[galaxy-commits] commit/galaxy-central: dannon: Initial commit of Galaxy Documentation.

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/6f91353f3eb0fa... + 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@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/e9ef7fdb2db87d... + 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/

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