.tox
dist
RELEASE-VERSION
+docs/build/
--- /dev/null
+# 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/HTS-Workflow.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/HTS-Workflow.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/HTS-Workflow"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/HTS-Workflow"
+ @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."
--- /dev/null
+Runfolder Processing
+====================
+
+Runfolder
+---------
+
+The PipelineRun class is designed to combine information
+from the following importers.
+
+* Image Analysis (one of the following)
+
+ * :class:`Firecrest`
+ * :class:`IPAR`
+
+* BaseCaller
+
+ * :class:`Bustard`
+
+* Sequence Alignment
+
+ * :class:`Gerald`
+
+.. automodule:: htsworkflow.pipelines.runfolder
+ :members:
+
+.. _Firecrest:
+
+Firecrest
+---------
+
+.. automodule:: htsworkflow.pipelines.firecrest
+ :members:
+
+.. _IPAR:
+
+IPAR
+----
+
+.. automodule:: htsworkflow.pipelines.ipar
+ :members:
+
+.. _Bustard:
+
+Bustard
+-------
+.. automodule:: htsworkflow.pipelines.bustard
+ :members:
+
+.. _Gerald:
+
+Gerald
+------
+
+.. automodule:: htsworkflow.pipelines.gerald
+ :members:
+
+.. _Eland:
+
+Eland
+-----
+
+.. automodule:: htsworkflow.pipelines.eland
+ :members:
+
+.. _Summary:
+
+Summary
+-------
+
+.. automodule:: htsworkflow.pipelines.summary
+ :members:
+
+Sequence Archival
+=================
+
+srf
+---
+
+.. automodule:: htsworkflow.pipelines.srf
+ :members:
+
+Fastq conversion
+================
+
+srf2fastq
+---------
+
+.. automodule:: htsworkflow.pipelines.srf2fastq
+ :members:
+
+qseq2fastq
+----------
+
+.. automodule:: htsworkflow.pipelines.qseq2fastq
+ :members:
+
+desplit_fastq
+-------------
+
+.. automodule:: htsworkflow.pipelines.desplit_fastq
+ :members:
+
+sequences
+---------
+
+.. automodule:: htsworkflow.pipelines.sequences
+ :members:
+
+Utilities
+=========
+
+.. automodule:: htsworkflow.pipelines.genome_mapper
+ :members:
+
+.. automodule:: htsworkflow.pipelines.genomemap
+ :members:
+
+.. automodule:: htsworkflow.pipelines.samplekey
+ :members:
+
+.. automodule:: htsworkflow.pipelines.recipe_parser
+ :members:
+
+Run Automation
+==============
+
+.. automodule:: htsworkflow.pipelines.configure_run
+ :members:
+
+.. automodule:: htsworkflow.pipelines.retrieve_config
+ :members:
+
+.. automodule:: htsworkflow.pipelines.run_status
+ :members:
--- /dev/null
+# -*- coding: utf-8 -*-
+#
+# HTS-Workflow documentation build configuration file, created by
+# sphinx-quickstart on Mon Jan 14 10:18:40 2013.
+#
+# 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
+
+# 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('.'))
+sys.path.insert(0, os.path.abspath('../../htsworkflow'))
+
+# -- 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.intersphinx', 'sphinx.ext.coverage', 'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# 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'HTS-Workflow'
+copyright = u'2013, Diane Trout'
+
+# 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 = '0.5'
+# The full version, including alpha/beta/rc tags.
+release = '0.5.4'
+
+# 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 = 'HTS-Workflowdoc'
+
+
+# -- 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', 'HTS-Workflow.tex', u'HTS-Workflow Documentation',
+ u'Diane Trout', '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', 'hts-workflow', u'HTS-Workflow Documentation',
+ [u'Diane Trout'], 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', 'HTS-Workflow', u'HTS-Workflow Documentation',
+ u'Diane Trout', 'HTS-Workflow', 'One line description of project.',
+ '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'
+
+
+# -- Options for Epub output ---------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = u'HTS-Workflow'
+epub_author = u'Diane Trout'
+epub_publisher = u'Diane Trout'
+epub_copyright = u'2013, Diane Trout'
+
+# The language of the text. It defaults to the language option
+# or en if the language is not set.
+#epub_language = ''
+
+# The scheme of the identifier. Typical schemes are ISBN or URL.
+#epub_scheme = ''
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#epub_identifier = ''
+
+# A unique identification for the text.
+#epub_uid = ''
+
+# A tuple containing the cover image and cover page html template filenames.
+#epub_cover = ()
+
+# HTML files that should be inserted before the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_pre_files = []
+
+# HTML files shat should be inserted after the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_post_files = []
+
+# A list of files that should not be packed into the epub file.
+#epub_exclude_files = []
+
+# The depth of the table of contents in toc.ncx.
+#epub_tocdepth = 3
+
+# Allow duplicate toc entries.
+#epub_tocdup = True
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'http://docs.python.org/': None}
--- /dev/null
+.. HTS-Workflow documentation master file, created by
+ sphinx-quickstart on Mon Jan 14 10:18:40 2013.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to HTS-Workflow's documentation!
+========================================
+
+Contents:
+
+.. toctree::
+ :maxdepth: 2
+
+ api
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
LOGGER = logging.getLogger(__name__)
-__docformat__ = "restructuredtext en"
-
class Firecrest(object):
+ """Gather information about older firecrest runs
+ """
XML_VERSION=1
# xml tag names
MATRIX = 'matrix'
def __init__(self, xml=None):
+ """Initialize a Firecrest object
+
+ consider using factory :function:firecrest
+
+ :param xml: xml serialzation element to initialze from [optional]
+ """
self.start = None
self.stop = None
self.version = None
time = property(_get_time, doc='return run time as seconds since epoch')
def dump(self):
+ """Report debugginf information
+ """
print "Starting cycle:", self.start
print "Ending cycle:", self.stop
print "Firecrest version:", self.version
print "user:", self.user
def get_elements(self):
+ """Return XML serialization structure.
+ """
attribs = {'version': str(Firecrest.XML_VERSION) }
root = ElementTree.Element(Firecrest.FIRECREST, attrib=attribs)
version = ElementTree.SubElement(root, Firecrest.SOFTWARE_VERSION)
-"""
-Core information needed to inspect a runfolder.
+"""Core information needed to inspect a runfolder.
"""
from glob import glob
import logging
from htsworkflow.pipelines import srf
class PipelineRun(object):
- """
- Capture "interesting" information about a pipeline run
+ """Capture "interesting" information about a pipeline run
+
+ :Variables:
+ - `pathname` location of the root of this runfolder
+ - `name` read only property containing name of run xml file
+ - `flowcell_id` read-only property containing flowcell id (bar code)
+ - `datadir` location of the runfolder data dir.
+ - `image_analysis` generic name for Firecrest or IPAR image analysis
+ - `bustard` summary base caller
+ - `gerald` summary of sequence alignment and quality control metrics
"""
XML_VERSION = 1
PIPELINE_RUN = 'PipelineRun'
FLOWCELL_ID = 'FlowcellID'
def __init__(self, pathname=None, flowcell_id=None, xml=None):
+ """Initialize a PipelineRun object
+
+ :Parameters:
+ - `pathname` the root directory of this run folder.
+ - `flowcell_id` the flowcell ID in case it can't be determined
+ - `xml` Allows initializing an object from a serialized xml file.
+
+ :Types:
+ - `pathname` str
+ - `flowcell_id` str
+ - `ElementTree` str
+ """
if pathname is not None:
self.pathname = os.path.normpath(pathname)
else:
self.set_elements(xml)
def _get_flowcell_id(self):
+ """Return the flowcell ID
+
+ Attempts to find the flowcell ID through several mechanisms.
+ """
# extract flowcell ID
if self._flowcell_id is None:
self._flowcell_id = self._get_flowcell_id_from_runinfo()
def _get_flowcell_id_from_flowcellid(self):
"""Extract flowcell id from a Config/FlowcellId.xml file
+
+ :return: flowcell_id or None if not found
"""
config_dir = os.path.join(self.pathname, 'Config')
flowcell_id_path = os.path.join(config_dir, 'FlowcellId.xml')
def _get_flowcell_id_from_runinfo(self):
"""Read RunInfo file for flowcell id
+
+ :return: flowcell_id or None if not found
"""
runinfo = os.path.join(self.pathname, 'RunInfo.xml')
if os.path.exists(runinfo):
if len(fc_nodes) == 1:
return fc_nodes[0].text
-
def _get_flowcell_id_from_path(self):
"""Guess a flowcell name from the path
+
+ :return: flowcell_id or None if not found
"""
path_fields = self.pathname.split('_')
if len(path_fields) > 0:
return self.gerald.runfolder_name
runfolder_name = property(_get_runfolder_name)
- def get_elements(self):
+ def _get_run_id(self):
+ """Return a identifer for a run.
+
+ For pre-multiplexing runs this is just the cycle range C1-123
+ For post-multiplexing runs the "suffix" that we add to
+ differentiate runs will be added to the range.
+ E.g. Unaligned_6mm may produce C1-200_6mm
"""
- make one master xml file from all of our sub-components.
+ pass
+
+ def get_elements(self):
+ """make one master xml file from all of our sub-components.
+
+ :return: an ElementTree containing all available pipeline
+ run xml compoents.
"""
root = ElementTree.Element(PipelineRun.PIPELINE_RUN)
flowcell = ElementTree.SubElement(root, PipelineRun.FLOWCELL_ID)
flowcell.text = self.flowcell_id
root.append(self.image_analysis.get_elements())
root.append(self.bustard.get_elements())
- root.append(self.gerald.get_elements())
+ if self.gerald:
+ root.append(self.gerald.get_elements())
return root
def set_elements(self, tree):
- # this file gets imported by all the others,
- # so we need to hide the imports to avoid a cyclic imports
+ """Initialize a PipelineRun object from an run.xml ElementTree.
+ :param tree: parsed ElementTree
+ :type tree: ElementTree
+ """
tag = tree.tag.lower()
if tag != PipelineRun.PIPELINE_RUN.lower():
raise ValueError('Pipeline Run Expecting %s got %s' % (
LOGGER.warn('PipelineRun unrecognized tag %s' % (tag,))
def _get_run_name(self):
- """
- Given a run tuple, find the latest date and use that as our name
+ """Compute the run name for the run xml file
+
+ Attempts to find the latest date from all of the run
+ components.
+
+ :return: run xml name
+ :rtype: str
"""
if self._name is None:
tmax = max(self.image_analysis.time, self.bustard.time, self.gerald.time)
name = property(_get_run_name)
def save(self, destdir=None):
+ """Save a run xml file.
+
+ :param destdir: Directory name to save too, uses current directory
+ if not specified.
+ :type destdir: str
+ """
if destdir is None:
destdir = ''
LOGGER.info("Saving run report " + self.name)
ElementTree.ElementTree(xml).write(dest_pathname)
def load(self, filename):
+ """Load a run xml into this object.
+
+ :Parameters:
+ - `filename` location of a run xml file
+
+ :Types:
+ - `filename` str
+ """
LOGGER.info("Loading run report from " + filename)
tree = ElementTree.parse(filename).getroot()
self.set_elements(tree)
Load and instantiate a Pipeline run from a run xml file
:Parameters:
- - `pathname` : location of an run xml file
+ - `pathname` location of an run xml file
:Returns: initialized PipelineRun object
"""
return run
def get_runs(runfolder, flowcell_id=None):
- """
- Search through a run folder for all the various sub component runs
- and then return a PipelineRun for each different combination.
+ """Find all runs associated with a runfolder.
+
+ We end up with multiple analysis runs as we sometimes
+ need to try with different parameters. This attempts
+ to return a list of all the various runs.
For example if there are two different GERALD runs, this will
generate two different PipelineRun objects, that differ
in there gerald component.
"""
- from htsworkflow.pipelines import firecrest
- from htsworkflow.pipelines import ipar
- from htsworkflow.pipelines import bustard
- from htsworkflow.pipelines import gerald
-
datadir = os.path.join(runfolder, 'Data')
LOGGER.info('Searching for runs in ' + datadir)
LOGGER.warn("Aligned directory %s without matching unalinged, skipping", aligned)
continue
- g = gerald.gerald(aligned)
print "scan for aligned then remove them from unaligned list"
try:
p = PipelineRun(runfolder, flowcell_id)
make a subprocess-friendly list of command line arguments to run solexa2srf
generates files like:
woldlab:080514_HWI-EAS229_0029_20768AAXX:8.srf
- site run name lane
+ site run name lane
run_name - most of the file name (run folder name is a good choice)
lanes - list of integers corresponding to which lanes to process
projects / htsworkflow.git / commitdiff