the API key, and then pull up a
+terminal. Now we'll use the display.py script in your galaxy/scripts/api
+directory for a short example::
+
+ % ./display.py my_key
http://localhost:4096/api/histories
+ Collection Members
+ ------------------
+ #1: /api/histories/8c49be448cfe29bc
+ name: Unnamed history
+ id: 8c49be448cfe29bc
+ #2: /api/histories/33b43b4e7093c91f
+ name: output test
+ id: 33b43b4e7093c91f
+
+The result is a Collection of the histories of the user specified by the API
+key (you). To look at the details of a particular history, say #1 above, do
+the following::
+
+ % ./display.py my_key
http://localhost:4096/api/histories/8c49be448cfe29bc
+ Member Information
+ ------------------
+ state_details: {'ok': 1, 'failed_metadata': 0, 'upload':
0, 'discarded': 0, 'running': 0, 'setting_metadata': 0,
'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
+ state: ok
+ contents_url: /api/histories/8c49be448cfe29bc/contents
+ id: 8c49be448cfe29bc
+ name: Unnamed history
+
+This gives detailed information about the specific member in question, in this
+case the History. To view history contents, do the following::
+
+
+ % ./display.py my_key
http://localhost:4096/api/histories/8c49be448cfe29bc/contents
+ Collection Members
+ ------------------
+ #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
+ name: Pasted Entry
+ type: file
+ id: 6f91353f3eb0fa4a
+
+What we have here is another Collection of items containing all of the datasets
+in this particular history. Finally, to view details of a particular dataset
+in this collection, execute the following::
+
+ % ./display.py my_key
http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb...
+ Member Information
+ ------------------
+ misc_blurb: 1 line
+ name: Pasted Entry
+ data_type: txt
+ deleted: False
+ file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
+ state: ok
+ download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
+ visible: True
+ genome_build: ?
+ model_class: HistoryDatasetAssociation
+ file_size: 17
+ metadata_data_lines: 1
+ id: 6f91353f3eb0fa4a
+ misc_info: uploaded txt file
+ metadata_dbkey: ?
+
+And now you've successfully used the API to request and select a history,
+browse the contents of that history, and then look at detailed information
+about a particular dataset.
+
+For a more comprehensive Data Library example, set the following option in your
+universe_wsgi.ini as well, and restart galaxy again::
+
+ admin_users = you(a)example.org
+ library_import_dir = /path/to/some/directory
+
+In the directory you specified for 'library_import_dir', create some
+subdirectories, and put (or symlink) files to import into Galaxy into those
+subdirectories.
+
+In Galaxy, create an account that matches the address you put in 'admin_users',
+then browse to that user's preferences and generate a new API Key. Copy the
+key to your clipboard and then use these scripts::
+
+ % ./display.py my_key
http://localhost:4096/api/libraries
+ Collection Members
+ ------------------
+
+ 0 elements in collection
+
+ % ./library_create_library.py my_key
http://localhost:4096/api/libraries api_test
'API Test Library'
+ Response
+ --------
+ /api/libraries/f3f73e481f432006
+ name: api_test
+ id: f3f73e481f432006
+
+ % ./display.py my_key
http://localhost:4096/api/libraries
+ Collection Members
+ ------------------
+ /api/libraries/f3f73e481f432006
+ name: api_test
+ id: f3f73e481f432006
+
+ % ./display.py my_key
http://localhost:4096/api/libraries/f3f73e481f432006
+ Member Information
+ ------------------
+ synopsis: None
+ contents_url: /api/libraries/f3f73e481f432006/contents
+ description: API Test Library
+ name: api_test
+
+ % ./display.py my_key
http://localhost:4096/api/libraries/f3f73e481f432006/contents
+ Collection Members
+ ------------------
+ /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
+ name: /
+ type: folder
+ id: 28202595c0d2591f61ddda595d2c3670
+
+ % ./library_create_folder.py my_key
http://localhost:4096/api/libraries/f3f73e481f432006/contents
28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
+ Response
+ --------
+ /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
+ name: api_test_folder1
+ id: 28202595c0d2591fa4f9089d2303fd89
+
+ % ./library_upload_from_import_dir.py my_key
http://localhost:4096/api/libraries/f3f73e481f432006/contents
28202595c0d2591fa4f9089d2303fd89 bed bed hg19
+ Response
+ --------
+ /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+ name: 2.bed
+ id: e9ef7fdb2db87d7b
+ /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
+ name: 3.bed
+ id: 3b7f6a31f80a5018
+
+ % ./display.py my_key
http://localhost:4096/api/libraries/f3f73e481f432006/contents
+ Collection Members
+ ------------------
+ /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
+ name: /
+ type: folder
+ id: 28202595c0d2591f61ddda595d2c3670
+ /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
+ name: /api_test_folder1
+ type: folder
+ id: 28202595c0d2591fa4f9089d2303fd89
+ /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+ name: /api_test_folder1/2.bed
+ type: file
+ id: e9ef7fdb2db87d7b
+ /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
+ name: /api_test_folder1/3.bed
+ type: file
+ id: 3b7f6a31f80a5018
+
+ % ./display.py my_key
http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db...
+ Member Information
+ ------------------
+ misc_blurb: 68 regions
+ metadata_endCol: 3
+ data_type: bed
+ metadata_columns: 6
+ metadata_nameCol: 4
+ uploaded_by: nate@...
+ metadata_strandCol: 6
+ name: 2.bed
+ genome_build: hg19
+ metadata_comment_lines: None
+ metadata_startCol: 2
+ metadata_chromCol: 1
+ file_size: 4272
+ metadata_data_lines: 68
+ message:
+ metadata_dbkey: hg19
+ misc_info: uploaded bed file
+ date_uploaded: 2010-06-22T17:01:51.266119
+ metadata_column_types: str, int, int, str, int, str
+
+Other parameters are valid when uploading, they are the same parameters as are
+used in the web form, like 'link_data_only' and etc.
+
+The request and response format should be considered alpha and are subject to change.
+
+
+API Controllers
+===============
+
+:mod:`datasets` Module
+----------------------
+
+.. automodule:: galaxy.web.api.datasets
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`forms` Module
+-------------------
+
+.. automodule:: galaxy.web.api.forms
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`genomes` Module
+---------------------
+
+.. automodule:: galaxy.web.api.genomes
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`histories` Module
+-----------------------
+
+.. automodule:: galaxy.web.api.histories
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`history_contents` Module
+------------------------------
+
+.. automodule:: galaxy.web.api.history_contents
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`libraries` Module
+-----------------------
+
+.. automodule:: galaxy.web.api.libraries
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`library_contents` Module
+------------------------------
+
+.. automodule:: galaxy.web.api.library_contents
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`permissions` Module
+-------------------------
+
+.. automodule:: galaxy.web.api.permissions
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`quotas` Module
+--------------------
+
+.. automodule:: galaxy.web.api.quotas
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`request_types` Module
+---------------------------
+
+.. automodule:: galaxy.web.api.request_types
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`requests` Module
+----------------------
+
+.. automodule:: galaxy.web.api.requests
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`roles` Module
+-------------------
+
+.. automodule:: galaxy.web.api.roles
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`samples` Module
+---------------------
+
+.. automodule:: galaxy.web.api.samples
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tools` Module
+-------------------
+
+.. automodule:: galaxy.web.api.tools
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`users` Module
+-------------------
+
+.. automodule:: galaxy.web.api.users
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`visualizations` Module
+----------------------------
+
+.. automodule:: galaxy.web.api.visualizations
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`workflows` Module
+-----------------------
+
+.. automodule:: galaxy.web.api.workflows
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.base.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.web.base.rst
@@ -0,0 +1,11 @@
+base Package
+============
+
+:mod:`controller` Module
+------------------------
+
+.. automodule:: galaxy.web.base.controller
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.controllers.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.web.controllers.rst
@@ -0,0 +1,235 @@
+controllers Package
+===================
+
+:mod:`controllers` Package
+--------------------------
+
+.. automodule:: galaxy.web.controllers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`admin` Module
+-------------------
+
+.. automodule:: galaxy.web.controllers.admin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`admin_toolshed` Module
+----------------------------
+
+.. automodule:: galaxy.web.controllers.admin_toolshed
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`async` Module
+-------------------
+
+.. automodule:: galaxy.web.controllers.async
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`cloud` Module
+-------------------
+
+.. automodule:: galaxy.web.controllers.cloud
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`data_admin` Module
+------------------------
+
+.. automodule:: galaxy.web.controllers.data_admin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`dataset` Module
+---------------------
+
+.. automodule:: galaxy.web.controllers.dataset
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`error` Module
+-------------------
+
+.. automodule:: galaxy.web.controllers.error
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`external_service` Module
+------------------------------
+
+.. automodule:: galaxy.web.controllers.external_service
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`external_services` Module
+-------------------------------
+
+.. automodule:: galaxy.web.controllers.external_services
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`forms` Module
+-------------------
+
+.. automodule:: galaxy.web.controllers.forms
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`history` Module
+---------------------
+
+.. automodule:: galaxy.web.controllers.history
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`library` Module
+---------------------
+
+.. automodule:: galaxy.web.controllers.library
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`library_admin` Module
+---------------------------
+
+.. automodule:: galaxy.web.controllers.library_admin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`library_common` Module
+----------------------------
+
+.. automodule:: galaxy.web.controllers.library_common
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`mobile` Module
+--------------------
+
+.. automodule:: galaxy.web.controllers.mobile
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`page` Module
+------------------
+
+.. automodule:: galaxy.web.controllers.page
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`request_type` Module
+--------------------------
+
+.. automodule:: galaxy.web.controllers.request_type
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`requests` Module
+----------------------
+
+.. automodule:: galaxy.web.controllers.requests
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`requests_admin` Module
+----------------------------
+
+.. automodule:: galaxy.web.controllers.requests_admin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`requests_common` Module
+-----------------------------
+
+.. automodule:: galaxy.web.controllers.requests_common
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`root` Module
+------------------
+
+.. automodule:: galaxy.web.controllers.root
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tag` Module
+-----------------
+
+.. automodule:: galaxy.web.controllers.tag
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tool_runner` Module
+-------------------------
+
+.. automodule:: galaxy.web.controllers.tool_runner
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`tracks` Module
+--------------------
+
+.. automodule:: galaxy.web.controllers.tracks
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`ucsc_proxy` Module
+------------------------
+
+.. automodule:: galaxy.web.controllers.ucsc_proxy
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`user` Module
+------------------
+
+.. automodule:: galaxy.web.controllers.user
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`visualization` Module
+---------------------------
+
+.. automodule:: galaxy.web.controllers.visualization
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`workflow` Module
+----------------------
+
+.. automodule:: galaxy.web.controllers.workflow
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.framework.helpers.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.web.framework.helpers.rst
@@ -0,0 +1,19 @@
+helpers Package
+===============
+
+:mod:`helpers` Package
+----------------------
+
+.. automodule:: galaxy.web.framework.helpers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`grids` Module
+-------------------
+
+.. automodule:: galaxy.web.framework.helpers.grids
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.web.framework.middleware.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.web.framework.middleware.rst
@@ -0,0 +1,51 @@
+middleware Package
+==================
+
+:mod:`middleware` Package
+-------------------------
+
+.. automodule:: galaxy.web.framework.middleware
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`profile` Module
+---------------------
+
+.. automodule:: galaxy.web.framework.middleware.profile
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`remoteuser` Module
+------------------------
+
+.. automodule:: galaxy.web.framework.middleware.remoteuser
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`static` Module
+--------------------
+
+.. automodule:: galaxy.web.framework.middleware.static
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`translogger` Module
+-------------------------
+
+.. automodule:: galaxy.web.framework.middleware.translogger
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`xforwardedhost` Module
+----------------------------
+
+.. automodule:: galaxy.web.framework.middleware.xforwardedhost
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.framework.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.web.framework.rst
@@ -0,0 +1,35 @@
+framework Package
+=================
+
+:mod:`framework` Package
+------------------------
+
+.. automodule:: galaxy.web.framework
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`base` Module
+------------------
+
+.. automodule:: galaxy.web.framework.base
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`openid_manager` Module
+----------------------------
+
+.. automodule:: galaxy.web.framework.openid_manager
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.web.framework.helpers
+ galaxy.web.framework.middleware
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.web.rst
@@ -0,0 +1,46 @@
+web Package
+===========
+
+:mod:`web` Package
+------------------
+
+.. automodule:: galaxy.web
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`buildapp` Module
+----------------------
+
+.. automodule:: galaxy.web.buildapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`form_builder` Module
+--------------------------
+
+.. automodule:: galaxy.web.form_builder
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`params` Module
+--------------------
+
+.. automodule:: galaxy.web.params
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.web.api
+ galaxy.web.base
+ galaxy.web.controllers
+ galaxy.web.framework
+ galaxy.web.security
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.security.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.web.security.rst
@@ -0,0 +1,11 @@
+security Package
+================
+
+:mod:`security` Package
+-----------------------
+
+.. automodule:: galaxy.web.security
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.community.controllers.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.community.controllers.rst
@@ -0,0 +1,59 @@
+controllers Package
+===================
+
+:mod:`controllers` Package
+--------------------------
+
+.. automodule:: galaxy.webapps.community.controllers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`admin` Module
+-------------------
+
+.. automodule:: galaxy.webapps.community.controllers.admin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`common` Module
+--------------------
+
+.. automodule:: galaxy.webapps.community.controllers.common
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`hg` Module
+----------------
+
+.. automodule:: galaxy.webapps.community.controllers.hg
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`repository` Module
+------------------------
+
+.. automodule:: galaxy.webapps.community.controllers.repository
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`upload` Module
+--------------------
+
+.. automodule:: galaxy.webapps.community.controllers.upload
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`workflow` Module
+----------------------
+
+.. automodule:: galaxy.webapps.community.controllers.workflow
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.community.framework.middleware.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst
@@ -0,0 +1,19 @@
+middleware Package
+==================
+
+:mod:`middleware` Package
+-------------------------
+
+.. automodule:: galaxy.webapps.community.framework.middleware
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`hg` Module
+----------------
+
+.. automodule:: galaxy.webapps.community.framework.middleware.hg
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.community.framework.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.community.framework.rst
@@ -0,0 +1,18 @@
+framework Package
+=================
+
+:mod:`framework` Package
+------------------------
+
+.. automodule:: galaxy.webapps.community.framework
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.webapps.community.framework.middleware
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.community.model.migrate.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.community.model.migrate.rst
@@ -0,0 +1,11 @@
+migrate Package
+===============
+
+:mod:`check` Module
+-------------------
+
+.. automodule:: galaxy.webapps.community.model.migrate.check
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.community.model.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.community.model.rst
@@ -0,0 +1,26 @@
+model Package
+=============
+
+:mod:`model` Package
+--------------------
+
+.. automodule:: galaxy.webapps.community.model
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`mapping` Module
+---------------------
+
+.. automodule:: galaxy.webapps.community.model.mapping
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.webapps.community.model.migrate
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.community.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.community.rst
@@ -0,0 +1,45 @@
+community Package
+=================
+
+:mod:`community` Package
+------------------------
+
+.. automodule:: galaxy.webapps.community
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`app` Module
+-----------------
+
+.. automodule:: galaxy.webapps.community.app
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`buildapp` Module
+----------------------
+
+.. automodule:: galaxy.webapps.community.buildapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`config` Module
+--------------------
+
+.. automodule:: galaxy.webapps.community.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.webapps.community.controllers
+ galaxy.webapps.community.framework
+ galaxy.webapps.community.model
+ galaxy.webapps.community.security
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.community.security.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.community.security.rst
@@ -0,0 +1,11 @@
+security Package
+================
+
+:mod:`security` Package
+-----------------------
+
+.. automodule:: galaxy.webapps.community.security
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst
@@ -0,0 +1,19 @@
+controllers Package
+===================
+
+:mod:`controllers` Package
+--------------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.controllers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`common` Module
+--------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.controllers.common
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst
@@ -0,0 +1,11 @@
+framework Package
+=================
+
+:mod:`framework` Package
+------------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.framework
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.demo_sequencer.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.demo_sequencer.rst
@@ -0,0 +1,51 @@
+demo_sequencer Package
+======================
+
+:mod:`demo_sequencer` Package
+-----------------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`app` Module
+-----------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.app
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`buildapp` Module
+----------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.buildapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`config` Module
+--------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`registry` Module
+----------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.registry
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.webapps.demo_sequencer.controllers
+ galaxy.webapps.demo_sequencer.framework
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6
doc/source/lib/galaxy.webapps.reports.controllers.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst
@@ -0,0 +1,59 @@
+controllers Package
+===================
+
+:mod:`controllers` Package
+--------------------------
+
+.. automodule:: galaxy.webapps.reports.controllers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`jobs` Module
+------------------
+
+.. automodule:: galaxy.webapps.reports.controllers.jobs
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`root` Module
+------------------
+
+.. automodule:: galaxy.webapps.reports.controllers.root
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sample_tracking` Module
+-----------------------------
+
+.. automodule:: galaxy.webapps.reports.controllers.sample_tracking
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`system` Module
+--------------------
+
+.. automodule:: galaxy.webapps.reports.controllers.system
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`users` Module
+-------------------
+
+.. automodule:: galaxy.webapps.reports.controllers.users
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`workflows` Module
+-----------------------
+
+.. automodule:: galaxy.webapps.reports.controllers.workflows
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.reports.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.reports.rst
@@ -0,0 +1,42 @@
+reports Package
+===============
+
+:mod:`reports` Package
+----------------------
+
+.. automodule:: galaxy.webapps.reports
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`app` Module
+-----------------
+
+.. automodule:: galaxy.webapps.reports.app
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`buildapp` Module
+----------------------
+
+.. automodule:: galaxy.webapps.reports.buildapp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`config` Module
+--------------------
+
+.. automodule:: galaxy.webapps.reports.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.webapps.reports.controllers
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.rst
@@ -0,0 +1,20 @@
+webapps Package
+===============
+
+:mod:`webapps` Package
+----------------------
+
+.. automodule:: galaxy.webapps
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy.webapps.community
+ galaxy.webapps.demo_sequencer
+ galaxy.webapps.reports
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.workflow.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.workflow.rst
@@ -0,0 +1,11 @@
+workflow Package
+================
+
+:mod:`modules` Module
+---------------------
+
+.. automodule:: galaxy.workflow.modules
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy_utils.rst
--- /dev/null
+++ b/doc/source/lib/galaxy_utils.rst
@@ -0,0 +1,10 @@
+galaxy_utils Package
+====================
+
+Subpackages
+-----------
+
+.. toctree::
+
+ galaxy_utils.sequence
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy_utils.sequence.rst
--- /dev/null
+++ b/doc/source/lib/galaxy_utils.sequence.rst
@@ -0,0 +1,43 @@
+sequence Package
+================
+
+:mod:`fasta` Module
+-------------------
+
+.. automodule:: galaxy_utils.sequence.fasta
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`fastq` Module
+-------------------
+
+.. automodule:: galaxy_utils.sequence.fastq
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`sequence` Module
+----------------------
+
+.. automodule:: galaxy_utils.sequence.sequence
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`transform` Module
+-----------------------
+
+.. automodule:: galaxy_utils.sequence.transform
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+:mod:`vcf` Module
+-----------------
+
+.. automodule:: galaxy_utils.sequence.vcf
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/log_tempfile.rst
--- /dev/null
+++ b/doc/source/lib/log_tempfile.rst
@@ -0,0 +1,7 @@
+log_tempfile Module
+===================
+
+.. automodule:: log_tempfile
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/mimeparse.rst
--- /dev/null
+++ b/doc/source/lib/mimeparse.rst
@@ -0,0 +1,7 @@
+mimeparse Module
+================
+
+.. automodule:: mimeparse
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/modules.rst
--- /dev/null
+++ b/doc/source/lib/modules.rst
@@ -0,0 +1,13 @@
+lib
+===
+
+.. toctree::
+ :maxdepth: 4
+
+ fpconst
+ galaxy
+ galaxy_utils
+ log_tempfile
+ mimeparse
+ pkg_resources
+ psyco_full
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/pkg_resources.rst
--- /dev/null
+++ b/doc/source/lib/pkg_resources.rst
@@ -0,0 +1,7 @@
+pkg_resources Module
+====================
+
+.. automodule:: pkg_resources
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r
77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/psyco_full.rst
--- /dev/null
+++ b/doc/source/lib/psyco_full.rst
@@ -0,0 +1,7 @@
+psyco_full Module
+=================
+
+.. automodule:: psyco_full
+ :members:
+ :undoc-members:
+ :show-inheritance:
Repository URL:
https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from
bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.