Read the Docs build information
Build id: 966897
Project: beliveau-lab-tigerfish
Version: latest
Commit: 18bf5564e4c596686811aa017f9157aa5cb6feaf
Date: 2022-06-02T17:01:40.931170Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-06-02T17:01:42.925701Z, end-time: 2022-06-02T17:01:48.365621Z, duration: 5, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:beliveau-lab/TigerFISH.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-06-02T17:01:48.607210Z, end-time: 2022-06-02T17:01:48.976102Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 18bf556 updated defined_coords_output

[rtd-command-info] start-time: 2022-06-02T17:01:49.220501Z, end-time: 2022-06-02T17:01:49.284598Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-06-02T17:01:50.343623Z, end-time: 2022-06-02T17:01:55.232810Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-06-02T17:01:55.462131Z, end-time: 2022-06-02T17:01:57.311909Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (22.1.2)
Collecting setuptools<58.3.0
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 62.3.2
    Uninstalling setuptools-62.3.2:
      Successfully uninstalled setuptools-62.3.2
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-06-02T17:01:57.585353Z, end-time: 2022-06-02T17:02:09.311808Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2
Collecting mock==1.0.1
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Collecting pillow==5.4.1
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Collecting sphinx
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Collecting docutils>=0.11
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Collecting Jinja2>=2.3
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Collecting Pygments>=2.0
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Collecting requests>=2.5.0
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Collecting sphinxcontrib-devhelp
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Collecting packaging
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Collecting imagesize
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Collecting sphinxcontrib-qthelp
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Collecting importlib-metadata>=4.4
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Collecting sphinxcontrib-htmlhelp>=2.0.0
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Collecting sphinxcontrib-applehelp
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Collecting docutils>=0.11
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Collecting pytz>=2015.7
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Collecting typing-extensions>=3.6.4
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Collecting charset-normalizer~=2.0.0
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Collecting urllib3<1.27,>=1.21.1
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Collecting pyparsing!=3.0.5,>=2.0.2
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=a1ba2689db9c8f8116620ddc1d04bd420799bdeb8ded1021861da3f46979ed01
  Stored in directory: /tmp/pip-ephem-wheel-cache-cye5bgvv/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=df7345f6efd6cce0b0026bfae5e055eecbf946537552a65623bcbb592946773f
  Stored in directory: /tmp/pip-ephem-wheel-cache-cye5bgvv/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: snowballstemmer, pytz, mock, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.1 certifi-2022.5.18.1 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 importlib-metadata-4.11.4 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.27.1 snowballstemmer-2.2.0 sphinx-5.0.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.2.0 urllib3-1.26.9 zipp-3.8.0

[rtd-command-info] start-time: 2022-06-02T17:02:09.602367Z, end-time: 2022-06-02T17:02:19.284304Z, duration: 9, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting Sphinx==4.4.0
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Collecting Pygments==2.11.2
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Requirement already satisfied: sphinx_rtd_theme==1.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from -r docs/requirements.txt (line 6)) (1.0.0)
Collecting sphinx-tabs==3.2.0
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Collecting readthedocs-sphinx-search==0.1.1
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Collecting myst_parser==0.16.1
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Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.3)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.27.1)
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Building wheels for collected packages: sphinx-intl, sphinxemoji, rstcheck, livereload
  Building wheel for sphinx-intl (setup.py): started
  Building wheel for sphinx-intl (setup.py): finished with status 'done'
  Created wheel for sphinx-intl: filename=sphinx_intl-2.0.1-py3-none-any.whl size=11640 sha256=274fc5624bfd070ff0a87e72731352aaca59ae39f5c5c86edfbb355e4eb98e17
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  Created wheel for sphinxemoji: filename=sphinxemoji-0.2.0-py3-none-any.whl size=44427 sha256=28fabaedbeab8b461cf8a7f7b0835ee71ed88ac625be5b340407e8af83bc4780
  Stored in directory: /tmp/pip-ephem-wheel-cache-3a2o2pcx/wheels/09/10/81/0438103576aeaea47d55fe341a8e89d7561afc4e414741bf87
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  Created wheel for livereload: filename=livereload-2.6.3-py2.py3-none-any.whl size=24724 sha256=507847c9479fd5fdd0e41a66705194ff5c010b686fa8b0252755bc825bb36827
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Successfully built sphinx-intl sphinxemoji rstcheck livereload
Installing collected packages: sphinx-notfound-page, tornado, six, readthedocs-sphinx-search, pyyaml, Pygments, mdurl, docutils, colorama, Sphinx, rstcheck, markdown-it-py, livereload, click, sphinxemoji, sphinxcontrib-httpdomain, sphinx-tabs, sphinx-prompt, sphinx-intl, sphinx-autobuild, mdit-py-plugins, myst_parser
  Attempting uninstall: Pygments
    Found existing installation: Pygments 2.12.0
    Uninstalling Pygments-2.12.0:
      Successfully uninstalled Pygments-2.12.0
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  Attempting uninstall: Sphinx
    Found existing installation: Sphinx 5.0.0
    Uninstalling Sphinx-5.0.0:
      Successfully uninstalled Sphinx-5.0.0
Successfully installed Pygments-2.11.2 Sphinx-4.4.0 click-8.1.3 colorama-0.4.4 docutils-0.16 livereload-2.6.3 markdown-it-py-2.1.0 mdit-py-plugins-0.3.0 mdurl-0.1.1 myst_parser-0.16.1 pyyaml-6.0 readthedocs-sphinx-search-0.1.1 rstcheck-3.3.1 six-1.16.0 sphinx-autobuild-2021.3.14 sphinx-intl-2.0.1 sphinx-notfound-page-0.8 sphinx-prompt-1.4.0 sphinx-tabs-3.2.0 sphinxcontrib-httpdomain-1.8.0 sphinxemoji-0.2.0 tornado-6.1

[rtd-command-info] start-time: 2022-06-02T17:02:20.749096Z, end-time: 2022-06-02T17:02:20.817156Z, duration: 0, exit-code: 0
cat docs/source/conf.py
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- Path setup --------------------------------------------------------------

# 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
import subprocess
from configparser import RawConfigParser
import sphinx_rtd_theme

sys.path.insert(0, os.path.abspath(os.path.join("..", "..")))

#sys.path.insert(0, os.path.abspath('..'))
#sys.path.append(os.path.dirname(__file__))

#try:
#    import numpydoc
#except ModuleNotFoundError:
#    subprocess.run(["pip", "install", "numpydoc"], check=True)


# -- Project information -----------------------------------------------------

project = 'Tigerfish'
copyright = '2022, Robin Aguilar'
author = 'Robin Aguilar'

# The full version, including alpha/beta/rc tags
release = '2022'


# -- General configuration ---------------------------------------------------

#def get_version():
#    """Return package version from setup.cfg."""
#    config = RawConfigParser()
#    config.read(os.path.join('.', 'setup.cfg'))
#    return config.get('metadata', 'version')

# 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.duration',
    'sphinx.ext.doctest',
    'sphinx.ext.autodoc',
    'sphinx_tabs.tabs',
    'sphinx-prompt',
    'sphinx_search.extension',
    'sphinx.ext.autosummary',
    'sphinx.ext.intersphinx',
    'sphinxemoji.sphinxemoji'
]


nbsphinx_execute = "never"

#autosummary_generate = True
#autodoc_default_options = {
#    "members": True,
#    "inherited-members": True,
#    "member-order": "bysource",
#}

#numpydoc_show_class_members = True
#numpydoc_show_inherited_class_members = True
#numpydoc_attributes_as_param_list = True
#intersphinx_mapping = {
#    "pandas": ("https://pandas.pydata.org/docs", None),
#    "sklearn": ("https://scikit-learn.org/stable", None),
#    "numpy": ("https://numpy.org/doc/stable", None),
#    "matplotlib": ("https://matplotlib.org", None),
#}

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']


# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ["build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]


# -- 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_static_path = ["_static"]

master_doc = "index"
source_suffix = [".rst", ".md"]

html_theme_options = {
    "style_nav_header_background": "#343131",
    "logo_only": True,
}

html_css_files = [
    "custom.css",
]

# 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_logo = "_static/tigerfish.png"




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'beliveau-lab-tigerfish',
    'name': u'TigerFISH',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://beliveau-lab-tigerfish.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/source/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'beliveau-lab',
    'proxied_api_host': '/_',
    'github_repo': 'TigerFISH',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '18bf5564',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/beliveau-lab-tigerfish/builds/966897/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2022-06-02T17:02:21.011252Z, end-time: 2022-06-02T17:02:22.380205Z, duration: 1, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.4.0
loading translations [en]... done
making output directory... done
[autosummary] generating autosummary for: cli.rst, faq.rst, index.rst, parameters.rst, snakemake_view.rst, tutorials.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 6 source files that are out of date
updating environment: [new config] 6 added, 0 changed, 0 removed
reading sources... [ 16%] cli
reading sources... [ 33%] faq
reading sources... [ 50%] index
reading sources... [ 66%] parameters
reading sources... [ 83%] snakemake_view
reading sources... [100%] tutorials

/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:13: WARNING: Title underline too short.

Named Arguments in `config.yml <https://github.com/beliveau-lab/TigerFISH/blob/master/example_run/main/main_pipeline/config.yml>`_ for main workflow
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:95: WARNING: Title underline too short.

Named Arguments in `config.yml <https://github.com/beliveau-lab/TigerFISH/blob/master/example_run/postprocess/config.yml>`_ for the Post-process workflow
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:95: WARNING: Title underline too short.

Named Arguments in `config.yml <https://github.com/beliveau-lab/TigerFISH/blob/master/example_run/postprocess/config.yml>`_ for the Post-process workflow
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:2: WARNING: Duplicate explicit target name: "config.yml".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/faq.rst:40: WARNING: Title underline too short.

How do I do <insert task> with Tigerfish?
---------------------------------------
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How do I do <insert task> with Tigerfish?
---------------------------------------
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`Main workflow <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/main_pipeline/Snakefile>`_
^^^^^^^^^^^^^
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generate_bt2_indices
------------------
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generate_bt2_indices
------------------
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`generate_jf_idx <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/generate_jf_idx.py>`_
-----------------
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`generate_jf_idx <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/generate_jf_idx.py>`_
-----------------
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`split_bed <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/split_bed.py>`_
---------
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`split_bed <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/split_bed.py>`_
---------
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`repeat_ID <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/repeat_ID.py>`_
---------
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`repeat_ID <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/repeat_ID.py>`_
---------
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`design_probes <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/design_probes.py>`_
-------------
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`design_probes <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/design_probes.py>`_
-------------
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`kmer_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/kmer_filter.py>`_
-----------
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`kmer_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/kmer_filter.py>`_
-----------
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`probe_mer_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/probe_mer_filter.py>`_
----------------
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`probe_mer_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/probe_mer_filter.py>`_
----------------
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`alignment_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/alignment_filter.py>`_
----------------
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`alignment_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/alignment_filter.py>`_
----------------
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`gather_repeat_regions (checkpoint) <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/split_filter.py>`_
---------------------
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`gather_repeat_regions (checkpoint) <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/split_filter.py>`_
---------------------
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`summary <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/finish_summary.py>`_
-------
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`summary <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/finish_summary.py>`_
-------
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`Post-process Workflow <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/Snakefile>`_
^^^^^^^^^^^^^^^^^^^^^
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`Post-process Workflow <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/Snakefile>`_
^^^^^^^^^^^^^^^^^^^^^
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`gather_repeat_regions <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/split_filter_region.py>`_
---------------------
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`gather_repeat_regions <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/split_filter_region.py>`_
---------------------
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`align_probes <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/generate_alignments.py>`_
------------
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`align_probes <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/generate_alignments.py>`_
------------
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`derived_beds <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/make_derived_beds.py>`_
------------
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`derived_beds <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/make_derived_beds.py>`_
------------
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`get_region_bed <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/get_region_bed.py>`_
--------------
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`get_region_bed <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/get_region_bed.py>`_
--------------
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maximum 1 argument(s) allowed, 22 supplied.

.. code-block:: bash
      "bedtools intersect -wa -wb -a {input.derived_bed} -b {input.genome_bin} > {output.alignments_out} |"
   "bedtools intersect -wa -wb -a {input.repeat_bed} -b {input.genome_bin} > {output.repeat_out}"
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`get_alignments <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/get_alignments.py>`_
--------------
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`get_alignments <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/get_alignments.py>`_
--------------
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`generate_chromomap <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/make_chromomap.R>`_
------------------
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`generate_chromomap <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/postprocess/scripts/make_chromomap.R>`_
------------------
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