Commit ab24c60f authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Add sphinx-doc based documentation

parent 2a3a33d6
# Minimal makefile for Sphinx documentation
# You can set these variables from the command line.
SPHINXBUILD = sphinx-build
SPHINXPROJ = PSOT-proteinsequenceobservationtool
SOURCEDIR = source
BUILDDIR = build
# Put it first so that "make" without argument is like "make help".
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=python -msphinx
set SOURCEDIR=source
set BUILDDIR=build
set SPHINXPROJ=PSOT-proteinsequenceobservationtool
if "%1" == "" goto help
if errorlevel 9009 (
echo.The Sphinx module was not found. Make sure you have Sphinx installed,
echo.then set the SPHINXBUILD environment variable to point to the full
echo.path of the 'sphinx-build' executable. Alternatively you may add the
echo.Sphinx directory to PATH.
echo.If you don't have Sphinx installed, grab it from
exit /b 1
goto end
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# PSOT - protein sequence observation tool documentation build configuration file, created by
# sphinx-quickstart on Wed Jul 26 11:24:20 2017.
# 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.
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.autodoc']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = 'PSOT - protein sequence observation tool'
copyright = '2017, Lukas Jelonek'
author = 'Lukas Jelonek'
# 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 = '0.2'
# The full version, including alpha/beta/rc tags.
release = '0.2'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = []
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'sphinx_rtd_theme'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
# html_theme_options = {}
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
# -- Options for HTMLHelp output ------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'PSOT-proteinsequenceobservationtooldoc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
# 'preamble': '',
# Latex figure (float) alignment
# 'figure_align': 'htbp',
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'PSOT-proteinsequenceobservationtool.tex', 'PSOT - protein sequence observation tool Documentation',
'Lukas Jelonek', 'manual'),
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'psot-proteinsequenceobservationtool', 'PSOT - protein sequence observation tool Documentation',
[author], 1)
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'PSOT-proteinsequenceobservationtool', 'PSOT - protein sequence observation tool Documentation',
author, 'PSOT-proteinsequenceobservationtool', 'One line description of project.',
.. PSOT - protein sequence observation tool documentation master file, created by
sphinx-quickstart on Wed Jul 26 11:24:20 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to PSOT - protein sequence observation tool's documentation!
.. toctree::
:maxdepth: 2
:caption: Contents:
Indices and tables
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
.. highlight:: yaml
A module specifies exactly one analysis that can be run within PSOT. Each
module has a default configuration that is specified in its manifest. During the
execution a module will run through two phases: the analysis and the conversion
phase. The phases are implemented as commandline tools that have at least the
following parameters:
* analysis
* ``--fasta`` - the fasta file to process
* ``--output`` - the result file/directory
* convert
* ``--result`` - the result from the analysis step
* ``--output`` - the converted json file
A module manifest has the following structure::
# Module manifest for the blastp against swissprot analysis
# The name of the module. Is needed for the list-analyses option, for custom
# configurations and custom profiles
name: 'blastp_swissprot'
# Short description of the analysis
info: 'blastp analysis against swissprot'
# The name of the script for the analysis step. Must take a --fasta parameter
script: ''
database: '/vol/biodb/uniprot/uniprot_sprot.fasta'
evalue: 1e-10
# The name of the result to json converter script. Must take one parameter, the
# result file from the analysis_script
script: ''
dbxref: UniProtKB/Swiss-Prot
These parameters can be overridden in the profile.
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