Commit cbea8ee5 authored by aknecht2's avatar aknecht2
Browse files

Added initial sphinx doc tree & build stuff. Using the sphinx markdown theme....

Added initial sphinx doc tree & build stuff.  Using the sphinx markdown theme.  Use 'make html' to build the docs.
parent ae6f874b
......@@ -9,3 +9,5 @@ examples/all_files.list
chipathlon/test/auth.yaml
meta/*.json
meta/data/*.json
doc/source/_static
doc/source/_templates
......@@ -48,7 +48,7 @@ class IdrGenerator(ModuleGenerator):
def create_final_results(self, run):
"""
:param run: The target run to generate jobs for.
:type run: :py:class:chipathlon.run.Run
:type run: :py:class:`~chipathlon.run.Run`
"""
module_jobs = [self.workflow_jobs[job_name] for job_name in self.module.get_job_names({})]
peak_results = self._find_prev_results(run)
......
......@@ -198,10 +198,13 @@ class ModuleGenerator(object):
were necessary to get to the current results. Based on the existance
of previous results / current results in the database, we add jobs to
the workflow.
If result exists -> Do nothing. No need to add jobs since the result
already exists. Result will be downloaded at a future step.
already exists. Result will be downloaded at a future step.
If result doesn't exist and prev_result does -> Queue download jobs
for previous results, then add jobs normally.
for previous results, then add jobs normally.
If result doesn't exists and prev_result doesn't -> Add jobs normally.
"""
final_results = self.create_final_results(run)
......
......@@ -355,14 +355,53 @@ class WorkflowJob(object):
:type outputs: list
Creates an actual Pegasus.Dax3.Job instance from the provided
information:
- inputs should be a list of dictionaries:
[{"name": FILE_NAME, "type": "file", "file": FILE_OBJECT},
{"name": ARUGMENT_NAME, "type": "argument", "value": ARGUMENT_VALUE},...]
- additional_files should be a list of dictionaries:
[{"name": FILE_NAME, "type": "file", "file": FILE_OBJECT},...]
- outputs should be a list of dictionaries:
[{"name": FILE_NAME, "transfer": True/False, "type": "file", "file": FILE_OBJECT},...]
information. Inputs, additional_inputs, and outputs should
all be a list of dictionaries:
**inputs**
.. code-block:: python
[
{
"name": "FULL-FILE-NAME",
"type": "file",
"file": PEGASUS-FILE-OBJECT
},
{
"name": "ARGUMENT-NAME",
"type": "argument",
"value": ARGUMENT-VALUE
},
...
]
**additional_inputs**
.. code-block:: python
[
{
"name": "FULL-FILE-NAME",
"type": "file",
"file": PEGASUS-FILE-OBJECT
},
...
]
**outputs**
.. code-block:: python
[
{
"name": "FULL-FILE-NAME",
"type": "file",
"transfer": True/False,
"file": PEGASUS-FILE-OBJECT
},
...
]
"""
if self._params_are_valid(inputs, additional_inputs, outputs):
job = Job(self.executable)
......
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = chipathlon
SOURCEDIR = source
BUILDDIR = build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
import sphinx_rtd_theme
# -*- coding: utf-8 -*-
#
# chipathlon documentation build configuration file, created by
# sphinx-quickstart on Tue Apr 11 15:50:17 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 = u'chipathlon'
copyright = u'2017, Avi Knecht'
author = u'Avi Knecht'
# 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 = u'1.0'
# The full version, including alpha/beta/rc tags.
release = u'1.0.1'
# 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'
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
# 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 = 'chipathlondoc'
# -- 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, 'chipathlon.tex', u'chipathlon Documentation',
u'Avi Knecht', '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, 'chipathlon', u'chipathlon 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, 'chipathlon', u'chipathlon Documentation',
author, 'chipathlon', 'One line description of project.',
'Miscellaneous'),
]
MongoDB
==============
.. autoclass:: chipathlon.db.MongoDB
:members:
Examples
==========
**Config**
.. code-block:: yaml
notify:
pegasus_home: "/usr/share/pegasus/"
email: "avi@kurtknecht.com"
profile:
pegasus:
style: "glite"
condor:
grid_resource: "pbs"
universe: "vanilla"
batch_queue: "batch"
env:
PYTHONPATH: "/home/swanson/aknecht/.conda/envs/ih_env/lib/python2.7/site-packages/"
PATH: "/home/swanson/aknecht/.conda/envs/ih_env/bin:/bin/:/usr/bin/:/usr/local/bin/"
PEGASUS_HOME: "/usr/"
**Run**
.. code-block:: yaml
genomes:
mm9:
bowtie2: /work/ladunga/SHARED/mouse/mm9/mm9.genome.fa
bwa: /work/ladunga/SHARED/mouse/mm9/mm9.genome.fa
chrom.sizes: /work/ladunga/SHARED/mouse/mm9/mm9.chrom.sizes
runs:
- align: bwa
assembly: mm9
controls: &id001
- ENCFF001NIM
file_type: fastq
idr: &id002
- ENCFF001NIP
- ENCFF001NIS
peak: spp
peak_type: narrow
signals: &id003
- ENCFF001NIP
- ENCFF001NIS
- align: bowtie2
assembly: mm9
controls: *id001
file_type: fastq
idr: *id002
peak: spp
peak_type: narrow
signals: *id003
Generators
===========
Module Generator
-----------------
.. autoclass:: chipathlon.generators.module_generator.ModuleGenerator
:members:
Align Generator
------------------
.. autoclass:: chipathlon.generators.align_generator.AlignGenerator
:members:
Remove Duplicate Generator
---------------------------
.. autoclass:: chipathlon.generators.remove_duplicates_generator.RemoveDuplicatesGenerator
:members:
Peak Call Generator
--------------------
.. autoclass:: chipathlon.generators.peak_call_generator.PeakCallGenerator
:members:
Idr Generator
---------------
.. autoclass:: chipathlon.generators.idr_generator.IdrGenerator
:members:
Genome
==============
.. autoclass:: chipathlon.genome.Genome
:members:
.. chipathlon documentation master file, created by
sphinx-quickstart on Tue Apr 11 15:50:17 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to chipathlon's documentation!
======================================
`GitHub <https://git.unl.edu/aknecht2/chipathlon/>`_
.. toctree::
:maxdepth: 2
:caption: Contents:
introduction
installation
examples
workflow
workflow_module
workflow_job
generators
run
genome
result
db
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
Installation
==============
Dependencies for chipathlon
----------------------------
*
Dependencies for running workflows
-----------------------------------
* gem
* zerone
* macs2
* spp
* ccat
* peakranger
* music
* samtools
* bamtools
* picard
* bwa
* bowtie2
Introduction
=============
Chipathlon is an open-source library for running multiple peak calling tools in
parallel. `Pegasus <pegasus.isi.edu>`_ is used to create and submit workflows
to super computers.
Chipathlon is currently being worked on. For help and questions, please
contact: avi@kurtknecht.com.
Result
==============
.. autoclass:: chipathlon.result.Result
:members:
Run
==============
.. autoclass:: chipathlon.run.Run
:members:
Workflow
=========
.. autoclass:: chipathlon.workflow.Workflow
:members:
Workflow Job
==============
.. autoclass:: chipathlon.workflow_job.WorkflowJob
:members:
Workflow Module
=================
.. autoclass:: chipathlon.workflow_module.WorkflowModule
:members:
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